Merge pull request #645 from effigies/mnt/refurb

STY: Miscellaneous cleanups

Author: effigies

.circleci/config.yml

@@ -32,12 +32,12 @@ docs_deploy: &docs
         name: Deploy docs to gh-pages branch
         command: gh-pages --no-history --dotfiles --message "doc(update) [skip ci]" --dist docs/_build/html
 
-version: 2
+version: 2.1
 jobs:
 
   build_docs:
     docker:
-      - image: python:3.7.4
+      - image: cimg/python:3.11
     working_directory: /tmp/gh-pages
     environment:
       - FSLOUTPUTTYPE: NIFTI

docs/conf.py

@@ -89,7 +89,7 @@
 napoleon_custom_sections = [("Inputs", "Parameters"), ("Outputs", "Parameters")]
 
 # Intersphinx
-intersphinx_mapping = {"https://docs.python.org/3/": None}
+intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}
 
 # Linkcode
 # The following is used by sphinx.ext.linkcode to provide links to github

pydra/__init__.py

@@ -11,15 +11,28 @@
 
 import logging
 
-logger = logging.getLogger("pydra")
+import __main__
+import attr
+
+from . import mark
+from .engine import AuditFlag, DockerTask, ShellCommandTask, Submitter, Workflow, specs
+
+__all__ = (
+    "Submitter",
+    "Workflow",
+    "AuditFlag",
+    "ShellCommandTask",
+    "DockerTask",
+    "specs",
+    "mark",
+)
 
 try:
     from ._version import __version__
 except ImportError:
     pass
 
-from .engine import Submitter, Workflow, AuditFlag, ShellCommandTask, DockerTask, specs
-from . import mark
+logger = logging.getLogger("pydra")
 
 
 def check_latest_version():
@@ -29,8 +42,6 @@ def check_latest_version():
 
 
 # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL
-import __main__
-
 if not hasattr(__main__, "__file__"):
     from .engine.core import TaskBase
 
@@ -39,8 +50,6 @@ def check_latest_version():
 
 
 # attr run_validators is set to False, but could be changed using use_validator
-import attr
-
 attr.set_run_validators(False)
 
 

pydra/engine/audit.py

@@ -1,12 +1,16 @@
 """Module to keep track of provenance information."""
 import os
-from pathlib import Path
 import json
 import attr
 from ..utils.messenger import send_message, make_message, gen_uuid, now, AuditFlag
 from .helpers import ensure_list, gather_runtime_info, hash_file
 from .specs import attr_fields, File, Directory
 
+try:
+    import importlib_resources
+except ImportError:
+    import importlib.resources as importlib_resources  # type: ignore
+
 
 class Audit:
     """Handle provenance tracking and resource utilization."""
@@ -133,9 +137,8 @@ def audit_message(self, message, flags=None):
 
         """
         if self.develop:
-            with open(
-                Path(os.path.dirname(__file__)) / ".." / "schema/context.jsonld"
-            ) as fp:
+            context_file = importlib_resources.files("pydra") / "schema/context.jsonld"
+            with context_file.open() as fp:
                 context = json.load(fp)
         else:
             context = {

pydra/engine/core.py

@@ -491,7 +491,7 @@ def _run(self, rerun=False, **kwargs):
         lockfile = self.cache_dir / (checksum + ".lock")
         # Eagerly retrieve cached - see scenarios in __init__()
         self.hooks.pre_run(self)
-        logger.debug(f"'%s' is attempting to acquire lock on %s", self.name, lockfile)
+        logger.debug("'%s' is attempting to acquire lock on %s", self.name, lockfile)
         with SoftFileLock(lockfile):
             if not (rerun or self.task_rerun):
                 result = self.result()
@@ -1105,7 +1105,7 @@ async def _run(self, submitter=None, rerun=False, **kwargs):
         lockfile = self.cache_dir / (checksum + ".lock")
         self.hooks.pre_run(self)
         logger.debug(
-            f"'%s' is attempting to acquire lock on %s with Pydra lock",
+            "'%s' is attempting to acquire lock on %s with Pydra lock",
             self.name,
             lockfile,
         )
@@ -1231,7 +1231,7 @@ def _collect_outputs(self):
                         err_file = getattr(self, val.name).output_dir / "_error.pklz"
                     raise ValueError(
                         f"Task {val.name} raised an error, full crash report is here: "
-                        f"{str(err_file)}"
+                        f"{err_file}"
                     )
         return attr.evolve(output, **output_wf)
 

pydra/engine/helpers_file.py

@@ -606,7 +606,7 @@ def template_update(inputs, output_dir, state_ind=None, map_copyfiles=None):
     for fld in fields_templ:
         if fld.type not in [str, ty.Union[str, bool]]:
             raise Exception(
-                f"fields with output_file_template"
+                "fields with output_file_template"
                 " has to be a string or Union[str, bool]"
             )
         dict_mod[fld.name] = template_update_single(
@@ -638,7 +638,7 @@ def template_update_single(
     if spec_type == "input":
         if field.type not in [str, ty.Union[str, bool]]:
             raise Exception(
-                f"fields with output_file_template"
+                "fields with output_file_template"
                 "has to be a string or Union[str, bool]"
             )
         inp_val_set = inputs_dict_st[field.name]

pydra/engine/helpers_state.py

@@ -344,7 +344,7 @@ def _add_name(mlist, name):
             if "." in elem or elem.startswith("_"):
                 pass
             else:
-                mlist[i] = "{}.{}".format(name, mlist[i])
+                mlist[i] = f"{name}.{mlist[i]}"
         elif isinstance(elem, list):
             mlist[i] = _add_name(elem, name)
         elif isinstance(elem, tuple):

pydra/engine/state.py

@@ -454,13 +454,11 @@ def _remove_repeated(self, previous_splitters):
                     f"{self.other_states}"
                 )
 
-        repeated = set(
-            [
-                (el, previous_splitters.count(el))
-                for el in previous_splitters
-                if previous_splitters.count(el) > 1
-            ]
-        )
+        repeated = {
+            (el, previous_splitters.count(el))
+            for el in previous_splitters
+            if previous_splitters.count(el) > 1
+        }
         if repeated:
             # assuming that I want to remove from right
             previous_splitters.reverse()

pydra/engine/tests/conftest.py

@@ -0,0 +1,23 @@
+import pytest
+from pydra import set_input_validator
+
+try:
+    import importlib_resources
+except ImportError:
+    import importlib.resources as importlib_resources
+
+
+@pytest.fixture(scope="package")
+def data_tests_dir():
+    test_nii = importlib_resources.files("pydra").joinpath(
+        "engine", "tests", "data_tests"
+    )
+    with importlib_resources.as_file(test_nii) as path:
+        yield path
+
+
+@pytest.fixture()
+def use_validator():
+    set_input_validator(flag=True)
+    yield None
+    set_input_validator(flag=False)

pydra/engine/tests/data_tests/loading.py

@@ -1,6 +1,3 @@
-import os
-
-
 def loading(filename):
     with open(filename) as f:
         txt = f.read()