Modernize GitHub Actions workflows to match bigplanet

Updated both tests.yml and docs.yml to use modern GitHub Actions patterns following the bigplanet repository's recently updated workflows.

tests.yml changes:
- Updated to test only ubuntu-22.04 and Python 3.9 initially (will expand after tests pass)
- Removed conda dependency, now uses direct pip install
- Updated actions versions: checkout@v5, setup-python@v5
- Added pip caching for faster CI runs
- Removed shell: bash -l {0} requirements (not needed without conda)
- Added diagnostic test step to verify pytest works
- Added per-test timeout (300s) to prevent hanging tests
- Updated codecov action to v4 with token support
- Improved test result publishing with better naming
- Removed unnecessary "Get unique id" step
- Changed branch from [master, main] to just [main]

docs.yml changes:
- Updated actions/checkout to v5 (from v2)
- Updated conda-incubator/setup-miniconda to v3 (from v2)
- Updated github-pages-deploy-action to v4 (from 4.1.2)
- Changed branch from [master, main] to just [main]
- Removed commented pull_request section

These changes align with modern GitHub Actions best practices and match the patterns successfully used in the bigplanet repository. Once tests pass on ubuntu-22.04 + Python 3.9, we can expand the matrix to include additional OS and Python versions as documented in bigplanet.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

Author: RoryBarnes

.github/workflows/docs.yml

@@ -2,20 +2,18 @@ name: docs
 
 on:
   push:
-    branches: [master, main]
-  #pull_request: TODO: Enable me
-  #  branches:[master, main]
+    branches: [main]
 
 jobs:
   tests:
     name: "Build docs"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v5
 
       - name: Set up Python
         id: setup_python
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: vplanet
           environment-file: environment.yml
@@ -41,7 +39,7 @@ jobs:
           touch _build/html/.nojekyll
 
       - name: Publish
-        uses: JamesIves/github-pages-deploy-action@4.1.2
+        uses: JamesIves/github-pages-deploy-action@v4
         # NOTE: Triggered only when the PR is *merged* (event_name == 'push')
         if: steps.build.outcome == 'success' && github.event_name == 'push'
         with:

.github/workflows/tests.yml

@@ -2,74 +2,71 @@ name: tests
 
 on:
   push:
-    branches: [master, main]
+    branches: [main]
   pull_request:
-    branches: [master, main]
+    branches: [main]
 
 jobs:
   tests:
-    name: 'Run tests on py${{ matrix.python-version }}'
-    runs-on: ubuntu-latest
+    name: 'py${{ matrix.python-version }} on ${{ matrix.os }}'
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - python-version: '3.6'
-          - python-version: '3.7'
-          - python-version: '3.8'
-          - python-version: '3.9'
-          # - python-version: '3.10'
+        os: [ubuntu-22.04]
+        python-version: ["3.9"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
-      - name: Set up Python
-        id: setup_python
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
-          activate-environment: vplanet
-          environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
 
-      - name: Install vplanet
-        id: install
-        if: steps.setup_python.outcome == 'success'
-        shell: bash -l {0}
+      - name: Install VPLanet
         run: |
+          python -m pip install --upgrade pip
           python -m pip install vplanet
 
       - name: Install vspace
-        id: tools
-        if: steps.install.outcome == 'success'
-        shell: bash -l {0}
         run: |
           python -m pip install -e .
 
-      - name: Run tests
-        if: steps.install.outcome == 'success'
-        shell: bash -l {0}
-        run: python -m pytest -v tests --junitxml=junit/test-results.xml --cov=vspace/ --cov-report=xml
+      - name: Install test dependencies
+        run: |
+          python -m pip install pytest pytest-cov pytest-timeout
 
-      - name: Get unique id
-        id: unique-id
-        env:
-          STRATEGY_CONTEXT: ${{ toJson(strategy) }}
+      - name: Run diagnostic test
+        timeout-minutes: 3
         run: |
-          export JOB_ID=`echo $STRATEGY_CONTEXT | md5sum`
-          echo "::set-output name=id::$JOB_ID"
+          # First run a simple unit test to verify pytest works
+          echo "Running single unit test as diagnostic..."
+          python -m pytest tests/Vspace_Explicit/test_vspace_explicit.py -v -s
 
-      - name: Publish unit test results
-        uses: EnricoMi/publish-unit-test-result-action@v2
-        if: always()
-        with:
-          files: junit/test-*.xml
+      - name: Run tests
+        timeout-minutes: 20
+        run: |
+          # Run all tests with verbose output, capture disabled to see subprocess output, and per-test timeout
+          python -m pytest tests/ -v -s --timeout=300 --junitxml=junit/test-results-${{ matrix.os }}-${{ matrix.python-version }}.xml --cov=vspace --cov-report=xml --cov-report=term
 
-      - name: CodeCov
-        uses: codecov/codecov-action@v2.1.0
+      - name: Upload coverage to Codecov
+        # Only upload from one runner to avoid redundant API calls
+        if: matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.9'
+        uses: codecov/codecov-action@v4
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
-        #shell: bash -l {0}
-        #run: |
-        #  bash <(curl -s https://codecov.io/bash)
+          flags: ${{ matrix.os }}-py${{ matrix.python-version }}
+          name: ${{ matrix.os }}-py${{ matrix.python-version }}
+          fail_ci_if_error: false
+
+      - name: Publish test results
+        uses: EnricoMi/publish-unit-test-result-action@v2
+        if: always() && runner.os == 'Linux'
+        with:
+          files: junit/test-*.xml
+          check_name: Test Results (py${{ matrix.python-version }} on ${{ matrix.os }})