diff --git a/dfols/__init__.py b/dfols/__init__.py index b91fea0..78d73de 100644 --- a/dfols/__init__.py +++ b/dfols/__init__.py @@ -39,9 +39,11 @@ from __future__ import absolute_import, division, print_function, unicode_literals # DFO-LS version -__version__ = '1.5.4' +__version__ = '1.6' # Main solver & exit flags from .solver import * __all__ = ['solve', 'OptimResults'] +from .evaluations_database import * +__all__ += ['EvaluationDatabase'] diff --git a/dfols/controller.py b/dfols/controller.py index 4fee084..c68175d 100644 --- a/dfols/controller.py +++ b/dfols/controller.py @@ -414,6 +414,48 @@ def initialise_random_directions(self, number_of_samples, num_directions, params return None + def initialise_from_database(self, eval_database, number_of_samples, params): + # Here, eval_database has at least one entry, and the base index has already been used + # to evaluate (x0,r0), which has already been added to self.model + # Now, find exactly n feasible perturbations (either from database or new evals) and add them to the model + base_idx, perturbation_idx, new_perturbations = eval_database.select_starting_evals(self.delta, + xl=self.model.xbase + self.model.sl, + xu=self.model.xbase + self.model.su, + projections=self.model.projections, + tol=params("database.new_direction_tol"), + dykstra_max_iters=params("dykstra.max_iters"), + dykstra_tol=params("dykstra.d_tol")) + + # Add suitable pre-existing evaluations + for i, idx in enumerate(perturbation_idx): + module_logger.info("Adding pre-existing evaluation %g to initial model" % idx) + x, rx = eval_database.get_eval(idx) + self.model.change_point(i + 1, x - self.model.xbase, rx, -idx) # use eval_num = -idx + + if new_perturbations is not None: + num_perturbations = new_perturbations.shape[0] + module_logger.debug("Adding %g new evaluations to initial model" % num_perturbations) + for i in range(num_perturbations): + new_point = (eval_database.get_x(base_idx) - self.model.xbase) + new_perturbations[i,:] # new_perturbations[i,:] has length <= self.delta + + # Evaluate objective + x = self.model.as_absolute_coordinates(new_point) + rvec_list, obj_list, num_samples_run, exit_info = self.evaluate_objective(x, number_of_samples, params) + + # Handle exit conditions (f < min obj value or maxfun reached) + if exit_info is not None: + if num_samples_run > 0: + self.model.save_point(x, np.mean(rvec_list[:num_samples_run, :], axis=0), num_samples_run, + self.nx, x_in_abs_coords=True) + return exit_info # return & quit + + # Otherwise, add new results (increments model.npt_so_far) + self.model.change_point(len(perturbation_idx) + 1 + i, x - self.model.xbase, rvec_list[0, :], self.nx) # expect step, not absolute x + for j in range(1, num_samples_run): + self.model.add_new_sample(len(perturbation_idx) + 1 + i, rvec_extra=rvec_list[j, :]) + + return None + def add_new_direction_while_growing(self, number_of_samples, params, min_num_steps=0): num_steps = max(params('growing.num_new_dirns_each_iter'), min_num_steps) step_length = params('growing.delta_scale_new_dirns') * self.delta diff --git a/dfols/evaluations_database.py b/dfols/evaluations_database.py new file mode 100644 index 0000000..2486289 --- /dev/null +++ b/dfols/evaluations_database.py @@ -0,0 +1,208 @@ +""" +Class to create/store database of existing evaluations, and routines to select +existing evaluations to build an initial linear model +""" +import logging +import numpy as np + +from .util import apply_scaling, dykstra +from .trust_region import ctrsbox_geometry, trsbox_geometry + +__all__ = ['EvaluationDatabase'] + +module_logger = logging.getLogger(__name__) + + +# Class to store set of evaluations (x, rx) +class EvaluationDatabase(object): + def __init__(self, eval_list=None, starting_eval=None): + # eval_list is a list of tuples (x, rx) + self._evals = [] + if eval_list is not None: + for e in eval_list: + self._evals.append(e) + + # Which evaluation index should be the starting point of the optimization? + self.starting_eval = None + if starting_eval is not None and 0 <= starting_eval <= len(self._evals): + self.starting_eval = starting_eval + + def __len__(self): + return len(self._evals) + + def append(self, x, rx, make_starting_eval=False): + self._evals.append((x, rx)) + if make_starting_eval: + self.starting_eval = len(self) - 1 + + def set_starting_eval(self, index): + if 0 <= index < len(self): + self.starting_eval = index + else: + raise IndexError("Invalid index %g given current set of %g evaluations" % (index, len(self))) + + def get_starting_eval_idx(self): + if len(self) == 0: + raise RuntimeError("No evaluations available, no suitable starting evaluation ") + elif self.starting_eval is None: + module_logger.warning("Starting evaluation index not set, using most recently appended evaluation") + self.starting_eval = len(self) - 1 + + return self.starting_eval + + def get_eval(self, index): + # Return (x, rx) for given index + if 0 <= index < len(self): + return self._evals[index][0], self._evals[index][1] + else: + raise IndexError("Invalid index %g given current set of %g evaluations" % (index, len(self))) + + def get_x(self, index): + return self.get_eval(index)[0] + + def get_rx(self, index): + return self.get_eval(index)[1] + + def apply_scaling(self, scaling_changes): + # Adjust all input x values based on scaling + if scaling_changes is not None: + for i in range(len(self)): + x, rx = self._evals[i] + self._evals[i] = (apply_scaling(x, scaling_changes), rx) + return + + def select_starting_evals(self, delta, xl=None, xu=None, projections=[], tol=1e-8, + dykstra_max_iters=100, dykstra_tol=1e-10): + # Given a database 'evals' with prescribed starting index, and initial trust-region radius delta > 0 + # determine a subset of the database to use + + # The bounds xl <= x <= xu and projection list are used to determine where to evaluate any new points + # (ensuring they are feasible) + + if delta <= 0.0: + raise RuntimeError("delta must be strictly positive") + if len(self) == 0: + raise RuntimeError("Need at least one evaluation to select starting evaluations") + + base_idx = self.get_starting_eval_idx() + xbase = self.get_x(self.get_starting_eval_idx()) + n = len(xbase) + module_logger.debug("Selecting starting evaluations from existing database") + module_logger.debug("Have %g evaluations to choose from" % len(self)) + module_logger.debug("Using base index %g" % base_idx) + + # For linear interpolation, we will use the matrix + # M = [[1, 0], [0, L]] where L has rows (xi-xbase)/delta + # So, just build a large matrix Lfull with everything + n_perturbations = len(self) - 1 + Lfull = np.zeros((n_perturbations, n)) + row_idx = 0 + for i in range(n_perturbations + 1): + if i == base_idx: + continue + Lfull[row_idx, :] = (self.get_x(i) - xbase) / delta # Lfull[i,:] = (xi-xbase) / delta + row_idx += 1 + + xdist = np.linalg.norm(Lfull, axis=1) # xdist[i] = ||Lfull[i,:]|| = ||xi-xbase|| / delta + # module_logger.debug("xdist =", xdist) + + # We ideally want xdist ~ 1, so reweight these distances based on that (large xdist_reweighted --> xdist ~ 1 --> good) + xdist_reweighted = 1.0 / np.maximum(xdist, 1.0 / xdist) + # module_logger.debug("xdist_reweighted =", xdist_reweighted) + + if n_perturbations == 0: + module_logger.debug("Only one evaluation available, just selecting that") + return base_idx, [], delta * np.eye(n) + + # Now, find as many good perturbations as we can + # Good = not too far from xbase (relative to delta) and sufficiently linearly independent + # from other selected perturbations (i.e. Lfull[perturbation_idx,:] well-conditioned + # and len(perturbation_idx) <= n + perturbation_idx = [] # what point indices to use as perturbations + + for iter in range(min(n_perturbations, n)): + # Add one more good perturbation, if available + # Note: can only add at most the number of available perturbations, or n perturbations, whichever is smaller + if iter == 0: + # First perturbation: every direction is equally good, so pick the point closest to the + # trust-region boundary + idx = int(np.argmax(xdist_reweighted)) + module_logger.debug("Adding index %g with ||xi-xbase|| / delta = %g" % (idx if idx < base_idx else idx+1, xdist[idx])) + perturbation_idx.append(idx) + else: + Q, R = np.linalg.qr(Lfull[perturbation_idx, :].T, mode='reduced') + # module_logger.debug("Current perturbation_idx =", perturbation_idx) + L_rem = Lfull @ (np.eye(n) - Q @ Q.T) # part of (xi-xbase)/delta orthogonal to current perturbations + # rem_size = fraction of original length ||xi-xbase||/delta that is orthogonal to current perturbations + # all entries are in [0,1], and is zero for already selected perturbations + rem_size = np.linalg.norm(L_rem, axis=1) / xdist + rem_size[perturbation_idx] = 0 # ensure this holds exactly + # module_logger.debug("rem_size =", rem_size) + # module_logger.debug("rem_size * xdist_reweighted =", rem_size * xdist_reweighted) + + # We want a point with large rem_size and xdist ~ 1 (i.e. xdist_reweighted large) + idx = int(np.argmax(rem_size * xdist_reweighted)) + if rem_size[idx] * xdist_reweighted[idx] > tol: + # This ensures new perturbation is sufficiently linearly independent of existing perturbations + # (and also ensures idx hasn't already been chosen) + module_logger.debug("Adding index %g" % (idx if idx < base_idx else idx+1)) + perturbation_idx.append(idx) + else: + module_logger.debug("No more linearly independent directions, quitting") + break + + # Find new linearly independent directions + if len(perturbation_idx) < n: + module_logger.debug("Selecting %g new linearly independent directions" % (n - len(perturbation_idx))) + Q, _ = np.linalg.qr(Lfull[perturbation_idx, :].T, mode='complete') + new_perturbations = delta * Q[:, len(perturbation_idx):].T + + # Make perturbations feasible w.r.t. xl <= x <= xu and projections + # Note: if len(projections) > 0, then the projection list *already* includes bounds + # Don't need to make pre-existing evaluations feasible, since we already have r(x) for these + + # Start construction of interpolation matrix for later + L = np.zeros((n, n), dtype=float) + L[:len(perturbation_idx), :] = Lfull[perturbation_idx, :] + L[len(perturbation_idx):, :] = new_perturbations / delta + + # Since we already have a full set of linearly independent directions, + # we do this by moving each infeasible perturbation to a geometry-improving location + for i in range(new_perturbations.shape[0]): + xnew = xbase + new_perturbations[i, :] + # Check feasibility + if len(projections) == 0: + # Bounds only + feasible = np.all(xnew >= xl) and np.all(xnew <= xu) + else: + # Projections + xnew_C = dykstra(projections, xnew, max_iter=dykstra_max_iters, tol=dykstra_tol) + feasible = np.linalg.norm(xnew - xnew_C) < dykstra_tol + + if feasible: + # Skip feasible points, nothing to do + continue + + # If infeasible, build Lagrange polynomial and move to geometry-improving location in B(xbase,delta) + # which will automatically be feasible + module_logger.debug("Moving default %g-th new perturbation to ensure feasibility" % i) + c = 0.0 # Lagrange polynomial centered at xbase + ei = np.zeros((n,), dtype=float) + ei[len(perturbation_idx) + i] = 1.0 + g = np.linalg.solve(L, ei) / delta # divide by delta because L is scaled by 1/delta + if len(projections) == 0: + new_perturbations[i, :] = trsbox_geometry(xbase, c, g, xl, xu, delta) + else: + new_perturbations[i, :] = ctrsbox_geometry(xbase, c, g, projections, delta) + + # Update L after replacement + L[len(perturbation_idx) + i, :] = new_perturbations[i,:] / delta + else: + module_logger.debug("Full set of directions found, no need for new evaluations") + new_perturbations = None + + # perturbation_idx in [0, ..., n_perturbations-1], reset to be actual indices + for i in range(len(perturbation_idx)): + if perturbation_idx[i] >= base_idx: + perturbation_idx[i] += 1 + return base_idx, perturbation_idx, new_perturbations diff --git a/dfols/params.py b/dfols/params.py index 7fe9ac2..d34c5f1 100644 --- a/dfols/params.py +++ b/dfols/params.py @@ -122,6 +122,9 @@ def __init__(self, n, npt, maxfun, objfun_has_noise=False): self.params["func_tol.tr_step"] = 1-1e-1 self.params["func_tol.max_iters"] = 500 self.params["sfista.max_iters_scaling"] = 2.0 + + # Evaluation database + self.params["database.new_direction_tol"] = 1e-8 self.params_changed = {} for p in self.params: @@ -284,6 +287,8 @@ def param_type(self, key, npt): type_str, nonetype_ok, lower, upper = 'int', False, 0, None elif key == "sfista.max_iters_scaling": type_str, nonetype_ok, lower, upper = 'float', False, 1.0, None + elif key == "database.new_direction_tol": + type_str, nonetype_ok, lower, upper = 'float', False, 0.0, None else: assert False, "ParameterList.param_type() has unknown key: %s" % key return type_str, nonetype_ok, lower, upper diff --git a/dfols/solver.py b/dfols/solver.py index f61d7da..cd099e6 100644 --- a/dfols/solver.py +++ b/dfols/solver.py @@ -39,6 +39,7 @@ from .controller import * from .diagnostic_info import * +from .evaluations_database import * from .params import * from .util import * @@ -70,13 +71,16 @@ def __init__(self, xmin, rmin, objmin, jacmin, nf, nx, nruns, exit_flag, exit_ms self.EXIT_TR_INCREASE_ERROR = EXIT_TR_INCREASE_ERROR self.EXIT_LINALG_ERROR = EXIT_LINALG_ERROR self.EXIT_FALSE_SUCCESS_WARNING = EXIT_FALSE_SUCCESS_WARNING + self.max_resid_length_print = 20 # don't print self.resid in __str__ if length >= this value + self.max_jac_length_print = 40 # don't print self.jacobian in __str__ if length >= this value + def __str__(self): # Result of calling print(soln) output = "****** DFO-LS Results ******\n" if self.flag != self.EXIT_INPUT_ERROR: output += "Solution xmin = %s\n" % str(self.x) - if len(self.resid) < 100: + if len(self.resid) < self.max_resid_length_print: output += "Residual vector = %s\n" % str(self.resid) else: output += "Not showing residual vector because it is too long; check self.resid\n" @@ -84,7 +88,7 @@ def __str__(self): output += "Needed %g objective evaluations (at %g points)\n" % (self.nf, self.nx) if self.nruns > 1: output += "Did a total of %g runs\n" % self.nruns - if self.jacobian is not None and np.size(self.jacobian) < 200: + if self.jacobian is not None and np.size(self.jacobian) < self.max_jac_length_print: output += "Approximate Jacobian = %s\n" % str(self.jacobian) elif self.jacobian is None: output += "No Jacobian returned\n" @@ -93,7 +97,7 @@ def __str__(self): if self.diagnostic_info is not None: output += "Diagnostic information available; check self.diagnostic_info\n" output += "Solution xmin was evaluation point %g\n" % self.xmin_eval_num - if self.jacmin_eval_nums is not None and len(self.jacmin_eval_nums) < 100: + if self.jacmin_eval_nums is not None and len(self.jacmin_eval_nums) < self.max_resid_length_print: output += "Approximate Jacobian formed using evaluation points %s\n" % str(self.jacmin_eval_nums) elif self.jacmin_eval_nums is None: output += "Approximate Jacobian not formed using problem information, disregard\n" @@ -152,58 +156,77 @@ def from_dict(soln_dict): def solve_main(objfun, x0, argsf, xl, xu, projections, npt, rhobeg, rhoend, maxfun, nruns_so_far, nf_so_far, nx_so_far, nsamples, params, diagnostic_info, scaling_changes, h=None, lh=None, argsh=(), prox_uh=None, argsprox=None, r0_avg_old=None, r0_nsamples_old=None, default_growing_method_set_by_user=None, do_logging=True, print_progress=False): + + if type(x0) == EvaluationDatabase: + x0_is_eval_database = True + x0_vec = x0.get_x(x0.get_starting_eval_idx()) + else: + x0_vec = x0 + x0_is_eval_database = False + n = len(x0_vec) + # Evaluate at x0 (keep nf, nx correct and check for f < 1e-12) # The hard bit is determining what m = len(r0) should be, and allocating memory appropriately if r0_avg_old is None: - number_of_samples = max(nsamples(rhobeg, rhobeg, 0, nruns_so_far), 1) - # Evaluate the first time... - nf = nf_so_far + 1 - nx = nx_so_far + 1 - r0, obj0 = eval_least_squares_with_regularisation(objfun, remove_scaling(x0, scaling_changes), h, - argsf=argsf, argsh=argsh, verbose=do_logging, eval_num=nf, pt_num=nx, - full_x_thresh=params("logging.n_to_print_whole_x_vector"), - check_for_overflow=params("general.check_objfun_for_overflow")) - m = len(r0) - - # Now we have m, we can evaluate the rest of the times - rvec_list = np.zeros((number_of_samples, m)) - obj_list = np.zeros((number_of_samples,)) - rvec_list[0, :] = r0 - obj_list[0] = obj0 - num_samples_run = 1 exit_info = None + if x0_is_eval_database: + # We have already got r(x0), so just extract this information + nf = nf_so_far + nx = nx_so_far + num_samples_run = 1 + r0_avg = x0.get_rx(x0.get_starting_eval_idx()) + m = len(r0_avg) + module_logger.info("Using pre-existing evaluation %g as starting point" % (x0.get_starting_eval_idx())) + else: + number_of_samples = max(nsamples(rhobeg, rhobeg, 0, nruns_so_far), 1) + # Evaluate the first time... + nf = nf_so_far + 1 + nx = nx_so_far + 1 + r0, obj0 = eval_least_squares_with_regularisation(objfun, remove_scaling(x0_vec, scaling_changes), h, + argsf=argsf, argsh=argsh, verbose=do_logging, eval_num=nf, pt_num=nx, + full_x_thresh=params("logging.n_to_print_whole_x_vector"), + check_for_overflow=params("general.check_objfun_for_overflow")) + m = len(r0) + + # Now we have m, we can evaluate the rest of the times + rvec_list = np.zeros((number_of_samples, m)) + obj_list = np.zeros((number_of_samples,)) + rvec_list[0, :] = r0 + obj_list[0] = obj0 + num_samples_run = 1 + + for i in range(1, number_of_samples): # skip first eval - already did this + if nf >= maxfun: + exit_info = ExitInformation(EXIT_MAXFUN_WARNING, "Objective has been called MAXFUN times") + nruns_so_far += 1 + break # stop evaluating at x0 - for i in range(1, number_of_samples): # skip first eval - already did this - if nf >= maxfun: - exit_info = ExitInformation(EXIT_MAXFUN_WARNING, "Objective has been called MAXFUN times") - nruns_so_far += 1 - break # stop evaluating at x0 + nf += 1 + # Don't increment nx for x0 - we did this earlier + rvec_list[i, :], obj_list[i] = eval_least_squares_with_regularisation(objfun, remove_scaling(x0_vec, scaling_changes), h, + argsf=argsf, argsh=argsh, verbose=do_logging, eval_num=nf, pt_num=nx, + full_x_thresh=params("logging.n_to_print_whole_x_vector"), + check_for_overflow=params("general.check_objfun_for_overflow")) + num_samples_run += 1 - nf += 1 - # Don't increment nx for x0 - we did this earlier - rvec_list[i, :], obj_list[i] = eval_least_squares_with_regularisation(objfun, remove_scaling(x0, scaling_changes), h, - argsf=argsf, argsh=argsh, verbose=do_logging, eval_num=nf, pt_num=nx, - full_x_thresh=params("logging.n_to_print_whole_x_vector"), - check_for_overflow=params("general.check_objfun_for_overflow")) - num_samples_run += 1 + r0_avg = np.mean(rvec_list[:num_samples_run, :], axis=0) - r0_avg = np.mean(rvec_list[:num_samples_run, :], axis=0) # NOTE: modify objvalue here if h is None: if sumsq(r0_avg) <= params("model.abs_tol"): exit_info = ExitInformation(EXIT_SUCCESS, "Objective is sufficiently small") else: - if sumsq(r0_avg) + h(remove_scaling(x0, scaling_changes), *argsh)<= params("model.abs_tol"): + if sumsq(r0_avg) + h(remove_scaling(x0_vec, scaling_changes), *argsh)<= params("model.abs_tol"): exit_info = ExitInformation(EXIT_SUCCESS, "Objective is sufficiently small") if exit_info is not None: xmin_eval_num = 0 jacmin_eval_nums = np.array([0], dtype=int) - return x0, r0_avg, sumsq(r0_avg), None, num_samples_run, nf, nx, nruns_so_far+1, exit_info, diagnostic_info, xmin_eval_num, jacmin_eval_nums + return x0_vec, r0_avg, sumsq(r0_avg), None, num_samples_run, nf, nx, nruns_so_far+1, exit_info, diagnostic_info, xmin_eval_num, jacmin_eval_nums else: # have old r0 information (e.g. from previous restart), use this instead - # m = len(r0_avg_old) + m = len(r0_avg_old) r0_avg = r0_avg_old num_samples_run = r0_nsamples_old nf = nf_so_far @@ -213,7 +236,7 @@ def solve_main(objfun, x0, argsf, xl, xu, projections, npt, rhobeg, rhoend, maxf if default_growing_method_set_by_user is not None and (not default_growing_method_set_by_user): # If m>=n, the default growing method (use_full_rank_interp) is best # However, this can fail for m= n+1 finished_growing = (control.model.npt() >= control.model.num_pts) # have we finished growing the initial set yet? # Save list of last N successful steps: whether they failed to be an improvement over fsave @@ -942,8 +972,16 @@ def solve_main(objfun, x0, argsf, xl, xu, projections, npt, rhobeg, rhoend, maxf def solve(objfun, x0, h=None, lh=None, prox_uh=None, argsf=(), argsh=(), argsprox=(), bounds=None, projections=[], npt=None, rhobeg=None, rhoend=1e-8, maxfun=None, nsamples=None, user_params=None, objfun_has_noise=False, scaling_within_bounds=False, do_logging=True, print_progress=False): - x0 = x0.astype(float) - n = len(x0) + + if type(x0) == EvaluationDatabase: + assert len(x0) > 0, "evaluation database x0 cannot be empty" + assert 0 <= x0.get_starting_eval_idx() < len(x0), "evaluation database must have valid starting index set" + x0_is_eval_database = True + n = len(x0.get_x(x0.get_starting_eval_idx())) + else: + x0 = np.array(x0).astype(float) + n = len(x0) + x0_is_eval_database = False # Set missing inputs (if not specified) to some sensible defaults if bounds is None: @@ -969,7 +1007,8 @@ def solve(objfun, x0, h=None, lh=None, prox_uh=None, argsf=(), argsh=(), argspro if npt is None: npt = n + 1 if rhobeg is None: - rhobeg = 0.1 if scaling_within_bounds else 0.1 * max(np.max(np.abs(x0)), 1.0) + x0_norm = np.max(np.abs(x0.get_x(x0.get_starting_eval_idx()))) if x0_is_eval_database else np.max(np.abs(x0)) + rhobeg = 0.1 if scaling_within_bounds else 0.1 * max(x0_norm, 1.0) if maxfun is None: maxfun = min(100 * (n + 1), 1000) # 100 gradients, capped at 1000 if nsamples is None: @@ -1004,7 +1043,10 @@ def solve(objfun, x0, h=None, lh=None, prox_uh=None, argsf=(), argsh=(), argspro scale = xu - xl scaling_changes = (shift, scale) - x0 = apply_scaling(x0, scaling_changes) + if x0_is_eval_database: + x0.apply_scaling(scaling_changes) + else: + x0 = apply_scaling(x0, scaling_changes) xl = apply_scaling(xl, scaling_changes) xu = apply_scaling(xu, scaling_changes) @@ -1033,13 +1075,19 @@ def solve(objfun, x0, h=None, lh=None, prox_uh=None, argsf=(), argsh=(), argspro if exit_info is None and maxfun <= 0: exit_info = ExitInformation(EXIT_INPUT_ERROR, "maxfun must be strictly positive") - if exit_info is None and np.shape(x0) != (n,): - exit_info = ExitInformation(EXIT_INPUT_ERROR, "x0 must be a vector") + if exit_info is None: + if x0_is_eval_database: + for i in range(len(x0)): + if np.shape(x0.get_x(i)) != (n,): + exit_info = ExitInformation(EXIT_INPUT_ERROR, "All input vectors x0 must have the same shape") + else: + if np.shape(x0) != (n,): + exit_info = ExitInformation(EXIT_INPUT_ERROR, "x0 must be a vector") - if exit_info is None and np.shape(x0) != np.shape(xl): + if exit_info is None and np.shape(xl) != (n,): exit_info = ExitInformation(EXIT_INPUT_ERROR, "lower bounds must have same shape as x0") - if exit_info is None and np.shape(x0) != np.shape(xu): + if exit_info is None and np.shape(xu) != (n,): exit_info = ExitInformation(EXIT_INPUT_ERROR, "upper bounds must have same shape as x0") if exit_info is None and np.min(xu - xl) < 2.0 * rhobeg: @@ -1090,22 +1138,24 @@ def solve(objfun, x0, h=None, lh=None, prox_uh=None, argsf=(), argsh=(), argspro return results # Enforce arbitrary constraint bounds on x0 - if projections: - xp = dykstra(projections,x0,max_iter=params("dykstra.max_iters"),tol=params("dykstra.d_tol")) - if not np.allclose(xp,x0): - warnings.warn("x0 not feasible w.r.t given constraints, adjusting", RuntimeWarning) - x0 = xp.copy() - - # Enforce lower & upper bounds on x0 - idx = (x0 < xl) - if np.any(idx): - warnings.warn("x0 below lower bound, adjusting", RuntimeWarning) - x0[idx] = xl[idx] - - idx = (x0 > xu) - if np.any(idx): - warnings.warn("x0 above upper bound, adjusting", RuntimeWarning) - x0[idx] = xu[idx] + if not x0_is_eval_database: + # Don't need to enforce any constraints for pre-existing evaluations (since we already have the objective value) + if projections: + xp = dykstra(projections,x0,max_iter=params("dykstra.max_iters"),tol=params("dykstra.d_tol")) + if not np.allclose(xp,x0): + warnings.warn("x0 not feasible w.r.t given constraints, adjusting", RuntimeWarning) + x0 = xp.copy() + + # Enforce lower & upper bounds on x0 + idx = (x0 < xl) + if np.any(idx): + warnings.warn("x0 below lower bound, adjusting", RuntimeWarning) + x0[idx] = xl[idx] + + idx = (x0 > xu) + if np.any(idx): + warnings.warn("x0 above upper bound, adjusting", RuntimeWarning) + x0[idx] = xu[idx] # Call main solver (first time) diagnostic_info = DiagnosticInfo() diff --git a/docs/build/doctrees/advanced.doctree b/docs/build/doctrees/advanced.doctree index fc38b0a..ff74e83 100755 Binary files a/docs/build/doctrees/advanced.doctree and b/docs/build/doctrees/advanced.doctree differ diff --git a/docs/build/doctrees/contributors.doctree b/docs/build/doctrees/contributors.doctree index fc2153b..3774c3b 100644 Binary files a/docs/build/doctrees/contributors.doctree and b/docs/build/doctrees/contributors.doctree differ diff --git a/docs/build/doctrees/diagnostic.doctree b/docs/build/doctrees/diagnostic.doctree index d72c0c0..aa78645 100755 Binary files a/docs/build/doctrees/diagnostic.doctree and b/docs/build/doctrees/diagnostic.doctree differ diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle index 2cab4b4..dad2380 100755 Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ diff --git a/docs/build/doctrees/history.doctree b/docs/build/doctrees/history.doctree index 4ef2fa0..4ee9c3a 100755 Binary files a/docs/build/doctrees/history.doctree and b/docs/build/doctrees/history.doctree differ diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree index 62b4d6e..024f58f 100755 Binary files a/docs/build/doctrees/index.doctree and b/docs/build/doctrees/index.doctree differ diff --git a/docs/build/doctrees/info.doctree b/docs/build/doctrees/info.doctree index 30b630f..816ef9e 100755 Binary files a/docs/build/doctrees/info.doctree and b/docs/build/doctrees/info.doctree differ diff --git a/docs/build/doctrees/install.doctree b/docs/build/doctrees/install.doctree index b2f86a4..792439a 100755 Binary files a/docs/build/doctrees/install.doctree and b/docs/build/doctrees/install.doctree differ diff --git a/docs/build/doctrees/userguide.doctree b/docs/build/doctrees/userguide.doctree index 1386dc4..955921e 100755 Binary files a/docs/build/doctrees/userguide.doctree and b/docs/build/doctrees/userguide.doctree differ diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo index 0849250..77669f2 100644 --- a/docs/build/html/.buildinfo +++ b/docs/build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 -# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 412cd91ff985b9489bd71148f8919cdf +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: e7c5306abb68a1486dd06854499b3f9f tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build/html/.buildinfo.bak b/docs/build/html/.buildinfo.bak new file mode 100644 index 0000000..0849250 --- /dev/null +++ b/docs/build/html/.buildinfo.bak @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 412cd91ff985b9489bd71148f8919cdf +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build/html/_sources/contributors.rst.txt b/docs/build/html/_sources/contributors.rst.txt index 48212de..2732936 100644 --- a/docs/build/html/_sources/contributors.rst.txt +++ b/docs/build/html/_sources/contributors.rst.txt @@ -3,7 +3,7 @@ Contributors Main author ----------- -* `Lindon Roberts `_ (University of Sydney) +* `Lindon Roberts `_ (University of Melbourne) Contributors ------------ diff --git a/docs/build/html/_sources/history.rst.txt b/docs/build/html/_sources/history.rst.txt index fd82d86..114d3d5 100644 --- a/docs/build/html/_sources/history.rst.txt +++ b/docs/build/html/_sources/history.rst.txt @@ -84,3 +84,8 @@ Version 1.5.4 (11 Feb 2025) --------------------------- * Bugfix when printing results from a run which terminated early * Add ability to save/load results to/from a dictionary + +Version 1.6 (10 Sep 2025) +------------------------- +* Allow use of evaluation database as :code:`x0` to reduce number of objective evaluations required in initialization phase +* When printing solution object, reduce the maximum length of residual/Jacobian vectors that are fully displayed diff --git a/docs/build/html/_sources/userguide.rst.txt b/docs/build/html/_sources/userguide.rst.txt index 0e72ab8..7f4ceac 100644 --- a/docs/build/html/_sources/userguide.rst.txt +++ b/docs/build/html/_sources/userguide.rst.txt @@ -33,6 +33,11 @@ The input :code:`objfun` is a Python function which takes an input :math:`x\in\m The input :code:`x0` is the starting point for the solver, and (where possible) should be set to be the best available estimate of the true solution :math:`x_{min}\in\mathbb{R}^n`. It should be specified as a one-dimensional NumPy array (i.e. with :code:`x0.shape == (n,)`). As DFO-LS is a local solver, providing different values for :code:`x0` may cause it to return different solutions, with possibly different objective values. +In newer version of DFO-LS (v1.6 onwards), the input :code:`x0` may instead by an instance of a :code:`dfols.EvaluationDatabase`, which stores a collection +of previously evaluated points and their associated vectors of residuals. One of these points is designated the starting point for the solver, and the other +points may be used by DFO-LS to build its first approximation to :code:`objfun`, reducing the number of evaluations required to begin the main iteration. +See the example below for more details for how to use this functionality. + The output of :code:`dfols.solve` is an object containing: * :code:`soln.x` - an estimate of the solution, :math:`x_{min}\in\mathbb{R}^n`, a one-dimensional NumPy array. @@ -436,6 +441,164 @@ The solution found by DFO-LS is: We can see that 3 of the 5 components of the solution are very close to zero. Note that many LASSO-type algorithms can produce a solution with many entries being exactly zero, but DFO-LS can only make them very small (related to how it calculates a new point with trust-region constraints). +Using Initial Evaluation Database +--------------------------------- +Since DFO-LS v1.6, the input :code:`x0` may instead be an instance of a :code:`dfols.EvaluationDatabase` class containing a collection of previously evaluated +points and their associated vectors of residuals. One of these points must be flagged as the starting point for the solver (otherwise, the most recently added +point is used). DFO-LS will automaticaly select some (but possibly none/all) of the other points to help build its first internal approximation to the objective, +which reduces the number of times the objective must be evaluated during the initialization phase, before the main algorithm can begin. + +For example, suppose we want to use DFO-LS to minimize the Watson test function (Problem 20 from [MGH1981]_). Using the standard starting point, our code looks like + + .. code-block:: python + + import numpy as np + import dfols + + # Define the objective function + def watson(x): + n = len(x) + m = 31 + fvec = np.zeros((m,), dtype=float) + for i in range(1, 30): # i=1,...,29 + div = float(i) / 29.0 + s1 = 0.0 + dx = 1.0 + for j in range(2, n + 1): # j = 2,...,n + s1 = s1 + (j - 1) * dx * x[j - 1] + dx = div * dx + s2 = 0.0 + dx = 1.0 + for j in range(1, n + 1): # j = 1,...,n + s2 = s2 + dx * x[j - 1] + dx = div * dx + fvec[i - 1] = s1 - s2 ** 2 - 1.0 + fvec[29] = x[0] + fvec[30] = x[1] - x[0] ** 2 - 1.0 + return fvec + + # Define the starting point + n = 6 + x0 = 0.5 * np.ones((n,), dtype=float) + + # Show extra output to demonstrate the impact of using an initial evaluation database + import logging + logging.basicConfig(level=logging.INFO, format='%(message)s') + + # Call DFO-LS + soln = dfols.solve(watson, x0) + + # Display output + print(soln) + +In the output of this code, we can check that DFO-LS finds the unique minimizer of this function. We can also see that before the main loop can begin, +DFO-LS needs to evaluate the objective at the given starting point, and 6 extra points (since this problem has 6 variables to be minimized): + + .. code-block:: none + + Function eval 1 at point 1 has obj = 16.4308311759923 at x = [...] + Initialising (coordinate directions) + Function eval 2 at point 2 has obj = 28.9196967094733 at x = [...] + Function eval 3 at point 3 has obj = 22.0866904737059 at x = [...] + Function eval 4 at point 4 has obj = 20.6560889343479 at x = [...] + Function eval 5 at point 5 has obj = 19.2914312375462 at x = [...] + Function eval 6 at point 6 has obj = 18.0373781384725 at x = [...] + Function eval 7 at point 7 has obj = 16.8946356501339 at x = [...] + Beginning main loop + Function eval 8 at point 8 has obj = 8.45207899459595 at x = [...] + Function eval 9 at point 9 has obj = 2.54949692496583 at x = [...] + ... + Function eval 90 at point 90 has obj = 0.00228767005355292 at x = [...] + Did a total of 1 run(s) + + ****** DFO-LS Results ****** + Solution xmin = [-0.01572509 1.01243487 -0.23299162 1.26043004 -1.51372886 0.99299641] + Not showing residual vector because it is too long; check self.resid + Objective value f(xmin) = 0.002287670054 + Needed 90 objective evaluations (at 90 points) + Not showing approximate Jacobian because it is too long; check self.jacobian + Solution xmin was evaluation point 89 + Approximate Jacobian formed using evaluation points [87 85 76 89 86 88 84] + Exit flag = 0 + Success: rho has reached rhoend + **************************** + +Instead of this, we can build a database of points where we have previously evaluated the objective, marking one of them as the starting point +for the algorithm. DFO-LS will then select some/all (but possibly none) of the other points and use them as initial evaluations, allowing it to begin +the main loop faster. In general, DFO-LS will select points that are: + +* Not too close/far from the selected starting point (relative to the initial trust-region radius, input :code:`rhobeg`) +* Not in similar directions (relative to the selected starting point) to other selected initial points. For example, if several points differ from + the selected starting point in only the first variable, at most one of these will be selected. + +The following code demonstrates how an evaluation database may be constructed and given to DFO-LS: + + .. code-block:: python + + # Assuming numpy and dfols already imported, watson function already defined + + # Build a database of evaluations + eval_db = dfols.EvaluationDatabase() + + # Define the starting point and add it to the database + n = 6 + x0 = 0.5 * np.ones((n,), dtype=float) + eval_db.append(x0, watson(x0), make_starting_eval=True) + # make_starting_eval=True --> use this point as the starting point for DFO-LS + + # Add other points to the database + # Note: x0, x1 and x2 are colinear, so at least one of x1 and x2 will not be included in the initial model + x1 = np.ones((n,), dtype=float) + x2 = np.zeros((n,), dtype=float) + x3 = np.arange(n).astype(float) + eval_db.append(x1, watson(x1)) + eval_db.append(x2, watson(x2)) + eval_db.append(x3, watson(x3)) + + # Show extra output to demonstrate the impact of using an initial evaluation database + import logging + logging.basicConfig(level=logging.INFO, format='%(message)s') + + # Call DFO-LS + soln = dfols.solve(watson, x0) + + # Display output + print(soln) + +Running this code, we get the same (correct) answer but using fewer evaluations of the objective in the main call to :code:`dfols.solve()`. +The logging information reveals that :code:`x0` was used as the starting point, and :code:`x1` and :code:`x3` were used to build the initial model. +This means that only 4 evaluations of the objective were required in the initialization phase. + + .. code-block:: none + + Using pre-existing evaluation 0 as starting point + Adding pre-existing evaluation 1 to initial model + Adding pre-existing evaluation 3 to initial model + Function eval 1 at point 1 has obj = 15.1910664616598 at x = [...] + Function eval 2 at point 2 has obj = 15.2288491702299 at x = [...] + Function eval 3 at point 3 has obj = 15.228054997542 at x = [...] + Function eval 4 at point 4 has obj = 15.3011037277481 at x = [...] + Beginning main loop + Function eval 5 at point 5 has obj = 13.5524099633802 at x = [...] + Function eval 6 at point 6 has obj = 7.33371957636104 at x = [...] + ... + Function eval 81 at point 81 has obj = 0.00228767005355266 at x = [...] + Did a total of 1 run(s) + + ****** DFO-LS Results ****** + Solution xmin = [-0.01572509 1.01243487 -0.23299163 1.26043009 -1.51372893 0.99299643] + Not showing residual vector because it is too long; check self.resid + Objective value f(xmin) = 0.002287670054 + Needed 81 objective evaluations (at 81 points) + Not showing approximate Jacobian because it is too long; check self.jacobian + Solution xmin was evaluation point 77 + Approximate Jacobian formed using evaluation points [76 73 79 74 77 75 80] + Exit flag = 0 + Success: rho has reached rhoend + **************************** + +Note that the indices of the evaluation database mentioned in the log refer to the order in which the points were added to the evaluation database. + Example: Noisy Objective Evaluation ----------------------------------- As described in :doc:`info`, derivative-free algorithms such as DFO-LS are particularly useful when :code:`objfun` has noise. Let's modify the previous example to include random noise in our objective evaluation, and compare it to SciPy's derivative-based solver (the below results came from using SciPy v1.13.0): @@ -708,3 +871,6 @@ References .. [B2017] Amir Beck, `First-Order Methods in Optimization `_, SIAM (2017). + +.. [MGH1981] + Jorge J. More, Burton S. Garbow and Kenneth E. Hillstrom, `Testing Unconstrained Optimization Software `_, *ACM Transactions on Mathematical Software*, 7:1 (1981), pp. 17-41. diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css index 30fee9d..4738b2e 100644 --- a/docs/build/html/_static/basic.css +++ b/docs/build/html/_static/basic.css @@ -1,12 +1,5 @@ /* - * basic.css - * ~~~~~~~~~ - * * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ /* -- main layout ----------------------------------------------------------- */ @@ -115,15 +108,11 @@ img { /* -- search page ----------------------------------------------------------- */ ul.search { - margin: 10px 0 0 20px; - padding: 0; + margin-top: 10px; } ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; + padding: 5px 0; } ul.search li a { @@ -752,14 +741,6 @@ abbr, 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format("woff2"),url(fonts/Roboto-Slab-Bold.woff?bed5564a116b05148e3b3bea6fb1162a) format("woff");font-display:block} \ No newline at end of file diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js index d06a71d..0398ebb 100644 --- a/docs/build/html/_static/doctools.js +++ b/docs/build/html/_static/doctools.js @@ -1,12 +1,5 @@ /* - * doctools.js - * ~~~~~~~~~~~ - * * Base JavaScript utilities for all Sphinx HTML documentation. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ "use strict"; diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js index 72ca8b0..ed97cc3 100644 --- a/docs/build/html/_static/documentation_options.js +++ b/docs/build/html/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '1.5.4', + VERSION: '1.6', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/build/html/_static/js/versions.js b/docs/build/html/_static/js/versions.js new file mode 100644 index 0000000..4958195 --- /dev/null +++ b/docs/build/html/_static/js/versions.js @@ -0,0 +1,228 @@ +const themeFlyoutDisplay = "hidden"; +const themeVersionSelector = true; +const themeLanguageSelector = true; + +if (themeFlyoutDisplay === "attached") { + function renderLanguages(config) { + if (!config.projects.translations.length) { + return ""; + } + + // Insert the current language to the options on the selector + let languages = config.projects.translations.concat(config.projects.current); + languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name)); + + const languagesHTML = ` +
+
Languages
+ ${languages + .map( + (translation) => ` +
+ ${translation.language.code} +
+ `, + ) + .join("\n")} +
+ `; + return languagesHTML; + } + + function renderVersions(config) { + if (!config.versions.active.length) { + return ""; + } + const versionsHTML = ` +
+
Versions
+ ${config.versions.active + .map( + (version) => ` +
+ ${version.slug} +
+ `, + ) + .join("\n")} +
+ `; + return versionsHTML; + } + + function renderDownloads(config) { + if (!Object.keys(config.versions.current.downloads).length) { + return ""; + } + const downloadsNameDisplay = { + pdf: "PDF", + epub: "Epub", + htmlzip: "HTML", + }; + + const downloadsHTML = ` +
+
Downloads
+ ${Object.entries(config.versions.current.downloads) + .map( + ([name, url]) => ` +
+ ${downloadsNameDisplay[name]} +
+ `, + ) + .join("\n")} +
+ `; + return downloadsHTML; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const flyout = ` +
+ + Read the Docs + v: ${config.versions.current.slug} + + +
+
+ ${renderLanguages(config)} + ${renderVersions(config)} + ${renderDownloads(config)} +
+
On Read the Docs
+
+ Project Home +
+
+ Builds +
+
+ Downloads +
+
+
+
Search
+
+
+ +
+
+
+
+ + Hosted by Read the Docs + +
+
+ `; + + // Inject the generated flyout into the body HTML element. + document.body.insertAdjacentHTML("beforeend", flyout); + + // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout. + document + .querySelector("#flyout-search-form") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); + }) +} + +if (themeLanguageSelector || themeVersionSelector) { + function onSelectorSwitch(event) { + const option = event.target.selectedIndex; + const item = event.target.options[option]; + window.location.href = item.dataset.url; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const versionSwitch = document.querySelector( + "div.switch-menus > div.version-switch", + ); + if (themeVersionSelector) { + let versions = config.versions.active; + if (config.versions.current.hidden || config.versions.current.type === "external") { + versions.unshift(config.versions.current); + } + const versionSelect = ` + + `; + + versionSwitch.innerHTML = versionSelect; + versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + + const languageSwitch = document.querySelector( + "div.switch-menus > div.language-switch", + ); + + if (themeLanguageSelector) { + if (config.projects.translations.length) { + // Add the current language to the options on the selector + let languages = config.projects.translations.concat( + config.projects.current, + ); + languages = languages.sort((a, b) => + a.language.name.localeCompare(b.language.name), + ); + + const languageSelect = ` + + `; + + languageSwitch.innerHTML = languageSelect; + languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + else { + languageSwitch.remove(); + } + } + }); +} + +document.addEventListener("readthedocs-addons-data-ready", function (event) { + // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav. + document + .querySelector("[role='search'] input") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js index 250f566..c7fe6c6 100644 --- a/docs/build/html/_static/language_data.js +++ b/docs/build/html/_static/language_data.js @@ -1,19 +1,12 @@ /* - * language_data.js - * ~~~~~~~~~~~~~~~~ - * * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/docs/build/html/_static/pygments.css b/docs/build/html/_static/pygments.css index 0d49244..5f2b0a2 100644 --- a/docs/build/html/_static/pygments.css +++ b/docs/build/html/_static/pygments.css @@ -6,26 +6,26 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: .highlight .hll { background-color: #ffffcc } .highlight { background: #eeffcc; } .highlight .c { color: #408090; font-style: italic } /* Comment */ -.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .err { border: 1px solid #F00 } /* Error */ .highlight .k { color: #007020; font-weight: bold } /* Keyword */ -.highlight .o { color: #666666 } /* Operator */ +.highlight .o { color: #666 } /* Operator */ .highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */ .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */ .highlight .cp { color: #007020 } /* Comment.Preproc */ .highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */ .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */ -.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */ +.highlight .cs { color: #408090; background-color: #FFF0F0 } /* Comment.Special */ .highlight .gd { color: #A00000 } /* Generic.Deleted */ .highlight .ge { font-style: italic } /* Generic.Emph */ .highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ -.highlight .gr { color: #FF0000 } /* Generic.Error */ +.highlight .gr { color: #F00 } /* Generic.Error */ .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ .highlight .gi { color: #00A000 } /* Generic.Inserted */ -.highlight .go { color: #333333 } /* Generic.Output */ -.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */ +.highlight .go { color: #333 } /* Generic.Output */ +.highlight .gp { color: #C65D09; font-weight: bold } /* Generic.Prompt */ .highlight .gs { font-weight: bold } /* Generic.Strong */ .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */ -.highlight .gt { color: #0044DD } /* Generic.Traceback */ +.highlight .gt { color: #04D } /* Generic.Traceback */ .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */ .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */ .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */ @@ -33,43 +33,43 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */ .highlight .kt { color: #902000 } /* Keyword.Type */ .highlight .m { color: #208050 } /* Literal.Number */ -.highlight .s { color: #4070a0 } /* Literal.String */ -.highlight .na { color: #4070a0 } /* Name.Attribute */ +.highlight .s { color: #4070A0 } /* Literal.String */ +.highlight .na { color: #4070A0 } /* Name.Attribute */ .highlight .nb { color: #007020 } /* Name.Builtin */ -.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */ -.highlight .no { color: #60add5 } /* Name.Constant */ -.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */ -.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */ +.highlight .nc { color: #0E84B5; font-weight: bold } /* Name.Class */ +.highlight .no { color: #60ADD5 } /* Name.Constant */ +.highlight .nd { color: #555; font-weight: bold } /* Name.Decorator */ +.highlight .ni { color: #D55537; font-weight: bold } /* Name.Entity */ .highlight .ne { color: #007020 } /* Name.Exception */ -.highlight .nf { color: #06287e } /* Name.Function */ +.highlight .nf { color: #06287E } /* Name.Function */ .highlight .nl { color: #002070; font-weight: bold } /* Name.Label */ -.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */ +.highlight .nn { color: #0E84B5; font-weight: bold } /* Name.Namespace */ .highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */ -.highlight .nv { color: #bb60d5 } /* Name.Variable */ +.highlight .nv { color: #BB60D5 } /* Name.Variable */ .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */ -.highlight .w { color: #bbbbbb } /* Text.Whitespace */ +.highlight .w { color: #BBB } /* Text.Whitespace */ .highlight .mb { color: #208050 } /* Literal.Number.Bin */ .highlight .mf { color: #208050 } /* Literal.Number.Float */ .highlight .mh { color: #208050 } /* Literal.Number.Hex */ .highlight .mi { color: #208050 } /* Literal.Number.Integer */ .highlight .mo { color: #208050 } /* Literal.Number.Oct */ -.highlight .sa { color: #4070a0 } /* Literal.String.Affix */ -.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */ -.highlight .sc { color: #4070a0 } /* Literal.String.Char */ -.highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */ -.highlight .sd { color: #4070a0; 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@@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") { // and returns the new score. /* score: result => { - const [docname, title, anchor, descr, score, filename] = result + const [docname, title, anchor, descr, score, filename, kind] = result return score }, */ @@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") { }; } +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + const _removeChildren = (element) => { while (element && element.lastChild) element.removeChild(element.lastChild); }; @@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => { const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; const contentRoot = document.documentElement.dataset.content_root; - const [docName, title, anchor, descr, score, _filename] = item; + const [docName, title, anchor, descr, score, _filename, kind] = item; let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); let requestUrl; let linkUrl; if (docBuilder === "dirhtml") { @@ -99,7 +104,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -115,9 +120,11 @@ const _finishSearch = (resultCount) => { "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." ); else - Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +144,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +183,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -219,6 +255,7 @@ const Search = { searchSummary.classList.add("search-summary"); searchSummary.innerText = ""; const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); searchList.classList.add("search"); const out = document.getElementById("search-results"); @@ -239,16 +276,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,22 +312,40 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) - results.push([ + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", null, - score, + score + boost, filenames[file], + SearchResultKind.title, ]); } } @@ -308,46 +354,48 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +409,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -432,6 +485,7 @@ const Search = { descr, score, filenames[match[0]], + SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -459,21 +513,27 @@ const Search = { // perform the search on the required terms searchTerms.forEach((word) => { const files = []; + // find documents, if any, containing the query word in their text/title term indices + // use Object.hasOwnProperty to avoid mismatching against prototype properties const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, + { files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term }, + { files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, score: Scorer.title }, ]; // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -489,16 +549,16 @@ const Search = { // set score for the word in each file recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; + if (!scoreMap.has(file)) scoreMap.set(file, new Map()); + const fileScores = scoreMap.get(file); + fileScores.set(word, record.score); }); }); // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -530,7 +590,7 @@ const Search = { break; // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + const score = Math.max(...wordList.map((w) => scoreMap.get(file).get(w))); // add result to the result list results.push([ docNames[file], @@ -539,6 +599,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.text, ]); } return results; @@ -549,8 +610,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/docs/build/html/advanced.html b/docs/build/html/advanced.html index 00ebe77..368f597 100644 --- a/docs/build/html/advanced.html +++ b/docs/build/html/advanced.html @@ -1,24 +1,22 @@ + + - Advanced Usage — DFO-LS v1.5.4 documentation - - + Advanced Usage — DFO-LS v1.6 documentation + + - - - - - - - - + + + + + + @@ -37,9 +35,6 @@ DFO-LS -
- 1.5.4 -
diff --git a/docs/build/html/contributors.html b/docs/build/html/contributors.html index 4ac629b..481c229 100644 --- a/docs/build/html/contributors.html +++ b/docs/build/html/contributors.html @@ -1,23 +1,21 @@ + + - Contributors — DFO-LS v1.5.4 documentation - - + Contributors — DFO-LS v1.6 documentation + + - - - - - - - + + + + + @@ -35,9 +33,6 @@ DFO-LS -
- 1.5.4 -
@@ -90,7 +85,7 @@

Contributors

Main author

diff --git a/docs/build/html/diagnostic.html b/docs/build/html/diagnostic.html index 49a22d4..00d9125 100644 --- a/docs/build/html/diagnostic.html +++ b/docs/build/html/diagnostic.html @@ -1,24 +1,22 @@ + + - Diagnostic Information — DFO-LS v1.5.4 documentation - - + Diagnostic Information — DFO-LS v1.6 documentation + + - - - - - - - - + + + + + + @@ -37,9 +35,6 @@ DFO-LS -
- 1.5.4 -
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html index aa7b49a..575c9c6 100644 --- a/docs/build/html/genindex.html +++ b/docs/build/html/genindex.html @@ -1,22 +1,20 @@ + + - Index — DFO-LS v1.5.4 documentation - - + Index — DFO-LS v1.6 documentation + + - - - - - - - + + + + + @@ -33,9 +31,6 @@ DFO-LS -
- 1.5.4 -
diff --git a/docs/build/html/history.html b/docs/build/html/history.html index 0e3329a..62559cf 100644 --- a/docs/build/html/history.html +++ b/docs/build/html/history.html @@ -1,23 +1,21 @@ + + - Version History — DFO-LS v1.5.4 documentation - - + Version History — DFO-LS v1.6 documentation + + - - - - - - - + + + + + @@ -36,9 +34,6 @@ DFO-LS -
- 1.5.4 -
@@ -72,6 +67,7 @@
  • Version 1.5.2 (28 Oct 2024)
  • Version 1.5.3 (30 Oct 2024)
  • Version 1.5.4 (11 Feb 2025)
    • +
  • Version 1.6 (10 Sep 2025)
  • Contributors
    • @@ -221,6 +217,13 @@

    Version 1.5.4 (11 Feb 2025) +

    Version 1.6 (10 Sep 2025)

    +
      +

    • Allow use of evaluation database as x0 to reduce number of objective evaluations required in initialization phase

      • +

    • When printing solution object, reduce the maximum length of residual/Jacobian vectors that are fully displayed

      • +
    +

    diff --git a/docs/build/html/index.html b/docs/build/html/index.html index b072139..8494522 100644 --- a/docs/build/html/index.html +++ b/docs/build/html/index.html @@ -1,24 +1,22 @@ + + - DFO-LS: Derivative-Free Optimizer for Least-Squares Minimization — DFO-LS v1.5.4 documentation - - + DFO-LS: Derivative-Free Optimizer for Least-Squares Minimization — DFO-LS v1.6 documentation + + - - - - - - - - + + + + + + @@ -36,9 +34,6 @@ DFO-LS -
    - 1.5.4 -
    @@ -84,8 +79,8 @@

    DFO-LS: Derivative-Free Optimizer for Least-Squares Minimization

    -

    Release: 1.5.4

    -

    Date: 11 February 2025

    +

    Release: 1.6

    +

    Date: 10 September 2025

    Author: Lindon Roberts

    DFO-LS is a flexible package for finding local solutions to nonlinear least-squares minimization problems (with optional regularizer and constraints), without requiring any derivatives of the objective. DFO-LS stands for Derivative-Free Optimizer for Least-Squares.

    That is, DFO-LS solves

    @@ -143,6 +138,7 @@

    DFO-LS: Derivative-Free Optimizer for Least-Squares MinimizationAdding Bounds and More Output
  • Adding General Convex Constraints
  • Adding a Regularizer
    • +
  • Using Initial Evaluation Database
  • Example: Noisy Objective Evaluation
  • Example: Parameter Estimation/Data Fitting
  • Example: Solving a Nonlinear System of Equations
    • @@ -193,6 +189,7 @@

    DFO-LS: Derivative-Free Optimizer for Least-Squares MinimizationVersion 1.5.2 (28 Oct 2024)
  • Version 1.5.3 (30 Oct 2024)
  • Version 1.5.4 (11 Feb 2025)
    • +
  • Version 1.6 (10 Sep 2025)
  • Contributors
      diff --git a/docs/build/html/info.html b/docs/build/html/info.html index 575c939..b1d4e5b 100644 --- a/docs/build/html/info.html +++ b/docs/build/html/info.html @@ -1,24 +1,22 @@ + + - Overview — DFO-LS v1.5.4 documentation - - + Overview — DFO-LS v1.6 documentation + + - - - - - - - - + + + + + + @@ -37,9 +35,6 @@ DFO-LS -
      - 1.5.4 -
      diff --git a/docs/build/html/install.html b/docs/build/html/install.html index a607dc2..50858fc 100644 --- a/docs/build/html/install.html +++ b/docs/build/html/install.html @@ -1,23 +1,21 @@ + + - Installing DFO-LS — DFO-LS v1.5.4 documentation - - + Installing DFO-LS — DFO-LS v1.6 documentation + + - - - - - - - + + + + + @@ -36,9 +34,6 @@ DFO-LS -
      - 1.5.4 -
      diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv index 6af97ea..6e114c2 100644 Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ diff --git a/docs/build/html/search.html b/docs/build/html/search.html index 867e393..877dbd4 100644 --- a/docs/build/html/search.html +++ b/docs/build/html/search.html @@ -1,23 +1,21 @@ + + - Search — DFO-LS v1.5.4 documentation - - + Search — DFO-LS v1.6 documentation + + - - - - - - - + + + + + @@ -36,9 +34,6 @@ DFO-LS -
      - 1.5.4 -
      diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js index 4cd082d..8d78da1 100644 --- a/docs/build/html/searchindex.js +++ b/docs/build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["advanced", "contributors", "diagnostic", "history", "index", "info", "install", "userguide"], "filenames": ["advanced.rst", "contributors.rst", "diagnostic.rst", "history.rst", "index.rst", "info.rst", "install.rst", "userguide.rst"], "titles": ["Advanced Usage", "Contributors", "Diagnostic Information", "Version History", "DFO-LS: Derivative-Free Optimizer for Least-Squares Minimization", "Overview", "Installing DFO-LS", "Using DFO-LS"], "terms": {"thi": [0, 2, 3, 4, 5, 6, 7], "section": [0, 2, 3, 7], "describ": [0, 5, 7], "differ": [0, 3, 5, 7], "option": [0, 3, 4, 5, 6], "user": [0, 4, 5, 7], "avail": [0, 7], "dfo": [0, 2, 3], "l": [0, 2, 3], "In": [0, 2, 5, 7], "last": [0, 2], "us": [0, 2, 3, 4], "we": [0, 2, 5, 7], "introduc": [0, 3], "dfol": [0, 2, 6, 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\ No newline at end of file diff --git a/docs/build/html/userguide.html b/docs/build/html/userguide.html index cb4220f..46abb97 100644 --- a/docs/build/html/userguide.html +++ b/docs/build/html/userguide.html @@ -1,24 +1,22 @@ + + - Using DFO-LS — DFO-LS v1.5.4 documentation - - + Using DFO-LS — DFO-LS v1.6 documentation + + - - - - - - - - + + + + + + @@ -37,9 +35,6 @@ DFO-LS -
      - 1.5.4 -
      @@ -60,6 +55,7 @@
    • Adding Bounds and More Output
    • Adding General Convex Constraints
    • Adding a Regularizer
      • +
    • Using Initial Evaluation Database
    • Example: Noisy Objective Evaluation
    • Example: Parameter Estimation/Data Fitting
    • Example: Solving a Nonlinear System of Equations
      • @@ -124,6 +120,10 @@

      How to use DFO-LSobjfun is a Python function which takes an input \(x\in\mathbb{R}^n\) and returns the vector of residuals \([r_1(x)\: \cdots \: r_m(x)]\in\mathbb{R}^m\). Both the input and output of objfun must be one-dimensional NumPy arrays (i.e. with x.shape == (n,) and objfun(x).shape == (m,)).

      The input x0 is the starting point for the solver, and (where possible) should be set to be the best available estimate of the true solution \(x_{min}\in\mathbb{R}^n\). It should be specified as a one-dimensional NumPy array (i.e. with x0.shape == (n,)). As DFO-LS is a local solver, providing different values for x0 may cause it to return different solutions, with possibly different objective values.

      +

      In newer version of DFO-LS (v1.6 onwards), the input x0 may instead by an instance of a dfols.EvaluationDatabase, which stores a collection +of previously evaluated points and their associated vectors of residuals. One of these points is designated the starting point for the solver, and the other +points may be used by DFO-LS to build its first approximation to objfun, reducing the number of evaluations required to begin the main iteration. +See the example below for more details for how to use this functionality.

      The output of dfols.solve is an object containing:

    • +
    +

    Using Initial Evaluation Database

    +

    Since DFO-LS v1.6, the input x0 may instead be an instance of a dfols.EvaluationDatabase class containing a collection of previously evaluated +points and their associated vectors of residuals. One of these points must be flagged as the starting point for the solver (otherwise, the most recently added +point is used). DFO-LS will automaticaly select some (but possibly none/all) of the other points to help build its first internal approximation to the objective, +which reduces the number of times the objective must be evaluated during the initialization phase, before the main algorithm can begin.

    +

    For example, suppose we want to use DFO-LS to minimize the Watson test function (Problem 20 from [MGH1981]). Using the standard starting point, our code looks like

    +
    +
    import numpy as np
+import dfols
+
+# Define the objective function
+def watson(x):
+    n = len(x)
+    m = 31
+    fvec = np.zeros((m,), dtype=float)
+    for i in range(1, 30):  # i=1,...,29
+        div = float(i) / 29.0
+        s1 = 0.0
+        dx = 1.0
+        for j in range(2, n + 1):  # j = 2,...,n
+            s1 = s1 + (j - 1) * dx * x[j - 1]
+            dx = div * dx
+        s2 = 0.0
+        dx = 1.0
+        for j in range(1, n + 1):  # j = 1,...,n
+            s2 = s2 + dx * x[j - 1]
+            dx = div * dx
+        fvec[i - 1] = s1 - s2 ** 2 - 1.0
+    fvec[29] = x[0]
+    fvec[30] = x[1] - x[0] ** 2 - 1.0
+    return fvec
+
+# Define the starting point
+n = 6
+x0 = 0.5 * np.ones((n,), dtype=float)
+
+# Show extra output to demonstrate the impact of using an initial evaluation database
+import logging
+logging.basicConfig(level=logging.INFO, format='%(message)s')
+
+# Call DFO-LS
+soln = dfols.solve(watson, x0)
+
+# Display output
+print(soln)
+
    +
    +
    +

    In the output of this code, we can check that DFO-LS finds the unique minimizer of this function. We can also see that before the main loop can begin, +DFO-LS needs to evaluate the objective at the given starting point, and 6 extra points (since this problem has 6 variables to be minimized):

    +
    +
    Function eval 1 at point 1 has obj = 16.4308311759923 at x = [...]
+Initialising (coordinate directions)
+Function eval 2 at point 2 has obj = 28.9196967094733 at x = [...]
+Function eval 3 at point 3 has obj = 22.0866904737059 at x = [...]
+Function eval 4 at point 4 has obj = 20.6560889343479 at x = [...]
+Function eval 5 at point 5 has obj = 19.2914312375462 at x = [...]
+Function eval 6 at point 6 has obj = 18.0373781384725 at x = [...]
+Function eval 7 at point 7 has obj = 16.8946356501339 at x = [...]
+Beginning main loop
+Function eval 8 at point 8 has obj = 8.45207899459595 at x = [...]
+Function eval 9 at point 9 has obj = 2.54949692496583 at x = [...]
+...
+Function eval 90 at point 90 has obj = 0.00228767005355292 at x = [...]
+Did a total of 1 run(s)
+
+****** DFO-LS Results ******
+Solution xmin = [-0.01572509  1.01243487 -0.23299162  1.26043004 -1.51372886  0.99299641]
+Not showing residual vector because it is too long; check self.resid
+Objective value f(xmin) = 0.002287670054
+Needed 90 objective evaluations (at 90 points)
+Not showing approximate Jacobian because it is too long; check self.jacobian
+Solution xmin was evaluation point 89
+Approximate Jacobian formed using evaluation points [87 85 76 89 86 88 84]
+Exit flag = 0
+Success: rho has reached rhoend
+****************************
+
    +
    +
    +

    Instead of this, we can build a database of points where we have previously evaluated the objective, marking one of them as the starting point +for the algorithm. DFO-LS will then select some/all (but possibly none) of the other points and use them as initial evaluations, allowing it to begin +the main loop faster. In general, DFO-LS will select points that are:

    +
      +

    • Not too close/far from the selected starting point (relative to the initial trust-region radius, input rhobeg)

      • +

    • Not in similar directions (relative to the selected starting point) to other selected initial points. For example, if several points differ from +the selected starting point in only the first variable, at most one of these will be selected.

      • +
    +

    The following code demonstrates how an evaluation database may be constructed and given to DFO-LS:

    +
    +
    # Assuming numpy and dfols already imported, watson function already defined
+
+# Build a database of evaluations
+eval_db = dfols.EvaluationDatabase()
+
+# Define the starting point and add it to the database
+n = 6
+x0 = 0.5 * np.ones((n,), dtype=float)
+eval_db.append(x0, watson(x0), make_starting_eval=True)
+# make_starting_eval=True --> use this point as the starting point for DFO-LS
+
+# Add other points to the database
+# Note: x0, x1 and x2 are colinear, so at least one of x1 and x2 will not be included in the initial model
+x1 = np.ones((n,), dtype=float)
+x2 = np.zeros((n,), dtype=float)
+x3 = np.arange(n).astype(float)
+eval_db.append(x1, watson(x1))
+eval_db.append(x2, watson(x2))
+eval_db.append(x3, watson(x3))
+
+# Show extra output to demonstrate the impact of using an initial evaluation database
+import logging
+logging.basicConfig(level=logging.INFO, format='%(message)s')
+
+# Call DFO-LS
+soln = dfols.solve(watson, x0)
+
+# Display output
+print(soln)
+
    +
    +
    +

    Running this code, we get the same (correct) answer but using fewer evaluations of the objective in the main call to dfols.solve(). +The logging information reveals that x0 was used as the starting point, and x1 and x3 were used to build the initial model. +This means that only 4 evaluations of the objective were required in the initialization phase.

    +
    +
    Using pre-existing evaluation 0 as starting point
+Adding pre-existing evaluation 1 to initial model
+Adding pre-existing evaluation 3 to initial model
+Function eval 1 at point 1 has obj = 15.1910664616598 at x = [...]
+Function eval 2 at point 2 has obj = 15.2288491702299 at x = [...]
+Function eval 3 at point 3 has obj = 15.228054997542 at x = [...]
+Function eval 4 at point 4 has obj = 15.3011037277481 at x = [...]
+Beginning main loop
+Function eval 5 at point 5 has obj = 13.5524099633802 at x = [...]
+Function eval 6 at point 6 has obj = 7.33371957636104 at x = [...]
+...
+Function eval 81 at point 81 has obj = 0.00228767005355266 at x = [...]
+Did a total of 1 run(s)
+
+****** DFO-LS Results ******
+Solution xmin = [-0.01572509  1.01243487 -0.23299163  1.26043009 -1.51372893  0.99299643]
+Not showing residual vector because it is too long; check self.resid
+Objective value f(xmin) = 0.002287670054
+Needed 81 objective evaluations (at 81 points)
+Not showing approximate Jacobian because it is too long; check self.jacobian
+Solution xmin was evaluation point 77
+Approximate Jacobian formed using evaluation points [76 73 79 74 77 75 80]
+Exit flag = 0
+Success: rho has reached rhoend
+****************************
+
    +
    +
    +

    Note that the indices of the evaluation database mentioned in the log refer to the order in which the points were added to the evaluation database.

    +

    Example: Noisy Objective Evaluation

    As described in Overview, derivative-free algorithms such as DFO-LS are particularly useful when objfun has noise. Let’s modify the previous example to include random noise in our objective evaluation, and compare it to SciPy’s derivative-based solver (the below results came from using SciPy v1.13.0):

    # DFO-LS example: minimize the noisy Rosenbrock function
-from __future__ import print_function
-import numpy as np
-import dfols
+from __future__ import print_function
+import numpy as np
+import dfols
 
 # Define the objective function
-def rosenbrock(x):
+def rosenbrock(x):
     return np.array([10.0 * (x[1] - x[0] ** 2), 1.0 - x[0]])
 
 # Modified objective function: add 1% Gaussian noise
-def rosenbrock_noisy(x):
+def rosenbrock_noisy(x):
     return rosenbrock(x) * (1.0 + 1e-2 * np.random.normal(size=(2,)))
 
 # Define the starting point
@@ -534,7 +691,7 @@ 
    Example: Noisy Objective Evaluationprint(soln)
 
 # Compare with a derivative-based solver
-import scipy.optimize as opt
+import scipy.optimize as opt
 soln = opt.least_squares(rosenbrock_noisy, x0)
 
 print("")
@@ -614,9 +771,9 @@ 
    Example: Parameter Estimation/Data Fitting
    # DFO-LS example: data fitting problem
 # Originally from:
 # https://uk.mathworks.com/help/optim/ug/lsqcurvefit.html
-from __future__ import print_function
-import numpy as np
-import dfols
+from __future__ import print_function
+import numpy as np
+import dfols
 
 # Observations
 tdata = np.array([0.9, 1.5, 13.8, 19.8, 24.1, 28.2, 35.2,
@@ -625,7 +782,7 @@ 
    Example: Parameter Estimation/Data Fitting-0.4, -1.3, -1.5])
 
 # Model is y(t) = x[0] * exp(x[1] * t)
-def prediction_error(x):
+def prediction_error(x):
     return ydata - x[0] * np.exp(x[1] * tdata)
 
 # Define the starting point
@@ -669,14 +826,15 @@ 
    Example: Parameter Estimation/Data FittingData Fitting Results
+Data Fitting Results
+
 
    To generate this plot, run:
    
 
    
 
    # Plot calibrated model vs. observations
 ts = np.linspace(0.0, 90.0)
 ys = soln.x[0] * np.exp(soln.x[1] * ts)
 
-import matplotlib.pyplot as plt
+import matplotlib.pyplot as plt
 plt.figure(1)
 ax = plt.gca()  # current axes
 ax.plot(ts, ys, 'k-', label='Model')
@@ -702,15 +860,15 @@ 
    Example: Solving a Nonlinear System of Equations# Originally from:
 # http://support.sas.com/documentation/cdl/en/imlug/66112/HTML/default/viewer.htm#imlug_genstatexpls_sect004.htm
 
-from __future__ import print_function
-from math import exp
-import numpy as np
-import dfols
+from __future__ import print_function
+from math import exp
+import numpy as np
+import dfols
 
 # Want to solve:
 #   x1 + x2 - x1*x2 + 2 = 0
 #   x1 * exp(-x2) - 1   = 0
-def nonlinear_system(x):
+def nonlinear_system(x):
     return np.array([x[0] + x[1] - x[0]*x[1] + 2,
                      x[0] * exp(-x[1]) - 1.0])
 
@@ -765,6 +923,10 @@ 
    References(1,2)
 
    Amir Beck, First-Order Methods in Optimization, SIAM (2017).
    
 
    
+
    
+[MGH1981]
+
    Jorge J. More, Burton S. Garbow and Kenneth E. Hillstrom, Testing Unconstrained Optimization Software, ACM Transactions on Mathematical Software, 7:1 (1981), pp. 17-41.
    
+
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makeindex, version 2.17 [TeX Live 2023] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file DFOLS.idx...done (0 entries accepted, 0 rejected). 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(pdftex.def) Requested size: 352.31625pt x 270.79639pt. - [21 <./data_fitting.png>] [22] [23] [24 - -] + [24 <./data_fitting.png>] [25] [26] Chapter 4. -[25] [26] -Underfull \hbox (badness 6725) in paragraph at lines 1516--1518 +[27 + +] [28] +Underfull \hbox (badness 6725) in paragraph at lines 1703--1705 []\T1/txtt/m/n/10 regression.increase_num_extra_steps_with_restart \T1/qtm/m/n/ 10 - The amount to in-crease \T1/txtt/m/n/10 regression. [] -[27] [28] [29] [30] -Chapter 5. -[31 +[29] [30] [31] [32 -] [32] +] +Chapter 5. +[33] [34] Chapter 6. -[33 +[35 -] [34] [35] [36 +] [36] [37] [38 ] Chapter 7. -[37] [38 +[39] [40 ] Chapter 8. -[39] [40 +[41] [42 -] (./DFOLS.ind) [41 +] (./DFOLS.ind) [43 ] (./DFOLS.aux) + *********** +LaTeX2e <2023-11-01> patch level 1 +L3 programming layer <2024-01-22> + *********** Package rerunfilecheck Info: File `DFOLS.out' has not changed. -(rerunfilecheck) Checksum: B1D090D924F9CAE29B25AFECFC8CF68A;12063. +(rerunfilecheck) Checksum: B8D2C0D2FC673CBE8A323F2B3C55D7BA;12492. ) Here is how much of TeX's memory you used: - 16273 strings out of 480247 - 271557 string characters out of 5896151 - 632502 words of memory out of 5000000 - 33688 multiletter control sequences out of 15000+600000 - 526530 words of font info for 75 fonts, out of 8000000 for 9000 + 20160 strings out of 476182 + 357968 string characters out of 5795595 + 1997975 words of memory out of 5000000 + 41617 multiletter control sequences out of 15000+600000 + 615340 words of font info for 83 fonts, out of 8000000 for 9000 15 hyphenation exceptions out of 8191 - 70i,20n,76p,887b,609s stack positions out of 5000i,500n,10000p,200000b,80000s -{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/ -fonts/enc/dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q --ec.enc}< -/usr/share/texmf/fonts/type1/public/tex-gyre/qtmri.pfb> -Output written on DFOLS.pdf (45 pages, 387990 bytes). + 72i,20n,83p,1194b,719s stack positions out of 10000i,1000n,20000p,200000b,200000s + +Output written on DFOLS.pdf (47 pages, 397982 bytes). 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\renewcommand{\releasename}{Release} @@ -86,10 +86,10 @@ \sphinxAtStartPar -\sphinxstylestrong{Release:} 1.5.4 +\sphinxstylestrong{Release:} 1.6 \sphinxAtStartPar -\sphinxstylestrong{Date:} 11 February 2025 +\sphinxstylestrong{Date:} 10 September 2025 \sphinxAtStartPar \sphinxstylestrong{Author:} \sphinxhref{https://lindonroberts.github.io/}{Lindon Roberts} @@ -446,6 +446,12 @@ \section{How to use DFO\sphinxhyphen{}LS} The input \sphinxcode{\sphinxupquote{x0}} is the starting point for the solver, and (where possible) should be set to be the best available estimate of the true solution \(x_{min}\in\mathbb{R}^n\). It should be specified as a one\sphinxhyphen{}dimensional NumPy array (i.e. with \sphinxcode{\sphinxupquote{x0.shape == (n,)}}). As DFO\sphinxhyphen{}LS is a local solver, providing different values for \sphinxcode{\sphinxupquote{x0}} may cause it to return different solutions, with possibly different objective values. +\sphinxAtStartPar +In newer version of DFO\sphinxhyphen{}LS (v1.6 onwards), the input \sphinxcode{\sphinxupquote{x0}} may instead by an instance of a \sphinxcode{\sphinxupquote{dfols.EvaluationDatabase}}, which stores a collection +of previously evaluated points and their associated vectors of residuals. One of these points is designated the starting point for the solver, and the other +points may be used by DFO\sphinxhyphen{}LS to build its first approximation to \sphinxcode{\sphinxupquote{objfun}}, reducing the number of evaluations required to begin the main iteration. +See the example below for more details for how to use this functionality. + \sphinxAtStartPar The output of \sphinxcode{\sphinxupquote{dfols.solve}} is an object containing: \begin{itemize} @@ -556,7 +562,7 @@ \section{How to use DFO\sphinxhyphen{}LS} \begin{quote} \begin{sphinxVerbatim}[commandchars=\\\{\}] -\PYG{k+kn}{import} \PYG{n+nn}{json} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{json} \PYG{n}{soln\PYGZus{}dict} \PYG{o}{=} \PYG{n}{soln}\PYG{o}{.}\PYG{n}{to\PYGZus{}dict}\PYG{p}{(}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} convert soln to serializable dict object} \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{dfols\PYGZus{}results.json}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}}\PYG{l+s+s1}{w}\PYG{l+s+s1}{\PYGZsq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{f}\PYG{p}{:} \PYG{n}{json}\PYG{o}{.}\PYG{n}{dump}\PYG{p}{(}\PYG{n}{soln\PYGZus{}dict}\PYG{p}{,} \PYG{n}{f}\PYG{p}{,} \PYG{n}{indent}\PYG{o}{=}\PYG{l+m+mi}{2}\PYG{p}{)} @@ -571,7 +577,7 @@ \section{How to use DFO\sphinxhyphen{}LS} \begin{quote} \begin{sphinxVerbatim}[commandchars=\\\{\}] -\PYG{k+kn}{import} \PYG{n+nn}{json} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{json} \PYG{n}{soln\PYGZus{}dict} \PYG{o}{=} \PYG{k+kc}{None} \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{dfols\PYGZus{}results.json}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{f}\PYG{p}{:} \PYG{n}{soln\PYGZus{}dict} \PYG{o}{=} \PYG{n}{json}\PYG{o}{.}\PYG{n}{load}\PYG{p}{(}\PYG{n}{f}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} read JSON into dict} @@ -699,12 +705,12 @@ \section{A Simple Example} \begin{sphinxVerbatim}[commandchars=\\\{\}] \PYG{c+c1}{\PYGZsh{} DFO\PYGZhy{}LS example: minimize the Rosenbrock function} -\PYG{k+kn}{from} \PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}} \PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} -\PYG{k+kn}{import} \PYG{n+nn}{numpy} \PYG{k}{as} \PYG{n+nn}{np} -\PYG{k+kn}{import} \PYG{n+nn}{dfols} +\PYG{k+kn}{from}\PYG{+w}{ }\PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}}\PYG{+w}{ }\PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{numpy}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{np} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{dfols} \PYG{c+c1}{\PYGZsh{} Define the objective function} -\PYG{k}{def} \PYG{n+nf}{rosenbrock}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} +\PYG{k}{def}\PYG{+w}{ }\PYG{n+nf}{rosenbrock}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} \PYG{k}{return} \PYG{n}{np}\PYG{o}{.}\PYG{n}{array}\PYG{p}{(}\PYG{p}{[}\PYG{l+m+mf}{10.0} \PYG{o}{*} \PYG{p}{(}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{*}\PYG{o}{*} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{,} \PYG{l+m+mf}{1.0} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} Define the starting point} @@ -795,7 +801,7 @@ \section{Adding Bounds and More Output} \begin{quote} \begin{sphinxVerbatim}[commandchars=\\\{\}] -\PYG{k+kn}{import} \PYG{n+nn}{logging} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{logging} \PYG{n}{logging}\PYG{o}{.}\PYG{n}{basicConfig}\PYG{p}{(}\PYG{n}{level}\PYG{o}{=}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{INFO}\PYG{p}{,} \PYG{n+nb}{format}\PYG{o}{=}\PYG{l+s+s1}{\PYGZsq{}}\PYG{l+s+si}{\PYGZpc{}(message)s}\PYG{l+s+s1}{\PYGZsq{}}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} ... (call dfols.solve)} @@ -895,11 +901,11 @@ \section{Adding General Convex Constraints} \begin{quote} \begin{sphinxVerbatim}[commandchars=\\\{\}] -\PYG{k+kn}{import} \PYG{n+nn}{numpy} \PYG{k}{as} \PYG{n+nn}{np} -\PYG{k+kn}{import} \PYG{n+nn}{dfols} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{numpy}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{np} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{dfols} \PYG{c+c1}{\PYGZsh{} Define the objective function} -\PYG{k}{def} \PYG{n+nf}{rosenbrock}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} +\PYG{k}{def}\PYG{+w}{ }\PYG{n+nf}{rosenbrock}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} \PYG{k}{return} \PYG{n}{np}\PYG{o}{.}\PYG{n}{array}\PYG{p}{(}\PYG{p}{[}\PYG{l+m+mf}{10.0} \PYG{o}{*} \PYG{p}{(}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{*}\PYG{o}{*} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{,} \PYG{l+m+mf}{1.0} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} Define the starting point} @@ -991,8 +997,8 @@ \section{Adding a Regularizer} \begin{sphinxVerbatim}[commandchars=\\\{\}] \PYG{c+c1}{\PYGZsh{} DFO\PYGZhy{}LS example: regularized least\PYGZhy{}squares regression} -\PYG{k+kn}{import} \PYG{n+nn}{numpy} \PYG{k}{as} \PYG{n+nn}{np} -\PYG{k+kn}{import} \PYG{n+nn}{dfols} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{numpy}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{np} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{dfols} \PYG{n}{n} \PYG{o}{=} \PYG{l+m+mi}{5} \PYG{c+c1}{\PYGZsh{} dimension of x} \PYG{n}{m} \PYG{o}{=} \PYG{l+m+mi}{10} \PYG{c+c1}{\PYGZsh{} number of residuals, i.e. dimension of b} @@ -1049,6 +1055,187 @@ \section{Adding a Regularizer} Note that many LASSO\sphinxhyphen{}type algorithms can produce a solution with many entries being exactly zero, but DFO\sphinxhyphen{}LS can only make them very small (related to how it calculates a new point with trust\sphinxhyphen{}region constraints). +\section{Using Initial Evaluation Database} +\label{\detokenize{userguide:using-initial-evaluation-database}} +\sphinxAtStartPar +Since DFO\sphinxhyphen{}LS v1.6, the input \sphinxcode{\sphinxupquote{x0}} may instead be an instance of a \sphinxcode{\sphinxupquote{dfols.EvaluationDatabase}} class containing a collection of previously evaluated +points and their associated vectors of residuals. One of these points must be flagged as the starting point for the solver (otherwise, the most recently added +point is used). DFO\sphinxhyphen{}LS will automaticaly select some (but possibly none/all) of the other points to help build its first internal approximation to the objective, +which reduces the number of times the objective must be evaluated during the initialization phase, before the main algorithm can begin. + +\sphinxAtStartPar +For example, suppose we want to use DFO\sphinxhyphen{}LS to minimize the Watson test function (Problem 20 from \sphinxcite{userguide:mgh1981}). Using the standard starting point, our code looks like +\begin{quote} + +\begin{sphinxVerbatim}[commandchars=\\\{\}] +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{numpy}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{np} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{dfols} + +\PYG{c+c1}{\PYGZsh{} Define the objective function} +\PYG{k}{def}\PYG{+w}{ }\PYG{n+nf}{watson}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} + \PYG{n}{n} \PYG{o}{=} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)} + \PYG{n}{m} \PYG{o}{=} \PYG{l+m+mi}{31} + \PYG{n}{fvec} \PYG{o}{=} \PYG{n}{np}\PYG{o}{.}\PYG{n}{zeros}\PYG{p}{(}\PYG{p}{(}\PYG{n}{m}\PYG{p}{,}\PYG{p}{)}\PYG{p}{,} \PYG{n}{dtype}\PYG{o}{=}\PYG{n+nb}{float}\PYG{p}{)} + \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{30}\PYG{p}{)}\PYG{p}{:} \PYG{c+c1}{\PYGZsh{} i=1,...,29} + \PYG{n}{div} \PYG{o}{=} \PYG{n+nb}{float}\PYG{p}{(}\PYG{n}{i}\PYG{p}{)} \PYG{o}{/} \PYG{l+m+mf}{29.0} + \PYG{n}{s1} \PYG{o}{=} \PYG{l+m+mf}{0.0} + \PYG{n}{dx} \PYG{o}{=} \PYG{l+m+mf}{1.0} + \PYG{k}{for} \PYG{n}{j} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{n} \PYG{o}{+} \PYG{l+m+mi}{1}\PYG{p}{)}\PYG{p}{:} \PYG{c+c1}{\PYGZsh{} j = 2,...,n} + \PYG{n}{s1} \PYG{o}{=} \PYG{n}{s1} \PYG{o}{+} \PYG{p}{(}\PYG{n}{j} \PYG{o}{\PYGZhy{}} \PYG{l+m+mi}{1}\PYG{p}{)} \PYG{o}{*} \PYG{n}{dx} \PYG{o}{*} \PYG{n}{x}\PYG{p}{[}\PYG{n}{j} \PYG{o}{\PYGZhy{}} \PYG{l+m+mi}{1}\PYG{p}{]} + \PYG{n}{dx} \PYG{o}{=} \PYG{n}{div} \PYG{o}{*} \PYG{n}{dx} + \PYG{n}{s2} \PYG{o}{=} \PYG{l+m+mf}{0.0} + \PYG{n}{dx} \PYG{o}{=} \PYG{l+m+mf}{1.0} + \PYG{k}{for} \PYG{n}{j} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{l+m+mi}{1}\PYG{p}{,} \PYG{n}{n} \PYG{o}{+} \PYG{l+m+mi}{1}\PYG{p}{)}\PYG{p}{:} \PYG{c+c1}{\PYGZsh{} j = 1,...,n} + \PYG{n}{s2} \PYG{o}{=} \PYG{n}{s2} \PYG{o}{+} \PYG{n}{dx} \PYG{o}{*} \PYG{n}{x}\PYG{p}{[}\PYG{n}{j} \PYG{o}{\PYGZhy{}} \PYG{l+m+mi}{1}\PYG{p}{]} + \PYG{n}{dx} \PYG{o}{=} \PYG{n}{div} \PYG{o}{*} \PYG{n}{dx} + \PYG{n}{fvec}\PYG{p}{[}\PYG{n}{i} \PYG{o}{\PYGZhy{}} \PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{=} \PYG{n}{s1} \PYG{o}{\PYGZhy{}} \PYG{n}{s2} \PYG{o}{*}\PYG{o}{*} \PYG{l+m+mi}{2} \PYG{o}{\PYGZhy{}} \PYG{l+m+mf}{1.0} + \PYG{n}{fvec}\PYG{p}{[}\PYG{l+m+mi}{29}\PYG{p}{]} \PYG{o}{=} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} + \PYG{n}{fvec}\PYG{p}{[}\PYG{l+m+mi}{30}\PYG{p}{]} \PYG{o}{=} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{*}\PYG{o}{*} \PYG{l+m+mi}{2} \PYG{o}{\PYGZhy{}} \PYG{l+m+mf}{1.0} + \PYG{k}{return} \PYG{n}{fvec} + +\PYG{c+c1}{\PYGZsh{} Define the starting point} +\PYG{n}{n} \PYG{o}{=} \PYG{l+m+mi}{6} +\PYG{n}{x0} \PYG{o}{=} \PYG{l+m+mf}{0.5} \PYG{o}{*} \PYG{n}{np}\PYG{o}{.}\PYG{n}{ones}\PYG{p}{(}\PYG{p}{(}\PYG{n}{n}\PYG{p}{,}\PYG{p}{)}\PYG{p}{,} \PYG{n}{dtype}\PYG{o}{=}\PYG{n+nb}{float}\PYG{p}{)} + +\PYG{c+c1}{\PYGZsh{} Show extra output to demonstrate the impact of using an initial evaluation database} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{logging} +\PYG{n}{logging}\PYG{o}{.}\PYG{n}{basicConfig}\PYG{p}{(}\PYG{n}{level}\PYG{o}{=}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{INFO}\PYG{p}{,} \PYG{n+nb}{format}\PYG{o}{=}\PYG{l+s+s1}{\PYGZsq{}}\PYG{l+s+si}{\PYGZpc{}(message)s}\PYG{l+s+s1}{\PYGZsq{}}\PYG{p}{)} + +\PYG{c+c1}{\PYGZsh{} Call DFO\PYGZhy{}LS} +\PYG{n}{soln} \PYG{o}{=} \PYG{n}{dfols}\PYG{o}{.}\PYG{n}{solve}\PYG{p}{(}\PYG{n}{watson}\PYG{p}{,} \PYG{n}{x0}\PYG{p}{)} + +\PYG{c+c1}{\PYGZsh{} Display output} +\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{soln}\PYG{p}{)} +\end{sphinxVerbatim} +\end{quote} + +\sphinxAtStartPar +In the output of this code, we can check that DFO\sphinxhyphen{}LS finds the unique minimizer of this function. We can also see that before the main loop can begin, +DFO\sphinxhyphen{}LS needs to evaluate the objective at the given starting point, and 6 extra points (since this problem has 6 variables to be minimized): +\begin{quote} + +\begin{sphinxVerbatim}[commandchars=\\\{\}] +Function eval 1 at point 1 has obj = 16.4308311759923 at x = [...] +Initialising (coordinate directions) +Function eval 2 at point 2 has obj = 28.9196967094733 at x = [...] +Function eval 3 at point 3 has obj = 22.0866904737059 at x = [...] +Function eval 4 at point 4 has obj = 20.6560889343479 at x = [...] +Function eval 5 at point 5 has obj = 19.2914312375462 at x = [...] +Function eval 6 at point 6 has obj = 18.0373781384725 at x = [...] +Function eval 7 at point 7 has obj = 16.8946356501339 at x = [...] +Beginning main loop +Function eval 8 at point 8 has obj = 8.45207899459595 at x = [...] +Function eval 9 at point 9 has obj = 2.54949692496583 at x = [...] +... +Function eval 90 at point 90 has obj = 0.00228767005355292 at x = [...] +Did a total of 1 run(s) + +****** DFO\PYGZhy{}LS Results ****** +Solution xmin = [\PYGZhy{}0.01572509 1.01243487 \PYGZhy{}0.23299162 1.26043004 \PYGZhy{}1.51372886 0.99299641] +Not showing residual vector because it is too long; check self.resid +Objective value f(xmin) = 0.002287670054 +Needed 90 objective evaluations (at 90 points) +Not showing approximate Jacobian because it is too long; check self.jacobian +Solution xmin was evaluation point 89 +Approximate Jacobian formed using evaluation points [87 85 76 89 86 88 84] +Exit flag = 0 +Success: rho has reached rhoend +**************************** +\end{sphinxVerbatim} +\end{quote} + +\sphinxAtStartPar +Instead of this, we can build a database of points where we have previously evaluated the objective, marking one of them as the starting point +for the algorithm. DFO\sphinxhyphen{}LS will then select some/all (but possibly none) of the other points and use them as initial evaluations, allowing it to begin +the main loop faster. In general, DFO\sphinxhyphen{}LS will select points that are: +\begin{itemize} +\item {} +\sphinxAtStartPar +Not too close/far from the selected starting point (relative to the initial trust\sphinxhyphen{}region radius, input \sphinxcode{\sphinxupquote{rhobeg}}) + +\item {} +\sphinxAtStartPar +Not in similar directions (relative to the selected starting point) to other selected initial points. For example, if several points differ from +the selected starting point in only the first variable, at most one of these will be selected. + +\end{itemize} + +\sphinxAtStartPar +The following code demonstrates how an evaluation database may be constructed and given to DFO\sphinxhyphen{}LS: +\begin{quote} + +\begin{sphinxVerbatim}[commandchars=\\\{\}] +\PYG{c+c1}{\PYGZsh{} Assuming numpy and dfols already imported, watson function already defined} + +\PYG{c+c1}{\PYGZsh{} Build a database of evaluations} +\PYG{n}{eval\PYGZus{}db} \PYG{o}{=} \PYG{n}{dfols}\PYG{o}{.}\PYG{n}{EvaluationDatabase}\PYG{p}{(}\PYG{p}{)} + +\PYG{c+c1}{\PYGZsh{} Define the starting point and add it to the database} +\PYG{n}{n} \PYG{o}{=} \PYG{l+m+mi}{6} +\PYG{n}{x0} \PYG{o}{=} \PYG{l+m+mf}{0.5} \PYG{o}{*} \PYG{n}{np}\PYG{o}{.}\PYG{n}{ones}\PYG{p}{(}\PYG{p}{(}\PYG{n}{n}\PYG{p}{,}\PYG{p}{)}\PYG{p}{,} \PYG{n}{dtype}\PYG{o}{=}\PYG{n+nb}{float}\PYG{p}{)} +\PYG{n}{eval\PYGZus{}db}\PYG{o}{.}\PYG{n}{append}\PYG{p}{(}\PYG{n}{x0}\PYG{p}{,} \PYG{n}{watson}\PYG{p}{(}\PYG{n}{x0}\PYG{p}{)}\PYG{p}{,} \PYG{n}{make\PYGZus{}starting\PYGZus{}eval}\PYG{o}{=}\PYG{k+kc}{True}\PYG{p}{)} +\PYG{c+c1}{\PYGZsh{} make\PYGZus{}starting\PYGZus{}eval=True \PYGZhy{}\PYGZhy{}\PYGZgt{} use this point as the starting point for DFO\PYGZhy{}LS} + +\PYG{c+c1}{\PYGZsh{} Add other points to the database} +\PYG{c+c1}{\PYGZsh{} Note: x0, x1 and x2 are colinear, so at least one of x1 and x2 will not be included in the initial model} +\PYG{n}{x1} \PYG{o}{=} \PYG{n}{np}\PYG{o}{.}\PYG{n}{ones}\PYG{p}{(}\PYG{p}{(}\PYG{n}{n}\PYG{p}{,}\PYG{p}{)}\PYG{p}{,} \PYG{n}{dtype}\PYG{o}{=}\PYG{n+nb}{float}\PYG{p}{)} +\PYG{n}{x2} \PYG{o}{=} \PYG{n}{np}\PYG{o}{.}\PYG{n}{zeros}\PYG{p}{(}\PYG{p}{(}\PYG{n}{n}\PYG{p}{,}\PYG{p}{)}\PYG{p}{,} \PYG{n}{dtype}\PYG{o}{=}\PYG{n+nb}{float}\PYG{p}{)} +\PYG{n}{x3} \PYG{o}{=} \PYG{n}{np}\PYG{o}{.}\PYG{n}{arange}\PYG{p}{(}\PYG{n}{n}\PYG{p}{)}\PYG{o}{.}\PYG{n}{astype}\PYG{p}{(}\PYG{n+nb}{float}\PYG{p}{)} +\PYG{n}{eval\PYGZus{}db}\PYG{o}{.}\PYG{n}{append}\PYG{p}{(}\PYG{n}{x1}\PYG{p}{,} \PYG{n}{watson}\PYG{p}{(}\PYG{n}{x1}\PYG{p}{)}\PYG{p}{)} +\PYG{n}{eval\PYGZus{}db}\PYG{o}{.}\PYG{n}{append}\PYG{p}{(}\PYG{n}{x2}\PYG{p}{,} \PYG{n}{watson}\PYG{p}{(}\PYG{n}{x2}\PYG{p}{)}\PYG{p}{)} +\PYG{n}{eval\PYGZus{}db}\PYG{o}{.}\PYG{n}{append}\PYG{p}{(}\PYG{n}{x3}\PYG{p}{,} \PYG{n}{watson}\PYG{p}{(}\PYG{n}{x3}\PYG{p}{)}\PYG{p}{)} + +\PYG{c+c1}{\PYGZsh{} Show extra output to demonstrate the impact of using an initial evaluation database} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{logging} +\PYG{n}{logging}\PYG{o}{.}\PYG{n}{basicConfig}\PYG{p}{(}\PYG{n}{level}\PYG{o}{=}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{INFO}\PYG{p}{,} \PYG{n+nb}{format}\PYG{o}{=}\PYG{l+s+s1}{\PYGZsq{}}\PYG{l+s+si}{\PYGZpc{}(message)s}\PYG{l+s+s1}{\PYGZsq{}}\PYG{p}{)} + +\PYG{c+c1}{\PYGZsh{} Call DFO\PYGZhy{}LS} +\PYG{n}{soln} \PYG{o}{=} \PYG{n}{dfols}\PYG{o}{.}\PYG{n}{solve}\PYG{p}{(}\PYG{n}{watson}\PYG{p}{,} \PYG{n}{x0}\PYG{p}{)} + +\PYG{c+c1}{\PYGZsh{} Display output} +\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{soln}\PYG{p}{)} +\end{sphinxVerbatim} +\end{quote} + +\sphinxAtStartPar +Running this code, we get the same (correct) answer but using fewer evaluations of the objective in the main call to \sphinxcode{\sphinxupquote{dfols.solve()}}. +The logging information reveals that \sphinxcode{\sphinxupquote{x0}} was used as the starting point, and \sphinxcode{\sphinxupquote{x1}} and \sphinxcode{\sphinxupquote{x3}} were used to build the initial model. +This means that only 4 evaluations of the objective were required in the initialization phase. +\begin{quote} + +\begin{sphinxVerbatim}[commandchars=\\\{\}] +Using pre\PYGZhy{}existing evaluation 0 as starting point +Adding pre\PYGZhy{}existing evaluation 1 to initial model +Adding pre\PYGZhy{}existing evaluation 3 to initial model +Function eval 1 at point 1 has obj = 15.1910664616598 at x = [...] +Function eval 2 at point 2 has obj = 15.2288491702299 at x = [...] +Function eval 3 at point 3 has obj = 15.228054997542 at x = [...] +Function eval 4 at point 4 has obj = 15.3011037277481 at x = [...] +Beginning main loop +Function eval 5 at point 5 has obj = 13.5524099633802 at x = [...] +Function eval 6 at point 6 has obj = 7.33371957636104 at x = [...] +... +Function eval 81 at point 81 has obj = 0.00228767005355266 at x = [...] +Did a total of 1 run(s) + +****** DFO\PYGZhy{}LS Results ****** +Solution xmin = [\PYGZhy{}0.01572509 1.01243487 \PYGZhy{}0.23299163 1.26043009 \PYGZhy{}1.51372893 0.99299643] +Not showing residual vector because it is too long; check self.resid +Objective value f(xmin) = 0.002287670054 +Needed 81 objective evaluations (at 81 points) +Not showing approximate Jacobian because it is too long; check self.jacobian +Solution xmin was evaluation point 77 +Approximate Jacobian formed using evaluation points [76 73 79 74 77 75 80] +Exit flag = 0 +Success: rho has reached rhoend +**************************** +\end{sphinxVerbatim} +\end{quote} + +\sphinxAtStartPar +Note that the indices of the evaluation database mentioned in the log refer to the order in which the points were added to the evaluation database. + + \section{Example: Noisy Objective Evaluation} \label{\detokenize{userguide:example-noisy-objective-evaluation}} \sphinxAtStartPar @@ -1057,16 +1244,16 @@ \section{Example: Noisy Objective Evaluation} \begin{sphinxVerbatim}[commandchars=\\\{\}] \PYG{c+c1}{\PYGZsh{} DFO\PYGZhy{}LS example: minimize the noisy Rosenbrock function} -\PYG{k+kn}{from} \PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}} \PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} -\PYG{k+kn}{import} \PYG{n+nn}{numpy} \PYG{k}{as} \PYG{n+nn}{np} -\PYG{k+kn}{import} \PYG{n+nn}{dfols} +\PYG{k+kn}{from}\PYG{+w}{ }\PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}}\PYG{+w}{ }\PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{numpy}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{np} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{dfols} \PYG{c+c1}{\PYGZsh{} Define the objective function} -\PYG{k}{def} \PYG{n+nf}{rosenbrock}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} +\PYG{k}{def}\PYG{+w}{ }\PYG{n+nf}{rosenbrock}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} \PYG{k}{return} \PYG{n}{np}\PYG{o}{.}\PYG{n}{array}\PYG{p}{(}\PYG{p}{[}\PYG{l+m+mf}{10.0} \PYG{o}{*} \PYG{p}{(}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{*}\PYG{o}{*} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{,} \PYG{l+m+mf}{1.0} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} Modified objective function: add 1\PYGZpc{} Gaussian noise} -\PYG{k}{def} \PYG{n+nf}{rosenbrock\PYGZus{}noisy}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} +\PYG{k}{def}\PYG{+w}{ }\PYG{n+nf}{rosenbrock\PYGZus{}noisy}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} \PYG{k}{return} \PYG{n}{rosenbrock}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)} \PYG{o}{*} \PYG{p}{(}\PYG{l+m+mf}{1.0} \PYG{o}{+} \PYG{l+m+mf}{1e\PYGZhy{}2} \PYG{o}{*} \PYG{n}{np}\PYG{o}{.}\PYG{n}{random}\PYG{o}{.}\PYG{n}{normal}\PYG{p}{(}\PYG{n}{size}\PYG{o}{=}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{,}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} Define the starting point} @@ -1087,7 +1274,7 @@ \section{Example: Noisy Objective Evaluation} \PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{soln}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} Compare with a derivative\PYGZhy{}based solver} -\PYG{k+kn}{import} \PYG{n+nn}{scipy}\PYG{n+nn}{.}\PYG{n+nn}{optimize} \PYG{k}{as} \PYG{n+nn}{opt} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{scipy}\PYG{n+nn}{.}\PYG{n+nn}{optimize}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{opt} \PYG{n}{soln} \PYG{o}{=} \PYG{n}{opt}\PYG{o}{.}\PYG{n}{least\PYGZus{}squares}\PYG{p}{(}\PYG{n}{rosenbrock\PYGZus{}noisy}\PYG{p}{,} \PYG{n}{x0}\PYG{p}{)} \PYG{n+nb}{print}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{)} @@ -1183,9 +1370,9 @@ \section{Example: Parameter Estimation/Data Fitting} \PYG{c+c1}{\PYGZsh{} DFO\PYGZhy{}LS example: data fitting problem} \PYG{c+c1}{\PYGZsh{} Originally from:} \PYG{c+c1}{\PYGZsh{} https://uk.mathworks.com/help/optim/ug/lsqcurvefit.html} -\PYG{k+kn}{from} \PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}} \PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} -\PYG{k+kn}{import} \PYG{n+nn}{numpy} \PYG{k}{as} \PYG{n+nn}{np} -\PYG{k+kn}{import} \PYG{n+nn}{dfols} +\PYG{k+kn}{from}\PYG{+w}{ }\PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}}\PYG{+w}{ }\PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{numpy}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{np} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{dfols} \PYG{c+c1}{\PYGZsh{} Observations} \PYG{n}{tdata} \PYG{o}{=} \PYG{n}{np}\PYG{o}{.}\PYG{n}{array}\PYG{p}{(}\PYG{p}{[}\PYG{l+m+mf}{0.9}\PYG{p}{,} \PYG{l+m+mf}{1.5}\PYG{p}{,} \PYG{l+m+mf}{13.8}\PYG{p}{,} \PYG{l+m+mf}{19.8}\PYG{p}{,} \PYG{l+m+mf}{24.1}\PYG{p}{,} \PYG{l+m+mf}{28.2}\PYG{p}{,} \PYG{l+m+mf}{35.2}\PYG{p}{,} @@ -1194,7 +1381,7 @@ \section{Example: Parameter Estimation/Data Fitting} \PYG{o}{\PYGZhy{}}\PYG{l+m+mf}{0.4}\PYG{p}{,} \PYG{o}{\PYGZhy{}}\PYG{l+m+mf}{1.3}\PYG{p}{,} \PYG{o}{\PYGZhy{}}\PYG{l+m+mf}{1.5}\PYG{p}{]}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} Model is y(t) = x[0] * exp(x[1] * t)} -\PYG{k}{def} \PYG{n+nf}{prediction\PYGZus{}error}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} +\PYG{k}{def}\PYG{+w}{ }\PYG{n+nf}{prediction\PYGZus{}error}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} \PYG{k}{return} \PYG{n}{ydata} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{*} \PYG{n}{np}\PYG{o}{.}\PYG{n}{exp}\PYG{p}{(}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{*} \PYG{n}{tdata}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} Define the starting point} @@ -1254,7 +1441,7 @@ \section{Example: Parameter Estimation/Data Fitting} \PYG{n}{ts} \PYG{o}{=} \PYG{n}{np}\PYG{o}{.}\PYG{n}{linspace}\PYG{p}{(}\PYG{l+m+mf}{0.0}\PYG{p}{,} \PYG{l+m+mf}{90.0}\PYG{p}{)} \PYG{n}{ys} \PYG{o}{=} \PYG{n}{soln}\PYG{o}{.}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{*} \PYG{n}{np}\PYG{o}{.}\PYG{n}{exp}\PYG{p}{(}\PYG{n}{soln}\PYG{o}{.}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{*} \PYG{n}{ts}\PYG{p}{)} -\PYG{k+kn}{import} \PYG{n+nn}{matplotlib}\PYG{n+nn}{.}\PYG{n+nn}{pyplot} \PYG{k}{as} \PYG{n+nn}{plt} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{matplotlib}\PYG{n+nn}{.}\PYG{n+nn}{pyplot}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{plt} \PYG{n}{plt}\PYG{o}{.}\PYG{n}{figure}\PYG{p}{(}\PYG{l+m+mi}{1}\PYG{p}{)} \PYG{n}{ax} \PYG{o}{=} \PYG{n}{plt}\PYG{o}{.}\PYG{n}{gca}\PYG{p}{(}\PYG{p}{)} \PYG{c+c1}{\PYGZsh{} current axes} \PYG{n}{ax}\PYG{o}{.}\PYG{n}{plot}\PYG{p}{(}\PYG{n}{ts}\PYG{p}{,} \PYG{n}{ys}\PYG{p}{,} \PYG{l+s+s1}{\PYGZsq{}}\PYG{l+s+s1}{k\PYGZhy{}}\PYG{l+s+s1}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{label}\PYG{o}{=}\PYG{l+s+s1}{\PYGZsq{}}\PYG{l+s+s1}{Model}\PYG{l+s+s1}{\PYGZsq{}}\PYG{p}{)} @@ -1285,15 +1472,15 @@ \section{Example: Solving a Nonlinear System of Equations} \PYG{c+c1}{\PYGZsh{} Originally from:} \PYG{c+c1}{\PYGZsh{} http://support.sas.com/documentation/cdl/en/imlug/66112/HTML/default/viewer.htm\PYGZsh{}imlug\PYGZus{}genstatexpls\PYGZus{}sect004.htm} -\PYG{k+kn}{from} \PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}} \PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} -\PYG{k+kn}{from} \PYG{n+nn}{math} \PYG{k+kn}{import} \PYG{n}{exp} -\PYG{k+kn}{import} \PYG{n+nn}{numpy} \PYG{k}{as} \PYG{n+nn}{np} -\PYG{k+kn}{import} \PYG{n+nn}{dfols} +\PYG{k+kn}{from}\PYG{+w}{ }\PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}}\PYG{+w}{ }\PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function} +\PYG{k+kn}{from}\PYG{+w}{ }\PYG{n+nn}{math}\PYG{+w}{ }\PYG{k+kn}{import} \PYG{n}{exp} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{numpy}\PYG{+w}{ }\PYG{k}{as}\PYG{+w}{ }\PYG{n+nn}{np} +\PYG{k+kn}{import}\PYG{+w}{ }\PYG{n+nn}{dfols} \PYG{c+c1}{\PYGZsh{} Want to solve:} \PYG{c+c1}{\PYGZsh{} x1 + x2 \PYGZhy{} x1*x2 + 2 = 0} \PYG{c+c1}{\PYGZsh{} x1 * exp(\PYGZhy{}x2) \PYGZhy{} 1 = 0} -\PYG{k}{def} \PYG{n+nf}{nonlinear\PYGZus{}system}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} +\PYG{k}{def}\PYG{+w}{ }\PYG{n+nf}{nonlinear\PYGZus{}system}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{:} \PYG{k}{return} \PYG{n}{np}\PYG{o}{.}\PYG{n}{array}\PYG{p}{(}\PYG{p}{[}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{+} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{\PYGZhy{}} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{o}{*}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]} \PYG{o}{+} \PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{*} \PYG{n}{exp}\PYG{p}{(}\PYG{o}{\PYGZhy{}}\PYG{n}{x}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{)} \PYG{o}{\PYGZhy{}} \PYG{l+m+mf}{1.0}\PYG{p}{]}\PYG{p}{)} @@ -2073,6 +2260,19 @@ \section{Version 1.5.4 (11 Feb 2025)} \end{itemize} + +\section{Version 1.6 (10 Sep 2025)} +\label{\detokenize{history:version-1-6-10-sep-2025}}\begin{itemize} +\item {} +\sphinxAtStartPar +Allow use of evaluation database as \sphinxcode{\sphinxupquote{x0}} to reduce number of objective evaluations required in initialization phase + +\item {} +\sphinxAtStartPar +When printing solution object, reduce the maximum length of residual/Jacobian vectors that are fully displayed + +\end{itemize} + \sphinxstepscope @@ -2083,7 +2283,7 @@ \section{Main author} \label{\detokenize{contributors:main-author}}\begin{itemize} \item {} \sphinxAtStartPar -\sphinxhref{https://lindonroberts.github.io/}{Lindon Roberts} (University of Sydney) +\sphinxhref{https://lindonroberts.github.io/}{Lindon Roberts} (University of Melbourne) \end{itemize} @@ -2132,6 +2332,9 @@ \chapter{Acknowledgements} \bibitem[B2017]{userguide:b2017} \sphinxAtStartPar Amir Beck, \sphinxhref{https://doi.org/10.1137/1.9781611974997}{First\sphinxhyphen{}Order Methods in Optimization}, SIAM (2017). +\bibitem[MGH1981]{userguide:mgh1981} +\sphinxAtStartPar +Jorge J. More, Burton S. Garbow and Kenneth E. Hillstrom, \sphinxhref{https://doi.org/10.1145/355934.355936}{Testing Unconstrained Optimization Software}, \sphinxstyleemphasis{ACM Transactions on Mathematical Software}, 7:1 (1981), pp. 17\sphinxhyphen{}41. \bibitem[CFMR2018]{advanced:cfmr2018} \sphinxAtStartPar Coralia Cartis, Jan Fiala, Benjamin Marteau and Lindon Roberts, \sphinxhref{https://doi.org/10.1145/3338517}{Improving the Flexibility and Robustness of Model\sphinxhyphen{}Based Derivative\sphinxhyphen{}Free Optimization Solvers}, \sphinxstyleemphasis{ACM Transactions on Mathematical Software}, 45:3 (2019), pp. 32:1\sphinxhyphen{}32:41 {[}\sphinxhref{https://arxiv.org/abs/1804.00154}{preprint}{]} diff --git a/docs/build/latex/DFOLS.toc b/docs/build/latex/DFOLS.toc index 10ab062..a43f50c 100755 --- a/docs/build/latex/DFOLS.toc +++ b/docs/build/latex/DFOLS.toc @@ -10,7 +10,7 @@ \contentsline {section}{\numberline {2.1}When to use DFO\sphinxhyphen {}LS}{5}{section.2.1}% \contentsline {section}{\numberline {2.2}Parameter Fitting}{5}{section.2.2}% \contentsline {section}{\numberline {2.3}Solving Nonlinear Systems of Equations}{6}{section.2.3}% -\contentsline {section}{\numberline {2.4}Details of the DFO\sphinxhyphen {}LS Algorithm}{7}{section.2.4}% +\contentsline {section}{\numberline {2.4}Details of the DFO\sphinxhyphen {}LS Algorithm}{6}{section.2.4}% \contentsline {section}{\numberline {2.5}References}{7}{section.2.5}% \contentsline {chapter}{\numberline {3}Using DFO\sphinxhyphen {}LS}{9}{chapter.3}% \contentsline {section}{\numberline {3.1}Nonlinear Least\sphinxhyphen {}Squares Minimization}{9}{section.3.1}% @@ -20,52 +20,54 @@ \contentsline {section}{\numberline {3.5}Adding Bounds and More Output}{13}{section.3.5}% \contentsline {section}{\numberline {3.6}Adding General Convex Constraints}{15}{section.3.6}% \contentsline {section}{\numberline {3.7}Adding a Regularizer}{16}{section.3.7}% -\contentsline {section}{\numberline {3.8}Example: Noisy Objective Evaluation}{18}{section.3.8}% -\contentsline {section}{\numberline {3.9}Example: Parameter Estimation/Data Fitting}{20}{section.3.9}% -\contentsline {section}{\numberline {3.10}Example: Solving a Nonlinear System of Equations}{22}{section.3.10}% -\contentsline {section}{\numberline {3.11}References}{23}{section.3.11}% -\contentsline {chapter}{\numberline {4}Advanced Usage}{25}{chapter.4}% -\contentsline {section}{\numberline {4.1}General Algorithm Parameters}{25}{section.4.1}% -\contentsline {section}{\numberline {4.2}Logging and Output}{25}{section.4.2}% -\contentsline {section}{\numberline {4.3}Initialization of Points}{26}{section.4.3}% -\contentsline {section}{\numberline {4.4}Trust Region Management}{26}{section.4.4}% -\contentsline {section}{\numberline {4.5}Termination on Small Objective Value}{26}{section.4.5}% -\contentsline {section}{\numberline {4.6}Termination on Slow Progress}{26}{section.4.6}% -\contentsline {section}{\numberline {4.7}Stochastic Noise Information}{27}{section.4.7}% -\contentsline {section}{\numberline {4.8}Interpolation Management}{27}{section.4.8}% -\contentsline {section}{\numberline {4.9}Regression Model Management}{27}{section.4.9}% -\contentsline {section}{\numberline {4.10}Multiple Restarts}{27}{section.4.10}% -\contentsline {section}{\numberline {4.11}Dynamically Growing Initial Set}{28}{section.4.11}% -\contentsline {section}{\numberline {4.12}Dykstra’s Algorithm}{29}{section.4.12}% -\contentsline {section}{\numberline {4.13}Checking Matrix Rank}{29}{section.4.13}% -\contentsline {section}{\numberline {4.14}Handling regularizer}{29}{section.4.14}% -\contentsline {section}{\numberline {4.15}References}{30}{section.4.15}% -\contentsline {chapter}{\numberline {5}Diagnostic Information}{31}{chapter.5}% -\contentsline {section}{\numberline {5.1}Current Iterate}{31}{section.5.1}% -\contentsline {section}{\numberline {5.2}Trust Region}{31}{section.5.2}% -\contentsline {section}{\numberline {5.3}Model Interpolation}{32}{section.5.3}% -\contentsline {section}{\numberline {5.4}Iteration Count}{32}{section.5.4}% -\contentsline {section}{\numberline {5.5}Algorithm Progress}{32}{section.5.5}% -\contentsline {chapter}{\numberline {6}Version History}{33}{chapter.6}% -\contentsline {section}{\numberline {6.1}Version 1.0 (6 Feb 2018)}{33}{section.6.1}% -\contentsline {section}{\numberline {6.2}Version 1.0.1 (20 Feb 2018)}{33}{section.6.2}% -\contentsline {section}{\numberline {6.3}Version 1.0.2 (20 Jun 2018)}{33}{section.6.3}% -\contentsline {section}{\numberline {6.4}Version 1.1 (16 Jan 2019)}{33}{section.6.4}% -\contentsline {section}{\numberline {6.5}Version 1.1.1 (5 Apr 2019)}{34}{section.6.5}% -\contentsline {section}{\numberline {6.6}Version 1.2 (12 Feb 2020)}{34}{section.6.6}% -\contentsline {section}{\numberline {6.7}Version 1.2.1 (13 Feb 2020)}{34}{section.6.7}% -\contentsline {section}{\numberline {6.8}Version 1.2.2 (26 Feb 2021)}{34}{section.6.8}% -\contentsline {section}{\numberline {6.9}Version 1.2.3 (1 Jun 2021)}{34}{section.6.9}% -\contentsline {section}{\numberline {6.10}Version 1.3.0 (8 Nov 2021)}{34}{section.6.10}% -\contentsline {section}{\numberline {6.11}Version 1.4.0 (29 Jan 2024)}{35}{section.6.11}% -\contentsline {section}{\numberline {6.12}Version 1.4.1 (11 Apr 2024)}{35}{section.6.12}% -\contentsline {section}{\numberline {6.13}Version 1.5.0 (11 Sep 2024)}{35}{section.6.13}% -\contentsline {section}{\numberline {6.14}Version 1.5.1 (10 Oct 2024)}{35}{section.6.14}% -\contentsline {section}{\numberline {6.15}Version 1.5.2 (28 Oct 2024)}{35}{section.6.15}% -\contentsline {section}{\numberline {6.16}Version 1.5.3 (30 Oct 2024)}{35}{section.6.16}% -\contentsline {section}{\numberline {6.17}Version 1.5.4 (11 Feb 2025)}{35}{section.6.17}% -\contentsline {chapter}{\numberline {7}Contributors}{37}{chapter.7}% -\contentsline {section}{\numberline {7.1}Main author}{37}{section.7.1}% -\contentsline {section}{\numberline {7.2}Contributors}{37}{section.7.2}% -\contentsline {chapter}{\numberline {8}Acknowledgements}{39}{chapter.8}% -\contentsline {chapter}{Bibliography}{41}{chapter*.3}% +\contentsline {section}{\numberline {3.8}Using Initial Evaluation Database}{18}{section.3.8}% +\contentsline {section}{\numberline {3.9}Example: Noisy Objective Evaluation}{21}{section.3.9}% +\contentsline {section}{\numberline {3.10}Example: Parameter Estimation/Data Fitting}{23}{section.3.10}% +\contentsline {section}{\numberline {3.11}Example: Solving a Nonlinear System of Equations}{25}{section.3.11}% +\contentsline {section}{\numberline {3.12}References}{26}{section.3.12}% +\contentsline {chapter}{\numberline {4}Advanced Usage}{27}{chapter.4}% +\contentsline {section}{\numberline {4.1}General Algorithm Parameters}{27}{section.4.1}% +\contentsline {section}{\numberline {4.2}Logging and Output}{27}{section.4.2}% +\contentsline {section}{\numberline {4.3}Initialization of Points}{28}{section.4.3}% +\contentsline {section}{\numberline {4.4}Trust Region Management}{28}{section.4.4}% +\contentsline {section}{\numberline {4.5}Termination on Small Objective Value}{28}{section.4.5}% +\contentsline {section}{\numberline {4.6}Termination on Slow Progress}{28}{section.4.6}% +\contentsline {section}{\numberline {4.7}Stochastic Noise Information}{28}{section.4.7}% +\contentsline {section}{\numberline {4.8}Interpolation Management}{29}{section.4.8}% +\contentsline {section}{\numberline {4.9}Regression Model Management}{29}{section.4.9}% +\contentsline {section}{\numberline {4.10}Multiple Restarts}{29}{section.4.10}% +\contentsline {section}{\numberline {4.11}Dynamically Growing Initial Set}{30}{section.4.11}% +\contentsline {section}{\numberline {4.12}Dykstra’s Algorithm}{31}{section.4.12}% +\contentsline {section}{\numberline {4.13}Checking Matrix Rank}{31}{section.4.13}% +\contentsline {section}{\numberline {4.14}Handling regularizer}{31}{section.4.14}% +\contentsline {section}{\numberline {4.15}References}{31}{section.4.15}% +\contentsline {chapter}{\numberline {5}Diagnostic Information}{33}{chapter.5}% +\contentsline {section}{\numberline {5.1}Current Iterate}{33}{section.5.1}% +\contentsline {section}{\numberline {5.2}Trust Region}{33}{section.5.2}% +\contentsline {section}{\numberline {5.3}Model Interpolation}{33}{section.5.3}% +\contentsline {section}{\numberline {5.4}Iteration Count}{34}{section.5.4}% +\contentsline {section}{\numberline {5.5}Algorithm Progress}{34}{section.5.5}% +\contentsline {chapter}{\numberline {6}Version History}{35}{chapter.6}% +\contentsline {section}{\numberline {6.1}Version 1.0 (6 Feb 2018)}{35}{section.6.1}% +\contentsline {section}{\numberline {6.2}Version 1.0.1 (20 Feb 2018)}{35}{section.6.2}% +\contentsline {section}{\numberline {6.3}Version 1.0.2 (20 Jun 2018)}{35}{section.6.3}% +\contentsline {section}{\numberline {6.4}Version 1.1 (16 Jan 2019)}{35}{section.6.4}% +\contentsline {section}{\numberline {6.5}Version 1.1.1 (5 Apr 2019)}{35}{section.6.5}% +\contentsline {section}{\numberline {6.6}Version 1.2 (12 Feb 2020)}{35}{section.6.6}% +\contentsline {section}{\numberline {6.7}Version 1.2.1 (13 Feb 2020)}{36}{section.6.7}% +\contentsline {section}{\numberline {6.8}Version 1.2.2 (26 Feb 2021)}{36}{section.6.8}% +\contentsline {section}{\numberline {6.9}Version 1.2.3 (1 Jun 2021)}{36}{section.6.9}% +\contentsline {section}{\numberline {6.10}Version 1.3.0 (8 Nov 2021)}{36}{section.6.10}% +\contentsline {section}{\numberline {6.11}Version 1.4.0 (29 Jan 2024)}{36}{section.6.11}% +\contentsline {section}{\numberline {6.12}Version 1.4.1 (11 Apr 2024)}{36}{section.6.12}% +\contentsline {section}{\numberline {6.13}Version 1.5.0 (11 Sep 2024)}{36}{section.6.13}% +\contentsline {section}{\numberline {6.14}Version 1.5.1 (10 Oct 2024)}{36}{section.6.14}% +\contentsline {section}{\numberline {6.15}Version 1.5.2 (28 Oct 2024)}{37}{section.6.15}% +\contentsline {section}{\numberline {6.16}Version 1.5.3 (30 Oct 2024)}{37}{section.6.16}% +\contentsline {section}{\numberline {6.17}Version 1.5.4 (11 Feb 2025)}{37}{section.6.17}% +\contentsline {section}{\numberline {6.18}Version 1.6 (10 Sep 2025)}{37}{section.6.18}% +\contentsline {chapter}{\numberline {7}Contributors}{39}{chapter.7}% +\contentsline {section}{\numberline {7.1}Main author}{39}{section.7.1}% +\contentsline {section}{\numberline {7.2}Contributors}{39}{section.7.2}% +\contentsline {chapter}{\numberline {8}Acknowledgements}{41}{chapter.8}% +\contentsline {chapter}{Bibliography}{43}{chapter*.3}% diff --git a/docs/build/latex/Makefile b/docs/build/latex/Makefile index e4653f2..3d4f1c9 100755 --- a/docs/build/latex/Makefile +++ b/docs/build/latex/Makefile @@ -49,7 +49,8 @@ tar: all-$(FMT) rm -r $(ARCHIVEPREFIX)docs-$(FMT) gz: tar - gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz + # -n to omit mtime from gzip headers + gzip -n -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz bz2: tar bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar diff --git a/docs/build/latex/sphinx.sty b/docs/build/latex/sphinx.sty index 6c31f32..8837485 100755 --- a/docs/build/latex/sphinx.sty +++ b/docs/build/latex/sphinx.sty @@ -3,10 +3,13 @@ % % Adapted from the old python.sty, mostly written by Fred Drake, % by Georg Brandl. -% +% This has now grown to become a full-fledged LaTeX support, split +% among multiple files, some of which provide features unavailable +% from usual LaTeX packages in interaction with the mark-up produced +% by the Sphinx LaTeX writer. \NeedsTeXFormat{LaTeX2e}[1995/12/01] -\ProvidesPackage{sphinx}[2023/03/19 v6.2.0 LaTeX package (Sphinx markup)] +\ProvidesPackage{sphinx}[2024/11/23 v8.2.0 Sphinx LaTeX package (sphinx-doc)] % provides \ltx@ifundefined % (many packages load ltxcmds: graphicx does for pdftex and lualatex but @@ -34,26 +37,26 @@ } %% important build warnings use an undefined reference to induce latexmk %% into complaining (once per warning) at very end of console output -\newcommand\sphinxbuildwarning[1]{% - \ifcsname sphinx_emitted_#1\endcsname +\newcommand\sphinxbuildwarning[2][]{% + \ifcsname sphinx_emitted_#2\endcsname \else - \global\expandafter\let\csname sphinx_emitted_#1\endcsname\@empty + \global\expandafter\let\csname sphinx_emitted_#2\endcsname\@empty \AtEndDocument{\hbox{% should the printing of text be made conditional on - % some boolean? + % some boolean? (7.4.0 answers this by adding an + % optional argument and testing it here for emptiness + % but no usage is made of this novelty yet.) + \if\relax\detokenize{#1}\relax + % No [], print a red warning text at very end of document \bfseries\color{red}% - \@nameuse{sphinx_buildwarning_#1}% + \@nameuse{sphinx_buildwarning_#2}% + \fi % place an undefined reference deliberately \let\nfss@text\@gobble % no ?? - \ref{!!\@nameuse{sphinx_buildwarning_#1}}% - }}% + \ref{!!\@nameuse{sphinx_buildwarning_#2}}% + }% + }% \fi } -\@namedef{sphinx_buildwarning_coloursyntax}{% - The colours whose definition used xcolor syntax were set to white - as xcolor was not found; check the latex log warnings for details} -\@namedef{sphinx_buildwarning_colorblend}{% - Command \string\sphinxcolorblend\space seen but ignored in tables - as xcolor was not found; check the latex log warnings for details} \@namedef{sphinx_buildwarning_badtitlesec}{% Your system has titlesec version 2.10.1 which causes disappearance of section numbers; check the latex log warning for details} @@ -63,29 +66,28 @@ \@namedef{sphinx_buildwarning_badfootnotes}{% Footnote rendering may have had problems, due to extra package or document class; check latex log for instructions}% - +\@namedef{sphinx_buildwarning_badiconpackage}{% + You have set iconpackage=\spx@opt@iconpackage, but this LaTeX package + is not found}% %% OPTION HANDLING % - % We generally first handle options then load packages, but we need -% \definecolor from xcolor/color to handle the options. +% \definecolor and \colorlet from xcolor to handle the options. +% Support for colour options +% -------------------------- +% At 7.4.0, package xcolor is required (which has allowed to get rid of +% annoying fall-back branches). Internals here got refactored to some extent. +% % MEMO: xcolor \fcolorbox coloured boxes render better in some PDF viewers % than with color package \fcolorbox. Since 1.6.3, Sphinx uses only its own % custom variant of \fcolorbox when handling code-blocks. But \fcolorbox -% appears also in Pygmentize output mark-up. Also, since 5.3.0, 'sphinxsetup' -% color options get a richer input syntax if Sphinx knows xcolor is loaded, -% and the \sphinxcolorblend (for tables) is made available only if xcolor is -% loaded. -\IfFileExists{xcolor.sty}{ +% appears also in Pygmentize output mark-up. % Should Sphinx load xcolor with its dvipsnames and svgnames options? - \RequirePackage{xcolor} -}{ - \RequirePackage{color} -} +\RequirePackage{xcolor} -% the \colorlet of xcolor (if at all loaded) is overkill for most internal use +% the \colorlet of xcolor is overkill for our internal usage here \newcommand{\sphinxcolorlet}[2] {\expandafter\let\csname\@backslashchar color@#1\expandafter\endcsname \csname\@backslashchar color@#2\endcsname } @@ -93,6 +95,8 @@ % (5.3.0) Allow colour options to use both the \definecolor and the \colorlet % syntaxes, for example VerbatimColor={gray}{0.9} or VerbatimColor=red!10 % In the latter case we need the real \colorlet from xcolor package. +% Prior to 7.4.0 xcolor was not required and thus \spx@colorlet was configured +% to raise a warning in case of absence of xcolor. \def\spx@defineorletcolor#1{% \def\spx@definedcolor{{#1}}% \futurelet\spx@token\spx@defineorlet} @@ -101,21 +105,17 @@ \expandafter\spx@definecolor\else\expandafter\spx@colorlet\fi} \def\spx@colorlet#1\relax{\expandafter\colorlet\spx@definedcolor{#1}} \def\spx@definecolor{\expandafter\definecolor\spx@definedcolor} -% -\@ifpackageloaded{xcolor}% - {}% - {% xcolor not loaded because it was not found in the LaTeX installation -\def\spx@colorlet#1\relax{% - \sphinxbuildwarning{coloursyntax}% - \PackageWarning{sphinx}{% -Sorry, the #1 syntax requires package xcolor,\MessageBreak -which was not found on your TeX/LaTeX installation.\MessageBreak -\@spaces\expandafter\@firstofone\spx@definedcolor\MessageBreak -will be set to white}% - \expandafter\definecolor\spx@definedcolor{rgb}{1,1,1}% - }% end of redefinition of \spx@colorlet - }% end of xcolor not found branch - +% These internals refactored at 7.4.0: +\newcommand*{\spx@DeclareColorOption}[3][]{% +% #1 = almost always "sphinx" but left empty for a few for legacy reasons +% #2 = option name, but internal colour name is #1#2 (i.e. with prefix) +% #3 = initial default colour with either \definecolor or \colorlet syntax + % Set the initial default + \spx@defineorletcolor{#1#2}#3\relax + % Set the key handler to accept both \definecolor and \colorlet syntax + % The key name does not have the #1 prefix from the colour name + \define@key{sphinx}{#2}{\spx@defineorletcolor{#1#2}##1\relax}% +}% % Handle options via "kvoptions" (later loaded by hyperref anyhow) \RequirePackage{kvoptions} @@ -156,13 +156,19 @@ will be set to white}% \DeclareStringOption[-1]{numfigreset} \DeclareBoolOption[false]{nonumfigreset} \DeclareBoolOption[false]{mathnumfig} +\DeclareStringOption[.]{mathnumsep} \define@key{sphinx}{bookmarksdepth}{\AtBeginDocument{\hypersetup{bookmarksdepth=#1}}} \AtBeginDocument{\define@key{sphinx}{bookmarksdepth}{\hypersetup{bookmarksdepth=#1}}} % \DeclareBoolOption[false]{usespart}% not used + +% Code-blocks +% ----------- +% % INFO: the keys for padding and border widths were extended at 5.1.0, % and legacy names for user interface were kept, but their definitions % are delayed further down. The legacy internally used dimen registers % \sphinxverbatimborder and \sphinxverbatimsep got removed at 6.2.0. +% More code-blocks related options are found in "CSS" part below. \DeclareBoolOption[true]{verbatimwithframe} \DeclareBoolOption[true]{verbatimwrapslines} \DeclareBoolOption[false]{verbatimforcewraps} @@ -180,70 +186,50 @@ will be set to white}% \DeclareStringOption % must use braces to hide the brackets [{\makebox[2\fontcharwd\font`\x][r]{\textcolor{red}{\tiny$\m@th\hookrightarrow$}}}]% {verbatimcontinued} -% topic boxes + +% Topic boxes +% ----------- % % 5.1.0 added new keys for configuration. The legacy keys shadowsep, -% shadowsize, shadowrule were kept for backward compatibility. Unfortunately -% this had bugs due to typos, which got fixed later at 6.1.2. +% shadowsize, shadowrule were kept for backward compatibility. +% 5.1.2 fixed some bugs. % % All configuration is now to be found in the "CSS" section below. % -% \sphinxshadowsep, \sphinxshadowsize, \sphinxshadowrule \dimen registers -% became at 5.1.0 either no-op or, for the latter, were used under an aliased -% name. They got removed at 6.2.0. -% -% notices/admonitions -% -% 5.1.0 added much customizability to warning, caution, attention, danger and -% error types of notices via an enhanced sphinxheavybox environment. -% -% 6.2.0 added the possibility to use the same kind of rendering also for -% note, hint, important, and tip. -% -% Legacy user interface for options was kept working. All of it is handled in -% the "CSS" section below. -% -% These 6.2.0 added booleans serve internally. There is no reason for user to -% know about them, except if it is desired to toggle mid-way in the document -% whether note, hint, important, and tip should use the "lightbox" or the -% "heavybox" rendering. -\DeclareBoolOption[false]{heavynote} -\DeclareBoolOption[false]{heavyhint} -\DeclareBoolOption[false]{heavyimportant} -\DeclareBoolOption[false]{heavytip} -% footnotes +% 6.2.0 removed \sphinxshadowsep, \sphinxshadowsize, \sphinxshadowrule +% \dimen registers + +% Footnotes +% --------- \DeclareStringOption[\mbox{ }]{AtStartFootnote} % we need a public macro name for direct use in latex file \newcommand*{\sphinxAtStartFootnote}{\spx@opt@AtStartFootnote} % no such need for this one, as it is used inside other macros \DeclareStringOption[\leavevmode\unskip]{BeforeFootnote} -% some font styling. + +% Some font styling +% ----------------- +% TODO: the replacement of old syntax \py@HeaderFamily as used +% in sphinxlatexstyle{page,headings}.sty and sphinx{manual,howto}.cls +% has never been really put in place. Hence this isolated tidbit here. \DeclareStringOption[\sffamily\bfseries]{HeaderFamily} -% colours -% same problems as for dimensions: we want the key handler to use \definecolor. -% first, some colours with no prefix, for backward compatibility -\newcommand*{\sphinxDeclareColorOption}[2]{% - % set the initial default; only \definecolor syntax for defaults! - \definecolor{#1}#2% - % set the key handler to accept both \definecolor and \colorlet syntax - \define@key{sphinx}{#1}{\spx@defineorletcolor{#1}##1\relax}% -}% -\sphinxDeclareColorOption{TitleColor}{{rgb}{0.126,0.263,0.361}} -\sphinxDeclareColorOption{InnerLinkColor}{{rgb}{0.208,0.374,0.486}} -\sphinxDeclareColorOption{OuterLinkColor}{{rgb}{0.216,0.439,0.388}} -\sphinxDeclareColorOption{VerbatimColor}{{gray}{0.95}} -\sphinxDeclareColorOption{VerbatimBorderColor}{{RGB}{32,32,32}} -% all other colours will be named with a "sphinx" prefix -\newcommand*{\sphinxDeclareSphinxColorOption}[2]{% - % set the initial default; only \definecolor syntax for defaults! - \definecolor{sphinx#1}#2% - % set the key handler to accept both \definecolor and \colorlet syntax - \define@key{sphinx}{#1}{\spx@defineorletcolor{sphinx#1}##1\relax}% -}% -% table row colors -\sphinxDeclareSphinxColorOption{TableRowColorHeader}{{gray}{0.86}} -\sphinxDeclareSphinxColorOption{TableRowColorOdd}{{gray}{0.92}} -\sphinxDeclareSphinxColorOption{TableRowColorEven}{{gray}{0.98}} + +% Some legacy colour options +% -------------------------- +% +\spx@DeclareColorOption{TitleColor}{{rgb}{0.126,0.263,0.361}} +\spx@DeclareColorOption{InnerLinkColor}{{rgb}{0.208,0.374,0.486}} +\spx@DeclareColorOption{OuterLinkColor}{{rgb}{0.216,0.439,0.388}} +% The Verbatim ones are "legacy" only since 5.1.0... call it "new-legacy" ;-) +\spx@DeclareColorOption{VerbatimColor}{{RGB}{242,242,242}}% same as {gray}{0.95} +\spx@DeclareColorOption{VerbatimBorderColor}{{RGB}{32,32,32}} +% All other colours will be internally assigned a "sphinx" prefix + +% Table row colors (since 6.0.0) +% ---------------- +\spx@DeclareColorOption[sphinx]{TableRowColorHeader}{{gray}{0.86}} +\spx@DeclareColorOption[sphinx]{TableRowColorOdd}{{gray}{0.92}} +\spx@DeclareColorOption[sphinx]{TableRowColorEven}{{gray}{0.98}} % if not set, the "Merge" colour will keep in sync with the "Row" colour \def\sphinxTableMergeColorHeader{sphinxTableRowColorHeader} \define@key{sphinx}{TableMergeColorHeader}{% @@ -261,37 +247,67 @@ will be set to white}% \def\sphinxTableMergeColorEven{sphinxTableMergeColorEven}% }% % Default color chosen to be as in minted.sty LaTeX package! -\sphinxDeclareSphinxColorOption{VerbatimHighlightColor}{{rgb}{0.878,1,1}} -% admonition boxes, "light" style -% border color defaults to black -% at 6.2.0 also background color is possible, but it then triggers -% usage of the "sphinxheavybox" from sphinxlatexadmonitions.sty. -\sphinxDeclareSphinxColorOption{noteBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{hintBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{importantBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{tipBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{noteBgColor}{{rgb}{1,1,1}} -\sphinxDeclareSphinxColorOption{hintBgColor}{{rgb}{1,1,1}} -\sphinxDeclareSphinxColorOption{importantBgColor}{{rgb}{1,1,1}} -\sphinxDeclareSphinxColorOption{tipBgColor}{{rgb}{1,1,1}} -% admonition boxes, "heavy" style -% border color defaults to black and background color to white -% As long as the color are not explicitly set via user options, -% the sphinxpackageboxes.sty code will actually not use them anyhow. -\sphinxDeclareSphinxColorOption{warningBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{cautionBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{attentionBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{dangerBorderColor}{{rgb}{0,0,0}} -\sphinxDeclareSphinxColorOption{errorBorderColor}{{rgb}{0,0,0}} -% BgColor should have been from the start BackgroundColor for better -% match with CSS property names, but this is legacy interface -% which is too late to change because the internal color names -% and not only the option names have been documented at user level. -\sphinxDeclareSphinxColorOption{warningBgColor}{{rgb}{1,1,1}} -\sphinxDeclareSphinxColorOption{cautionBgColor}{{rgb}{1,1,1}} -\sphinxDeclareSphinxColorOption{attentionBgColor}{{rgb}{1,1,1}} -\sphinxDeclareSphinxColorOption{dangerBgColor}{{rgb}{1,1,1}} -\sphinxDeclareSphinxColorOption{errorBgColor}{{rgb}{1,1,1}} +\spx@DeclareColorOption[sphinx]{VerbatimHighlightColor}{{rgb}{0.878,1,1}} + +% Notices/admonitions +% ------------------- +% +% 5.1.0 added much customizability to warning, caution, attention, danger and +% error types of notices via an enhanced sphinxheavybox environment. +% +% 6.2.0 added the possibility to use the same kind of rendering also for +% note, hint, important, and tip. +% +% Legacy user interface for options was kept working. All of it is handled in +% the "CSS" section below. +% +% 6.2.0 added booleans to serve internally as a record of whether the +% note, hint, important and tip admonitions used the legacy "lightbox" or +% the then enhanced "heavybox" environment. +% +% 7.4.0 uses "heavybox" environment from sphinxlatexadmonitions in all cases, +% hence the booleans mentioned above have been removed as well as the rather +% complex TeX code which was done so that these booleans were made true if +% and only if the CSS-named keys had been made usage of via 'sphinxsetup'. +% +% The "light style" implemented in sphinxlatexadmonitions.sty as +% "sphinxlightbox" is not used. Also, admonitions by default have a "title +% row", and the corresponding options are only named in the CSS style which is +% implemented further below. Here we define options having a legacy name. +% +% seealso directive is also using "heavybox" at 7.4.0 acquiring the same +% customizability as admonitions. +% todo directive also. +\definecolor{sphinx-admonition-bgcolor} {RGB}{247, 247, 247}% #F7F7F7 +\definecolor{sphinx-admonition-bordercolor} {RGB}{134, 152, 155}% #86989B +\definecolor{sphinx-warning-bordercolor} {RGB}{148, 0, 0}% #940000 +\definecolor{sphinx-error-bordercolor} {RGB}{180, 0, 0}% #B40000 +\spx@DeclareColorOption[sphinx]{noteBorderColor} {sphinx-admonition-bordercolor} +\spx@DeclareColorOption[sphinx]{hintBorderColor} {sphinx-admonition-bordercolor} +\spx@DeclareColorOption[sphinx]{importantBorderColor}{sphinx-admonition-bordercolor} +\spx@DeclareColorOption[sphinx]{tipBorderColor} {sphinx-admonition-bordercolor} +\spx@DeclareColorOption[sphinx]{seealsoBorderColor} {sphinx-admonition-bordercolor}% 7.4.0 +\spx@DeclareColorOption[sphinx]{todoBorderColor} {sphinx-admonition-bordercolor}% 7.4.0 +% +\spx@DeclareColorOption[sphinx]{noteBgColor} {sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{hintBgColor} {sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{importantBgColor}{sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{tipBgColor} {sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{seealsoBgColor} {sphinx-admonition-bgcolor}% 7.4.0 +\spx@DeclareColorOption[sphinx]{todoBgColor} {sphinx-admonition-bgcolor}% 7.4.0 +% +\spx@DeclareColorOption[sphinx]{warningBorderColor} {sphinx-warning-bordercolor} +\spx@DeclareColorOption[sphinx]{cautionBorderColor} {sphinx-warning-bordercolor} +\spx@DeclareColorOption[sphinx]{attentionBorderColor}{sphinx-warning-bordercolor} +\spx@DeclareColorOption[sphinx]{dangerBorderColor} {sphinx-warning-bordercolor} +\spx@DeclareColorOption[sphinx]{errorBorderColor} {sphinx-error-bordercolor} +% +\spx@DeclareColorOption[sphinx]{warningBgColor} {sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{cautionBgColor} {sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{attentionBgColor}{sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{dangerBgColor} {sphinx-admonition-bgcolor} +\spx@DeclareColorOption[sphinx]{errorBgColor} {sphinx-admonition-bgcolor} +% %%%%%%%% % % Additions of CSS-like keys at 5.1.0 (and possibility of rounded boxes) @@ -324,14 +340,30 @@ will be set to white}% % finally been removed entirely. No more \dimen register is used here only % storage in macros. % +% Restyling at 7.4.0 with new defaults for all admonition types +% ------------------------------------------------------------- +% +% So far the 5.1.0 added possibilities for fancier boxes had been used by +% default only for code-blocks, and admonitions kept their old-fashioned +% legacy styles. At 7.4.0, as a follow-up to the revamped styles of +% admonitions in the HTML sphinx13 theme (PR #12439), it is decided to +% apply similar styling for PDF output. Also the seealso directive +% is handled as an admonition with the same customizability. And the +% todo directive. +% +% 8.1.0: style separately topic, contents, and sidebar directives +% --------------------------------------------------------------- +% +% And use some title row also for them (but without icon, per default). +% \def\spxstring@none{none} \def\spxstring@clone{clone} % % Border keys -% +% At 7.4.0 refactoring to avoid defining legacy \spx@@border +% macros which are (now) used nowhere, only @top, @right, @bottom, @left. \def\spx@tempa#1{% #1 = macro prefix \expandafter\spx@tempb - \csname #1border\expandafter\endcsname \csname #1border@top\expandafter\endcsname \csname #1border@right\expandafter\endcsname \csname #1border@bottom\expandafter\endcsname @@ -340,103 +372,122 @@ will be set to white}% \csname #1border@opentrue\expandafter\endcsname \csname #1border@openfalse\endcsname }% -\def\spx@tempb #1#2#3#4#5#6#7#8#9{% #9 = option prefix - \define@key{sphinx}{#9border-top-width}{\def#2{##1}}% - \define@key{sphinx}{#9border-right-width}{\def#3{##1}}% - \define@key{sphinx}{#9border-bottom-width}{\def#4{##1}}% - \define@key{sphinx}{#9border-left-width}{\def#5{##1}}% - \define@key{sphinx}{#9border-width}{% - \def#1{##1}% MEMO: not immediately expanded, should this be changed? - \def#2{#1}\let#3#2\let#4#2\let#5#2% +\def\spx@tempb #1#2#3#4#5#6#7#8#9{% #8 = option prefix + \define@key{sphinx}{#8border-top-width}{\def#1{##1}}% + \define@key{sphinx}{#8border-right-width}{\def#2{##1}}% + \define@key{sphinx}{#8border-bottom-width}{\def#3{##1}}% + \define@key{sphinx}{#8border-left-width}{\def#4{##1}}% + \define@key{sphinx}{#8border-width}{% + % MEMO: not immediately expanded, should this be changed? + \def#1{##1}\let#2#1\let#3#1\let#4#1% }% - \newif#6% - \define@key{sphinx}{#9box-decoration-break}% + \newif#5% + % 6.2.0 has added support for box-decoration-break also to admonition + % directives, formerly the option setting was ignored for them. + \define@key{sphinx}{#8box-decoration-break}% {\begingroup\edef\spx@tempa{##1}\expandafter\endgroup - \ifx\spx@tempa\spxstring@clone#8\else#7\fi}% - \spx@tempc{#9}% option prefix -} -\def\spx@tempc #1#2{% #1 = option prefix, #2 = legacy option name + \ifx\spx@tempa\spxstring@clone#7\else#6\fi}% + % 7.4.0 sets the default behaviour to "slice" not only for code-blocks but + % also for admonitions, as the latter now have a background colour each. + #6% + % #8 = option prefix (with underscore), #9 = legacy option name % keep legacy option names as aliases to new-named options - \expandafter\let\csname KV@sphinx@#2\expandafter\endcsname - \csname KV@sphinx@#1border-width\endcsname + \expandafter\let\csname KV@sphinx@#9\expandafter\endcsname + \csname KV@sphinx@#8border-width\endcsname % init border-width (fetches next argument) - \csname KV@sphinx@#1border-width\endcsname + \csname KV@sphinx@#8border-width\endcsname } -% MEMO: prior to 6.2.0 the \fboxrule value (0.4pt, a priori) was frozen here via -% a \dimen assignment done immediately. Now it remains \fboxrule until being used. +% MEMO: from 6.2.0 to 7.4.0 (excluive) \fboxrule was used in the first +% two, and was resolved only at location of use. At 7.4.0, we again +% use 0.4pt rather and not \fboxrule dimen register. % macro prefix option prefix legacy option init value -\spx@tempa{spx@pre@} {pre_} {verbatimborder} \fboxrule -\spx@tempa{spx@topic@} {div.topic_} {shadowrule} \fboxrule +\spx@tempa{spx@pre@} {pre_} {verbatimborder} {0.4pt} +\spx@tempa{spx@topic@} {div.topic_} {shadowrule} {0.5pt}% mod. at 7.4.0 +\spx@tempa{spx@contents@} {div.contents_} {shadowrule} {0.5pt}% 8.1.0 +\spx@tempa{spx@sidebar@} {div.sidebar_} {shadowrule} {1pt}% 8.1.0 +% let legacy shadowrule key set all topic/contents/sidebar border +% keys to the common value given by user to shadowrule +\def\KV@sphinx@shadowrule #1{% + \@nameuse{KV@sphinx@div.topic_border-width}{#1}% + \@nameuse{KV@sphinx@div.contents_border-width}{#1}% + \@nameuse{KV@sphinx@div.sidebar_border-width}{#1}% +}% \spx@tempa{spx@note@} {div.note_} {noteborder} {0.5pt} \spx@tempa{spx@hint@} {div.hint_} {hintborder} {0.5pt} \spx@tempa{spx@important@}{div.important_}{importantborder}{0.5pt} \spx@tempa{spx@tip@} {div.tip_} {tipborder} {0.5pt} +\spx@tempa{spx@seealso@} {div.seealso_} {seealsoborder} {0.5pt}% new at 7.4.0 +\spx@tempa{spx@todo@} {div.todo_} {todoborder} {0.5pt}% new at 7.4.0 \spx@tempa{spx@warning@} {div.warning_} {warningborder} {1pt} \spx@tempa{spx@caution@} {div.caution_} {cautionborder} {1pt} \spx@tempa{spx@attention@}{div.attention_}{attentionborder}{1pt} \spx@tempa{spx@danger@} {div.danger_} {dangerborder} {1pt} -\spx@tempa{spx@error@} {div.error_} {errorborder} {1pt} +\spx@tempa{spx@error@} {div.error_} {errorborder} {1.25pt}% mod. at 7.4.0 % this one new at 6.2.0: (we do not create a "legacy name" for it) -\spx@tempa{spx@box@} {box_} {box_border-width}\fboxrule -% Set default box-decoration-break style for codeblocks to slice -\spx@pre@border@opentrue % new default at 6.0.0: slice, not clone -% 6.2.0 has added support for box-decoration-break=slice to all -% other directives, formerly the option setting was ignored for them. +\spx@tempa{spx@box@} {box_} {box_border-width}{0.4pt} +% Reset default box-decoration-break style to "clone" for \sphinxbox, +% but anyhow this is ignored as \sphinxbox produces unbreakable boxes. +\spx@box@border@openfalse % Padding keys -% +% At 7.4.0, \spx@@padding internal macros removed, only @top, @right, +% @bottom, @left are actually needed by sphinxpackageboxes.sty. \def\spx@tempa#1{% \expandafter\spx@tempb - \csname #1padding\expandafter\endcsname \csname #1padding@top\expandafter\endcsname \csname #1padding@right\expandafter\endcsname \csname #1padding@bottom\expandafter\endcsname \csname #1padding@left\endcsname }% -\def\spx@tempb #1#2#3#4#5#6{% #6 = option prefix - \define@key{sphinx}{#6padding-top}{\def#2{##1}}% - \define@key{sphinx}{#6padding-right}{\def#3{##1}}% - \define@key{sphinx}{#6padding-bottom}{\def#4{##1}}% - \define@key{sphinx}{#6padding-left}{\def#5{##1}}% - \define@key{sphinx}{#6padding}{% - \def#1{##1}% - \def#2{#1}\let#3#2\let#4#2\let#5#2% +\def\spx@tempb #1#2#3#4#5#6#7#8#9{% #5 = option prefix + \define@key{sphinx}{#5padding-top}{\def#1{##1}}% + \define@key{sphinx}{#5padding-right}{\def#2{##1}}% + \define@key{sphinx}{#5padding-bottom}{\def#3{##1}}% + \define@key{sphinx}{#5padding-left}{\def#4{##1}}% + \define@key{sphinx}{#5padding}{% + \def#1{##1}\let#2#1\let#3#1\let#4#1% }% - % initialization (will fetch "init" argument next): - \csname KV@sphinx@#6padding\endcsname + % initial defaults + \def#1{#6}\def#2{#7}\def#3{#8}\def#4{#9}% } % MEMO: prior to 6.2.0 the \fboxsep value (3pt, a priori) was frozen here via -% a \dimen assignment done immediately. Now it remains \fboxsep until being used. -% #1 macro prefix #6 option prefix init value -\spx@tempa{spx@pre@} {pre_} \fboxsep -\spx@tempa{spx@topic@} {div.topic_} {5pt} -% MEMO: prior to 6.2.0, "note" type admonitions used sphinxlightbox automatically -% and had no interface to set the padding parameters needed by sphinxheavybox. -% At 6.2.0 they acquired such interface and the default is set as for legacy -% default of "warning" type. I hesitated using \fboxsep, but if I did I would -% then need to explain how to change "note etc..." into behaving exactly -% as "warning etc...", which goes via the \dimexpr here which is too scary to -% put sanely into documentation. -\spx@tempa{spx@note@} {div.note_} {\dimexpr.6\baselineskip-\spx@note@border\relax} -\spx@tempa{spx@hint@} {div.hint_} {\dimexpr.6\baselineskip-\spx@hint@border\relax} -\spx@tempa{spx@important@}{div.important_} {\dimexpr.6\baselineskip-\spx@important@border\relax} -\spx@tempa{spx@tip@} {div.tip_} {\dimexpr.6\baselineskip-\spx@tip@border\relax} -% MEMO: prior to 5.1.0 padding was not separately customizable from border -% width for warning type admonitions. The below keeps the legacy behavior of a -% constant borderwidth+padding. The dim expression is not evaluated yet, only -% at time of use (so that it dynamically adapts to the border width setting). -% MEMO: I could use everywhere \spx@notice@border, as sphinxadmonition environment -% configures it to hold the \spx@@border value. -\spx@tempa{spx@warning@} {div.warning_} {\dimexpr.6\baselineskip-\spx@warning@border\relax} -\spx@tempa{spx@caution@} {div.caution_} {\dimexpr.6\baselineskip-\spx@caution@border\relax} -\spx@tempa{spx@attention@}{div.attention_} {\dimexpr.6\baselineskip-\spx@attention@border\relax} -\spx@tempa{spx@danger@} {div.danger_} {\dimexpr.6\baselineskip-\spx@danger@border\relax} -\spx@tempa{spx@error@} {div.error_} {\dimexpr.6\baselineskip-\spx@error@border\relax} -\spx@tempa{spx@box@} {box_} \fboxsep +% a \dimen assignment done immediately. From 6.2.0 to 7.4.0 an unfrozen +% \fboxsep was used, and at 7.4.0 it is again explicit 3pt. +% The defaults for admonitions were all modified at 7.4.0. +% For topic/contents and all admonitions the horizontal padding plus borders +% are put inside the text area (i.e. do not go into the margins). +% In order for perfect exact same vertical alignment of contents from all such +% directives, the value of horizontal border-width+padding is kept constant +% (equal to 7.5pt since 7.4.0). +% 8.1.0 styles separately topic, contents, and sidebar. +% #1 macro prefix #6 option prefix top right bottom left +\spx@tempa{spx@pre@} {pre_} {3pt}{3pt}{3pt}{3pt} +\spx@tempa{spx@topic@} {div.topic_} {6pt}{7pt}{6pt}{7pt}% mod. at 8.1.0 +% contents styling inherits at 8.1.0 the former 7.4.0 topic defaults +\spx@tempa{spx@contents@} {div.contents_} {10pt}{7pt}{12pt}{7pt}% 8.1.0 +\spx@tempa{spx@sidebar@} {div.sidebar_} {6pt}{6.5pt}{6pt}{6.5pt}% 8.1.0 +% 7.4.0 drops legacy settings which linked strangely padding with border width +\spx@tempa{spx@note@} {div.note_} {6pt}{7pt}{6pt}{7pt} +\spx@tempa{spx@hint@} {div.hint_} {6pt}{7pt}{6pt}{7pt} +\spx@tempa{spx@important@}{div.important_} {6pt}{7pt}{6pt}{7pt} +\spx@tempa{spx@tip@} {div.tip_} {6pt}{7pt}{6pt}{7pt} +\spx@tempa{spx@seealso@} {div.seealso_} {6pt}{7pt}{6pt}{7pt} +\spx@tempa{spx@todo@} {div.todo_} {6pt}{7pt}{6pt}{7pt} +\spx@tempa{spx@warning@} {div.warning_} {6pt}{6.5pt}{6pt}{6.5pt} +\spx@tempa{spx@caution@} {div.caution_} {6pt}{6.5pt}{6pt}{6.5pt} +\spx@tempa{spx@attention@}{div.attention_} {6pt}{6.5pt}{6pt}{6.5pt} +\spx@tempa{spx@danger@} {div.danger_} {6pt}{6.5pt}{6pt}{6.5pt} +\spx@tempa{spx@error@} {div.error_} {6pt}{6.25pt}{6pt}{6.25pt} +\spx@tempa{spx@box@} {box_} {3pt}{3pt}{3pt}{3pt} % define legacy verbatimsep key as alias of pre_padding key \expandafter\let\expandafter\KV@sphinx@verbatimsep\csname KV@sphinx@pre_padding\endcsname -% define legacy shadowsep key as alias of div.topic_padding key -\expandafter\let\expandafter\KV@sphinx@shadowsep\csname KV@sphinx@div.topic_padding\endcsname +% let legacy shadowsep key set all topic/contents/sidebar padding +% keys to the common value given by user to shadosep +\def\KV@sphinx@shadowsep #1{% + \@nameuse{KV@sphinx@div.topic_padding}{#1}% + \@nameuse{KV@sphinx@div.contents_padding}{#1}% + \@nameuse{KV@sphinx@div.sidebar_padding}{#1}% +}% % Corner radii keys % @@ -450,30 +501,42 @@ will be set to white}% \csname #1radius@bottomright\expandafter\endcsname \csname #1radius@bottomleft\endcsname }% -\def\spx@tempb #1#2#3#4#5{% #5 = option prefix +\def\spx@tempb #1#2#3#4#5#6#7#8#9{% #5 = option prefix \define@key{sphinx}{#5border-top-left-radius}{\def#1{##1}}% \define@key{sphinx}{#5border-top-right-radius}{\def#2{##1}}% \define@key{sphinx}{#5border-bottom-right-radius}{\def#3{##1}}% \define@key{sphinx}{#5border-bottom-left-radius}{\def#4{##1}}% \define@key{sphinx}{#5border-radius}{\def#1{##1}\let#2#1\let#3#1\let#4#1}% - \csname KV@sphinx@#5border-radius\endcsname % fetches next argument + \def#1{#6}\def#2{#7}\def#3{#8}\def#4{#9}% } % The init value for corner radius in code-blocks was \z@ (i.e. 0pt) prior -% to 6.0.0., then 3pt, then \fboxsep at 6.2.0 as padding is \fboxsep, -% and \fboxsep=3pt per default (also with platex). -% macro prefix option prefix init value -\spx@tempa{spx@pre@} {pre_} \fboxsep -\spx@tempa{spx@topic@} {div.topic_} \z@ -\spx@tempa{spx@note@} {div.note_} \z@ -\spx@tempa{spx@hint@} {div.hint_} \z@ -\spx@tempa{spx@important@}{div.important_} \z@ -\spx@tempa{spx@tip@} {div.tip_} \z@ -\spx@tempa{spx@warning@} {div.warning_} \z@ -\spx@tempa{spx@caution@} {div.caution_} \z@ -\spx@tempa{spx@attention@}{div.attention_} \z@ -\spx@tempa{spx@danger@} {div.danger_} \z@ -\spx@tempa{spx@error@} {div.error_} \z@ -\spx@tempa{spx@box@} {box_} \fboxsep +% to 6.0.0., then 3pt, then \fboxsep at 6.2.0 as padding was also \fboxsep. +% At 7.4.0: +% - the 3pt is used (which is normal value of \fboxsep). +% - some admonitions use rounded corners as well. +% - topic boxed have only their bottom right corner rounded. +% At 8.1.0 topic, contents and sidebar separately styled. +% macro prefix option prefix tl tr br bl +\spx@tempa{spx@pre@} {pre_} {3pt}{3pt}{3pt}{3pt} +% use four rounded corners (and no shadow) for topic at 8.1.0 +\spx@tempa{spx@topic@} {div.topic_} {8pt}{8pt}{8pt}{8pt} +% contents inherits at 8.1.0 the 7.4.0 former styling of topic +\spx@tempa{spx@contents@} {div.contents_} \z@ \z@ {12pt} \z@ +% make sidebard distinctive as we can't really safely implement +% it with text flowing around it, but rather as a full width block +\spx@tempa{spx@sidebar@} {div.sidebar_} {12pt}\z@ {12pt} \z@ +\spx@tempa{spx@note@} {div.note_} {5pt}{5pt}{5pt}{5pt} +\spx@tempa{spx@hint@} {div.hint_} {5pt}{5pt}{5pt}{5pt} +\spx@tempa{spx@important@}{div.important_} \z@\z@\z@\z@ +\spx@tempa{spx@tip@} {div.tip_} {5pt}{5pt}{5pt}{5pt} +\spx@tempa{spx@seealso@} {div.seealso_} \z@\z@\z@\z@ +\spx@tempa{spx@todo@} {div.todo_} \z@\z@\z@\z@ +\spx@tempa{spx@warning@} {div.warning_} \z@\z@\z@\z@ +\spx@tempa{spx@caution@} {div.caution_} \z@\z@\z@\z@ +\spx@tempa{spx@attention@}{div.attention_} \z@\z@\z@\z@ +\spx@tempa{spx@danger@} {div.danger_} \z@\z@\z@\z@ +\spx@tempa{spx@error@} {div.error_} \z@\z@\z@\z@ +\spx@tempa{spx@box@} {box_} {3pt}{3pt}{3pt}{3pt} % Shadow keys % @@ -490,10 +553,14 @@ will be set to white}% % macro prefix \spx@tempa{spx@pre@} \spx@tempa{spx@topic@} +\spx@tempa{spx@contents@}% 8.1.0 +\spx@tempa{spx@sidebar@}% 8.1.0 \spx@tempa{spx@note@} \spx@tempa{spx@hint@} \spx@tempa{spx@important@} \spx@tempa{spx@tip@} +\spx@tempa{spx@seealso@}% 7.4.0 +\spx@tempa{spx@todo@}% 7.4.0 \spx@tempa{spx@warning@} \spx@tempa{spx@caution@} \spx@tempa{spx@attention@} @@ -521,13 +588,10 @@ will be set to white}% % used here. Since 6.2.0, expansion is delayed to time of use as for % the other dimensions handled above. This is synched with an added % encapsulation in \dimexpr...\relax by the "setup" from - % sphinxpackageboxes.sty. An induced regression had to be fixed in - % the sphinxShadowBox environment as it was using in an \ifdim the - % \spx@topic@shadow@yoffset macro, now holding by default 4pt+\z@ - % rather than an already digested 262144sp. The +\z@ is in case ##2 - % is empty. + % sphinxpackageboxes.sty. \else #1% - \def#6{##1}\def#7{##2+\z@}% + \def#6{##1}% + \if\relax\detokenize{##2}\relax\let#7#6\else\def#7{##2}\fi \if\relax\detokenize{##3}\relax#4\else#3\fi \fi }% @@ -535,12 +599,18 @@ will be set to white}% } \spx@tempa{spx@pre@} {pre_} \spx@tempa{spx@topic@} {div.topic_} -% This corresponds to the legacy parameters of ShadowBox - \spx@topic@shadow@setter 4pt 4pt {} \@nnil +\spx@tempa{spx@contents@} {div.contents_} +\spx@tempa{spx@sidebar@} {div.sidebar_} +% This corresponds to the legacy parameters for topic/contents/sidebar, +% but they are now only kept for contents + \spx@contents@shadow@setter 4pt 4pt {} \@nnil +% topic and sidebar default to no shadow \spx@tempa{spx@note@} {div.note_} \spx@tempa{spx@hint@} {div.hint_} \spx@tempa{spx@important@}{div.important_} \spx@tempa{spx@tip@} {div.tip_} +\spx@tempa{spx@seealso@} {div.seealso_} +\spx@tempa{spx@todo@} {div.todo_} \spx@tempa{spx@warning@} {div.warning_} \spx@tempa{spx@caution@} {div.caution_} \spx@tempa{spx@attention@}{div.attention_} @@ -548,24 +618,34 @@ will be set to white}% \spx@tempa{spx@error@} {div.error_} \spx@tempa{spx@box@} {box_} -% Support for legacy shadowsize (topic/contents) +% Support for legacy shadowsize (topic/contents/sidebar) % This definition was broken due to a typo at 5.1.0 and got fixed at 6.1.2 % MEMO: at 6.2.0 this no longer does \number\dimexpr in an \edef. Reason is to % keep in sync with div.topic_box-shadow handling of xoffset and yoffset. -% Attention in particular to \ifdim context, we add a \dimexpr to the one here. \define@key{sphinx}{shadowsize}{% \def\spx@topic@shadow@xoffset{#1}% - \let\spx@topic@shadow@yoffset\spx@topic@shadow@xoffset + \let\spx@contents@shadow@xoffset\spx@topic@shadow@xoffset + \let\spx@sidebar@shadow@xoffset \spx@topic@shadow@xoffset + \let\spx@topic@shadow@yoffset \spx@topic@shadow@xoffset + \let\spx@contents@shadow@yoffset\spx@topic@shadow@xoffset + \let\spx@sidebar@shadow@yoffset \spx@topic@shadow@xoffset \ifdim\dimexpr\spx@topic@shadow@xoffset=\z@ \spx@topic@withshadowfalse + \spx@contents@withshadowfalse + \spx@sidebar@withshadowfalse \else \spx@topic@withshadowtrue \spx@topic@insetshadowfalse + \spx@contents@withshadowtrue + \spx@contents@insetshadowfalse + \spx@sidebar@withshadowtrue + \spx@sidebar@insetshadowfalse \fi }% -% Color keys -% (four of them: border, background, shadow and the text color) +% Color keys, TeXextras key, keys for admonition titles with icon +% +% Historical remarks to be removed at some point: % % Some problems due to legacy naming scheme which had diverging conventions % for code-blocks (VerbatimBorderColor, VerbatimColor) and admonitions @@ -574,34 +654,42 @@ will be set to white}% % example sphinxwarningBgColor are also documented at user level, they are not % only internally used. % -% For topic directive, "legacy" (by this I mean Sphinx around 2016-2017 after -% my first additions to LaTeX) had no interface for colors, so I could change -% some internals with no breakage during 5.x up to 6.2.0. So topic -% (shadowbox) could be unified with admonitions (sphinxheavybox), and the -% "set-up" macros could all be moved into a single one in the -% sphinxpackageboxes.sty file, with only one argument holding the directive -% type. +% For topic directive, "legacy" (around 2016-2017) had no interface for +% colours, so some internals could be changed with no breakage during 5.x up +% to 6.2.0. For example topic (shadowbox) could be unified with admonitions +% (sphinxheavybox), and the "setup" macros could all be moved into a single +% one in the sphinxpackageboxes.sty file, with only one argument holding the +% directive type. % -% It was then needed only for sphinxlatexliterals.sty to let its +% It was then needed only by sphinxlatexliterals.sty to let its emitted % \spx@verb@boxes@fcolorbox@setup incorporate some extra adjustment. % -% We associate a boolean to each color, so that the box code can -% decide to insert a \color command or consider it is not needed. +% 7.4.0 removes usages of booleans relative to usage of a colour for +% background or border which were there to optimize the boxing code from +% sphinxpackageboxes.sty when colours where not needed. These were internal +% macros so their removal should not be considered breaking. +% We keep the infrastructure for "shadowcolor" and "textcolor" because the +% defaults for them remain not to have specific colour. +% +% 7.4.0 adds keys for admonition titles: for background and foreground colors, +% and for icons (whose defaults are picked from Free Fontawesome 5). \def\spx@tempa#1{% \expandafter\spx@tempb \csname if#1withshadowcolor\expandafter\endcsname - \csname if#1withbordercolor\expandafter\endcsname - \csname if#1withbackgroundcolor\expandafter\endcsname \csname if#1withtextcolor\endcsname }% -\def\spx@tempb#1#2#3#4{\newif#1\newif#2\newif#3\newif#4}% +\def\spx@tempb#1#2{\newif#1\newif#2}% % macro prefix \spx@tempa{spx@pre@} \spx@tempa{spx@topic@} +\spx@tempa{spx@contents@} +\spx@tempa{spx@sidebar@} \spx@tempa{spx@note@} \spx@tempa{spx@hint@} \spx@tempa{spx@important@} \spx@tempa{spx@tip@} +\spx@tempa{spx@seealso@} +\spx@tempa{spx@todo@} \spx@tempa{spx@warning@} \spx@tempa{spx@caution@} \spx@tempa{spx@attention@} @@ -611,29 +699,36 @@ will be set to white}% % \def\spx@tempa#1{% #1 = macro prefix \expandafter\spx@tempb - \csname #1withbordercolortrue\expandafter\endcsname - \csname #1withbackgroundcolortrue\expandafter\endcsname \csname #1withshadowcolortrue\expandafter\endcsname - \csname #1withtextcolortrue\endcsname + \csname #1withtextcolortrue\expandafter\endcsname + \csname #1TeXextras\endcsname } -\def\spx@tempb#1#2#3#4#5#6{% #5 = option prefix, #6 = color name prefix - \define@key{sphinx}{#5border-TeXcolor}% - {#1\spx@defineorletcolor{#6BorderColor}##1\relax}% - \define@key{sphinx}{#5background-TeXcolor}% - {#2\spx@defineorletcolor{#6BgColor}##1\relax}% - \define@key{sphinx}{#5box-shadow-TeXcolor}% - {#3\spx@defineorletcolor{#6ShadowColor}##1\relax}% - \define@key{sphinx}{#5TeXcolor}% - {#4\spx@defineorletcolor{#6TextColor}##1\relax}% +% 7.4.0 adds options for a title. They have an action only for admonitions, +% seealso and todo directives. +\def\spx@tempb#1#2#3#4#5{% #4 = option prefix, #5 = color name prefix + \define@key{sphinx}{#4border-TeXcolor}% + {\spx@defineorletcolor{#5BorderColor}##1\relax}% + \define@key{sphinx}{#4background-TeXcolor}% + {\spx@defineorletcolor{#5BgColor}##1\relax}% + \define@key{sphinx}{#4title-background-TeXcolor}% + {\spx@defineorletcolor{#5TtlBgColor}##1\relax}% + \define@key{sphinx}{#4title-foreground-TeXcolor}% + {\spx@defineorletcolor{#5TtlFgColor}##1\relax}% + \define@key{sphinx}{#4title-icon}% + {\@namedef{#5TtlIcon}{##1}}% + \define@key{sphinx}{#4box-shadow-TeXcolor}% + {#1\spx@defineorletcolor{#5ShadowColor}##1\relax}% + \define@key{sphinx}{#4TeXcolor}% + {#2\spx@defineorletcolor{#5TextColor}##1\relax}% + \define@key{sphinx}{#4TeXextras}% + {\def#3{##1}}% } % macro prefix option prefix color name prefix \spx@tempa{spx@pre@} {pre_} {Verbatim} % (memo: internal VerbatimShadowColor was formerly sphinxVerbatimShadowColor) % internal legacy color name is VerbatimColor not VerbatimBgColor, so redefine: \define@key{sphinx}{pre_background-TeXcolor}% - {\spx@pre@withbackgroundcolortrue\spx@defineorletcolor{VerbatimColor}#1\relax}% - \spx@pre@withbordercolortrue % 6.0.0 VerbatimBorderColor {RGB}{32,32,32} - \spx@pre@withbackgroundcolortrue % 6.0.0 VerbatimColor {gray}{0.95} + {\spx@defineorletcolor{VerbatimColor}#1\relax}% % Keep legacy option names working \expandafter\let\expandafter\KV@sphinx@VerbatimBorderColor \csname KV@sphinx@pre_border-TeXcolor\endcsname @@ -641,11 +736,17 @@ will be set to white}% \csname KV@sphinx@pre_background-TeXcolor\endcsname % (6.2.0 modified some internal namings for the colors of topic boxes) % macro prefix option prefix color name prefix -\spx@tempa{spx@topic@} {div.topic_} {sphinxtopic}% (no legacy interface) +% There was no legacy interface for topic/contents/sidebar +% 8.1.0 allows separate styling for topic/contents/sidebar +\spx@tempa{spx@topic@} {div.topic_} {sphinxtopic} +\spx@tempa{spx@contents@} {div.contents_} {sphinxcontents} +\spx@tempa{spx@sidebar@} {div.sidebar_} {sphinxsidebar} \spx@tempa{spx@note@} {div.note_} {sphinxnote} \spx@tempa{spx@hint@} {div.hint_} {sphinxhint} \spx@tempa{spx@important@}{div.important_} {sphinximportant} \spx@tempa{spx@tip@} {div.tip_} {sphinxtip} +\spx@tempa{spx@seealso@} {div.seealso_} {sphinxseealso} +\spx@tempa{spx@todo@} {div.todo_} {sphinxtodo} \spx@tempa{spx@warning@} {div.warning_} {sphinxwarning} \spx@tempa{spx@caution@} {div.caution_} {sphinxcaution} \spx@tempa{spx@attention@}{div.attention_} {sphinxattention} @@ -666,11 +767,12 @@ will be set to white}% \spx@tempa{div.error_} {error} % Keep legacy sphinxsetup BorderColor for =note, hint, ... - % which will not trigger sphinxheavybox - % Add "legacy" hintTextColor etc... that will not trigger sphinxheavybox + % Add "legacy" names BgColor (added at 7.4.0) and TextColor \def\spx@tempa#1#2{% #1 = CSS like option prefix, #2 = legacy option prefix \expandafter\let\csname KV@sphinx@#2BorderColor\expandafter\endcsname \csname KV@sphinx@#1border-TeXcolor\endcsname + \expandafter\let\csname KV@sphinx@#2BgColor\expandafter\endcsname + \csname KV@sphinx@#1background-TeXcolor\endcsname \expandafter\let\csname KV@sphinx@#2TextColor\expandafter\endcsname \csname KV@sphinx@#1TeXcolor\endcsname } @@ -679,28 +781,7 @@ will be set to white}% \spx@tempa{div.important_} {important} \spx@tempa{div.tip_} {tip} -% The TeXextras key -% -\def\spx@tempa#1{% #1 = macro prefix - \expandafter\spx@tempb\csname #1TeXextras\endcsname -} -\def\spx@tempb#1#2{% #2 = option prefix - \define@key{sphinx}{#2TeXextras}{\def#1{##1}}% -} -% macro prefix option prefix -\spx@tempa{spx@pre@} {pre_} -\spx@tempa{spx@topic@} {div.topic_} -\spx@tempa{spx@note@} {div.note_} -\spx@tempa{spx@hint@} {div.hint_} -\spx@tempa{spx@important@}{div.important_} -\spx@tempa{spx@tip@} {div.tip_} -\spx@tempa{spx@warning@} {div.warning_} -\spx@tempa{spx@caution@} {div.caution_} -\spx@tempa{spx@attention@}{div.attention_} -\spx@tempa{spx@danger@} {div.danger_} -\spx@tempa{spx@error@} {div.error_} -\spx@tempa{spx@box@} {box_} - % Add "legacy" hintTeXextras etc... that will not trigger sphinxheavybox + % Add "legacy" hintTeXextras etc... \def\spx@tempa#1#2{% #1 = CSS like option prefix, #2 = legacy option prefix \expandafter\let\csname KV@sphinx@#2TeXextras\expandafter\endcsname \csname KV@sphinx@#1TeXextras\endcsname @@ -710,64 +791,162 @@ will be set to white}% \spx@tempa{div.important_} {important} \spx@tempa{div.tip_} {tip} -% For note type admonitions, redefine all CSS-like named options to trigger -% the "heavybox" path. + % At 7.4.0, let topic/contents boxes acquire background and border colours + % and give the shadow some colour other than black + % 8.1.0 styles separately topic/contents/sidebar + % topic has no shadow but we keep 7.4.0 color in case it gets needed + \setkeys{sphinx}{% + div.topic_border-TeXcolor=sphinx-admonition-bordercolor, + div.topic_background-TeXcolor=sphinx-admonition-bgcolor, + div.topic_box-shadow-TeXcolor={RGB}{108,108,108}, + div.contents_border-TeXcolor=sphinx-admonition-bordercolor, + div.contents_background-TeXcolor=sphinx-admonition-bgcolor, + div.contents_box-shadow-TeXcolor={RGB}{108,108,108}, + div.sidebar_border-TeXcolor=sphinx-admonition-bordercolor, + div.sidebar_background-TeXcolor=sphinx-admonition-bgcolor, + div.sidebar_box-shadow-TeXcolor=sphinx-admonition-bordercolor!80,% #9eacaf + } + + +% 7.4.0 lets all types of admonitions style especially their titlss. +% The Sphinx default colours for admonition titles are copied from PR #12486 +% which modified sphinx13.css (see also earlier #12439) +% The actual code using the colours and icons whose defaults are set here +% is to be found in sphinxlatexadmonitions.sty. +% +% MEMO: unfortunately xcolor does NOT implement HSL but only HSB! +% So the sphinx13.css colours specified via hsl() got converted to RGB here +\definecolor{sphinx-admonition-title-bgcolor}{RGB}{229,229,229} % hsl(0, 0%, 90%); +\definecolor{sphinx-admonition-title-fgcolor}{RGB}{127,127,127} % hsl(0, 0%, 50%); +\definecolor{sphinx-warning-title-bgcolor} {RGB}{248,228,210} % hsl(28.5, 74%, 90%); +\definecolor{sphinx-warning-title-fgcolor} {RGB}{221,122,33} % hsl(28.5, 74%, 50%); +\definecolor{sphinx-note-title-bgcolor} {RGB}{208,222,250} % hsl(219.5, 84%, 90%); +\definecolor{sphinx-note-title-fgcolor} {RGB}{20,93,234} % hsl(219.5, 84%, 50%); +\definecolor{sphinx-success-title-bgcolor} {RGB}{220,239,230} % hsl(150, 36.7%, 90%); +\definecolor{sphinx-success-title-fgcolor} {RGB}{81,174,128} % hsl(150, 36.7%, 50%); +\definecolor{sphinx-error-title-bgcolor} {RGB}{238,220,220} % hsl(0, 37%, 90%); +\definecolor{sphinx-error-title-fgcolor} {RGB}{174,80,80} % hsl(0, 37%, 50%); +\definecolor{sphinx-todo-title-bgcolor} {RGB}{226,204,254} % hsl(266.8, 100%, 90%); +\definecolor{sphinx-todo-title-fgcolor} {RGB}{113,0,255} % hsl(266.8, 100%, 50%); + +% Now use the above colours as default settings, following the choices +% done in sphinx13.css +\setkeys{sphinx}{ + div.note_title-background-TeXcolor=sphinx-note-title-bgcolor, + div.note_title-foreground-TeXcolor=sphinx-note-title-fgcolor, +% + div.hint_title-background-TeXcolor=sphinx-success-title-bgcolor, + div.hint_title-foreground-TeXcolor=sphinx-success-title-fgcolor, + div.tip_title-background-TeXcolor=sphinx-success-title-bgcolor, + div.tip_title-foreground-TeXcolor=sphinx-success-title-fgcolor, + div.seealso_title-background-TeXcolor=sphinx-success-title-bgcolor, + div.seealso_title-foreground-TeXcolor=sphinx-success-title-fgcolor, + div.todo_title-background-TeXcolor=sphinx-todo-title-bgcolor, + div.todo_title-foreground-TeXcolor=sphinx-todo-title-fgcolor, +% + div.important_title-background-TeXcolor=sphinx-warning-title-bgcolor, + div.important_title-foreground-TeXcolor=sphinx-warning-title-fgcolor, + div.caution_title-background-TeXcolor=sphinx-warning-title-bgcolor, + div.caution_title-foreground-TeXcolor=sphinx-warning-title-fgcolor, + div.warning_title-background-TeXcolor=sphinx-warning-title-bgcolor, + div.warning_title-foreground-TeXcolor=sphinx-warning-title-fgcolor, +% + div.attention_title-background-TeXcolor=sphinx-error-title-bgcolor, + div.attention_title-foreground-TeXcolor=sphinx-error-title-fgcolor, + div.danger_title-background-TeXcolor=sphinx-error-title-bgcolor, + div.danger_title-foreground-TeXcolor=sphinx-error-title-fgcolor, + div.error_title-background-TeXcolor=sphinx-error-title-bgcolor, + div.error_title-foreground-TeXcolor=sphinx-error-title-fgcolor, % -% MEMO: the noteBorderColor and noteborder legacy options have already been -% re-created and they do not trigger the "heavybox" as their meaning will not -% be modified in the loop below contrarily to their CSS counterparts -% div.note_border-TeXcolor and div.note_border-width, and to the noteBgColor -% etc... which are handled below. +% 8.1.0 add title rows, but will not use icons per default, so +% the fgcolor setting will be used only if user uses title-icon key + div.topic_title-background-TeXcolor=sphinx-admonition-title-bgcolor, + div.topic_title-foreground-TeXcolor=sphinx-admonition-title-fgcolor, + div.contents_title-background-TeXcolor=sphinx-admonition-title-bgcolor, + div.contents_title-foreground-TeXcolor=sphinx-admonition-title-fgcolor, + div.sidebar_title-background-TeXcolor=sphinx-note-title-bgcolor, + div.sidebar_title-foreground-TeXcolor=sphinx-note-title-fgcolor, +} + +% 7.4.0 Support for icons in admonition titles +% We try to +% - get Sphinx PDF builds to process fine in absence of fontawesome5 +% - use fontawesome5 if present, but not if user prefers another package +% - provide an interface for using other LaTeX code for icons +% - provide an interface for using some other package than fontawesome5 +% Indeed we can't load fontawesome5 unconditionally even if available, +% as it proves incompatible with fontawesome package. +% We thus must delay its loading. +\IfFileExists{fontawesome5.sty}{% + \DeclareStringOption[fontawesome5]{iconpackage}% +}% +{% + \IfFileExists{fontawesome.sty} + {\DeclareStringOption[fontawesome]{iconpackage}} + {\DeclareStringOption[none]{iconpackage}}% +}% +\newcommand\spx@faIcon[2][]{}% +% The above \spx@faIcon which gobbles one mandatory and one optional +% argument is put into use only if both fontawesome5 and fontawesome +% LaTeX packages are not available, as part of the defaults for the +% div.*_title-icon keys (these keys can be redefined via the sphinxsetup +% interface). % -% This goes via rather hardcore TeX here. -\def\spx@tempa#1{\if\relax#1\expandafter\@gobble +\def\spxstring@fontawesome{fontawesome} +\def\spxstring@fontawesomev{fontawesome5} +\AtBeginDocument{% + \ifx\spx@opt@iconpackage\spxstring@none \else - \toks@{##1}% - \expandafter\def\csname KV@sphinx@div.note_#1\expandafter\endcsname - \the\toks0\expandafter{% - \csname spx@opt@heavynotetrue\expandafter\expandafter\expandafter\endcsname - \csname KV@sphinx@div.note_#1\endcsname{##1}}% - \expandafter\def\csname KV@sphinx@div.hint_#1\expandafter\endcsname - \the\toks0\expandafter{% - \csname spx@opt@heavyhinttrue\expandafter\expandafter\expandafter\endcsname - \csname KV@sphinx@div.hint_#1\endcsname{##1}}% - \expandafter\def\csname KV@sphinx@div.important_#1\expandafter\endcsname - \the\toks0\expandafter{% - \csname spx@opt@heavyimportanttrue\expandafter\expandafter\expandafter\endcsname - \csname KV@sphinx@div.important_#1\endcsname{##1}}% - \expandafter\def\csname KV@sphinx@div.tip_#1\expandafter\endcsname - \the\toks0\expandafter{% - \csname spx@opt@heavytiptrue\expandafter\expandafter\expandafter\endcsname - \csname KV@sphinx@div.tip_#1\endcsname{##1}}% + \IfFileExists{\spx@opt@iconpackage.sty} + {\RequirePackage{\spx@opt@iconpackage}% + \ifx\spx@opt@iconpackage\spxstring@fontawesomev + \renewcommand\spx@faIcon{\faIcon}% + \else + \ifx\spx@opt@iconpackage\spxstring@fontawesome + \renewcommand\spx@faIcon[2][]{\faicon{##2}}% + % The \ifdefined's are a bit silly because we know that + % fontawesome.sty does not provide it, but perhaps + % there can be some new release of that package? + \ifdefined\faicon@lightbulb\else + \let\faicon@lightbulb\faLightbulbO + \fi + \ifdefined\faicon@radiation\else + \let\faicon@radiation\faBolt + \fi + \ifdefined\faicon@pen\else + \let\faicon@pen\faPencil + \fi + % if neither has been required, \spx@faIcon will simply swallow + % its argument and it is up to user + % to set the various div.*_title-icon keys appropriately. + \fi\fi % + }% + {% + \sphinxbuildwarning{badiconpackage}% + \PackageWarningNoLine{sphinx}{% + You have set iconpackage=\spx@opt@iconpackage\MessageBreak + But \spx@opt@iconpackage.sty is not found by LaTeX} + }% \fi - \spx@tempa } -\spx@tempa{border-width}% - {border-top-width}{border-right-width}{border-bottom-width}{border-left-width}% - {box-decoration-break}% - {padding}% - {padding-top}{padding-right}{padding-bottom}{padding-left}% - {border-radius}% - {border-top-left-radius}{border-top-right-radius}% - {border-bottom-right-radius}{border-bottom-left-radius}% - {box-shadow}% - {border-TeXcolor}{background-TeXcolor}{box-shadow-TeXcolor}{TeXcolor}% - {TeXextras}% -\relax - -% Now we add at 6.2.0 BgColor et al. options which will trigger the -% "heavybox" as they are \let to the div._background-TeXColor option -% which has already been enhanced to set the boolean for rendering via -% "heavybox". This is in contrast with legacy BorderColor, -% and with the new TeXcolor and TeXextras. - \def\spx@tempa#1#2{% #1 = CSS like option prefix, #2 = legacy style option prefix - \expandafter\let\csname KV@sphinx@#2BgColor\expandafter\endcsname - \csname KV@sphinx@#1background-TeXcolor\endcsname - } - \spx@tempa{div.note_} {note} - \spx@tempa{div.hint_} {hint} - \spx@tempa{div.important_} {important} - \spx@tempa{div.tip_} {tip} + +\setkeys{sphinx}{ +% Icon defaults. + div.note_title-icon = \spx@faIcon{info-circle}, + div.hint_title-icon = \spx@faIcon[regular]{lightbulb}, + div.tip_title-icon = \spx@faIcon[regular]{lightbulb}, + div.seealso_title-icon = \spx@faIcon{share}, + div.todo_title-icon = \spx@faIcon{pen}, + div.important_title-icon = \spx@faIcon{pause-circle}, + div.caution_title-icon = \spx@faIcon{radiation}, + div.warning_title-icon = \spx@faIcon{exclamation-triangle}, + div.attention_title-icon = \spx@faIcon{exclamation-triangle}, + div.danger_title-icon = \spx@faIcon{radiation}, + div.error_title-icon = \spx@faIcon{times-circle}, +% MEMO: the new at 8.1.0 defaults for contents/topic/sidebar directives +% use no icons, they use \sphinxdotitlerow which detects automatically +% whether title-icon key has been set or not. +} \newif\ifspx@opt@box@addstrut \expandafter\def\csname KV@sphinx@box_addstrut\endcsname#1{% @@ -831,9 +1010,9 @@ will be set to white}% %% PASS OPTIONS % % pass options to hyperref; it must not have been loaded already -\input{sphinxoptionshyperref.sty} +\RequirePackage{sphinxoptionshyperref} % pass options to geometry; it must not have been loaded already -\input{sphinxoptionsgeometry.sty} +\RequirePackage{sphinxoptionsgeometry} %% COLOR (general) @@ -872,7 +1051,7 @@ will be set to white}% % % It will always be needed, so let's load it here \RequirePackage{graphicx} -\input{sphinxlatexgraphics.sty} +\RequirePackage{sphinxlatexgraphics} %% FRAMED ENVIRONMENTS @@ -918,30 +1097,34 @@ will be set to white}% } % Some of these defaults got already set. But we now list them all explicitly % for a complete initial configuration of reset storage. -% +% At 7.4.0, \fboxrule and \fboxsep replaced by 0.4pt and 3pt which are anyhow +% the defaults for these LaTeX dimensions. 8.2.0 corrected border-radius +% default back to 3pt (\fboxsep) not 0.4pt (\fboxrule). \let\spx@boxes@sphinxbox@defaults\@gobble \sphinxboxsetup{% - border-width=\fboxrule,% <-not really needed to avoid EOL space - padding=\fboxsep,% but done here out of habit - border-radius=\fboxsep,% - box-shadow=none,% -% As xcolor is perhaps not loaded we can not use background-TeXcolor=VerbatimColor -% which would not be compatible with \definecolor syntax. - border-TeXcolor={RGB}{32,32,32},% the default VerbatimBorderColor - background-TeXcolor={gray}{0.95},% the default VerbatimColor - box-shadow-TeXcolor={rgb}{0,0,0},% - TeXextras={},% - addstrut=false% (a final comma here would not hurt) + border-width=0.4pt, + padding=3pt, + border-radius=3pt, + box-shadow=none, +% MEMO: as xcolor is loaded, \spx@defineorletcolor has a "\colorlet" branch +% which makes this syntax acceptable and avoids duplicating here the values. + border-TeXcolor=VerbatimBorderColor, + background-TeXcolor=VerbatimColor, +% 7.4.0 modified the color of the shadow (anyhow box-shadow is set above to none +% so no shadow is drawn), to be as the new shadow colour of topic boxes. + box-shadow-TeXcolor={RGB}{108,108,108}, + TeXextras={}, + addstrut=false, }% \RequirePackage{sphinxpackageboxes} -\input{sphinxlatexadmonitions.sty} -\input{sphinxlatexliterals.sty} -\input{sphinxlatexshadowbox.sty} +\RequirePackage{sphinxlatexadmonitions} +\RequirePackage{sphinxlatexliterals} +\RequirePackage{sphinxlatexshadowbox} %% CONTAINERS % -\input{sphinxlatexcontainers.sty} +\RequirePackage{sphinxlatexcontainers} %% PYGMENTS @@ -951,17 +1134,17 @@ will be set to white}% %% TABLES % -\input{sphinxlatextables.sty} +\RequirePackage{sphinxlatextables} %% NUMBERING OF FIGURES, TABLES, AND LITERAL BLOCKS % -\input{sphinxlatexnumfig.sty} +\RequirePackage{sphinxlatexnumfig} %% LISTS % -\input{sphinxlatexlists.sty} +\RequirePackage{sphinxlatexlists} %% FOOTNOTES @@ -991,19 +1174,19 @@ will be set to white}% %% INDEX, BIBLIOGRAPHY, APPENDIX, TABLE OF CONTENTS % -\input{sphinxlatexindbibtoc.sty} +\RequirePackage{sphinxlatexindbibtoc} %% STYLING % -\input{sphinxlatexstylepage.sty} -\input{sphinxlatexstyleheadings.sty} -\input{sphinxlatexstyletext.sty} +\RequirePackage{sphinxlatexstylepage} +\RequirePackage{sphinxlatexstyleheadings} +\RequirePackage{sphinxlatexstyletext} %% MODULE RELEASE DATA AND OBJECT DESCRIPTIONS % -\input{sphinxlatexobjects.sty} +\RequirePackage{sphinxlatexobjects} % FIXME: this line should be dropped, as "9" is default anyhow. diff --git a/docs/build/latex/sphinx.xdy b/docs/build/latex/sphinx.xdy index 0dcf113..8df526e 100644 --- a/docs/build/latex/sphinx.xdy +++ b/docs/build/latex/sphinx.xdy @@ -99,7 +99,7 @@ ;; file, with a blank space after \IeC ;; Details of the syntax are explained at -;; http://xindy.sourceforge.net/doc/manual-3.html +;; https://xindy.sourceforge.net/doc/manual-3.html ;; In absence of :string, "xindy uses an auto-detection mechanism to decide, ;; if the pattern is a regular expression or not". But it is not obvious to ;; guess, for example "\\_" is not detected as RE but "\\P\{\}" is, so for diff --git a/docs/build/latex/sphinxlatexadmonitions.sty b/docs/build/latex/sphinxlatexadmonitions.sty index a31ae4c..0519903 100644 --- a/docs/build/latex/sphinxlatexadmonitions.sty +++ b/docs/build/latex/sphinxlatexadmonitions.sty @@ -1,53 +1,74 @@ %% NOTICES AND ADMONITIONS % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexadmonitions.sty}[2023/03/19 admonitions] +\ProvidesPackage{sphinxlatexadmonitions}[2024/10/11 v8.1.1 admonitions] % Provides support for this output mark-up from Sphinx latex writer: % -% - sphinxseealso environment added at 6.1.0 +% - sphinxseealso environment added at 6.1.0. +% +% - sphinxtodo environment added at 7.4.0. % % - sphinxadmonition (environment) -% This is a dispatch supporting +% This is a dispatch which formerly configured % -% - note, hint, important, tip (via sphinxlightbox) -% (also optionally via sphinxheavybox since 6.2.0) -% - warning, caution, attention, danger, error (via sphinxheavybox) +% - note, hint, important, tip to use sphinxlightbox (or optionally +% sphinxheavybox since 6.2.0), +% - warning, caution, attention, danger, error to use sphinxheavybox. % -% Each sphinx environment can be redefined by user. -% The defaults are customizable via various colour and dimension -% settings, cf sphinx docs (latex customization). +% Since 7.4.0 all admonitions use sphinxheavybox. % -% Requires: -\RequirePackage{sphinxpackageboxes} -\RequirePackage{framed}% used by sphinxheavybox +% - All environments sphinxnote, sphinxwarning, etc... can be redefined as +% will by user. Thay have a single parameter #1 which is the title. +% +% - Also redefinable by user are the one-argument commands +% * \sphinxstylenotetitle, +% * \sphinxstylewarningtitle, +% * etc.... one for each admonition type (also seealso and todo). % +% - At 7.4.0, all commands of previous item use \sphinxdotitlerow. +% (the 7.4.0 name, still usable, was \sphinxdotitlerowwithicon; the 8.1.0 +% version is also used for topic, contents and sidebar directives, see +% sphinxlatexshadowbox.sty, and handles both "with icon" and "without +% icon" situations). +% +% The sphinxlightbox environment is kept for backward compatibility, for user +% custom code which used it via custom definitions done in preamble or via +% raw latex directive. +% MEMO: here is for example how sphinxnote was formerly defined: +% (where #1 is the localized string Note, followed with a colon) +% \newenvironment{sphinxnote}[1] +% {\begin{sphinxlightbox}\sphinxstrong{#1} } +% {\end{sphinxlightbox}} +% Use this if you want to revert the 7.4.0 switch to usage of sphinxheavybox. +% (the 7.4.0 redefined \sphinxstylenotetitle will not work in sphinxlightbox, +% so \sphinxstrong{#1} which was its former default is used above). + % Dependencies (they do not need to be defined at time of loading): % % - of course the various colour and dimension options handled via sphinx.sty -% % - dimension register \spx@image@maxheight from sphinxlatexgraphics.sty +% - \savenotes/\spewnotes from sphinxpackagefootnote.sty +% - \ifspx@inframed defined in sphinx.sty +% - \spx@boxes@fcolorbox@setup from sphinxpackageboxes.sty % -% - \savenotes/\spewnotes from sphinxpackagefootnote (for sphinxheavybox) +\RequirePackage{framed} +% Those are required either before or after by sphinx.sty anyhow, but for +% clarity we list them here: +\RequirePackage{sphinxlatexgraphics} +\RequirePackage{sphinxpackagefootnote} +\RequirePackage{sphinxpackageboxes} % -% - \sphinxstylenotetitle, ..., \sphinxstylewarningtitle, etc... which are used by -% default in the corresponding sphinx environments to replace at 6.2.0 -% formerly hard-coded \sphinxstrong{#1} -% Their definitions are in sphinxlatexstyletext.sty. - - % Provides: (also in sphinxlatexliterals.sty) +% Only needed here by legacy (deprecated) sphinxlightbox environment. \providecommand*\sphinxvspacefixafterfrenchlists{% \ifvmode\ifdim\lastskip<\z@ \vskip\parskip\fi\else\par\fi } -% Some are quite plain -\newenvironment{sphinxseealso}[1]{\sphinxstyleseealsotitle{#1}}{} - % This \dimen register is a legacy relic from Sphinx 1.5 which is used now % only for sphinxlightbox. It is set in the sphinxadmonition environment. \newdimen\spx@notice@border - +% sphinxlightbox is now also a legacy relic, not used by Sphinx anymore \newenvironment{sphinxlightbox}{% \par \noindent{\color{spx@notice@bordercolor}% @@ -65,55 +86,28 @@ {\linewidth}{\spx@notice@border}}\hss}\allowbreak }% end of sphinxlightbox environment definition -% note/hint/important/tip notices -% -% Since 1.5 these environments are named individually to allow user to -% redefine them entirely. +% Since 1.5 these environments are named individually sphinxnote, sphinxhint, +% etc... to allow user to redefine them entirely. % -% The Sphinx definitions were done like this, prior to 6.2.0: +% The Sphinx definitions for note/hint/important/tip notices were done like +% this, prior to 6.2.0: % % \newenvironment{sphinxhint}[1] % {\begin{sphinxlightbox}\sphinxstrong{#1} }{\end{sphinxlightbox}} % -% The more complex definition below will branch to sphinxheavybox if a certain -% boolean associated to the notice type is true. This boolean is set to true -% whenever a CSS-named alike options for the notice type has been used in -% sphinxsetup. The old coding as above would still work, with the new options -% being then simply ignored. A user redefinition will probably either use -% directly sphinxlightbox or sphinxheavybox or something else, with no need to -% test the boolean. -% -% 6.2.0 also adds one layer of mark-up via \sphinxnotetitle etc..., because -% the former \sphinxstrong{#1} used a too generic \sphinxstrong. But -% perhaps the #1 should be passed over to sphinx{light,heavy}box as parameter. -% Unfortunately replacing these environments with one-parameter environments -% would be potentially a breaking change. Anyway, sphinxpackageboxes.sty does not -% provide a "titled" box; the caption of code-blocks is handled by extra -% code in sphinxVerbatim. -\newenvironment{sphinxnote}[1] - {\edef\spx@env{sphinx\ifspx@opt@heavynote heavy\else light\fi box}% - \expandafter\begin\expandafter{\spx@env}\sphinxstylenotetitle{#1}} - {\expandafter\end\expandafter{\spx@env}} -\newenvironment{sphinxhint}[1] - {\edef\spx@env{sphinx\ifspx@opt@heavyhint heavy\else light\fi box}% - \expandafter\begin\expandafter{\spx@env}\sphinxstylehinttitle{#1}} - {\expandafter\end\expandafter{\spx@env}} -\newenvironment{sphinximportant}[1] - {\edef\spx@env{sphinx\ifspx@opt@heavyimportant heavy\else light\fi box}% - \expandafter\begin\expandafter{\spx@env}\sphinxstyleimportanttitle{#1}} - {\expandafter\end\expandafter{\spx@env}} -\newenvironment{sphinxtip}[1] - {\edef\spx@env{sphinx\ifspx@opt@heavytip heavy\else light\fi box}% - \expandafter\begin\expandafter{\spx@env}\sphinxstyletiptitle{#1}} - {\expandafter\end\expandafter{\spx@env}} - -% warning/caution/attention/danger/error get more distinction +% Then from 6.2.0 to 7.4.0 (exclusive) a more complex definition decided +% to use either sphinxlightbox or sphinxheavybox according to whether +% some CSS-like options had been used, for example for a background color. +% +% 6.2.0 also added one layer of mark-up via \sphinxnotetitle etc..., because +% the former \sphinxstrong{#1} used a too generic \sphinxstrong. +% +% At 7.4.0, sphinxheavybox environment is default for all types of notices +% and also for the seealso and todo directives. % % Code adapted from framed.sty's "snugshade" environment. % Nesting works (inner frames do not allow page breaks). \newenvironment{sphinxheavybox}{\par - % 6.2.0 allows to not have to distinguish here between warning type notices - % which always use sphinxheavybox or note type notices which might use it. % (MEMO: it is not a problem here if there is no sphinxShadowColor, % as it used only if set) \spx@boxes@fcolorbox@setup{\spx@noticetype}% @@ -205,16 +199,80 @@ % Example: % \renewcommand{\sphinxwarningtitle}[1]{\textbf{#1}\par\smallskip % {\color{sphinxwarningBorderColor}\hrule height1pt}\smallskip} +% +% - Since 7.4.0, all types of notices use sphinxheavybox and the default +% for \sphinxstyletitle is mapped to using \sphinxdotitlerowwithicon{} +% +% MEMO: except for the generic admonition directive (which uses "note" type) +% the argument #1 in these environments has a postfixed colon originating +% in Sphinx LaTeX writer legacy code. The +% \sphinxremovefinalcolon utility in sphinxlatexstyletext.sty can be used as +% \sphinxremovefinalcolon{#1} from inside the definitions of +% \sphinxstylenotetitle et al. commands. + +% Important: even prior to 5.1.0 it was not really possible to use directly +% sphinxheavybox if not triggered from sphinxadmonition, because some +% parameters were defined in sphinxadmonition. This meant that the +% sphinxwarning, sphinxcaution etc... environments (defined below) could not +% be used directly in a document, they had to be triggered via +% sphinxadmonition. The sole data since 5.1.0 needed by sphinxheavybox is the +% type of the notice which sphinxadmonition stores into \spx@noticetype. +% +% In order to facilitate recycling or imitation of the sphinx +% environments, 7.4.0 inserts an extra \def\spx@noticetype{} in their +% definitions, so that they can be used independently of sphinxadmonition +% dispatcher. +% +% MEMO: direct usage of these environments does not execute the div._TeXextras +% and div._TexColor code, there are only done from the sphinxadmonition wrapper. +\newenvironment{sphinxnote}[1] + {\def\spx@noticetype{note}\begin{sphinxheavybox}\sphinxstylenotetitle{#1}} + {\end{sphinxheavybox}} +\newenvironment{sphinxhint}[1] + {\def\spx@noticetype{hint}\begin{sphinxheavybox}\sphinxstylehinttitle{#1}} + {\end{sphinxheavybox}} +\newenvironment{sphinxtip}[1] + {\def\spx@noticetype{tip}\begin{sphinxheavybox}\sphinxstyletiptitle{#1}} + {\end{sphinxheavybox}} +\newenvironment{sphinximportant}[1] + {\def\spx@noticetype{important}\begin{sphinxheavybox}\sphinxstyleimportanttitle{#1}} + {\end{sphinxheavybox}} \newenvironment{sphinxwarning}[1] - {\begin{sphinxheavybox}\sphinxstylewarningtitle{#1}}{\end{sphinxheavybox}} + {\def\spx@noticetype{warning}\begin{sphinxheavybox}\sphinxstylewarningtitle{#1}} + {\end{sphinxheavybox}} \newenvironment{sphinxcaution}[1] - {\begin{sphinxheavybox}\sphinxstylecautiontitle{#1}}{\end{sphinxheavybox}} + {\def\spx@noticetype{caution}\begin{sphinxheavybox}\sphinxstylecautiontitle{#1}} + {\end{sphinxheavybox}} \newenvironment{sphinxattention}[1] - {\begin{sphinxheavybox}\sphinxstyleattentiontitle{#1}}{\end{sphinxheavybox}} + {\def\spx@noticetype{attention}\begin{sphinxheavybox}\sphinxstyleattentiontitle{#1}} + {\end{sphinxheavybox}} \newenvironment{sphinxdanger}[1] - {\begin{sphinxheavybox}\sphinxstyledangertitle{#1}}{\end{sphinxheavybox}} + {\def\spx@noticetype{danger}\begin{sphinxheavybox}\sphinxstyledangertitle{#1}} + {\end{sphinxheavybox}} \newenvironment{sphinxerror}[1] - {\begin{sphinxheavybox}\sphinxstyleerrortitle{#1}}{\end{sphinxheavybox}} + {\def\spx@noticetype{error}\begin{sphinxheavybox}\sphinxstyleerrortitle{#1}} + {\end{sphinxheavybox}} +% The "see also" was quite plain until 7.4.0 as it simply did +% \newenvironment{sphinxseealso}[1]{\sphinxstyleseealsotitle{#1}}{} +% Here we need to manually insert execution of div.seealso_TeX{color,extras} values +\newenvironment{sphinxseealso}[1] + {\def\spx@noticetype{seealso}% + \begin{sphinxheavybox}\sphinxstyleseealsotitle{#1}% + \ifspx@seealso@withtextcolor\color{sphinxseealsoTextColor}\fi + \spx@seealso@TeXextras + } + {\end{sphinxheavybox}} +% There was no sphinxtodo environment until 7.4.0 because sphinx.ext.todo +% generated \begin{sphinxadmonition}{note}{Todo:} mark-up. +\newcounter{sphinxtodo}% to provide targets from todolist directive output +\newenvironment{sphinxtodo}[1] + {\refstepcounter{sphinxtodo}\def\spx@noticetype{todo}% + \begin{sphinxheavybox}\sphinxstyletodotitle{#1}% + \ifspx@todo@withtextcolor\color{sphinxtodoTextColor}\fi + \spx@todo@TeXextras + } + {\end{sphinxheavybox}} + % the main dispatch for all types of notices \newenvironment{sphinxadmonition}[2]{% #1=type, #2=heading @@ -227,16 +285,119 @@ % the more bulky "sphinx\spx@noticetype BgColor". \sphinxcolorlet{spx@notice@bordercolor}{sphinx#1BorderColor}% \sphinxcolorlet{spx@notice@bgcolor}{sphinx#1BgColor}% - \spx@notice@border \dimexpr\csname spx@#1@border\endcsname\relax + % At 7.4.0 there are no \spx@@boder macros anymore only top, left, + % bottom, right. For this legacy \spx@notice@border only needed by + % sphinxlightbox (which is not used by own Sphinx environments anymore) + % we thus use here @top + \spx@notice@border \dimexpr\csname spx@#1@border@top\endcsname\relax % trigger the sphinx environment, #2=heading is passed as argument \begin{sphinx#1}{#2}% + % MEMO: the heading #2 will be typeset before the next lines are executed % 6.2.0 support of div._TeX{color,extras} options \csname ifspx@\spx@noticetype @withtextcolor\endcsname \color{sphinx\spx@noticetype TextColor}% \fi + % Other code to be executed at start of contents (after title) \csname spx@\spx@noticetype @TeXextras\endcsname } - % workaround some LaTeX "feature" of \end command (can't use "sphinx#1" here) + % workaround some LaTeX "feature" of \end command (i.e. can't use "sphinx#1" here) {\edef\spx@temp{\noexpand\end{sphinx\spx@noticetype}}\spx@temp} +% TODO: allow these next three settings to be customized individually. +% This can however already be done at user level by \renewcommand +% inside renew'ed environments sphinxnote, sphinxhint etc... +\newcommand\sphinxtitlerowtoppadding{5pt} +\newcommand\sphinxtitlerowbottompadding{3pt} +\newcommand\sphinxtitlerowaftericonspacecmd{\hskip0.5em\relax} +% 7.4.0 used this longer name: +\newcommand\sphinxdotitlerowwithicon{\sphinxdotitlerow} +\newcommand\sphinxdotitlerow[2]{% #1=type, #2=heading (without final colon) + \begingroup + \kern-\spx@boxes@padding@top + \parskip\z@skip % the \parskip business is a workaround to a vertical + % glue issue showing in LaTeX earlier than 2023-06-01 + \noindent + \kern-\spx@boxes@padding@left % must have been configured by a prior + % \spx@boxes@fcolorbox@setup{} + % inherit settings from the enclosing box and modify what is needed + \spx@boxes@border@top =\z@ + \spx@boxes@border@right =\z@ + \spx@boxes@border@bottom =\z@ + \spx@boxes@border@left =\z@ + \spx@boxes@radius@bottomright@x=\z@ + \spx@boxes@radius@bottomright@y=\z@ + \spx@boxes@radius@bottomleft@x=\z@ + \spx@boxes@radius@bottomleft@x=\z@ + \spx@boxes@padding@top =\sphinxtitlerowtoppadding\relax + \spx@boxes@padding@bottom=\sphinxtitlerowbottompadding\relax + \spx@boxes@withshadowfalse + \sphinxcolorlet{spx@boxes@backgroundcolor}{sphinx#1TtlBgColor}% + \spx@boxes@fcolorbox{% + \parbox[t]{\linewidth}{% 7.4.0 used \makebox, but wrapping of long titles + % is needed for generic admonition or topic box. + \sphinxAtStartPar + % 8.1.0 auto-drops extra space if no icon + \sbox\z@{\@nameuse{sphinx#1TtlIcon}}% + \ifdim\wd\z@>\z@ + \textcolor{sphinx#1TtlFgColor}{% + \@nameuse{sphinx#1TtlIcon}% + % The next macro is located here for legacy reasons of earlier + % functioning of \spx@faIcon. When fontawesome{5,}.sty both + % are unavailable, it (formerly) gobbled this next macro. + % We leave it here now although it could be moved to after + % the closing brace. + \sphinxtitlerowaftericonspacecmd + }% + \fi + \sphinxstrong{#2}% + \strut + \par + }% + }% + \kern-\spx@boxes@padding@right + \par + \endgroup + \vskip-\parskip + \kern\spx@boxes@padding@top +} + +% #1 holds the localized name of the notice, postfixed with a colon. +% \sphinxremovefinalcolon{#1} will typeset #1 without the colon. +% Legacy definitions (done in sphinxlatexstyletext.sty) were all using +% a boring plain \sphinxstrong{#1}, now we use a coloured title row. +\newcommand\sphinxstylenotetitle [1]{\sphinxdotitlerow{note}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstylehinttitle [1]{\sphinxdotitlerow{hint}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstyleimportanttitle[1]{\sphinxdotitlerow{important}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstyletiptitle [1]{\sphinxdotitlerow{tip}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstylewarningtitle [1]{\sphinxdotitlerow{warning}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstylecautiontitle [1]{\sphinxdotitlerow{caution}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstyleattentiontitle[1]{\sphinxdotitlerow{attention}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstyledangertitle [1]{\sphinxdotitlerow{danger}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstyleerrortitle [1]{\sphinxdotitlerow{error}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstyleseealsotitle [1]{\sphinxdotitlerow{seealso}{\sphinxremovefinalcolon{#1}}} +\newcommand\sphinxstyletodotitle [1]{\sphinxdotitlerow{todo}{\sphinxremovefinalcolon{#1}}} +% +% A utility to remove a final colon. Removing last token is not easy in +% LaTeX, and there are additional complications: +% - some languages will make the : "active" in document body, +% - the generic admonition ends up using "note", so for \sphinxnotetitle to +% use it safely, the utility has to allow an input not having any final colon. +% - a bit far-fetched but maybe there is more than one colon inside the input +% (possible from a generic admonition title). +% Hence the scary code. +\newcommand\sphinxremovefinalcolon[1]{% #1 is the "active" : TeX token +% Prior to 7.4.0 this was defined with \protected\def but we do not +% see what usefulness this could have. +\renewcommand\sphinxremovefinalcolon[1]{% + % complications due to : possibly "active" + \begingroup\ifnum\catcode`:=\active + \def\x####1#1\relax{####1}% + \else\def\x####1:\relax{####1}\fi + \expandafter\endgroup\x##1\relax + % trick to let \x work also if input ##1 has no ending colon + \@gobblefour#1\relax:\relax\relax\relax + }% +}% end of wrapper to inject active : +\begingroup\catcode`:\active\expandafter\endgroup\sphinxremovefinalcolon: + \endinput diff --git a/docs/build/latex/sphinxlatexcontainers.sty b/docs/build/latex/sphinxlatexcontainers.sty index 93b2c8c..012d9ee 100644 --- a/docs/build/latex/sphinxlatexcontainers.sty +++ b/docs/build/latex/sphinxlatexcontainers.sty @@ -1,7 +1,7 @@ %% CONTAINER DIRECTIVES % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexcontainers.sty}[2021/05/03 containers] +\ProvidesPackage{sphinxlatexcontainers}[2021/05/03 containers] % The purpose of this file is to provide a dummy environment sphinxclass which % will be inserted for each class in each container directive. The class name diff --git a/docs/build/latex/sphinxlatexgraphics.sty b/docs/build/latex/sphinxlatexgraphics.sty index fd0aae6..f0c7c25 100644 --- a/docs/build/latex/sphinxlatexgraphics.sty +++ b/docs/build/latex/sphinxlatexgraphics.sty @@ -1,7 +1,7 @@ %% GRAPHICS % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexgraphics.sty}[2021/01/27 graphics] +\ProvidesPackage{sphinxlatexgraphics}[2024/08/13 v8.1.0 graphics] % Provides support for this output mark-up from Sphinx latex writer: % @@ -84,7 +84,8 @@ \ifin@ \setbox\spx@image@box \hbox{\includegraphics - [%#1,% contained only width and/or height and overruled anyhow + [#1,% contains only width and/or height which are overruled next + % but in future may contain page=N hence must be kept width=\spx@image@requiredwidth,height=\spx@image@requiredheight]% {#2}}% % \includegraphics does not set box dimensions to the exactly diff --git a/docs/build/latex/sphinxlatexindbibtoc.sty b/docs/build/latex/sphinxlatexindbibtoc.sty index 79e30a1..052d31e 100644 --- a/docs/build/latex/sphinxlatexindbibtoc.sty +++ b/docs/build/latex/sphinxlatexindbibtoc.sty @@ -1,7 +1,7 @@ %% INDEX, BIBLIOGRAPHY, APPENDIX, TABLE OF CONTENTS % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexindbibtoc.sty}[2021/01/27 index, bib., toc] +\ProvidesPackage{sphinxlatexindbibtoc}[2021/01/27 index, bib., toc] % Provides support for this output mark-up from Sphinx latex writer: % diff --git a/docs/build/latex/sphinxlatexlists.sty b/docs/build/latex/sphinxlatexlists.sty index 8e79355..4db3af2 100644 --- a/docs/build/latex/sphinxlatexlists.sty +++ b/docs/build/latex/sphinxlatexlists.sty @@ -1,7 +1,7 @@ %% ALPHANUMERIC LIST ITEMS % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexlists.sty}[2021/12/20 lists] +\ProvidesPackage{sphinxlatexlists}[2021/12/20 lists] % Provides support for this output mark-up from Sphinx latex writer: % - \sphinxsetlistlabels diff --git a/docs/build/latex/sphinxlatexliterals.sty b/docs/build/latex/sphinxlatexliterals.sty index 3a73a76..11991d9 100644 --- a/docs/build/latex/sphinxlatexliterals.sty +++ b/docs/build/latex/sphinxlatexliterals.sty @@ -1,7 +1,7 @@ %% LITERAL BLOCKS % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexliterals.sty}[2023/04/01 code-blocks and parsed literals] +\ProvidesPackage{sphinxlatexliterals}[2024/07/01 v7.4.0 code-blocks and parsed literals] % Provides support for this output mark-up from Sphinx latex writer: % @@ -34,6 +34,7 @@ % - needspace % - sphinxpackageboxes \RequirePackage{sphinxpackageboxes} +% 7.4.0 removes unneeded usage of \spx@boxes@border % also in sphinxlatexadmonitions.sty: % This is a workaround to a "feature" of French lists, when literal block @@ -224,7 +225,6 @@ \spx@boxes@border@right\z@ \spx@boxes@border@bottom\z@ \spx@boxes@border@left\z@ - \spx@boxes@border\z@ % MEMO: rounded corners still make sense in presence of a background % color, so we do not force the fcolorbox@rectangle here \fi @@ -512,6 +512,9 @@ \setbox\spx@tempboxa \vtop{\raggedright\hyphenpenalty\z@\exhyphenpenalty\z@ \doublehyphendemerits\z@\finalhyphendemerits\z@ +% Avoid TeX reporting Overfull \hbox'es during this measuring phase. Setting +% \hbadness to \@M to avoid Underfull reports is unneeded due to \raggedright. + \hfuzz\maxdimen \spx@everypar{}\noindent\strut\FV@Line\strut\spx@par \spx@verb@getwidths}% \ifdim\spx@verb@maxwidth> @@ -670,25 +673,18 @@ \def\sphinxVerbatim@Before {\sphinxVerbatim@Title\nointerlineskip \kern\dimexpr-\dp\strutbox+\sphinxbelowcaptionspace - % if no frame (code-blocks inside table cells), remove - % the top padding (better visually) - \ifspx@opt@verbatimwithframe\else - % but we must now check if there is a background color - % MEMO: "fcolorbox@setup" will have been done by time of use - \ifspx@boxes@withbackgroundcolor\else-\spx@boxes@padding@top\fi - \fi + % MEMO: prior to 7.4.0 a test was done for presence or + % not of a frame and if not top padding was removed if + % no background color. A background color is now always + % assumed, so this got removed. % caption package adds \abovecaptionskip vspace, remove it - \spx@ifcaptionpackage{-\abovecaptionskip}{}\relax}% + \spx@ifcaptionpackage{-\abovecaptionskip}{}\relax}% \else \vskip\sphinxverbatimsmallskipamount \def\sphinxVerbatim@After {\nointerlineskip\kern\dimexpr\dp\strutbox - \ifspx@opt@verbatimwithframe\else - % but we must now check if there is a background color - % MEMO: "fcolorbox@setup" will have been done by time of use - \ifspx@boxes@withbackgroundcolor\else-\spx@boxes@padding@bottom\fi - \fi - \spx@ifcaptionpackage{-\abovecaptionskip}{}\relax + % MEMO: 7.4.0 removes here too an optional removal of bottom padding + \spx@ifcaptionpackage{-\abovecaptionskip}{}\relax \sphinxVerbatim@Title}% \fi \def\@captype{literalblock}% diff --git a/docs/build/latex/sphinxlatexnumfig.sty b/docs/build/latex/sphinxlatexnumfig.sty index 6d72961..22fcbb0 100644 --- a/docs/build/latex/sphinxlatexnumfig.sty +++ b/docs/build/latex/sphinxlatexnumfig.sty @@ -1,7 +1,7 @@ %% NUMBERING OF FIGURES, TABLES, AND LITERAL BLOCKS % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexnumfig.sty}[2021/01/27 numbering] +\ProvidesPackage{sphinxlatexnumfig}[2024/07/31 v8.1.0 numbering] % Requires: remreset (old LaTeX only) % relates to numfig and numfig_secnum_depth configuration variables @@ -37,7 +37,11 @@ \def\theequation{\arabic{equation}}% \fi \else -\let\spx@preAthefigure\@empty +% See apologetic comments on TeX wizardry at bottom of file. +% The reason for this one is to catch case where there will be only +% the number with no prefix from enclosing sectioning (can happen +% with latex_toplevel_sectioning='part'). +\def\spx@preAthefigure{\expandafter\spx@magicsep@s\romannumeral-`0} \let\spx@preBthefigure\@empty % \ifspx@opt@usespart % <-- LaTeX writer could pass such a 'usespart' boolean % % as sphinx.sty package option @@ -51,7 +55,7 @@ \ifnum\spx@opt@numfigreset>0 \ltx@ifundefined{c@chapter} {} - {\g@addto@macro\spx@preAthefigure{\ifnum\c@chapter>\z@\arabic{chapter}.}% + {\g@addto@macro\spx@preAthefigure{\ifnum\c@chapter>\z@\arabic{chapter}\spx@magicsep}% \g@addto@macro\spx@preBthefigure{\fi}}% \fi \ifnum\spx@opt@numfigreset>1 @@ -61,7 +65,7 @@ \ifspx@opt@mathnumfig \@addtoreset{equation}{section}% \fi% - \g@addto@macro\spx@preAthefigure{\ifnum\c@section>\z@\arabic{section}.}% + \g@addto@macro\spx@preAthefigure{\ifnum\c@section>\z@\arabic{section}\spx@magicsep}% \g@addto@macro\spx@preBthefigure{\fi}% \fi \ifnum\spx@opt@numfigreset>2 @@ -71,7 +75,7 @@ \ifspx@opt@mathnumfig \@addtoreset{equation}{subsection}% \fi% - \g@addto@macro\spx@preAthefigure{\ifnum\c@subsection>\z@\arabic{subsection}.}% + \g@addto@macro\spx@preAthefigure{\ifnum\c@subsection>\z@\arabic{subsection}\spx@magicsep}% \g@addto@macro\spx@preBthefigure{\fi}% \fi \ifnum\spx@opt@numfigreset>3 @@ -81,7 +85,7 @@ \ifspx@opt@mathnumfig \@addtoreset{equation}{subsubsection}% \fi% - \g@addto@macro\spx@preAthefigure{\ifnum\c@subsubsection>\z@\arabic{subsubsection}.}% + \g@addto@macro\spx@preAthefigure{\ifnum\c@subsubsection>\z@\arabic{subsubsection}\spx@magicsep}% \g@addto@macro\spx@preBthefigure{\fi}% \fi \ifnum\spx@opt@numfigreset>4 @@ -91,7 +95,7 @@ \ifspx@opt@mathnumfig \@addtoreset{equation}{paragraph}% \fi% - \g@addto@macro\spx@preAthefigure{\ifnum\c@subparagraph>\z@\arabic{subparagraph}.}% + \g@addto@macro\spx@preAthefigure{\ifnum\c@subparagraph>\z@\arabic{subparagraph}\spx@magicsep}% \g@addto@macro\spx@preBthefigure{\fi}% \fi \ifnum\spx@opt@numfigreset>5 @@ -101,7 +105,7 @@ \ifspx@opt@mathnumfig \@addtoreset{equation}{subparagraph}% \fi% - \g@addto@macro\spx@preAthefigure{\ifnum\c@subsubparagraph>\z@\arabic{subsubparagraph}.}% + \g@addto@macro\spx@preAthefigure{\ifnum\c@subsubparagraph>\z@\arabic{subsubparagraph}\spx@magicsep}% \g@addto@macro\spx@preBthefigure{\fi}% \fi \expandafter\g@addto@macro @@ -114,9 +118,18 @@ \g@addto@macro\theliteralblock{\arabic{literalblock}}% \ifspx@opt@mathnumfig \let\theequation\spx@preAthefigure - \g@addto@macro\theequation{\arabic{equation}}% + \g@addto@macro\theequation{E}% \fi \fi }% end of big \AtBeginDocument +% Sorry for TeX wizardry here. We need to keep expandability. Explaining +% the mechanism is not really feasible to non TeX-experts, but the idea +% is to force next `\ifnum` conditional so we can check what comes next. +% All cases are accounted for (i.e. not an equation, or an equation at top +% level, or an equation in some section at some depth). +\def\spx@magicsep{\expandafter\spx@magicsep@i\romannumeral-`0} +\def\spx@magicsep@i#1{\if#1E\spx@opt@mathnumsep\arabic{equation}\else.#1\fi} +% +\def\spx@magicsep@s#1{\if#1E\arabic{equation}\else#1\fi} \endinput diff --git a/docs/build/latex/sphinxlatexobjects.sty b/docs/build/latex/sphinxlatexobjects.sty index 5d9b69b..1147a01 100644 --- a/docs/build/latex/sphinxlatexobjects.sty +++ b/docs/build/latex/sphinxlatexobjects.sty @@ -1,7 +1,7 @@ %% MODULE RELEASE DATA AND OBJECT DESCRIPTIONS % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexobjects.sty}[2023/07/23 documentation environments] +\ProvidesPackage{sphinxlatexobjects}[2025/02/11 documentation environments] % Provides support for this output mark-up from Sphinx latex writer: % @@ -279,18 +279,37 @@ \newcommand{\pysigstopmultiline}{\sphinxsigismultilinefalse\itemsep\sphinxsignaturesep}% % Production lists +% This simply outputs the lines as is, in monospace font. Refers #13326. +% (the left padding for multi-line alignment is from the nodes themselves, +% and latex is configured below to obey such horizontal whitespace). +% +% - The legacy code used longtable and hardcoded the separator as ::= +% via dedicated macros defined by the environment itself. +% - Here the separator is part of the node. Any extra LaTeX mark-up would +% have to originate from the writer itself to decorate it. +% - The legacy code used strangely \parindent and \indent. Possibly +% (unchecked) due to an earlier tabular usage, but a longtable does not +% work in paragraph mode, so \parindent was without effect and +% \indent only caused some extra blank line above display. +% - The table had some whitespace on its left, which we imitate here via +% \parindent usage (which works in our context...). % \newenvironment{productionlist}{% -% \def\sphinxoptional##1{{\Large[}##1{\Large]}} - \def\production##1##2{\\\sphinxcode{\sphinxupquote{##1}}&::=&\sphinxcode{\sphinxupquote{##2}}}% - \def\productioncont##1{\\& &\sphinxcode{\sphinxupquote{##1}}}% - \parindent=2em - \indent - \setlength{\LTpre}{0pt}% - \setlength{\LTpost}{0pt}% - \begin{longtable}[l]{lcl} + \bigskip % imitate close enough legacy vertical whitespace, which was + % visibly excessive + \ttfamily % needed for space tokens to have same width as letters + \parindent1em % width of a "quad", font-dependent, usually circa width of 2 + % letters + \obeylines % line in = line out + \parskip\z@skip % prevent the parskip vertical whitespace between lines, + % which are technically to LaTeX now each its own paragraph + \@vobeyspaces % obey whitespace + % now a technicality to, only locally to this environment, prevent the + % suppression of indentation of first line, if it comes right after + % \section. Cf package indentfirst from which the code is borrowed. + \let\@afterindentfalse\@afterindenttrue\@afterindenttrue }{% - \end{longtable} + \par % does not hurt... } % Definition lists; requested by AMK for HOWTO documents. Probably useful diff --git a/docs/build/latex/sphinxlatexshadowbox.sty b/docs/build/latex/sphinxlatexshadowbox.sty index a2a1a0e..53a3338 100644 --- a/docs/build/latex/sphinxlatexshadowbox.sty +++ b/docs/build/latex/sphinxlatexshadowbox.sty @@ -1,21 +1,37 @@ %% TOPIC AND CONTENTS BOXES % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexshadowbox.sty}[2023/03/19 sphinxShadowBox] +\ProvidesPackage{sphinxlatexshadowbox}[2024/07/28 v8.1.0 sphinxShadowBox] % Provides support for this output mark-up from Sphinx latex writer: % -% - sphinxShadowBox (environment) +% - Environments: sphinxtopic, sphinxcontents, and sphinxsidebar. +% +% These wrappers replace at 8.1.0 former direct use of sphinxShadowBox +% environment which did not allow separate styling. +% +% - Commands: \sphinxstyletopictitle, \sphinxstylecontentstitle, and +% \sphinxstylesidebartitle. +% +% At 8.1.0 they default to use \sphinxdotitlerow whose definiion is done in +% sphinxlatexadmonitions.sty. There is also \sphinxstylesidebarsubtitle +% which does not use \sphinxdotitlerow. % % Dependencies (they do not need to be defined at time of loading): % % - of course the various colour and dimension options handled via sphinx.sty % - dimension register \spx@image@maxheight from sphinxlatexgraphics.sty -% - \savenotes/\spewnotes from sphinxpackagefootnote +% - \savenotes/\spewnotes from sphinxpackagefootnote.sty % - \ifspx@inframed defined in sphinx.sty +% - \sphinxdotitlerow from sphinxlatexadmonitions.sty +% - \spx@boxes@fcolorbox@setup from sphinxpackageboxes.sty % -% Requires: \RequirePackage{framed} +% Those are required either before or after by sphinx.sty anyhow, but for +% clarity we list them here: +\RequirePackage{sphinxlatexgraphics} +\RequirePackage{sphinxpackagefootnote} +\RequirePackage{sphinxlatexadmonitions} \RequirePackage{sphinxpackageboxes} % At 5.1.0 the code formerly here in a definition of \spx@ShadowFBox has been @@ -45,9 +61,28 @@ % in contrast with the framing used for literal blocks, also based, but in a % more sophisticated way on usage of \MakeFramed/\endMakeFramed, and % adjusting to current text indentation. -\newenvironment{sphinxShadowBox} +% +% At 8.1.0, sphinxShadowBox takes an optional argument #1 and uses it as +% \spx@boxes@fcolorbox@setup{#1} rather than \spx@boxes@fcolorbox@setup{topic}. +% Some hesitation whether to move this line to newly added sphinxtopic, +% sphinxcontents and sphinxsidebar environmments. But anyhow the environment +% also requires later knowing a few more things: sphinxTextColor and +% spx@@texextras. +% +% The #1 defaulting to topic must be such that all parameters expected by +% \spx@boxes@fcolorbox@setup actually do exist, see CSS options in sphinx.sty +% which is what defines them for contents, topic, and sidebar. +% +% Fortunately the #1 is not needed in \end{sphinxShadowBox} so we don't have +% to work around a LaTeX conception bug that such #1 can not be used as is in +% the definition of the \end part of an environment. +% +% MEMO: the "shadow" is not really drawn directly by this environment but +% indirectly via the configuration which is passed over to \spx@boxes@fcolorbox, +% which is the macro creating frame and (perhaps but not necessarily) a shadow. +\newenvironment{sphinxShadowBox}[1][topic]% {% - \spx@boxes@fcolorbox@setup{topic}% + \spx@boxes@fcolorbox@setup{#1}% % we will use the dimen registers from sphinxpackageboxes.sty which now hold % the values from options related to topic/contents % MEMO: \spx@boxes@fcolorbox creates an \hbox but does not quit vertical @@ -56,7 +91,7 @@ \def\FrameCommand {\spx@boxes@fcolorbox}% % 6.2.0 adds support for div.topic_box-decoration-break=slice. % (it is yet undecided if slice style should inhibit a bottom shadow) - \ifspx@topic@border@open + \@nameuse{ifspx@#1@border@open}% \def\FirstFrameCommand {\spx@boxes@fcolorbox@setup@openbottom\FrameCommand}% \def\MidFrameCommand @@ -97,10 +132,10 @@ \@setminipage }% \color@begingroup % workaround upstream framed.sty bug - \ifspx@topic@withtextcolor - \color{sphinxtopicTextColor}% + \@nameuse{ifspx@#1@withtextcolor}% + \color{sphinx#1TextColor}% \fi - \spx@topic@TeXextras + \@nameuse{spx@#1@TeXextras}% }% {% insert the "endminipage" code \par\unskip @@ -113,4 +148,31 @@ \spewnotes } +% 8.1.0 +\newenvironment{sphinxtopic} + {\begin{sphinxShadowBox}[topic]}{\end{sphinxShadowBox}} +\newenvironment{sphinxcontents} + {\begin{sphinxShadowBox}[contents]}{\end{sphinxShadowBox}} +% Arguably sphinxsidebar should rather use a wrapfig or similar environment +% but this is so dysfunctional in LaTeX (except for self-written documents) +% so we prefer to not venture into such a potential quagmire and keep the +% legacy rendering using a full width display. +\newenvironment{sphinxsidebar} + {\begin{sphinxShadowBox}[sidebar]}{\end{sphinxShadowBox}} + +% TODO: decide if this should be in sphinxlatexstyletext.sty rather +% +% 8.1.0 styles topic/contents/sidebar with a title row, too. +% Prior to 8.1.0, definitions use \protected\def but there does not seem +% to be any reason so back to \newcommand. +\newcommand*\sphinxstyletopictitle[1]{\sphinxdotitlerow{topic}{#1}} +\newcommand*\sphinxstylecontentstitle[1]{\sphinxdotitlerow{contents}{#1}} +\newcommand*\sphinxstylesidebartitle[1]{\sphinxdotitlerow{sidebar}{#1}} +% No default color background for subtitle. The contents next are injected by +% LaTeX writer after a blank line in source hence will start a new paragrpah. +% The \sphinxAtStartPar here is only for coherence with other text paragraphs, +% but does not have serious necessity (its general role is to allow hyphenation +% for first word in narrow table cells). +\newcommand*\sphinxstylesidebarsubtitle[1]{\sphinxAtStartPar\textbf{#1}} + \endinput diff --git a/docs/build/latex/sphinxlatexstyleheadings.sty b/docs/build/latex/sphinxlatexstyleheadings.sty index b5e9c85..08773c0 100644 --- a/docs/build/latex/sphinxlatexstyleheadings.sty +++ b/docs/build/latex/sphinxlatexstyleheadings.sty @@ -1,9 +1,15 @@ %% TITLES % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexstyleheadings.sty}[2023/02/11 headings] +\ProvidesPackage{sphinxlatexstyleheadings}[2023/02/11 headings] \RequirePackage[nobottomtitles*]{titlesec} +% tests showed that this setting guarantees \section title has +% 3 lines of text following it on same page if near bottom. +\renewcommand\bottomtitlespace{6\baselineskip} +% the default setting of 0.2\textheight is about 11\baselineskip +% (for 10pt letterpaper documents) and may create large voids. + \@ifpackagelater{titlesec}{2016/03/15}% {\@ifpackagelater{titlesec}{2016/03/21}% {}% @@ -47,7 +53,6 @@ \titleformat{\subparagraph}{\normalsize\py@HeaderFamily}% {\py@TitleColor\thesubparagraph}{0.5em}{\py@TitleColor} - % Since Sphinx 1.5, users should use HeaderFamily key to 'sphinxsetup' rather % than defining their own \py@HeaderFamily command (which is still possible). % Memo: \py@HeaderFamily is also used by \maketitle as defined in diff --git a/docs/build/latex/sphinxlatexstylepage.sty b/docs/build/latex/sphinxlatexstylepage.sty index 4066129..53f9e48 100644 --- a/docs/build/latex/sphinxlatexstylepage.sty +++ b/docs/build/latex/sphinxlatexstylepage.sty @@ -1,16 +1,10 @@ %% PAGE STYLING % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexstylepage.sty}[2021/01/27 page styling] +\ProvidesPackage{sphinxlatexstylepage}[2021/01/27 page styling] % Separate paragraphs by space by default. -\IfFileExists{parskip-2001-04-09.sty}% since September 2018 TeXLive update -% new parskip.sty, but let it rollback to old one. -% hopefully TeX installation not broken and LaTeX kernel not too old - {\RequirePackage{parskip}[=v1]} -% standard one from 1989. Admittedly \section of article/book gives possibly -% anomalous spacing, but we can't require September 2018 release for some time. - {\RequirePackage{parskip}} +\RequirePackage{parskip} % Style parameters and macros used by most documents here \raggedbottom diff --git a/docs/build/latex/sphinxlatexstyletext.sty b/docs/build/latex/sphinxlatexstyletext.sty index d900090..d083cd9 100644 --- a/docs/build/latex/sphinxlatexstyletext.sty +++ b/docs/build/latex/sphinxlatexstyletext.sty @@ -1,45 +1,12 @@ %% TEXT STYLING % % change this info string if making any custom modification -\ProvidesFile{sphinxlatexstyletext.sty}[2023/07/23 text styling] +\ProvidesPackage{sphinxlatexstyletext}[2024/07/28 v8.1.0 text styling] -% Basically everything here consists of macros which are part of the latex -% markup produced by the Sphinx latex writer - -% But those arise rather from the default definitions of the respective -% latex environments done in sphinxlatexadmonitions.sty -\def\sphinxstylenotetitle #1{\sphinxstrong{#1} } -\let\sphinxstylehinttitle \sphinxstylenotetitle % #1 holds the localized notice name -\let\sphinxstyleimportanttitle\sphinxstylenotetitle % followed by a colon -\let\sphinxstyletiptitle \sphinxstylenotetitle -\let\sphinxstylewarningtitle \sphinxstylenotetitle -\let\sphinxstylecautiontitle \sphinxstylenotetitle -\let\sphinxstyleattentiontitle\sphinxstylenotetitle -\let\sphinxstyledangertitle \sphinxstylenotetitle -\let\sphinxstyleerrortitle \sphinxstylenotetitle -\def\sphinxstyleseealsotitle#1{\sphinxstrong{#1}\par\nopagebreak} -% -% A utility to remove a final colon. Removing last token is not easy in -% LaTeX, and there are additional complications: -% - some languages will make the : "active" in document body, -% - the generic admonition ends up using "note", so for \sphinxnotetitle to -% use it safely, the utility has to allow an input not having any final colon. -% - a bit far-fetched but maybe there is more than one colon inside the input -% (possible from a generic admonition title). -% Hence the scary code. -\def\sphinxremovefinalcolon#1{% #1 is the "active" : TeX token -\protected\def\sphinxremovefinalcolon ##1{% - % complications due to : possibly "active" - \begingroup\ifnum\catcode`:=\active - \def\x####1#1\relax{####1}% - \else\def\x####1:\relax{####1}\fi - \expandafter\endgroup\x##1\relax - % trick to let \x work also if input ##1 has no ending colon - \@gobblefour#1\relax:\relax\relax\relax - }% -}% end of wrapper to inject active : -\begingroup\catcode`:\active\expandafter\endgroup\sphinxremovefinalcolon: -% See doc/latex.rst for an example. +% 7.4.0 has moved all that is related to admonitions to sphinxlatexadmonitions.sty +% 8.1.0 has moved topic/contents/sidebar to sphinxlatexshadowbox.sty +% Most everything left here consists of macros which are part of the latex markup +% produced by the Sphinx LaTeX writer. % Some custom font markup commands. \protected\def\sphinxstrong#1{\textbf{#1}} @@ -73,10 +40,7 @@ {{\Large\sffamily#1}\nopagebreak\vspace{1mm}} \def\sphinxstyleindexlettergroupDefault #1% {{\Large\sffamily\sphinxnonalphabeticalgroupname}\nopagebreak\vspace{1mm}} -\protected\def\sphinxstyletopictitle #1{\textbf{#1}\par\medskip} -\let\sphinxstylesidebartitle\sphinxstyletopictitle \protected\def\sphinxstyleothertitle #1{\textbf{#1}} -\protected\def\sphinxstylesidebarsubtitle #1{~\\\textbf{#1} \smallskip} % \text.. commands do not allow multiple paragraphs % attention, this one is not self-delimiting \protected\def\sphinxstyletheadfamily {\sffamily} diff --git a/docs/build/latex/sphinxlatextables.sty b/docs/build/latex/sphinxlatextables.sty index 9e44532..4114955 100644 --- a/docs/build/latex/sphinxlatextables.sty +++ b/docs/build/latex/sphinxlatextables.sty @@ -1,7 +1,7 @@ %% TABLES (WITH SUPPORT FOR MERGED CELLS OF GENERAL CONTENTS) % % change this info string if making any custom modification -\ProvidesFile{sphinxlatextables.sty}[2022/08/15 tables]% +\ProvidesPackage{sphinxlatextables}[2024/07/01 v7.4.0 tables]% % Provides support for this output mark-up from Sphinx latex writer % and table templates: @@ -42,6 +42,11 @@ % - \sphinxthistablewithnocolorrowsstyle % - \sphinxthistablewithvlinesstyle % - \sphinxthistablewithnovlinesstyle +% +% Also provides user command (see docs) +% - \sphixncolorblend +% (Sphinx 7.4.0 now requires xcolor, so \sphinxcolorblend does not check +% its availability anymore) % % Executes \RequirePackage for: % @@ -103,6 +108,7 @@ \vbox{}% get correct baseline from above \LTpre\z@skip\LTpost\z@skip % set to zero longtable's own skips \edef\sphinxbaselineskip{\dimexpr\the\dimexpr\baselineskip\relax\relax}% + \spx@inframedtrue % message to sphinxheavybox }% % Compatibility with caption package \def\sphinxthelongtablecaptionisattop{% @@ -116,7 +122,9 @@ \def\sphinxatlongtableend{\@nobreakfalse % latex3/latex2e#173 \prevdepth\z@\vskip\sphinxtablepost\relax}% % B. Table with tabular or tabulary -\def\sphinxattablestart{\par\vskip\dimexpr\sphinxtablepre\relax}% +\def\sphinxattablestart{\par\vskip\dimexpr\sphinxtablepre\relax + \spx@inframedtrue % message to sphinxheavybox + }% \let\sphinxattableend\sphinxatlongtableend % This is used by tabular and tabulary templates \newcommand*\sphinxcapstartof[1]{% @@ -513,19 +521,6 @@ \fi } \def\sphinxcolorblend#1{\gdef\spx@colorblendparam{{#1}}\spx@table@hackCT@colorblend} -% Either xcolor.sty exists on user system and has been loaded by sphinx.sty, -% or it does not exist, so we can use \@ifpackageloaded without delaying. -\@ifpackageloaded{xcolor}% - {}% - {\def\sphinxcolorblend#1{% -\PackageWarning{sphinx}{This table uses \string\sphinxcolorblend\space - but xcolor is not in\MessageBreak - the TeX/LaTeX installation, the command will be\MessageBreak - ignored in this and the next tables}% - \global\let\sphinxcolorblend\@gobble - \sphinxbuildwarning{colorblend}% - }% - } %%%%%%%%%%%%%%%%%% @@ -564,7 +559,7 @@ % 99% or use case. Or perhaps some trick with storing in a \vbox and recovering % via some \vsplit but this becomes complicated... perhaps in future. % -% In passing we obtain baseline alignements across rows (only if +% In passing we obtain baseline alignments across rows (only if % \arraystretch is 1, as LaTeX's does not obey \arraystretch in "p" % multi-line contents, only first and last line...) % diff --git a/docs/build/latex/sphinxoptionsgeometry.sty b/docs/build/latex/sphinxoptionsgeometry.sty index af5a804..d0c59f0 100644 --- a/docs/build/latex/sphinxoptionsgeometry.sty +++ b/docs/build/latex/sphinxoptionsgeometry.sty @@ -1,7 +1,7 @@ %% OPTIONS FOR GEOMETRY % % change this info string if making any custom modification -\ProvidesFile{sphinxoptionsgeometry.sty}[2021/01/27 geometry] +\ProvidesPackage{sphinxoptionsgeometry}[2021/01/27 geometry] % geometry \ifx\kanjiskip\@undefined diff --git a/docs/build/latex/sphinxoptionshyperref.sty b/docs/build/latex/sphinxoptionshyperref.sty index b88f108..caf28e8 100644 --- a/docs/build/latex/sphinxoptionshyperref.sty +++ b/docs/build/latex/sphinxoptionshyperref.sty @@ -1,7 +1,7 @@ %% Bookmarks and hyperlinks % % change this info string if making any custom modification -\ProvidesFile{sphinxoptionshyperref.sty}[2021/01/27 hyperref] +\ProvidesPackage{sphinxoptionshyperref}[2021/01/27 hyperref] % to make pdf with correct encoded bookmarks in Japanese % this should precede the hyperref package diff --git a/docs/build/latex/sphinxpackageboxes.sty b/docs/build/latex/sphinxpackageboxes.sty index b0d3707..2345051 100644 --- a/docs/build/latex/sphinxpackageboxes.sty +++ b/docs/build/latex/sphinxpackageboxes.sty @@ -1,7 +1,12 @@ %% COLOURED BOXES % % change this info string if making any custom modification -\ProvidesPackage{sphinxpackageboxes}[2023/03/19 v6.2.0 advanced colored boxes] +\ProvidesPackage{sphinxpackageboxes}[2024/07/01 v7.4.0 advanced colored boxes] +% 7.4.0 removes usage of some booleans "...withbackgroundcolor" and +% "...withbordercolor" as well as \spx@boxes@border dimen which was +% actually really needed nowhere. This was done in sync with changes in +% sphinx.sty, sphinxlatexadmonitions.sty and sphinxlatexliterals.sty. +% % Optionally executes \RequirePackage for: % % - pict2e. Ideally we would like to use the v0.4a 2020/08/16 release of this @@ -78,15 +83,13 @@ %%%%%%%%%%%%%%%% % Internal registers, conditionals, colors to be configured by each caller % via a preliminary "setup" call -% \newif\ifspx@boxes@withshadow \newif\ifspx@boxes@insetshadow -\newif\ifspx@boxes@withbackgroundcolor +%%% \newif\ifspx@boxes@withbackgroundcolor % removed at 7.4.0 \newif\ifspx@boxes@withshadowcolor -\newif\ifspx@boxes@withbordercolor +%%% \newif\ifspx@boxes@withbordercolor % removed at 7.4.0 \newif\ifspx@boxes@shadowinbbox % -\newdimen\spx@boxes@border \newdimen\spx@boxes@border@top \newdimen\spx@boxes@border@right \newdimen\spx@boxes@border@bottom @@ -150,7 +153,6 @@ \spx@boxes@border@right \dimexpr\@nameuse{spx@#1@border@right}\relax \spx@boxes@border@bottom\dimexpr\@nameuse{spx@#1@border@bottom}\relax \spx@boxes@border@left \dimexpr\@nameuse{spx@#1@border@left}\relax - \spx@boxes@border \dimexpr\@nameuse{spx@#1@border}\relax % \spx@boxes@padding@top \dimexpr\@nameuse{spx@#1@padding@top}\relax \spx@boxes@padding@right \dimexpr\@nameuse{spx@#1@padding@right}\relax @@ -200,19 +202,9 @@ \spx@boxes@insetshadowfalse \fi % - \@nameuse{ifspx@#1@withbordercolor}% - \spx@boxes@withbordercolortrue \sphinxcolorlet{spx@boxes@bordercolor}{sphinx#1BorderColor}% - \else - \spx@boxes@withbordercolorfalse - \fi % - \@nameuse{ifspx@#1@withbackgroundcolor}% - \spx@boxes@withbackgroundcolortrue \sphinxcolorlet{spx@boxes@backgroundcolor}{sphinx#1BgColor}% - \else - \spx@boxes@withbackgroundcolorfalse - \fi % \@nameuse{ifspx@#1@withshadowcolor}% \spx@boxes@withshadowcolortrue @@ -447,14 +439,12 @@ \fi % BACKGROUND % draw background and move back to reference point - \ifspx@boxes@withbackgroundcolor {\color{spx@boxes@backgroundcolor}% \vrule\@height\ht\spx@tempboxa \@depth\dp\spx@tempboxa \@width\wd\spx@tempboxa \kern-\wd\spx@tempboxa }% - \fi % BOX SHADOW % draw shadow and move back to reference point \ifspx@boxes@withshadow @@ -494,13 +484,8 @@ }% end of \vbox \fi % end of shadow drawing, and we are back to horizontal reference point % BOX BORDER - \vbox{\ifspx@boxes@withbordercolor - \color{spx@boxes@bordercolor}% - \else - % 6.2.0: guard against a \color command in contents whose effect - % could leak to border at a pagebreak - \normalcolor - \fi + % 7.4.0 requires a set border color + \vbox{\color{spx@boxes@bordercolor}% \hrule\@height\spx@boxes@border@top \kern-\spx@boxes@border@top \setbox\spx@tempboxb\hb@xt@\wd\spx@tempboxa @@ -540,14 +525,13 @@ \def\spx@boxes@fcolorbox@insetshadow{% % BACKGROUND % draw background and move back to reference point - \ifspx@boxes@withbackgroundcolor + % 7.4.0 always assumes a background color {\color{spx@boxes@backgroundcolor}% \vrule\@height\ht\spx@tempboxa \@depth\dp\spx@tempboxa \@width\wd\spx@tempboxa \kern-\wd\spx@tempboxa }% - \fi % BOX SHADOW % draw shadow and move back to reference point \ifspx@boxes@withshadow @@ -589,13 +573,8 @@ }% end of \hbox, attention its depth is only |yoffset| if yoffset<0 \fi % end of inset shadow drawing, and we are back to horizontal reference point % BOX BORDER - \vbox{\ifspx@boxes@withbordercolor - \color{spx@boxes@bordercolor}% - \else - % 6.2.0: guard against a \color command in contents whose effect - % could leak to border at a pagebreak - \normalcolor - \fi + % 7.4.0 requires a set border color + \vbox{\color{spx@boxes@bordercolor}% \hrule\@height\spx@boxes@border@top \kern-\spx@boxes@border@top \setbox\spx@tempboxb\hb@xt@\wd\spx@tempboxa @@ -807,17 +786,11 @@ \fi \spx@boxes@border@defpath% must be redone after each \fillpath! (even if % was in a \put) - \ifspx@boxes@withbordercolor + % 7.4.0 requires a set border color \color{spx@boxes@bordercolor}% - \else - \normalcolor - \fi \fillpath - \ifspx@boxes@withbackgroundcolor + % and backgroundcolor command \color{spx@boxes@backgroundcolor}% - \else - \color{white}% - \fi \edef\spx@width{\number\dimexpr\spx@width-\spx@boxes@border@left -\spx@boxes@border@right sp}% \edef\spx@height{\number\dimexpr\spx@height-\spx@boxes@border@top diff --git a/docs/build/latex/sphinxpackagefootnote.sty b/docs/build/latex/sphinxpackagefootnote.sty index 5590123..7f2e291 100644 --- a/docs/build/latex/sphinxpackagefootnote.sty +++ b/docs/build/latex/sphinxpackagefootnote.sty @@ -1,6 +1,6 @@ \NeedsTeXFormat{LaTeX2e} \ProvidesPackage{sphinxpackagefootnote}% - [2022/08/15 v5.3.0 Sphinx custom footnotehyper package (Sphinx team)] + [2024/05/17 v7.3.x Sphinx custom footnotehyper package (Sphinx team)] %% %% Package: sphinxpackagefootnote %% Version: based on footnotehyper.sty 2021/02/04 v1.1d @@ -409,9 +409,10 @@ {\gdef\@thefnmark{?}% on first LaTeX run \refstepcounter{sphinxfootnotemark}\label{footnotemark.\thesphinxfootnotemark}% }% - {\sphinx@xdef@thefnmark{#1}% also defines \spx@footrefHref - \def\@makefnmark{% will be used by \H@@footnotemark + {\def\@makefnmark{% will be used by \H@@footnotemark \refstepcounter{sphinxfootnotemark}\label{footnotemark.\thesphinxfootnotemark}% + \sphinx@xdef@thefnmark{#1}% also defines \spx@footrefHref + % must be executed after \refstepcounter \hyper@linkstart{link}{\spx@footrefHref}% \spx@saved@makefnmark \hyper@linkend diff --git a/docs/build/latex/sphinxpackagesubstitutefont.sty b/docs/build/latex/sphinxpackagesubstitutefont.sty new file mode 100644 index 0000000..536bf20 --- /dev/null +++ b/docs/build/latex/sphinxpackagesubstitutefont.sty @@ -0,0 +1,21 @@ +%% a stub for obsoleted LaTeX package substitutefont +% The package substitutefont stopped being distributed with TeXLive +% around August 2023 and was moved to "obsolete" section. +% cf https://ctan.org/pkg/substitutefont +% Trying to load it raises a LaTeX build error since. + +% The \substitutefont has a LaTeX kernel replacement +% \DeclareFontFamilySubstitution +% which was added to LaTeX 2020-02-02 +% The aim of this stub is to do that replacement silently. + +% change this info string if making any custom modification +\ProvidesPackage{sphinxpackagesubstitutefont}[2023/15/11 v7.3.0 substitutefont stub] + +\ifdefined\DeclareFontFamilySubstitution + \def\substitutefont{\DeclareFontFamilySubstitution} +\else + \usepackage{substitutefont} +\fi + +\endinput diff --git a/docs/contributors.rst b/docs/contributors.rst index 48212de..2732936 100644 --- a/docs/contributors.rst +++ b/docs/contributors.rst @@ -3,7 +3,7 @@ Contributors Main author ----------- -* `Lindon Roberts `_ (University of Sydney) +* `Lindon Roberts `_ (University of Melbourne) Contributors ------------ diff --git a/docs/history.rst b/docs/history.rst index fd82d86..114d3d5 100644 --- a/docs/history.rst +++ b/docs/history.rst @@ -84,3 +84,8 @@ Version 1.5.4 (11 Feb 2025) --------------------------- * Bugfix when printing results from a run which terminated early * Add ability to save/load results to/from a dictionary + +Version 1.6 (10 Sep 2025) +------------------------- +* Allow use of evaluation database as :code:`x0` to reduce number of objective evaluations required in initialization phase +* When printing solution object, reduce the maximum length of residual/Jacobian vectors that are fully displayed diff --git a/docs/userguide.rst b/docs/userguide.rst index 0e72ab8..7f4ceac 100644 --- a/docs/userguide.rst +++ b/docs/userguide.rst @@ -33,6 +33,11 @@ The input :code:`objfun` is a Python function which takes an input :math:`x\in\m The input :code:`x0` is the starting point for the solver, and (where possible) should be set to be the best available estimate of the true solution :math:`x_{min}\in\mathbb{R}^n`. It should be specified as a one-dimensional NumPy array (i.e. with :code:`x0.shape == (n,)`). As DFO-LS is a local solver, providing different values for :code:`x0` may cause it to return different solutions, with possibly different objective values. +In newer version of DFO-LS (v1.6 onwards), the input :code:`x0` may instead by an instance of a :code:`dfols.EvaluationDatabase`, which stores a collection +of previously evaluated points and their associated vectors of residuals. One of these points is designated the starting point for the solver, and the other +points may be used by DFO-LS to build its first approximation to :code:`objfun`, reducing the number of evaluations required to begin the main iteration. +See the example below for more details for how to use this functionality. + The output of :code:`dfols.solve` is an object containing: * :code:`soln.x` - an estimate of the solution, :math:`x_{min}\in\mathbb{R}^n`, a one-dimensional NumPy array. @@ -436,6 +441,164 @@ The solution found by DFO-LS is: We can see that 3 of the 5 components of the solution are very close to zero. Note that many LASSO-type algorithms can produce a solution with many entries being exactly zero, but DFO-LS can only make them very small (related to how it calculates a new point with trust-region constraints). +Using Initial Evaluation Database +--------------------------------- +Since DFO-LS v1.6, the input :code:`x0` may instead be an instance of a :code:`dfols.EvaluationDatabase` class containing a collection of previously evaluated +points and their associated vectors of residuals. One of these points must be flagged as the starting point for the solver (otherwise, the most recently added +point is used). DFO-LS will automaticaly select some (but possibly none/all) of the other points to help build its first internal approximation to the objective, +which reduces the number of times the objective must be evaluated during the initialization phase, before the main algorithm can begin. + +For example, suppose we want to use DFO-LS to minimize the Watson test function (Problem 20 from [MGH1981]_). Using the standard starting point, our code looks like + + .. code-block:: python + + import numpy as np + import dfols + + # Define the objective function + def watson(x): + n = len(x) + m = 31 + fvec = np.zeros((m,), dtype=float) + for i in range(1, 30): # i=1,...,29 + div = float(i) / 29.0 + s1 = 0.0 + dx = 1.0 + for j in range(2, n + 1): # j = 2,...,n + s1 = s1 + (j - 1) * dx * x[j - 1] + dx = div * dx + s2 = 0.0 + dx = 1.0 + for j in range(1, n + 1): # j = 1,...,n + s2 = s2 + dx * x[j - 1] + dx = div * dx + fvec[i - 1] = s1 - s2 ** 2 - 1.0 + fvec[29] = x[0] + fvec[30] = x[1] - x[0] ** 2 - 1.0 + return fvec + + # Define the starting point + n = 6 + x0 = 0.5 * np.ones((n,), dtype=float) + + # Show extra output to demonstrate the impact of using an initial evaluation database + import logging + logging.basicConfig(level=logging.INFO, format='%(message)s') + + # Call DFO-LS + soln = dfols.solve(watson, x0) + + # Display output + print(soln) + +In the output of this code, we can check that DFO-LS finds the unique minimizer of this function. We can also see that before the main loop can begin, +DFO-LS needs to evaluate the objective at the given starting point, and 6 extra points (since this problem has 6 variables to be minimized): + + .. code-block:: none + + Function eval 1 at point 1 has obj = 16.4308311759923 at x = [...] + Initialising (coordinate directions) + Function eval 2 at point 2 has obj = 28.9196967094733 at x = [...] + Function eval 3 at point 3 has obj = 22.0866904737059 at x = [...] + Function eval 4 at point 4 has obj = 20.6560889343479 at x = [...] + Function eval 5 at point 5 has obj = 19.2914312375462 at x = [...] + Function eval 6 at point 6 has obj = 18.0373781384725 at x = [...] + Function eval 7 at point 7 has obj = 16.8946356501339 at x = [...] + Beginning main loop + Function eval 8 at point 8 has obj = 8.45207899459595 at x = [...] + Function eval 9 at point 9 has obj = 2.54949692496583 at x = [...] + ... + Function eval 90 at point 90 has obj = 0.00228767005355292 at x = [...] + Did a total of 1 run(s) + + ****** DFO-LS Results ****** + Solution xmin = [-0.01572509 1.01243487 -0.23299162 1.26043004 -1.51372886 0.99299641] + Not showing residual vector because it is too long; check self.resid + Objective value f(xmin) = 0.002287670054 + Needed 90 objective evaluations (at 90 points) + Not showing approximate Jacobian because it is too long; check self.jacobian + Solution xmin was evaluation point 89 + Approximate Jacobian formed using evaluation points [87 85 76 89 86 88 84] + Exit flag = 0 + Success: rho has reached rhoend + **************************** + +Instead of this, we can build a database of points where we have previously evaluated the objective, marking one of them as the starting point +for the algorithm. DFO-LS will then select some/all (but possibly none) of the other points and use them as initial evaluations, allowing it to begin +the main loop faster. In general, DFO-LS will select points that are: + +* Not too close/far from the selected starting point (relative to the initial trust-region radius, input :code:`rhobeg`) +* Not in similar directions (relative to the selected starting point) to other selected initial points. For example, if several points differ from + the selected starting point in only the first variable, at most one of these will be selected. + +The following code demonstrates how an evaluation database may be constructed and given to DFO-LS: + + .. code-block:: python + + # Assuming numpy and dfols already imported, watson function already defined + + # Build a database of evaluations + eval_db = dfols.EvaluationDatabase() + + # Define the starting point and add it to the database + n = 6 + x0 = 0.5 * np.ones((n,), dtype=float) + eval_db.append(x0, watson(x0), make_starting_eval=True) + # make_starting_eval=True --> use this point as the starting point for DFO-LS + + # Add other points to the database + # Note: x0, x1 and x2 are colinear, so at least one of x1 and x2 will not be included in the initial model + x1 = np.ones((n,), dtype=float) + x2 = np.zeros((n,), dtype=float) + x3 = np.arange(n).astype(float) + eval_db.append(x1, watson(x1)) + eval_db.append(x2, watson(x2)) + eval_db.append(x3, watson(x3)) + + # Show extra output to demonstrate the impact of using an initial evaluation database + import logging + logging.basicConfig(level=logging.INFO, format='%(message)s') + + # Call DFO-LS + soln = dfols.solve(watson, x0) + + # Display output + print(soln) + +Running this code, we get the same (correct) answer but using fewer evaluations of the objective in the main call to :code:`dfols.solve()`. +The logging information reveals that :code:`x0` was used as the starting point, and :code:`x1` and :code:`x3` were used to build the initial model. +This means that only 4 evaluations of the objective were required in the initialization phase. + + .. code-block:: none + + Using pre-existing evaluation 0 as starting point + Adding pre-existing evaluation 1 to initial model + Adding pre-existing evaluation 3 to initial model + Function eval 1 at point 1 has obj = 15.1910664616598 at x = [...] + Function eval 2 at point 2 has obj = 15.2288491702299 at x = [...] + Function eval 3 at point 3 has obj = 15.228054997542 at x = [...] + Function eval 4 at point 4 has obj = 15.3011037277481 at x = [...] + Beginning main loop + Function eval 5 at point 5 has obj = 13.5524099633802 at x = [...] + Function eval 6 at point 6 has obj = 7.33371957636104 at x = [...] + ... + Function eval 81 at point 81 has obj = 0.00228767005355266 at x = [...] + Did a total of 1 run(s) + + ****** DFO-LS Results ****** + Solution xmin = [-0.01572509 1.01243487 -0.23299163 1.26043009 -1.51372893 0.99299643] + Not showing residual vector because it is too long; check self.resid + Objective value f(xmin) = 0.002287670054 + Needed 81 objective evaluations (at 81 points) + Not showing approximate Jacobian because it is too long; check self.jacobian + Solution xmin was evaluation point 77 + Approximate Jacobian formed using evaluation points [76 73 79 74 77 75 80] + Exit flag = 0 + Success: rho has reached rhoend + **************************** + +Note that the indices of the evaluation database mentioned in the log refer to the order in which the points were added to the evaluation database. + Example: Noisy Objective Evaluation ----------------------------------- As described in :doc:`info`, derivative-free algorithms such as DFO-LS are particularly useful when :code:`objfun` has noise. Let's modify the previous example to include random noise in our objective evaluation, and compare it to SciPy's derivative-based solver (the below results came from using SciPy v1.13.0): @@ -708,3 +871,6 @@ References .. [B2017] Amir Beck, `First-Order Methods in Optimization `_, SIAM (2017). + +.. [MGH1981] + Jorge J. More, Burton S. Garbow and Kenneth E. Hillstrom, `Testing Unconstrained Optimization Software `_, *ACM Transactions on Mathematical Software*, 7:1 (1981), pp. 17-41. diff --git a/examples/existing_evaluations.py b/examples/existing_evaluations.py new file mode 100644 index 0000000..183d7f8 --- /dev/null +++ b/examples/existing_evaluations.py @@ -0,0 +1,66 @@ +""" +Demonstration of using database of existing evaluations to speed up DFO-LS + +Test problem is the 'Watson function': for details, see +J. J. More, B. S. Garbow, K. E. Hillstrom. Testing Unconstrained Optimization Software. +ACM Transactions on Mathematical Software, 7:1 (1981), pp. 17-41. +""" +import numpy as np +import dfols + +# Define the objective function +def watson(x): + n = len(x) + m = 31 + fvec = np.zeros((m,), dtype=float) + for i in range(1, 30): # i=1,...,29 + div = float(i) / 29.0 + s1 = 0.0 + dx = 1.0 + for j in range(2, n + 1): # j = 2,...,n + s1 = s1 + (j - 1) * dx * x[j - 1] + dx = div * dx + s2 = 0.0 + dx = 1.0 + for j in range(1, n + 1): # j = 1,...,n + s2 = s2 + dx * x[j - 1] + dx = div * dx + fvec[i - 1] = s1 - s2 ** 2 - 1.0 + fvec[29] = x[0] + fvec[30] = x[1] - x[0] ** 2 - 1.0 + return fvec + +# Define the starting point +n = 6 +x0 = 0.5 * np.ones((n,), dtype=float) + +# Show extra output to demonstrate the impact of using an initial evaluation database +import logging +logging.basicConfig(level=logging.INFO, format='%(message)s') + +# Call DFO-LS +soln = dfols.solve(watson, x0) + +# Display output +print(soln) + +# Build a database of evaluations +eval_db = dfols.EvaluationDatabase() + +# Define the starting point and add it to the database +eval_db.append(x0, watson(x0), make_starting_eval=True) +# make_starting_eval=True --> use this point as the starting point for DFO-LS + +# Add other points to the database +# Note: x0, x1 and x2 are colinear, so at least one of x1 and x2 will not be included in the initial model +x1 = np.ones((n,), dtype=float) +x2 = np.zeros((n,), dtype=float) +x3 = np.arange(n).astype(float) +eval_db.append(x1, watson(x1)) +eval_db.append(x2, watson(x2)) +eval_db.append(x3, watson(x3)) + +# Alternative run: initialize using evaluation database +# Turn on logging above to see which database points are selected to reduce the initialization cost +soln = dfols.solve(watson, eval_db) # replace x0 with eval_db +print(soln) \ No newline at end of file diff --git a/manual.pdf b/manual.pdf index 1b0a0ba..89b3d4e 100755 Binary files a/manual.pdf and b/manual.pdf differ