Extend pre-commit configuration (#339)

* Update .git-blame-ignore-revs
* Add pyproject.toml with configurations for isort, black and flake8
* Extend pre-commit configuration with isort, black, pyproject-flake8,
  check-yaml, end-of-file-fixer, trailing-whitespace and actionlint
* Address issues identified by flake8 and actionlint
* Prepare for pre-commit CI
* Add pre-commit to environment-dev.yml

---------

Co-authored-by: Robert Pincus <[email protected]>

.cmake-format.py

@@ -1,13 +1,13 @@
-with section("parse"):
+with section("parse"):  # noqa: F821
     additional_commands = {"check_python3_package": {"pargs": 1, "kwargs": {"CODE": 1}}}
 
-with section("format"):
+with section("format"):  # noqa: F821
     dangle_parens = True
     max_lines_hwrap = 0
     keyword_case = "upper"
     autosort = True
 
-with section("lint"):
+with section("lint"):  # noqa: F821
     # The formatter sometimes fails to fit the code into the line limit (C0301) and can
     # disagree with the linter regarding the indentation (C0307):
     disabled_codes = ["C0301", "C0307"]

.git-blame-ignore-revs

@@ -1,2 +1,4 @@
-# Formatted entire CMake code base with cmake-format
-45b43632309cff022326472a8be0fdd5efc8f5c8
+# Formatted entire codebase (#337)
+db7044f9c85b9675b0447d2162001f32b61e0e84
+cc0f75b44d536fd10fa0556474926e58bfbb3f4f
+71520f8bcc8af9611e2a0f70eb3278fcc3064343

.github/workflows/check-api.yml

@@ -33,5 +33,5 @@ jobs:
         $FC --version
         cmake -S . -B build \
          -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-         -DKERNEL_MODE=$RTE_KERNELS
+         -DKERNEL_MODE="$RTE_KERNELS"
         cmake --build build

.github/workflows/containerized-ci.yml

@@ -83,7 +83,7 @@ jobs:
       run: |
           cmake -S . -B build -G "Ninja" \
               -DCMAKE_BUILD_TYPE=${{ matrix.build-type }} \
-              -DRTE_ENABLE_SP=`test 'x${{ matrix.fpmodel }}' = xSP && echo ON || echo OFF` \
+              -DRTE_ENABLE_SP="$(test '${{ matrix.fpmodel }}' = SP && echo ON || echo OFF)" \
               -DKERNEL_MODE=${{ matrix.rte-kernels }} \
               -DBUILD_TESTING=ON
           cmake --build build

.github/workflows/continuous-integration.yml

@@ -101,7 +101,7 @@ jobs:
         if: matrix.gfortran-from == 'conda'
         run: |
           conda install -c conda-forge gfortran=${{ matrix.gfortran-version }} -y
-          echo "FC=gfortran" >> $GITHUB_ENV
+          echo "FC=gfortran" >> "$GITHUB_ENV"
       #
       # Install dependencies
       #
@@ -112,15 +112,15 @@ jobs:
       #
       - name: Adjust toolchain
         if: matrix.os == 'windows-2022'
-        run: echo "FC=${FC}.exe" >> $GITHUB_ENV
+        run: echo "FC=${FC}.exe" >> "$GITHUB_ENV"
       #
       # Build libraries, examples, and tests
       #
       - name: Build libraries and tests
         run: |
           cmake -S . -B build -G "Ninja" \
               -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-              -DRTE_ENABLE_SP=`test 'x${{ matrix.fpmodel }}' = xSP && echo ON || echo OFF` \
+              -DRTE_ENABLE_SP="$(test '${{ matrix.fpmodel }}' = SP && echo ON || echo OFF)" \
               -DBUILD_TESTING=ON
           cmake --build build
       #

.pre-commit-config.yaml

@@ -1,4 +1,18 @@
+ci:
+  autofix_prs: false
+  autoupdate_branch: develop
+
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.6
+    hooks:
+      - id: actionlint
   - repo: https://github.com/cheshirekow/cmake-format-precommit
     rev: v0.6.13
     hooks:
@@ -12,3 +26,15 @@ repos:
         name: cmake-lint (templates)
         types: [file]
         files: \.cmake\.in$
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.10.0
+    hooks:
+      - id: black
+  - repo: https://github.com/csachs/pyproject-flake8
+    rev: v7.0.0
+    hooks:
+      - id: pyproject-flake8

environment-dev.yml

@@ -21,6 +21,7 @@ dependencies:
   - netcdf-fortran
   - cmake
   - ninja
+  - pre-commit
 variables:
   FC: gfortran
   # Debugging flags below

examples/all-sky/make_problem_size_loop.py

@@ -76,10 +76,10 @@
         raise AssertionError("Need to supply cloud optics if providing aerosol optics")
 
     # Every combo of ncol, nlay
-    for l in args.nlay:
-        for i in args.ncol:
+    for ll in args.nlay:
+        for ii in args.ncol:
             print(
-                f"{args.executable} {i:6d} {l:4d} {args.nloops:3d} "
+                f"{args.executable} {ii:6d} {ll:4d} {args.nloops:3d} "
                 + f"{args.output_file} {args.k_distribution} "
                 + f"{args.cloud_optics} {args.aerosol_optics} "
             )

pyproject.toml

@@ -0,0 +1,7 @@
+[tool.isort]
+profile = "black"
+
+[tool.black]
+
+[tool.flake8]
+max-line-length = 88

tests/validation-plots.py

@@ -111,11 +111,11 @@ def main():
         try:
             try:
                 urllib.request.urlretrieve(construct_lbl_esgf_root(v), v + lbl_suffix)
-            except:
+            except Exception:
                 urllib.request.urlretrieve(
                     construct_lbl_esgf_root(v, esgf_node="dkrz"), v + lbl_suffix
                 )
-        except:
+        except Exception:
             raise Exception("Failed to download {0}".format(v + lbl_suffix))
 
     lbl = xr.open_mfdataset([v + lbl_suffix for v in fluxes], combine="by_coords").sel(