[NDSL] Add functionality to pre-commit

.github/workflows/ndsl-checks.yml

@@ -33,6 +33,7 @@ jobs:
             cd ndsl
             pip install -e .[develop]
             pip install -e ../GCMGridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist
+            pip install pylint==3.2.6
         - name: Run lint via pre-commit
           run: |
             cd ./GCMGridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/.pre-commit-config.yaml

@@ -4,22 +4,12 @@ default_language_version:
 files: pyMoist
 
 repos:
--   repo: https://github.com/psf/black
-    rev: 20.8b1
-    hooks:
-    - id: black
-      additional_dependencies: ["click==8.0.4"]
-
--   repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.4.2
-    hooks:
-    - id: isort
-      args: ["--profile", "black"]
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.4.1
     hooks:
     - id: mypy
+      description: Perform static type analysis of Python code
       name: mypy-pyMoist
       args: [
         --ignore-missing-imports,
@@ -35,31 +25,40 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:
+    - id: check-added-large-files
+    - id: check-ast
+    - id: check-case-conflict
+    - id: check-merge-conflict
     - id: check-toml
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
--   repo: https://github.com/pycqa/flake8
-    rev: 3.9.2
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.3.0
+  hooks:
+    -   id: codespell
+        name: codespell
+        description: Check for spelling errors
+        entry: codespell
+        args:  ["--ignore-words","GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/ignored_codespell.txt"]
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.0
+  hooks:
+    # Run the linter.
+    - id: ruff
+      name: ruff linting
+      args: [--fix ]
+    # Run the formatter.
+    - id: ruff-format
+      name: ruff formatting
+-   repo: local
     hooks:
-    - id: flake8
-      name: flake8
-      language_version: python3
-      args: [
-        "--exclude=docs",
-        "--ignore=W503,E302,E203,F841",
-        "--max-line-length=88"
-      ]
-      exclude: |
-        (?x)^(
-        .*/__init__.py |
-        )$
-    - id: flake8
-      name: flake8 __init__.py files
-      files: "__init__.py"
-      # ignore unused import error in __init__.py files
-      args: [
-        "--exclude=docs",
-        "--ignore=W503,E302,E203,F841,F401",
-        "--max-line-length=88",]
+    -   id: pylint
+        name: pylint
+        language: system
+        entry: pylint
+        args:
+        - --rcfile=GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/.pylintrc

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/.pylintrc

@@ -0,0 +1,6 @@
+[MAIN]
+ignore-patterns=^__init__.py$
+
+[FORMAT]
+# Maximum number of characters on a single line.
+max-line-length=100

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/README.md

@@ -14,4 +14,4 @@ The `interface` sub-directory contain the three-way bridge to and from GEOS.
 
 ## Develop
 
-- Run `pre-commit run --all-files` before comitting for code guidelines coherency.
+- Run `pre-commit run --all-files` before committing for code guidelines coherency.

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/ignored_codespell.txt

@@ -0,0 +1,3 @@
+THIRDPARTY
+dum
+te

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/aer_activation.py

@@ -1,14 +1,16 @@
 import copy
 
 from gt4py.cartesian.gtscript import PARALLEL, computation, exp, interval, log, sqrt
-
-import pyMoist.aer_activation_constants as constants
 from ndsl import QuantityFactory, StencilFactory, orchestrate
 from ndsl.constants import X_DIM, Y_DIM, Z_DIM
 from ndsl.dsl.typing import Float, FloatField, FloatFieldIJ, Int
-from pyMoist.numerical_recipes import Erf
+
+import pyMoist.aer_activation_constants as constants
+from pyMoist.numerical_recipes import error_function
 from pyMoist.types import FloatField_NModes
 
+# ruff: noqa: PLR0913,PLR0915
+
 
 def aer_activation_stencil(
     aero_dgn: FloatField_NModes,
@@ -67,7 +69,6 @@ def aer_activation_stencil(
     None
     """
     with computation(PARALLEL), interval(...):
-
         # Compute nwfa
         # Fortran AeroProps aero_kap is aero_hygroscopicity
         nfaux = 0.0
@@ -99,14 +100,17 @@ def aer_activation_stencil(
             n = 0
             while n < constants.n_modes:
                 ni[0, 0, 0][n] = max(
-                    aero_num[0, 0, 0][n] * air_den, constants.ZERO_PAR
+                    aero_num[0, 0, 0][n] * air_den,
+                    constants.ZERO_PAR,
                 )  # unit: [m-3]
                 rg[0, 0, 0][n] = max(
-                    aero_dgn[0, 0, 0][n] * 0.5 * 1.0e6, constants.ZERO_PAR
+                    aero_dgn[0, 0, 0][n] * 0.5 * 1.0e6,
+                    constants.ZERO_PAR,
                 )  # unit: [um]
                 sig0[0, 0, 0][n] = aero_sigma[0, 0, 0][n]  # unit: [um]
                 bibar[0, 0, 0][n] = max(
-                    aero_hygroscopicity[0, 0, 0][n], constants.ZERO_PAR
+                    aero_hygroscopicity[0, 0, 0][n],
+                    constants.ZERO_PAR,
                 )
                 n += 1
 
@@ -147,43 +151,32 @@ def aer_activation_stencil(
 
             # These variables are common to all modes and need only be computed once.
             dv = (
-                constants.DIJH2O0
-                * (constants.P0DIJ / plo)
-                * (tk / constants.T0DIJ) ** 1.94e00
+                constants.DIJH2O0 * (constants.P0DIJ / plo) * (tk / constants.T0DIJ) ** 1.94e00
             )  # [m^2/s] (p&k,2nd ed., p.503)
             surten = 76.10e-3 - 0.155e-3 * (tk - 273.15e00)  # [j/m^2]
             wpe = exp(
-                77.34491296 - 7235.424651 / tk - 8.2 * log(tk) + tk * 5.7113e-3
+                77.34491296 - 7235.424651 / tk - 8.2 * log(tk) + tk * 5.7113e-3,
             )  # [pa]
             dumw = sqrt(
-                constants.TWOPI * constants.WMOLMASS / constants.RGASJMOL / tk
+                constants.TWOPI * constants.WMOLMASS / constants.RGASJMOL / tk,
             )  # [s/m]
             dvprime = dv / (
-                (rdrp / (rdrp + constants.DELTAV))
-                + (dv * dumw / (rdrp * constants.ALPHAC))
+                (rdrp / (rdrp + constants.DELTAV)) + (dv * dumw / (rdrp * constants.ALPHAC))
             )  # [m^2/s] - eq. (17)
             xka = (
                 5.69 + 0.017 * (tk - 273.15)
             ) * 418.4e-5  # [j/m/s/k] (0.0238 j/m/s/k at 273.15 k)
             duma = sqrt(
-                constants.TWOPI * constants.AMOLMASS / constants.RGASJMOL / tk
+                constants.TWOPI * constants.AMOLMASS / constants.RGASJMOL / tk,
             )  # [s/m]
             xkaprime = xka / (
                 (rdrp / (rdrp + constants.DELTAT))
-                + (
-                    xka
-                    * duma
-                    / (rdrp * constants.ALPHAT * constants.DENH2O * constants.CPAIR)
-                )
+                + (xka * duma / (rdrp * constants.ALPHAT * constants.DENH2O * constants.CPAIR))
             )  # [j/m/s/k]
             g = 1.0 / (
-                (constants.DENH2O * constants.RGASJMOL * tk)
-                / (wpe * dvprime * constants.WMOLMASS)
+                (constants.DENH2O * constants.RGASJMOL * tk) / (wpe * dvprime * constants.WMOLMASS)
                 + ((constants.HEATVAP * constants.DENH2O) / (xkaprime * tk))
-                * (
-                    (constants.HEATVAP * constants.WMOLMASS) / (constants.RGASJMOL * tk)
-                    - 1.0
-                )
+                * ((constants.HEATVAP * constants.WMOLMASS) / (constants.RGASJMOL * tk) - 1.0)
             )  # [m^2/s]
             a = (2.0 * surten * constants.WMOLMASS) / (
                 constants.DENH2O * constants.RGASJMOL * tk
@@ -194,46 +187,34 @@ def aer_activation_stencil(
             )  # [1/m]
             gamma = (constants.RGASJMOL * tk) / (wpe * constants.WMOLMASS) + (
                 constants.WMOLMASS * constants.HEATVAP * constants.HEATVAP
-            ) / (
-                constants.CPAIR * plo * constants.AMOLMASS * tk
-            )  # [m^3/kg]
-            dum = sqrt(alpha * wupdraft / g)  # [1/m]
+            ) / (constants.CPAIR * plo * constants.AMOLMASS * tk)  # [m^3/kg]
+            dum: None = sqrt(alpha * wupdraft / g)  # [1/m]
             zeta = 2.0 * a * dum / 3.0  # [1]
 
             # These variables must be computed for each mode
             n = 0
             while n < constants.n_modes:
                 xlogsigm = log(sig0[0, 0, 0][n])  # [1]
                 smax = 0.0  # [1]
-                sm = (2.0 / sqrt(bibar[0, 0, 0][n])) * (
-                    a / (3.0 * rg[0, 0, 0][n])
-                ) ** 1.5  # [1]
-                eta = dum ** 3 / (
-                    constants.TWOPI * constants.DENH2O * gamma * ni[0, 0, 0][n]
-                )  # [1]
-                f1 = 0.5 * exp(2.50 * xlogsigm ** 2)  # [1]
+                sm = (2.0 / sqrt(bibar[0, 0, 0][n])) * (a / (3.0 * rg[0, 0, 0][n])) ** 1.5  # [1]
+                eta = dum**3 / (constants.TWOPI * constants.DENH2O * gamma * ni[0, 0, 0][n])  # [1]
+                f1 = 0.5 * exp(2.50 * xlogsigm**2)  # [1]
                 f2 = 1.0 + 0.25 * xlogsigm  # [1]
                 smax = (
                     smax
-                    + (
-                        f1 * (zeta / eta) ** 1.5
-                        + f2 * (sm ** 2 / (eta + 3.0 * zeta)) ** 0.75
-                    )
-                    / sm ** 2
+                    + (f1 * (zeta / eta) ** 1.5 + f2 * (sm**2 / (eta + 3.0 * zeta)) ** 0.75) / sm**2
                 )  # [1] - eq. (6)
                 n += 1
 
             smax = 1.0e00 / sqrt(smax)  # [1]
             n = 0
             u = 0.0
             while n < constants.n_modes:
-                sm = (2.0 / sqrt(bibar[0, 0, 0][n])) * (
-                    a / (3.0 * rg[0, 0, 0][n])
-                ) ** 1.5  # [1]
+                sm = (2.0 / sqrt(bibar[0, 0, 0][n])) * (a / (3.0 * rg[0, 0, 0][n])) ** 1.5  # [1]
                 xlogsigm = log(sig0[0, 0, 0][n])  # [1]
                 ac = rg[0, 0, 0][n] * (sm / smax) ** 0.66666666666666667  # [um]
                 u = log(ac / rg[0, 0, 0][n]) / (constants.SQRT2 * xlogsigm)  # [1]
-                fracactn = 0.5 * (1.0 - Erf(u))  # [1]
+                fracactn = 0.5 * (1.0 - error_function(u))  # [1]
                 nact[0, 0, 0][n] = fracactn * ni[0, 0, 0][n]  # [#/m^3]
                 n += 1
 
@@ -247,9 +228,7 @@ def aer_activation_stencil(
             nactl = min(nactl, 0.99 * numbinit)
 
         # Ice Clouds Calculation
-        if (tk <= constants.MAPL_TICE) and (
-            qi > constants.FLOAT_TINY or ql > constants.FLOAT_TINY
-        ):
+        if (tk <= constants.MAPL_TICE) and (qi > constants.FLOAT_TINY or ql > constants.FLOAT_TINY):
             numbinit = 0.0
             n = 0
             while n < constants.n_modes:
@@ -262,21 +241,14 @@ def aer_activation_stencil(
             nacti = (
                 constants.AI
                 * ((constants.MAPL_TICE - tk) ** constants.BI)
-                * (
-                    numbinit
-                    ** (constants.CI * (constants.MAPL_TICE - tk) + constants.DI)
-                )
+                * (numbinit ** (constants.CI * (constants.MAPL_TICE - tk) + constants.DI))
             )
 
         # apply limits for NACTL/NACTI
-        if nactl < constants.NN_MIN:
-            nactl = constants.NN_MIN
-        if nactl > constants.NN_MAX:
-            nactl = constants.NN_MAX
-        if nacti < constants.NN_MIN:
-            nacti = constants.NN_MIN
-        if nacti > constants.NN_MAX:
-            nacti = constants.NN_MAX
+        nactl = max(nactl, constants.NN_MIN)
+        nactl = min(nactl, constants.NN_MAX)
+        nacti = max(nacti, constants.NN_MIN)
+        nacti = min(nacti, constants.NN_MAX)
 
 
 class AerActivation:
@@ -287,15 +259,15 @@ class AerActivation:
     stencil_factory (StencilFactory): Factory for creating stencil computations.
     quantity_factory (QuantityFactory): Factory for creating quantities.
     n_modes (Int): Number of aerosol modes.
-    USE_AERSOL_NN (bool): Flag indicating whether to use neural network for aerosol.
+    use_aersol_nn (bool): Flag indicating whether to use neural network for aerosol.
     """
 
     def __init__(
         self,
         stencil_factory: StencilFactory,
         quantity_factory: QuantityFactory,
         n_modes: Int,
-        USE_AERSOL_NN: bool,
+        use_aersol_nn: bool,
     ) -> None:
         """
         Initialize the AerActivation class.
@@ -304,7 +276,7 @@ def __init__(
         stencil_factory (StencilFactory): Factory for creating stencil computations.
         quantity_factory (QuantityFactory): Factory for creating quantities.
         n_modes (Int): Number of aerosol modes.
-        USE_AERSOL_NN (bool): Flag indicating whether to use neural network for aerosol.
+        use_aersol_nn (bool): Flag indicating whether to use neural network for aerosol.
 
         Raises:
         NotImplementedError: If the number of modes is not equal to the expected number.
@@ -314,15 +286,15 @@ def __init__(
 
         if constants.n_modes != n_modes:
             raise NotImplementedError(
-                f"Coding limitation: 14 modes are expected, getting {n_modes}"
+                f"Coding limitation: 14 modes are expected, getting {n_modes}",
             )
 
-        if not USE_AERSOL_NN:
+        if not use_aersol_nn:
             raise NotImplementedError("Non NN Aerosol not implemented")
 
         # Temporary buffers
         nmodes_quantity_factory = AerActivation.make_nmodes_quantity_factory(
-            quantity_factory
+            quantity_factory,
         )
         self._nact = nmodes_quantity_factory.zeros(
             [X_DIM, Y_DIM, Z_DIM, "n_modes"],
@@ -362,7 +334,7 @@ def make_nmodes_quantity_factory(ijk_quantity_factory: QuantityFactory):
         nmodes_quantity_factory.set_extra_dim_lengths(
             **{
                 "n_modes": constants.n_modes,
-            }
+            },
         )
         return nmodes_quantity_factory
 

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/aer_activation_constants.py

@@ -1,8 +1,6 @@
 import numpy as np
-
 from ndsl.dsl.typing import Float
 
-
 """
 All global constants used for aer_actv_single_moment.F90
 """
@@ -58,5 +56,5 @@
 # Define how many modes in an aerosol
 n_modes = 14
 
-# Python euqivalent of Fortran's tiny(X)
+# Python equivalent of Fortran's tiny(X)
 FLOAT_TINY = np.finfo(Float).tiny