Merge branch 'main' of https://github.com/VirtualPlanetaryLaboratory/…

…vplanet into OutputOrder
VirtualPlanetaryLaboratory · Sep 12, 2024 · 1d4d1e8 · 1d4d1e8
2 parents 189ffee + d76bb0b
commit 1d4d1e8
Show file tree

Hide file tree

Showing 19 changed files with 220 additions and 109 deletions.
diff --git a/.github/workflows/pip-install.yml b/.github/workflows/pip-install.yml
@@ -5,44 +5,72 @@ on:
 
 jobs:
   build_wheels:
-    name: Build wheel
-    runs-on: ubuntu-latest
+    name: Building wheel for ${{ matrix.os }}:Python-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, ubuntu-22.04, macos-12, macos-13, macos-14]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        exclude:
+          - os: ubuntu-22.04
+            python-version: '3.6'
+          - os: macos-14
+            python-version: '3.6'
+          - os: macos-14
+            python-version: '3.7'
+      fail-fast: false
+
     steps:
       - uses: actions/checkout@v4
 
       - name: Set up Python
         id: setup_python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-
-      - uses: ilammy/msvc-dev-cmd@v1
+          python-version: ${{ matrix.python-version }}
 
-      - name: Install cibuildwheel
+      - name: Install packages
         run: |
-          python -m pip install cibuildwheel==2.12.1
+          python -m pip install -U pip
+          python -m pip install setuptools
+          python -m pip install cibuildwheel
 
-      - name: Build wheel
+      - name: Build wheel on Linux
+        if: runner.os == 'Linux'
         run: |
-          if [[ "$RUNNER_OS" == "Linux" || "$RUNNER_OS" == "macOS" ]]; then
-            python -m cibuildwheel --output-dir wheelhouse
-          else
-            echo "$RUNNER_OS not supported"
-            exit 1
-          fi           
+          python -m cibuildwheel --output-dir wheelhouse
         env:
           CIBW_BUILD: 'cp3?-*'
-          CIBW_SKIP: '*-manylinux_i686' 
+          CIBW_SKIP: '*-manylinux_i686'
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-        shell: bash
 
-      - uses: actions/upload-artifact@v3
+      - name: Build wheel on macOS
+        if: runner.os == 'macOS'
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+
+      - name: Upload wheel artifact
+        uses: actions/upload-artifact@v4
         with:
-          path: ./wheelhouse/*.whl
+          name: wheel-${{ matrix.os }}-${{ matrix.python-version }}
+          path: ./wheelhouse/
 
   build_sdist:
-    name: Build source distribution
-    runs-on: ubuntu-latest
+    name: Building source for ${{ matrix.os }}:Python-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, ubuntu-22.04, macos-12, macos-13, macos-14]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        exclude:
+          - os: ubuntu-22.04
+            python-version: '3.6'
+          - os: macos-14
+            python-version: '3.6'
+          - os: macos-14
+            python-version: '3.7'
+      fail-fast: false
+
     steps:
       - uses: actions/checkout@v4
         with:
@@ -52,27 +80,92 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: 3.9
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install packages
+        run: |
+          python -m pip install -U pip
+          python -m pip install setuptools
 
       - name: Build sdist
         run: python setup.py sdist
 
-      - uses: actions/upload-artifact@v4
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
         with:
-          path: dist/*.tar.gz
+          name: sdist-${{ matrix.os }}-${{ matrix.python-version }}
+          path: dist/
 
   upload_pypi:
     needs: [build_wheels, build_sdist]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+
     steps:
-      - uses: actions/download-artifact@v4
-        with:
-          name: artifact
+     - uses: actions/download-artifact@v4
+       with:
+          name: wheel-ubuntu-20.04-3.6.whl
+          path: wheelhouse
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: wheel-ubuntu-22.04-*
+          path: wheelhouse
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: wheel-macos-12-*
+          path: wheelhouse
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: wheel-macos-13-*
+          path: wheelhouse
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: wheel-macos-14-*
+          path: wheelhouse
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: sdist-ubuntu-20.04-*
+          path: dist
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: sdist-ubuntu-22.04-*
+          path: dist
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: sdist-macos-12-*
+          path: dist
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: sdist-macos-13-*
+          path: dist
+
+     - uses: actions/download-artifact@v4
+       with:
+          name: sdist-macos-14-*
           path: dist
 
+     - name: Install dependencies
+       run: |
+         python -m pip install --upgrade pip
+         python -m pip install twine
+
+     - name: Upload to PyPI
+       if: github.repository == 'VirtualPlanetaryLaboratory/vplanet'
+       run: python -m twine upload dist/* wheelhouse/*
+       env:
+         TWINE_USERNAME: __token__
+         TWINE_PASSWORD: ${{ secrets.pypi_password }}
+
       # Only push to PyPI if we're on the public repo!
-      - uses: pypa/gh-action-pypi-publish@release/v1
-        if: (!github.event.release.prerelease) && github.event_name == 'release' && github.event.action == 'published' && github.repository == 'VirtualPlanetaryLaboratory/vplanet'
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
+    #  - uses: pypa/gh-action-pypi-publish@release/v1
+    #    if: (!github.event.release.prerelease) && github.event_name == 'release' && github.event.action == 'published' && github.repository == 'VirtualPlanetaryLaboratory/vplanet'
+    #    with:
+    #       user: __token__
+    #       password: ${{ secrets.pypi_password }}
diff --git a/.github/workflows/sanitizer.yml b/.github/workflows/sanitizer.yml
@@ -7,8 +7,8 @@ on:
 
 jobs:
   sanitizer:
-    name: Run address-sanitizer on Ubuntu
-    runs-on: ubuntu-latest
+    name: Run address-sanitizer on macOS
+    runs-on: macos-13
     strategy:
       fail-fast: false
 

diff --git a/.github/workflows/tests-linux.yml b/.github/workflows/tests-linux.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-22.04]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
         exclude:
           - os: ubuntu-22.04
             python-version: '3.6'
@@ -46,32 +46,28 @@ jobs:
         shell: bash -l {0}
         run: |
           make opt
-          pytest --tb=short
+          pytest --tb=short --junitxml=junit/test-results.xml
 
-      - name: Check test ouptut created
+      - name: Check test output created
         id: check_test_file
         uses: andstor/file-existence-action@v3
         with:
-          files: "/home/runner/work/vplanet/vplanet/junit/test-results.xml"
+          files: "${{ github.workspace }}/junit/test-results.xml"
           fail: true
 
-      - name: Generate coverage
-        id: coverage
-        if: steps.test.outcome == 'success' && steps.check_test_file.outcome == 'success'
-        run: make coverage
-
-      - name: Get unique id
-        uses: Tiryoh/gha-jobid-action@v1
-        id: jobs
-
       - name: Publish unit test results
+        if: ${{ matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.9' }}
         uses: EnricoMi/publish-unit-test-result-action@v2
-        if: always()
         with:
           files: junit/test-*.xml
 
-      - name: CodeCov
-        if:  ${{ matrix.os }} == ubuntu-22.04 &&  ${{ matrix.python-version }} == '3.9'
+      - name: Generate coverage
+        id: coverage
+        if: ${{ matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.9' && steps.test.outcome == 'success' && steps.check_test_file.outcome == 'success' }}
+        run: make coverage
+
+      - name: Upload to CodeCov
+        if: ${{ matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.9' }}
         uses: codecov/codecov-action@v4
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

diff --git a/.github/workflows/tests-macos-intel.yml b/.github/workflows/tests-macos-intel.yml
@@ -10,8 +10,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-11, macos-12, macos-13]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
+        os: [macos-12, macos-13]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
       fail-fast: false
     steps:
       - uses: actions/checkout@v4
@@ -35,8 +35,11 @@ jobs:
         if: steps.setup_python.outcome == 'success'
         run: |
           make opt
-          pytest --tb=short
+          pytest --tb=short --junitxml=junit/test-results.xml
 
-      - name: Get unique id
-        uses: Tiryoh/gha-jobid-action@v1
-        id: jobs
+      - name: Check test ouptut created
+        id: check_test_file
+        uses: andstor/file-existence-action@v3
+        with:
+          files: "${{ github.workspace }}/junit/test-results.xml"
+          fail: true
diff --git a/.github/workflows/tests-macos-silicon.yml b/.github/workflows/tests-macos-silicon.yml
@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-14]
-        python-version: ['3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
       fail-fast: false
     steps:
       - uses: actions/checkout@v4
@@ -35,8 +35,12 @@ jobs:
         if: steps.setup_python.outcome == 'success'
         run: |
           make opt
-          pytest --tb=short
+          pytest --tb=short --junitxml=junit/test-results.xml
+
+      - name: Check test ouptut created
+        id: check_test_file
+        uses: andstor/file-existence-action@v3
+        with:
+          files: "${{ github.workspace }}/junit/test-results.xml"
+          fail: true
 
-      - name: Get unique id
-        uses: Tiryoh/gha-jobid-action@v1
-        id: jobs
diff --git a/.gitignore b/.gitignore
@@ -30,6 +30,7 @@ tests/Vspace_Log/Log_Test/
 *BP_CreateHDF5*
 *BP_Extract*
 *BP_Stats*
+junit/
 
 coverage.info
 .coverage

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,3 @@
+include VERSION
+include src/*.c
+include src/*.h
diff --git a/Makefile b/Makefile
@@ -30,7 +30,7 @@ legacy:
 	@echo "=========================================================================================================="
 
 debug:
-	-gcc -g -D DEBUG -o bin/vplanet src/*.c -lm -DGITVERSION=\"$(GITVERSION)\"
+	-gcc -g -D DEBUG -Wunused-but-set-variable -Wunused-variable -Wfloat-equal -o bin/vplanet src/*.c -lm -DGITVERSION=\"$(GITVERSION)\"
 
 debug_no_AE:
 	-gcc -g -o bin/vplanet src/*.c -lm -DGITVERSION=\"$(GITVERSION)\"
@@ -51,6 +51,9 @@ opt:
 cpp:
 	g++ -o bin/vplanet src/*.c -lm -O3 -fopenmp -fpermissive -w -DGITVERSION=\"$(GITVERSION)\"
 
+warnings:
+	clang -Weverything src/*.c -lm -O3 -DGITVERSION=\"$(GITVERSION)\"
+
 parallel:
 	gcc -o bin/vplanet src/*.c -lm -O3 -fopenmp -DGITVERSION=\"$(GITVERSION)\"
 
@@ -68,9 +71,12 @@ test:
 	-pytest --tb=short
 
 coverage:
-	-mkdir -p gcov && cd gcov && gcc -coverage -o ../bin/vplanet ../src/*.c -lm
-	-python -m pytest --tb=short tests --junitxml=junit/test-results.xml
-	-lcov --capture --directory gcov --output-file .coverage && genhtml .coverage --output-directory gcov/html
+	-rm -f ./gcov/*.gcda ./gcov/*.gcno ./.coverage
+	-mkdir -p ./gcov
+	-cd gcov && gcc -coverage -o ./../bin/vplanet ./../src/*.c -lm
+	-python -m pytest --tb=short tests --junitxml=./junit/test-results.xml
+	-lcov --capture --directory ./gcov --output-file ./.coverage
+	-genhtml ./.coverage --output-directory ./gcov/html
 
 docs:
 	-make -C docs html && echo 'Documentation available at `docs/.build/html/index.html`.'

diff --git a/README.md b/README.md
@@ -23,18 +23,18 @@
   </a>
   <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/pip-install.yml/badge.svg">
   <br>
-  <img src="https://img.shields.io/badge/Unit%20Tests-19,130-darkblue.svg">
+  <img src="https://img.shields.io/badge/Unit%20Tests-19,599-darkblue.svg">
   <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests-linux.yml/badge.svg">
-  <img src="https://img.shields.io/badge/Ubuntu%2020-Python%203.6--3.11-7d93c7.svg">
-  <img src="https://img.shields.io/badge/Ubuntu%2022-Python%203.7--3.11-7d93c7.svg">
+  <img src="https://img.shields.io/badge/Ubuntu%2020-Python%203.6--3.12-7d93c7.svg">
+  <img src="https://img.shields.io/badge/Ubuntu%2022-Python%203.7--3.12-7d93c7.svg">
   <a href="https://codecov.io/gh/VirtualPlanetaryLaboratory/vplanet">
     <img src="https://codecov.io/gh/VirtualPlanetaryLaboratory/vplanet/branch/main/graph/badge.svg?token=3LFJQO1M6H">
   </a>
   <br>
   <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests-macos-intel.yml/badge.svg">
-  <img src="https://img.shields.io/badge/MacOS%2011--13-Python%203.6--3.11-7d93c7.svg">
+  <img src="https://img.shields.io/badge/MacOS%2012--13-Python%203.6--3.12-7d93c7.svg">
   <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests-macos-silicon.yml/badge.svg">
-  <img src="https://img.shields.io/badge/MacOS%2014-Python%203.10--3.11-7d93c7.svg">  
+  <img src="https://img.shields.io/badge/MacOS%2014-Python%203.8--3.12-7d93c7.svg">  
   <br>
   <img src="https://img.shields.io/badge/Test%20Sims-70-darkblue.svg">
   <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/memcheck.yml/badge.svg">

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.5.6
+2.5.31