Update Python support (#735)

* Update Python support

* Match latest zstash python support

* Fixes try 2

* Further updates

* Address comments

* Address further comments

Author: forsyth2

.github/workflows/build_workflow.yml

@@ -37,23 +37,26 @@ jobs:
       - name: Checkout Code Repository
         uses: actions/checkout@v3
 
-      - name: Set up Python
+      - name: Set up Python 3.13
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.13
 
       # Run all pre-commit hooks on all the files.
       # Getting only staged files can be tricky in case a new PR is opened
       # since the action is run on a branch in detached head state.
       # This is the equivalent of running "pre-commit run --all-files" locally.
       # If you commit with the `--no-verify` flag, this check may fail.
       - 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' }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
     defaults:
       run:
         shell: bash -l {0}
@@ -63,11 +66,11 @@ jobs:
       - name: Cache Conda
         uses: actions/cache@v3
         env:
-          CACHE_NUMBER: 0
+          CACHE_NUMBER: 1 # Increment this to invalidate cache
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda/dev.yml') }}
+            hashFiles('conda/dev.yml') }}-python${{ matrix.python-version }}
 
       - name: Build Conda Environment
         uses: conda-incubator/setup-miniconda@v3
@@ -76,8 +79,23 @@ jobs:
           miniforge-variant: Miniforge3
           miniforge-version: latest
           environment-file: conda/dev.yml
-          channel-priority: strict
+          channel-priority: flexible # Changed from strict to flexible
           auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          use-only-tar-bz2: true
+
+      - name: Verify Environment and Fix Dependencies
+        run: |
+          conda info
+          conda list
+          # Ensure we have the right Python version
+          python --version
+          # Fix pip issues for Python 3.12+
+          if [[ "${{ matrix.python-version }}" == "3.12" ]] || [[ "${{ matrix.python-version }}" == "3.13" ]]; then
+            python -m ensurepip --upgrade || true
+            python -m pip install --upgrade --force-reinstall pip setuptools wheel
+          fi
 
       - if: ${{ needs.check-jobs-to-skip.outputs.should_skip != 'true' }}
         name: Show Conda Environment Info
@@ -87,7 +105,7 @@ jobs:
           conda list
 
       - name: Install `zppy` Package
-        run: pip install .
+        run: python -m pip install .
 
       # Does not run the integration tests, which require server access
       - name: Run Unit Tests
@@ -101,7 +119,7 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    timeout-minutes: 5
+    timeout-minutes: 10 # Increased timeout for docs
     steps:
       - uses: actions/checkout@v2
         with:
@@ -111,11 +129,11 @@ jobs:
       - name: Cache Conda
         uses: actions/cache@v3
         env:
-          CACHE_NUMBER: 0
+          CACHE_NUMBER: 1 # Match the build job cache number
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda/dev.yml') }}
+            hashFiles('conda/dev.yml') }}-docs
 
       - name: Build Conda Environment
         uses: conda-incubator/setup-miniconda@v3
@@ -124,8 +142,9 @@ jobs:
           miniforge-variant: Miniforge3
           miniforge-version: latest
           environment-file: conda/dev.yml
-          channel-priority: strict
+          channel-priority: flexible # Changed from strict to flexible
           auto-update-conda: true
+          python-version: "3.13" # Use stable Python version for docs
 
       - if: ${{ needs.check-jobs-to-skip.outputs.should_skip != 'true' }}
         name: Show Conda Environment Info

.pre-commit-config.yaml

@@ -13,29 +13,29 @@ repos:
 
   # Can run individually with `pre-commit run black --all-files`
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
 
   # Can run individually with `pre-commit run isort --all-files`
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
 
   # Can run individually with `pre-commit run flake8 --all-files`
   # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
   # https://github.com/pre-commit/pre-commit/issues/1206
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
+    rev: 7.3.0
     hooks:
       - id: flake8
         args: ["--config=setup.cfg"]
         additional_dependencies: [flake8-isort==6.1.1]
 
   # Can run individually with `pre-commit run mypy --all-files`
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.18.2
     hooks:
       - id: mypy
         args: ["--config=setup.cfg"]

conda/dev.yml

@@ -7,45 +7,43 @@
 name: zppy_dev
 channels:
   - conda-forge
-  - defaults
 dependencies:
   # Build
   # =======================
-  - python=3.9.13
-  - pip=22.2.2
+  - python >=3.11,<3.14
+  - pip
   # Base
   # =================
-  - configobj=5.0.6
-  - jinja2=3.1.2
+  - configobj>=5.0.6  # Changed from =5.0.6
+  - jinja2>=3.1.2     # Changed from =3.1.2
   - mache>=1.5.0
   - mpas_tools>=0.15.0
-  - pillow=9.2.0
+  - pillow>=9.2.0     # Changed from =9.2.0
   # Testing
   # =======================
   - pytest
   - pytest-cov
   # Documentation
   # If versions are updated, also update in `.github/workflows/build_workflow.yml`
   # =================
-  - sphinx=5.2.3
-  - sphinx_rtd_theme=1.0.0
-  - sphinx-multiversion=0.2.4
+  - sphinx >=5.2.0
+  - sphinx-multiversion >=0.2.4
+  - sphinx_rtd_theme >=1.0.0
   # Need to pin docutils because 0.17 has a bug with unordered lists
   # https://github.com/readthedocs/sphinx_rtd_theme/issues/1115
-  - docutils=0.16
+  # This issue has been resolved.
+  - docutils>=0.16    # Removed <0.17 constraint
   # Quality Assurance Tools
   # =======================
   # If versions are updated, also update 'rev' in `.pre-commit-config.yaml`
-  - black=24.10.0        # version from https://anaconda.org/conda-forge/black
-  - flake8=7.1.1         # version from https://anaconda.org/conda-forge/flake8
-  # This line also implicitly installs isort
-  - flake8-isort=6.1.1  # version from https://anaconda.org/conda-forge/flake8-isort
-  - mypy=1.11.2         # version from https://anaconda.org/conda-forge/mypy
-  - pre-commit=4.0.1    # version from https://anaconda.org/conda-forge/pre-commit
-  - tbump=6.9.0
+  - black ==25.1.0
+  - flake8 ==7.3.0
+  - isort ==6.0.1
+  - mypy ==1.18.2
+  - pre-commit ==4.3.0
+  - tbump >=6.9.0
   # Developer Tools
   # =======================
-  - tbump=6.9.0
   - ipykernel
 
 prefix: /opt/miniconda3/envs/zppy_dev

conda/meta.yaml

@@ -1,6 +1,5 @@
 {% set name = "zppy" %}
 {% set version = "3.0.0" %}
-{% set python_min = "3.9" %}
 
 package:
   name: {{ name|lower }}
@@ -17,19 +16,19 @@ build:
 
 requirements:
   host:
-    - python {{ python_min }}
+    - python >=3.11,<3.14
     - pip
     - setuptools
   run:
-    - python >={{ python_min }}
+    - python >=3.11,<3.14
     - configobj >=5.0.0,<6.0.0
     - jinja2 >=2.0.0
     - mache >=1.3.2
     - mpas_tools >=0.15.0
 
 test:
   requires:
-    - python {{ python_min }}
+    - python >=3.11,<3.14
     - pip
   imports:
     - zppy

pyproject.toml

@@ -4,7 +4,7 @@
 
 [tool.black]
 line-length = 88
-target-version = ['py36']
+target-version = ['py311']
 include = '\.pyi?$'
 exclude = '''
 /(

setup.cfg

@@ -48,7 +48,7 @@ exclude =
     venv
 
 [mypy]
-python_version = 3.9
+python_version = 3.13
 check_untyped_defs = True
 ignore_missing_imports = True
 warn_unused_ignores = True

setup.py

@@ -27,7 +27,7 @@ def package_files(directory, prefixes, extensions):
     author="Ryan Forsyth, Chris Golaz",
     author_email="[email protected], [email protected]",
     description="Post-processing software for E3SM",
-    python_requires=">=3.9",
+    python_requires=">=3.11,<3.14",
     packages=find_packages(include=["zppy", "zppy.*"]),
     package_data={"": data_files},
     entry_points={"console_scripts": ["zppy=zppy.__main__:main"]},