Modernizations and bug fixes

.github/workflows/auto-accept-ci-changes.yml

@@ -33,6 +33,8 @@ jobs:
         uses: dependabot/fetch-metadata@ffa630c65fa7e0ecfa0625b5ceda64399aea1b36 # v3.0.0
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
+          permission-contents: write
+          permission-pull-requests: write
 
       - name: Stop workflow if not minor update or patch update
         id: skip-condition

.github/workflows/cache_cleaner.yml

@@ -27,6 +27,8 @@ jobs:
 
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Cleanup
         run: |

.github/workflows/first_pull_request.yml

@@ -20,6 +20,7 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8.0.0
         with:
           script: |

.github/workflows/main.yml

@@ -35,24 +35,29 @@ jobs:
             files.pythonhosted.org:443
             github.com:443
             pypi.org:443
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Environment Caching
         uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
         with:
           path: |
             .tox
           key: ${{ runner.os }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-lint-${{ env.ESGF_TEST_DATA_VERSION }}
+
       - name: Run linting suite
         run: |
           python -m tox -e lint
@@ -71,22 +76,27 @@ jobs:
         with:
           disable-sudo: false
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
+
       - name: Install HDF5 (Linux)
         run: |
           sudo apt-get update
           sudo apt-get install -y libhdf5-dev
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Environment Caching
         uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
         with:
@@ -95,6 +105,7 @@ jobs:
             ~/.cache/xclim-testdata
             .tox
           key: ${{ runner.os }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-Python${{ matrix.python-version }}-${{ env.ESGF_TEST_DATA_VERSION }}
+
       - name: Test with tox
         run: |
           python -m tox
@@ -112,7 +123,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.11", "3.12", "3.13" ]
+        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -122,10 +133,12 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
@@ -134,24 +147,28 @@ jobs:
           environment-file: environment.yml
           create-args: >-
             python=${{ matrix.python-version }}
-            pytest-timeout
+
       - name: Install CLISOPS
         run: |
           python -m pip install --no-user --no-deps --editable .
+
       - name: Test Data Caching
         uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
         with:
           path: |
             ~/.cache/mini-esgf-data
             ~/.cache/xclim-testdata
           key: ${{ runner.os }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-conda-Python${{ matrix.python-version }}-${{ env.ESGF_TEST_DATA_VERSION }}
+
       - name: Check versions
         run: |
           micromamba list
           python -m pip check || true
+
       - name: Test with conda
         run: |
-          python -m pytest -m "not slow" --timeout=300 --numprocesses=logical --durations=10 --cov=clisops --cov-report=lcov
+          python -m pytest -m "not slow" --numprocesses=logical --durations=10 --cov=clisops --cov-report=lcov
+
       - name: Report Coverage
         uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
         with:
@@ -170,6 +187,7 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Coveralls Finished
         uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
         with:

.github/workflows/prepare-release.yml

@@ -21,10 +21,12 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Create Release
         uses: softprops/action-gh-release@153bb8e04406b158c6c84fc1615b65b24149a1fe # v2.6.1
         env:

.github/workflows/publish-pypi-production.yml

@@ -25,19 +25,24 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "${{ matrix.python-version }}"
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Build a binary wheel and a source tarball
         run: |
           python -m flit build
+
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0

.github/workflows/tag-testpypi-staging.yml

@@ -25,20 +25,25 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "${{ matrix.python-version }}"
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Build a binary wheel and a source tarball
         run: |
           python -m flit build
+
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
         with:

.github/workflows/upstream.yml

@@ -42,11 +42,13 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
           persist-credentials: false
+
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
@@ -56,21 +58,26 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             pytest-reportlog
+
       - name: Install CLISOPS
         run: |
           python -m pip install --no-deps --no-user --editable .
+
       - name: Install upstream versions
         run: |
           python -m pip install -r CI/requirements_upstream.txt
+
       - name: Check versions
         run: |
           micromamba list
           python -m pip check || true
+
       - name: Run Tests
         if: success()
         id: status
         run: |
           python -m pytest --durations=10 --cov=clisops --cov-report=term-missing --report-log output-${{ matrix.python-version }}-log.jsonl
+
       - name: Generate and publish the report
         if: |
           failure()

.gitignore

@@ -43,7 +43,7 @@ htmlcov/
 .coverage.*
 .cache
 nosetests.xml
-coverage.xml
+coverage.*
 *.cover
 .hypothesis/
 .pytest_cache/

.pre-commit-config.yaml

@@ -10,17 +10,21 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
-      - id: end-of-file-fixer
-      - id: fix-byte-order-marker
       - id: check-merge-conflict
+      - id: check-json
       - id: check-toml
       - id: check-yaml
       - id: debug-statements
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
       - id: mixed-line-ending
-      - id: no-commit-to-branch
-        args: [ '--branch', 'main' ]
       - id: name-tests-test
         args: [ '--pytest-test-first' ]
+      - id: no-commit-to-branch
+        args: [ '--branch', 'main' ]
+      - id: pretty-format-json
+        args: [ '--autofix', '--no-ensure-ascii', '--no-sort-keys' ]
+        exclude: .ipynb
       - id: trailing-whitespace
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.24.4
@@ -32,7 +36,7 @@ repos:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.15.15
     hooks:
       - id: ruff-check
         args: [ '--fix', '--show-fixes' ]
@@ -69,11 +73,11 @@ repos:
       - id: numpydoc-validation
         exclude: ^docs/|^tests/
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.30.0
+    rev: v8.30.1
     hooks:
       - id: gitleaks
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.37.1
+    rev: 0.37.2
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

.readthedocs.yml

@@ -12,9 +12,9 @@ sphinx:
 
 # Build configuration
 build:
-  os: ubuntu-24.04
+  os: "ubuntu-26.04"
   tools:
-    python: "mambaforge-23.11"
+    python: "miniforge3-25.11"
   jobs:
     post_create_environment:
       - mamba install --quiet --name ${READTHEDOCS_VERSION} -c conda-forge "python>=3.12,<3.13" "psy-maps>=1.5.0"

CONTRIBUTING.rst

@@ -86,34 +86,35 @@ Ready to contribute? Here's how to set up `clisops` for local development.
     Now you can make your changes locally!
 
 #.
-    When you are done making changes, check that you verify your changes with `flake8` and `black` and run the tests, including testing other Python versions with `tox`:
+    When you are done making changes, check that you verify your changes with `deptry`, `flake8`, and `ruff` and run the tests, including testing other Python versions with `tox`:
 
     .. code-block:: shell
 
         # For virtualenv environments:
-        $ pip install flake8 black pytest pytest-loguru tox
+        $ pip install flake8 ruff deptry pytest pytest-loguru tox
 
         # For Anaconda/Miniconda environments:
         $ conda install -c conda-forge flake8 black pytest pytest-loguru tox
 
-        $ flake8 clisops tests
-        $ black clisops tests
+        $ ruff check clisops tests
+	    $ flake8 --config=.flake8 clisops tests
+	    $ deptry .
         $ pytest
         $ tox
 
 #.
-    Before committing your changes, we ask that you install `pre-commit` in your virtualenv. `Pre-commit` runs git hooks that ensure that your code resembles that of the project and catches and corrects any small errors or inconsistencies when you `git commit`:
+    Before committing your changes, we ask that you install `prek` in your virtualenv. `prek` runs git hooks that ensure that your code resembles that of the project and catches and corrects any small errors or inconsistencies when you `git commit`:
 
     .. code-block:: shell
 
         # For virtualenv environments:
-        $ pip install pre-commit
+        $ pip install prek
 
         # For Anaconda/Miniconda environments:
-        $ conda install -c conda-forge pre-commit
+        $ conda install -c conda-forge prek
 
-        $ pre-commit install
-        $ pre-commit run --all-files
+        $ prek install
+        $ prek run --all-files
 
 #.
     Commit your changes and push your branch to GitHub: