Test infrastructure restoration

.coveragerc

@@ -0,0 +1,21 @@
+[run]
+# Coverage configuration for multiplanet
+source = multiplanet
+
+# Multiplanet uses a hybrid testing strategy:
+# 1. Unit tests (tests/unit/) - Import modules directly for code coverage
+# 2. Integration tests (tests/*/) - Call CLI via subprocess for end-to-end validation
+#
+# Unit tests provide code coverage metrics by importing multiplanet.multiplanet
+# and multiplanet.mpstatus modules directly. Integration tests validate the
+# user-facing CLI interface by calling multiplanet/mpstatus as subprocess commands.
+#
+# This approach combines the best of both worlds: measurable coverage from unit
+# tests and real-world validation from integration tests.
+
+[report]
+precision = 2
+show_missing = True
+
+[html]
+directory = htmlcov

.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@v3
+      - 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/pip-install.yml

@@ -8,27 +8,28 @@ on:
 jobs:
 
   build:
-    name: ${{ matrix.os }}:${{ matrix.python }}
+    name: 'py${{ matrix.python }} on ${{ matrix.os }}'
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python: ['3.7', '3.8', '3.9']
+        os: [macos-15-intel, macos-26, ubuntu-22.04, ubuntu-24.04]
+        python: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: ${{ matrix.python }}
+          allow-prereleases: true
 
       - name: Build
         run: |
-          python -m pip install -U pip pep517 twine setuptools_scm
-          python -m pep517.build .
+          python -m pip install -U pip build twine setuptools setuptools_scm wheel
+          python -m build
 
       - name: Test the sdist
         run: |
@@ -42,21 +43,22 @@ jobs:
           venv-wheel/bin/python -m pip install dist/multiplanet*.whl
           venv-wheel/bin/python -c "import multiplanet; print(multiplanet.__version__)"
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: dist-${{ matrix.os }}-${{ matrix.python }}
           path: dist/*
 
   upload_pypi:
     needs: [build]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
+    permissions:
+      id-token: write
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: dist-*
           path: dist
+          merge-multiple: true
 
-      - uses: pypa/gh-action-pypi-publish@master
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
+      - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -2,72 +2,81 @@ 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'
+        os: [ubuntu-22.04, ubuntu-24.04, macos-15-intel, macos-26]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
 
     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 dependencies
         run: |
-          python -m pip install vplanet
+          python -m pip install --upgrade pip
+          # Install public releases from PyPI
+          # BigPlanet v3.1.2+ includes all compatibility fixes
+          python -m pip install vplanet vspace bigplanet
 
       - name: Install multiplanet
-        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=multiplanet/ --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: |
+          # First run a simple unit test to verify pytest works
+          echo "Running single test as diagnostic..."
+          python -m pytest tests/Serial/test_serial.py -v -s
+
+      - name: Run tests
+        timeout-minutes: 20
         run: |
-          export JOB_ID=`echo $STRATEGY_CONTEXT | md5sum`
-          echo "::set-output name=id::$JOB_ID"
+          # Run all tests with verbose output, per-test timeout, and coverage
+          # Note: Coverage shows 0% because tests invoke CLI as subprocess (expected for CLI tools)
+          python -m pytest tests/ -v -s --timeout=300 --junitxml=junit/test-results-${{ matrix.os }}-${{ matrix.python-version }}.xml --cov=multiplanet --cov-report=xml --cov-report=term
 
-      - name: Publish unit test results
-        uses: EnricoMi/publish-unit-test-result-action@v1
-        if: always()
+      - 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
+          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
-          comment_mode: update last
+          check_name: Test Results (py${{ matrix.python-version }} on ${{ matrix.os }})
 
-      - name: CodeCov
-        uses: codecov/codecov-action@v2.1.0
+      - name: Publish test results (macOS)
+        uses: EnricoMi/publish-unit-test-result-action/composite@v2
+        if: always() && runner.os == 'macOS'
         with:
-          files: ./coverage.xml
-        #shell: bash -l {0}
-        #run: |
-        #  bash <(curl -s https://codecov.io/bash)
+          files: junit/test-*.xml
+          check_name: Test Results (py${{ matrix.python-version }} on ${{ matrix.os }})