Merge pull request #1326 from PCMDI/v4.0.0_alpha

v4.0.0_alpha version (`v4.0.0rc1`) release prepare

Author: lee1043

setup.cfg renamed to .flake8.cfg

@@ -31,10 +31,3 @@ exclude =
     venv
     *json
     *md
-
-
-
-[tool:pytest]
-junit_family = xunit2
-addopts = --cov=pcmdi_metrics --cov-report term --cov-report html:tests_coverage_reports/htmlcov --cov-report xml:tests_coverage_reports/coverage.xml -s --ignore tests/deprecated
-python_files = tests.py test_*.py

.github/workflows/build_workflow.yml

@@ -20,7 +20,7 @@ jobs:
       should_skip: ${{ steps.skip_check.outputs.should_skip }}
     steps:
       - id: skip_check
-        uses: fkirc/skip-duplicate-actions@master
+        uses: fkirc/skip-duplicate-actions@v5
         with:
           cancel_others: true
           paths_ignore: '["**/README.md", "**/docs/**", "**/ISSUE_TEMPLATE/**", "**/pull_request_template.md", "**/.vscode/**"]'
@@ -32,66 +32,61 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout Code Repository
-        uses: actions/checkout@v3
-        
+        uses: actions/checkout@v4
+
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.13'
 
       - name: Install and Run Pre-commit
-        uses: pre-commit/[email protected].0
+        uses: pre-commit/[email protected].1
 
   build:
     needs: check-jobs-to-skip
     if: ${{ needs.check-jobs-to-skip.outputs.should_skip != 'true' }} || ${{ github.event_name == 'push' }}
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     defaults:
       run:
         shell: bash -l {0}
     timeout-minutes: 15
     steps:
-      - uses: actions/checkout@v3
-
+      - uses: actions/checkout@v4
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
       - name: Set up Conda Environment
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          activate-environment: "pcmdi_metrics_ci"
+          activate-environment: pcmdi_metrics_ci
           environment-file: conda-env/ci.yml
           channel-priority: flexible
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           use-mamba: false
           conda-solver: classic
 
+      - name: Cache Conda Packages
+        uses: actions/cache@v4
+        with:
+          path: ~/conda_pkgs_dir
+          key: conda-${{ runner.os }}--${{ runner.arch }}--py${{ matrix.python-version }}--${{ steps.get-date.outputs.today }}--${{ hashFiles('conda-env/ci.yml') }}--${{ env.CACHE_NUMBER }}
+        env:
+          CACHE_NUMBER: 0
+
       - name: Verify Conda Environment
         run: |
           conda info
           conda list
           conda config --show-sources
           conda config --show
 
-      # Used for refreshing the cache every 24 hours to avoid inconsistencies of package
-      # versions between the CI pipeline and local installations.
-      - name: Get Date
-        id: get-date
-        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
-        shell: bash
-
-      - name: Cache Conda
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.CONDA }}/envs
-          key:
-            conda-${{ runner.os }}--${{ runner.arch }}--${{
-            steps.get-date.outputs.today }}-${{
-            hashFiles('conda-env/ci.yml') }}-${{ env.CACHE_NUMBER}}
-        env:
-          # Increase this value to reset cache if conda/dev.yml has not changed in the workflow
-          CACHE_NUMBER: 0
-
       - name: Install pcmdi_metrics
         # Source: https://github.com/conda/conda-build/issues/4251#issuecomment-1053460542
         run: |
@@ -111,48 +106,53 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    timeout-minutes: 5
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
 
       - name: Cache Conda
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
-          # Increase this value to reset cache if conda-env/ci.yml has not changed in the workflow
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-env/dev.yml') }}
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda-env/dev.yml') }}
 
       - name: Set up Conda Environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          activate-environment: "pcmdi_metrics_dev"
+          activate-environment: pcmdi_metrics_dev
+          environment-file: conda-env/dev.yml
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          environment-file: conda-env/dev.yml
           channel-priority: strict
           auto-update-conda: true
-          use-mamba: false  # Disable libmamba solver
+          use-mamba: false
+          conda-solver: classic
+          python-version: '3.13'
+
+      - name: Verify Conda Environment
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
 
       - name: Install pcmdi_metrics
-        # Source: https://github.com/conda/conda-build/issues/4251#issuecomment-1053460542
         run: |
-            python -m pip install --no-build-isolation --no-deps -e .
+          python -m pip install --no-build-isolation --no-deps -e .
 
       - name: Sphinx build
         run: |
           sphinx-build docs _build
-          
+
       - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
         with:
-          publish_branch: gh-pages 
+          publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: _build/
           force_orphan: true

.pre-commit-config.yaml

@@ -37,5 +37,5 @@ repos:
       rev: 7.3.0
       hooks:
           - id: flake8
-            args: ["--config=setup.cfg"]
+            args: ["--config=.flake8.cfg"]
             additional_dependencies: [flake8-isort]

CITATION.cff

@@ -39,5 +39,5 @@ keywords:
   - climatology
   - climate variability
 license: BSD-3-Clause
-version: '3.9.3'
-date-released: '2025-09-18'
+version: '4.0.0rc1'
+date-released: '2025-09-24'

MANIFEST.in

@@ -0,0 +1,4 @@
+# Ensure custom build backend and generator script are included in sdist
+recursive-include _custom_build *.py
+include share/setup_default_args.py
+include share/DefArgsCIA.json

README.md

@@ -126,6 +126,8 @@ Release Notes and History
 
 | <div style="width:300%">[Versions]</div> | Update summary   |
 | ------------- | ------------------------------------- |
+| [v4.0.0rc1]   | Pre-release of development version: Newerly support higher Python versions, `>= 3.10, < 3.14`
+| ------------- | ------------------------------------- |
 | [v3.9.3]      | Technical update
 | [v3.9.2]      | Technical update
 | [v3.9.1]      | New capability (**new modes for modes of variability metrics: EA, SCA**) and technical update
@@ -183,6 +185,7 @@ Release Notes and History
 </details>
 
 [Versions]: https://github.com/PCMDI/pcmdi_metrics/releases
+[v4.0.0rc1]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v4.0.0rc1
 [v3.9.3]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v3.9.3
 [v3.9.2]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v3.9.2
 [v3.9.1]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v3.9.1

_custom_build/backend.py

@@ -0,0 +1,57 @@
+from __future__ import annotations
+
+import os
+import runpy
+from pathlib import Path
+
+from setuptools import build_meta as _orig
+from setuptools.build_meta import *  # noqa: F401,F403 - re-export PEP 517 hooks
+
+_PROJECT_ROOT = Path(__file__).resolve().parent.parent
+_GENERATOR = _PROJECT_ROOT / "share" / "setup_default_args.py"
+
+
+def _run_prebuild_generator() -> None:
+    """Run the script that (re)generates share/DefArgsCIA.json if present.
+
+    Mirrors the behavior previously invoked in setup.py before packaging.
+    The script writes DefArgsCIA.json into the share directory.
+    """
+    if _GENERATOR.is_file():
+        # Execute in-place with cwd=share to preserve original behavior
+        share_dir = _GENERATOR.parent
+        cwd = os.getcwd()
+        try:
+            os.chdir(share_dir)
+            # runpy.run_path executes the script as __main__ without spawning a new process
+            runpy.run_path(str(_GENERATOR), run_name="__main__")
+        finally:
+            os.chdir(cwd)
+
+
+def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):  # type: ignore[override]
+    _run_prebuild_generator()
+    return _orig.build_wheel(wheel_directory, config_settings, metadata_directory)
+
+
+def build_sdist(sdist_directory, config_settings=None):  # type: ignore[override]
+    _run_prebuild_generator()
+    return _orig.build_sdist(sdist_directory, config_settings)
+
+
+def build_editable(wheel_directory, config_settings=None, metadata_directory=None):  # type: ignore[override]
+    # PEP 660 editable install hook (pip -e). Ensure the file exists here too.
+    _run_prebuild_generator()
+    return _orig.build_editable(wheel_directory, config_settings, metadata_directory)
+
+
+def prepare_metadata_for_build_wheel(metadata_directory, config_settings=None):  # type: ignore[override]
+    _run_prebuild_generator()
+    return _orig.prepare_metadata_for_build_wheel(metadata_directory, config_settings)
+
+
+def prepare_metadata_for_build_editable(metadata_directory, config_settings=None):  # type: ignore[override]
+    _run_prebuild_generator()
+    return _orig.prepare_metadata_for_build_editable(
+        metadata_directory, config_settings
+    )

conda-env/ci.yml

@@ -8,21 +8,21 @@ dependencies:
     # Base
     # ==================
     # NOTE: If versions are updated, also `additional_dependencies` list for mypy in `.pre-commit-config.yaml`
-    - python=3.10.10
-    - pip=23.1.2
-    - numpy >=2.0.0,<2.1.0
+    - python >=3.10,<3.14
+    - pip >=23.1.2
+    - numpy >=2.0.0,<3
     - cartopy >=0.22.0
     - matplotlib >=3.7.1
-    - cdp=1.7.0
-    - eofs=2.0.0
-    - seaborn=0.12.2
-    # - enso_metrics=1.1.5
-    - xcdat >=0.7.3
-    - xmltodict=0.13.0
-    - setuptools=67.7.2
-    - netcdf4>=1.6.3
-    - regionmask=0.12.1
-    - rasterio>=1.3.6
+    - cdp >=1.7.0
+    - eofs >=2.0.0
+    - seaborn >=0.12.2
+    #- enso_metrics >=1.1.5
+    - xcdat >=0.10.0
+    - xmltodict >=0.13.0
+    - setuptools >=67.7.2
+    - netcdf4 >=1.6.3
+    - regionmask >=0.12.1
+    - rasterio >=1.3.6
     - shapely >=2.0.1,<=2.0.6
     - numdifftools
     - nc-time-axis
@@ -32,8 +32,8 @@ dependencies:
     # ==================
     # Testing
     # ==================
-    - pre_commit=3.2.2
-    - pytest=7.3.1
-    - pytest-cov=4.0.0
+    - pre_commit >=3.2.2
+    - pytest >=7.3.1
+    - pytest-cov >=4.0.0
 
 prefix: /opt/miniconda3/envs/pmcdi_metrics_ci

conda-env/dev.yml

@@ -8,21 +8,21 @@ dependencies:
     # Base
     # ==================
     # NOTE: If versions are updated, also `additional_dependencies` list for mypy in `.pre-commit-config.yaml`
-    - python=3.10.10
-    - pip=23.1.2
-    - numpy >=2.0.0,<2.1.0
+    - python >=3.10,<3.14
+    - pip
+    - numpy >=2.0.0,<3
     - cartopy >=0.22.0
     - matplotlib >=3.7.1
-    - cdp=1.7.0
-    - eofs=2.0.0
-    - seaborn=0.12.2
-    # - enso_metrics=1.1.5
-    - xcdat >=0.7.3
-    - xmltodict=0.13.0
-    - setuptools=67.7.2
-    - netcdf4>=1.6.3
-    - regionmask=0.12.1
-    - rasterio>=1.3.6
+    - cdp >=1.7.0
+    - eofs >=2.0.0
+    - seaborn >=0.12.2
+    #- enso_metrics >=1.1.5
+    - xcdat >=0.10.0
+    - xmltodict >=0.13.0
+    - setuptools >=67.7.2
+    - netcdf4 >=1.6.3
+    - regionmask >=0.12.1
+    - rasterio >=1.3.6
     - shapely >=2.0.1,<=2.0.6
     - numdifftools
     - nc-time-axis
@@ -32,9 +32,9 @@ dependencies:
     # ==================
     # Testing
     # ==================
-    - pre_commit=3.2.2
-    - pytest=7.3.1
-    - pytest-cov=4.0.0
+    - pre_commit >=3.2.2
+    - pytest >=7.3.1
+    - pytest-cov >=4.0.0
     # ==================
     # Developer Tools
     # ==================

pcmdi_metrics/_version.py

@@ -1 +1 @@
-__version__ = "3.9.3"
+__version__ = "4.0.0rc1"