Lint

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

@@ -21,7 +21,14 @@ repos:
     hooks:
     - id: mypy
       name: mypy-pyMoist
-      args: [--config, GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/python/model/setup.cfg]
+      args: [
+        --ignore-missing-imports,
+        "--follow-imports=normal",
+        --namespace-packages,
+        --no-strict-optional,
+        --warn-unreachable,
+        --explicit-package-bases,
+      ]
       additional_dependencies: [types-PyYAML]
       files: pyMoist
 
@@ -39,7 +46,11 @@ repos:
     - id: flake8
       name: flake8
       language_version: python3
-      args: [--config, setup.cfg]
+      args: [
+        "--exclude=docs",
+        "--ignore=W503,E302,E203,F841",
+        "--max-line-length=88"
+      ]
       exclude: |
         (?x)^(
         .*/__init__.py |
@@ -48,4 +59,7 @@ repos:
       name: flake8 __init__.py files
       files: "__init__.py"
       # ignore unused import error in __init__.py files
-      args: ["--ignore=F401,E203", --config, setup.cfg]
+      args: [
+        "--exclude=docs",
+        "--ignore=W503,E302,E203,F841,F401",
+        "--max-line-length=88",]

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 comitting for code guidelines coherency.

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/interface/README.md

@@ -1,3 +1,3 @@
-# Interface between GEOS and pyMoist 
+# Interface between GEOS and pyMoist
 
-This is the `cffi` based interface between the GEOS Moist grid component and the `pyMoist` NDSL numerical code.
+This is the `cffi` based interface between the GEOS Moist grid component and the `pyMoist` NDSL numerical code.

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/setup.cfg

@@ -5,7 +5,7 @@ commit = True
 [bdist_wheel]
 universal = 1
 
-[flake8]
+[flake8] # WARNING: This configuration is duplicated in pre-commit-config.yaml due to pre-config lack of working dir
 exclude = docs
 ignore = W503,E302,E203,F841
 max-line-length = 88
@@ -24,7 +24,7 @@ sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
 known_first_party = pyMoist,ndsl
 known_third_party = f90nml,pytest,xarray,numpy,mpi4py,gt4py
 
-[mypy]
+[mypy] # WARNING: This configuration is duplicated in pre-commit-config.yaml due to pre-config lack of working dir
 ignore_missing_imports = True
 follow_imports = normal
 namespace_packages = True

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/setup.py

@@ -9,8 +9,6 @@
 with open("README.md", encoding="utf-8") as readme_file:
     readme = readme_file.read()
 
-requirements = []
-
 test_requirements = ["pytest", "pytest-subtests", "serialbox", "coverage"]
 ndsl_requirements = ["ndsl @ git+https://github.com/NOAA-GFDL/NDSL.git@2024.04.00"]
 develop_requirements = test_requirements + ndsl_requirements + ["pre-commit"]
@@ -32,8 +30,8 @@
         "Natural Language :: English",
         "Programming Language :: Python :: 3.11",
     ],
-    description="pyMoist is the NDSL version of NASA GMAO's GEOS Moist physics.",
-    install_requires=requirements,
+    description=("pyMoist is the NDSL version of NASA GMAO's GEOS Moist physics."),
+    install_requires=[],
     extras_require=extras_requires,
     license="BSD license",
     long_description=readme,

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/tests/conftest.py

@@ -1,7 +1,8 @@
+import savepoint
+
 import ndsl.stencils.testing.conftest
 from ndsl.stencils.testing.conftest import *  # noqa: F403,F401
 
-import savepoint
 
 # Point to an __init__.py where all the TestX are improted
 ndsl.stencils.testing.conftest.translate = savepoint  # type: ignore

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/tests/savepoint/translate_radiation_coupling.py

@@ -1,5 +1,5 @@
-from ndsl.stencils.testing.translate import TranslateFortranData2Py
 from ndsl import Namelist, StencilFactory
+from ndsl.stencils.testing.translate import TranslateFortranData2Py
 from pyMoist.radiation_coupling import RadiationCoupling
 
 
@@ -11,10 +11,10 @@ def __init__(
         stencil_factory: StencilFactory,
     ):
         super().__init__(grid, stencil_factory)
-        self.compute_func = RadiationCoupling(   # type: ignore
+        self.compute_func = RadiationCoupling(  # type: ignore
             self.stencil_factory,
             self.grid.quantity_factory,
-            do_qa=namelist.do_qa
+            do_qa=namelist.do_qa,
         )
 
         # ADAPT BELOW TO INPUTS
@@ -31,7 +31,6 @@ def __init__(
         #     "q": self.grid.compute_dict(),
         # }
 
-
     def compute_from_storage(self, inputs):
         self.compute_func(**inputs)
         return inputs