Fix: Adding Pace and PySHiELD unit tests back in to workflow

.github/workflows/lint.yaml

@@ -6,21 +6,21 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-        - name: Checkout repository
-          uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-        - name: Setup Python 3.11
-          uses: actions/setup-python@v5
-          with:
-            python-version: '3.11'
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
 
-        - name: Install pre-commit
-          run: |
-            pip install pre-commit
-        - name: Run lint via pre-commit
-          run: |
-            pre-commit run --all-files
+      - name: Install pre-commit
+        run: |
+          pip install pre-commit
+      - name: Run lint via pre-commit
+        run: |
+          pre-commit run --all-files
 
-        - name: Check advection code consistency
-          run: |
-            ./.github/workflows/scripts/ensure_xppm_yppm_consistency.sh
+      - name: Check advection code consistency
+        run: |
+          ./.github/workflows/scripts/ensure_xppm_yppm_consistency.sh

.github/workflows/pace_tests.yaml

@@ -1,15 +1,10 @@
-# TODO: Re-activate after PR 60
-# TODO: Temporarily removing tests due to dependent changes in
-#       Pace#129, PyFV3#64 PRs; tests should be reverted back after
-#       these PRs are merged.
+name: "pace main tests"
+on:
+  pull_request:
 
-# name: "pace main tests"
-# on:
-#   pull_request:
-
-# jobs:
-#   pace_main_tests:
-#     uses: NOAA-GFDL/pace/.github/workflows/main_unit_tests.yaml@develop
-#     with:
-#       component_trigger: true
-#       component_name: pyFV3
+jobs:
+  pace_main_tests:
+    uses: NOAA-GFDL/pace/.github/workflows/main_unit_tests.yaml@develop
+    with:
+      component_trigger: true
+      component_name: pyFV3

.github/workflows/pyshield_tests.yaml

@@ -1,11 +1,10 @@
-# TODO: Reactivate after PR 60
-# name: "pySHiELD translate tests"
-# on:
-#   pull_request:
+name: "pySHiELD translate tests"
+on:
+  pull_request:
 
-# jobs:
-#   pyshield_translate_tests:
-#     uses:  NOAA-GFDL/PySHiELD/.github/workflows/translate.yaml@develop
-#     with:
-#       component_trigger: true
-#       component_name: pyFV3
+jobs:
+  pyshield_translate_tests:
+    uses: NOAA-GFDL/PySHiELD/.github/workflows/translate.yaml@develop
+    with:
+      component_trigger: true
+      component_name: pyFV3

.github/workflows/translate.yaml

@@ -32,7 +32,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: 'recursive'
-          repository:  noaa-gfdl/pyFV3
+          repository: noaa-gfdl/pyFV3
           path: pyFV3
 
       - name: Checkout hash that triggered CI
@@ -43,14 +43,14 @@ jobs:
 
       - name: External trigger install NDSL packages
         if: ${{inputs.component_trigger}}
-        run:  |
+        run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
           cd NDSL && pip3 install .[test] && cd ../
           pip3 install .[test]
 
       - name: Install pyFV3 packages
         if: ${{ ! inputs.component_trigger }}
-        run : |
+        run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
           pip install .[ndsl,test]
 
@@ -73,7 +73,7 @@ jobs:
       - name: NumPy FvTp2d
         run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
-          coverage run --rcfile=setup.cfg -m pytest \
+          coverage run --rcfile=pyproject.toml -m pytest \
               -v -s --data_path=${{ env.DATA_PATH }} \
               --backend=numpy \
               --which_modules=FvTp2d \
@@ -82,18 +82,18 @@ jobs:
 
       - name: Numpy D_SW
         run: |
-         cd ${GITHUB_WORKSPACE}/pyFV3
-         coverage run --rcfile=setup.cfg -m pytest \
-              -v -s --data_path=${{ env.DATA_PATH }} \
-              --backend=numpy \
-              --which_modules=D_SW \
-              --threshold_overrides_file=./tests/savepoint/translate/overrides/standard.yaml \
-              ./tests/savepoint
+          cd ${GITHUB_WORKSPACE}/pyFV3
+          coverage run --rcfile=pyproject.toml -m pytest \
+               -v -s --data_path=${{ env.DATA_PATH }} \
+               --backend=numpy \
+               --which_modules=D_SW \
+               --threshold_overrides_file=./tests/savepoint/translate/overrides/standard.yaml \
+               ./tests/savepoint
 
       - name: Numpy Remapping
         run: |
           cd ${GITHUB_WORKSPACE}/pyFV3
-          coverage run --rcfile=setup.cfg -m pytest \
+          coverage run --rcfile=pyproject.toml -m pytest \
               -v -s --data_path=${{ env.DATA_PATH }} \
               --backend=numpy \
               --which_modules=Remapping \
@@ -107,7 +107,7 @@ jobs:
           export PACE_FLOAT_PRECISION=64
           export OMP_NUM_THREADS=1
           export PACE_LOGLEVEL=Debug
-          mpiexec -mca orte_abort_on_non_zero_status 1 -np 6 --oversubscribe coverage run --rcfile=setup.cfg -m mpi4py -m pytest \
+          mpiexec -mca orte_abort_on_non_zero_status 1 -np 6 --oversubscribe coverage run --rcfile=pyproject.toml -m mpi4py -m pytest \
             -v -s --data_path=${{ env.DATA_PATH }} \
             --backend=dace:cpu \
             -m parallel \

.pre-commit-config.yaml

@@ -2,51 +2,59 @@ default_language_version:
   python: python3
 
 repos:
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 25.1.0
     hooks:
-    - id: black
-      additional_dependencies: ["click==8.0.4"]
+      - id: black
+        additional_dependencies: ["click==8.0.4"]
 
--   repo: https://github.com/pre-commit/mirrors-isort
+  - repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
-    - id: isort
-      args: ["--profile", "black"]
+      - id: isort
+        args: ["--profile", "black"]
 
--   repo: https://github.com/pre-commit/mirrors-mypy
+  - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.17.0
     hooks:
-    - id: mypy
-      name: mypy-fv3core
-      args: [--config-file, setup.cfg]
-      additional_dependencies: [types-PyYAML]
-      files: pyFV3
-      exclude: |
-        (?x)^(
-        pyFV3/stencils/fv_subgridz.py |
-        pyFV3/tests/conftest.py
-        )$
--   repo: https://github.com/pre-commit/pre-commit-hooks
+      - id: mypy
+        name: mypy-fv3core
+        args: [--config-file, pyproject.toml]
+        additional_dependencies: [types-PyYAML]
+        files: pyFV3
+        exclude: |
+          (?x)^(
+          pyFV3/stencils/fv_subgridz.py |
+          pyFV3/tests/conftest.py
+          )$
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-    - id: check-toml
-    - id: check-yaml
-    - id: end-of-file-fixer
-    - id: trailing-whitespace
--   repo: https://github.com/pycqa/flake8
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/pycqa/flake8
     rev: 7.3.0
     hooks:
-    - id: flake8
-      name: flake8
-      language_version: python3
-      args: [--config, setup.cfg]
-      exclude: |
-        (?x)^(
-        .*/__init__.py |
-        )$
-    - id: flake8
-      name: flake8 __init__.py files
-      files: "__init__.py"
+      - id: flake8
+        name: flake8
+        language_version: python3
+        additional_dependencies: [Flake8-pyproject]
+        exclude: |
+          (?x)^(
+          .*/__init__.py |
+          )$
+      - id: flake8
+        name: flake8 __init__.py files
+        additional_dependencies: [Flake8-pyproject]
+        files: "__init__.py"
       # ignore unused import error in __init__.py files
-      args: ["--ignore=F401,E203", --config, setup.cfg]
+
+  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.15.0
+    hooks:
+      - id: pretty-format-toml
+        args: [--autofix, --indent, "2"]
+      - id: pretty-format-yaml
+        args: [--autofix, --preserve-quotes, --indent, "2", --offset, "2"]

pyproject.toml

@@ -1,57 +1,92 @@
 [build-system]
-requires = ["setuptools >= 77.0.3"]
 build-backend = "setuptools.build_meta"
+requires = ["setuptools >= 77.0.3"]
 
 [project]
-name = "pyfv3"
-version = "0.2.0"
+authors = [{name = "NOAA - Geophysical Fluid Dynamics Laboratory", email = "oliver.elbert@noaa.gov"}]
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Intended Audience :: Developers",
+  "Natural Language :: English",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.11"
+]
 dependencies = [
-    "f90nml>=1.1.0",
-    "numpy==1.26.4",
-    "xarray",
+  "f90nml>=1.1.0",
+  "numpy==1.26.4",
+  "xarray"
 ]
-requires-python = ">=3.11,<3.12"
-authors = [{name = "NOAA - Geophysical Fluid Dynamics Laboratory", email = "oliver.elbert@noaa.gov"}]
 description = "PyFV3 is a NDSL-based FV3 dynamical core for atmospheric models."
-readme = "README.md"
 license = "Apache-2.0"
 license-files = ["LICENSE.md"]
-classifiers = [
-    "Development Status :: 2 - Pre-Alpha",
-    "Intended Audience :: Developers",
-    "Natural Language :: English",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
-]
+name = "pyfv3"
+readme = "README.md"
+requires-python = ">=3.11,<3.12"
+version = "0.2.0"
 
 [project.optional-dependencies]
-test = [
-    "coverage",
-    "pytest",
-    "pytest-subtests",
-    "serialbox",
-]
-ndsl = ["ndsl @ git+https://github.com/NOAA-GFDL/NDSL.git@develop"]
-develop = [
-    "pyfv3[test]",
-    "pyfv3[ndsl]",
-    "pre-commit",
+dev = [
+  "pyfv3[test]",
+  "pyfv3[ndsl]",
+  "pre-commit",
+  "flake8-pyproject"
 ]
 extras = [
-    "pyfv3[test]",
-    "pyfv3[ndsl]",
-    "pyfv3[develop]",
+  "pyfv3[test]",
+  "pyfv3[ndsl]",
+  "pyfv3[dev]"
+]
+ndsl = ["ndsl @ git+https://github.com/NOAA-GFDL/NDSL.git@develop"]
+test = [
+  "coverage",
+  "pytest",
+  "pytest-subtests",
+  "serialbox"
 ]
 
 [project.urls]
 Repository = "https://github.com/NOAA-GFDL/pyFV3"
 
-[tool.setuptools.packages.find]
-include = ["pyfv3", "pyfv3.*"]
-
-[tool.setuptools]
-include-package-data = true
+[tool.aliases]
 
 [tool.black]
 line-length = 88
 target_version = ['py311']
+
+[tool.coverage.run]
+branch = true
+omit = ["tests/*", "*gt_cache*", ".dacecache*", "external/*", "__init__.py"]
+parallel = true
+source_pkgs = ["pyfv3"]
+
+[tool.flake8]
+exclude = ["docs"]
+extend-ignore = ["W503", "E302", "E203", "F841"]
+max-line-length = 88
+per-file-ignores = "__init__.py: F401"
+
+[tool.isort]
+default_section = "THIRDPARTY"
+force_grid_wrap = 0
+include_trailing_comma = true
+known_first_party = "pyfv3,ndsl,pyshield"
+known_third_party = "f90nml,pytest,xarray,numpy,mpi4py,gt4py"
+line_length = 88
+lines_after_imports = 2
+multi_line_output = 3
+sections = "FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER"
+use_parentheses = true
+
+[tool.mypy]
+explicit_package_bases = true
+follow_imports = "normal"
+ignore_missing_imports = true
+namespace_packages = true
+strict_optional = false
+warn_unreachable = true
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+include = ["pyfv3", "pyfv3.*"]