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fixing ci pipeline for python3.9 and python3.13 #435
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5db7314
adding libffi to windows ci pipeline
ye11owSub 2147ef1
bump pillow version
ye11owSub 2fe1c16
refactoring testLoadPWG
ye11owSub 1306de6
removing usage of cgi lib
ye11owSub df8de68
moving all pyton dependencies from github/workflow to pyproject.toml
ye11owSub 5b83fe9
adding strategy for python versions
ye11owSub 3ed37a1
fixing type annotation for python3.9
ye11owSub 742f7c0
fixes after review
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -7,28 +7,30 @@ jobs: | |
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| runs-on: ubuntu-22.04 | ||
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| strategy: | ||
| matrix: | ||
| python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] | ||
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| steps: | ||
| - uses: actions/[email protected] | ||
| - uses: actions/checkout@v4 | ||
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| - name: Set up Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: Install system dependencies | ||
| run: > | ||
| sudo apt-get update; | ||
| sudo apt-get --no-install-recommends install | ||
| catch2 | ||
| cmake | ||
| libfreetype6-dev | ||
| libglew-dev | ||
| libglm-dev | ||
| libmsgpack-dev | ||
| libnetcdf-dev | ||
| libpng-dev | ||
| libxml2-dev | ||
| python-is-python3 | ||
| python3-biopython | ||
| python3-dev | ||
| python3-setuptools | ||
| python3-numpy | ||
| python3-pip | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get --no-install-recommends install \ | ||
| catch2 \ | ||
| libfreetype6-dev \ | ||
| libglew-dev \ | ||
| libglm-dev \ | ||
| libmsgpack-dev \ | ||
| libnetcdf-dev \ | ||
| libpng-dev \ | ||
| libxml2-dev | ||
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| - name: Install collada2gltf | ||
| run: | | ||
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@@ -38,7 +40,7 @@ jobs: | |
| - name: Get additional sources | ||
| run: | | ||
| git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git | ||
| cp -R mmtf-cpp/include/mmtf* include/ | ||
| cp -R mmtf-cpp/include/* include/ | ||
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| - name: Build | ||
| run: | | ||
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@@ -51,87 +53,123 @@ jobs: | |
| run: | | ||
| pymol -ckqy testing/testing.py --run all | ||
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| build-Windows: | ||
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| runs-on: windows-latest | ||
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| strategy: | ||
| matrix: | ||
| python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] | ||
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| env: | ||
| CONDA_ROOT: ${{github.workspace}}\..\tmp\miniforge | ||
| MINIFORGE_EXEC: ${{github.workspace}}\..\tmp\miniforge.exe | ||
| CONDA_ENV_NAME: "testing_env" | ||
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| steps: | ||
| - uses: actions/[email protected] | ||
| - name: Download Miniforge | ||
| shell: cmd | ||
| run: |- | ||
| if not exist %CONDA_ROOT% mkdir %CONDA_ROOT% | ||
| curl -L -o %MINIFORGE_EXEC% https://github.com/conda-forge/miniforge/releases/download/24.11.0-0/Miniforge3-24.11.0-0-Windows-x86_64.exe | ||
| start /wait %MINIFORGE_EXEC% /S /D=%CONDA_ROOT% | ||
| - uses: actions/checkout@v4 | ||
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| - name: Set up Miniforge | ||
| shell: cmd | ||
| run: |- | ||
| CALL %CONDA_ROOT%\\Scripts\\activate.bat | ||
| conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 catch2=2.13.3 glm libnetcdf collada2gltf biopython msgpack-python pip python-build | ||
| - name: Install Miniforge | ||
| run: | | ||
| choco install miniforge3 | ||
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| - name: Conda info | ||
| shell: cmd | ||
| run: |- | ||
| CALL %CONDA_ROOT%\\Scripts\\activate.bat | ||
| conda info | ||
| - name: Add conda to PATH | ||
| run: | | ||
| echo "$env:CONDA" | Out-File -Append -FilePath $env:GITHUB_PATH | ||
| echo "$env:CONDA\Scripts" | Out-File -Append -FilePath $env:GITHUB_PATH | ||
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| - name: Set up Miniforge | ||
| run: | | ||
| conda init powershell | ||
| conda create --name $env:CONDA_ENV_NAME -c conda-forge -c schrodinger ` | ||
| python=${{ matrix.python-version }} ` | ||
| pip ` | ||
| catch2=2.13.3 ` | ||
| cxx-compiler ` | ||
| collada2gltf ` | ||
| freetype ` | ||
| glew ` | ||
| glm ` | ||
| libpng ` | ||
| libxml2 ` | ||
| libnetcdf ` | ||
| libffi | ||
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| - name: Get additional sources | ||
| shell: cmd | ||
| run: | | ||
| conda deactivate | ||
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| conda activate $env:CONDA_ENV_NAME | ||
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| git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git | ||
| cp -R mmtf-cpp/include/mmtf* %CONDA_ROOT%/Library/include/ | ||
| Copy-Item -Recurse -Path mmtf-cpp/include\* -Destination "$env:CONDA_PREFIX\Library\include" | ||
| git clone --depth 1 --single-branch --branch cpp_master https://github.com/msgpack/msgpack-c.git | ||
| cp -R msgpack-c/include/msgpack* %CONDA_ROOT%/Library/include/ | ||
| Copy-Item -Recurse -Path msgpack-c/include\* -Destination "$env:CONDA_PREFIX\Library\include" | ||
| dir $env:CONDA_PREFIX\Library\include | ||
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| - name: Build PyMOL | ||
| shell: cmd | ||
| run: | | ||
| CALL %CONDA_ROOT%\\Scripts\\activate.bat | ||
| conda activate $env:CONDA_ENV_NAME | ||
| pip install -v --config-settings testing=True .[dev] | ||
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| - name: Test | ||
| shell: cmd | ||
| run: | | ||
| CALL %CONDA_ROOT%\\Scripts\\activate.bat | ||
| pymol -ckqy testing\\testing.py --run all | ||
| conda activate $env:CONDA_ENV_NAME | ||
| pymol -ckqy testing\testing.py --run all | ||
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| build-MacOS: | ||
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| runs-on: macos-latest | ||
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| strategy: | ||
| matrix: | ||
| python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] | ||
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| env: | ||
| CONDA_ROOT: "/tmp/miniforge" | ||
| CONDA_ENV_NAME: "testing_env" | ||
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| steps: | ||
| - uses: actions/[email protected] | ||
| - name: Set up Miniforge and Build | ||
| run: |- | ||
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| - name: Download Miniforge | ||
| run: | | ||
| curl -L -o $CONDA_ROOT.sh https://github.com/conda-forge/miniforge/releases/download/24.11.0-0/Miniforge3-MacOSX-x86_64.sh | ||
| bash $CONDA_ROOT.sh -b -p $CONDA_ROOT | ||
| export PATH="$CONDA_ROOT/bin:$PATH" | ||
| conda config --set quiet yes | ||
| conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 catch2=2.13.3 glm libnetcdf collada2gltf biopython msgpack-python pip python-build | ||
| conda info | ||
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| - name: Add conda to PATH | ||
| run: | | ||
| echo "${CONDA_ROOT}/bin" >> "$GITHUB_PATH" | ||
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| - name: Set up Miniforge | ||
| run: | | ||
| conda create --name $CONDA_ENV_NAME -c conda-forge -c schrodinger \ | ||
| python=${{ matrix.python-version }} \ | ||
| pip \ | ||
| catch2=2.13.3 \ | ||
| collada2gltf \ | ||
| freetype \ | ||
| glew \ | ||
| glm \ | ||
| libpng \ | ||
| libxml2 \ | ||
| libnetcdf | ||
|
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| - name: Get additional sources | ||
| run: | | ||
| source activate $CONDA_ENV_NAME | ||
| git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git | ||
| cp -R mmtf-cpp/include/mmtf* ${CONDA_ROOT}/include/ | ||
| cp -R mmtf-cpp/include/* ${CONDA_PREFIX}/include/ | ||
| git clone --depth 1 --single-branch --branch cpp_master https://github.com/msgpack/msgpack-c.git | ||
| cp -R msgpack-c/include/msgpack* ${CONDA_ROOT}/include/ | ||
| cp -R msgpack-c/include/* ${CONDA_PREFIX}/include/ | ||
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| - name: Build PyMOL | ||
| run: |- | ||
| run: | | ||
| source activate $CONDA_ENV_NAME | ||
| export MACOSX_DEPLOYMENT_TARGET=12.0 | ||
| export PATH="$CONDA_ROOT/bin:$PATH" | ||
| pip install -v --config-settings testing=True '.[dev]' | ||
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| - name: Test | ||
| run: |- | ||
| export PATH="$CONDA_ROOT/bin:$PATH" | ||
| run: | | ||
| source activate $CONDA_ENV_NAME | ||
| pymol -ckqy testing/testing.py --run all | ||
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Probably correct, but what caused this to be needed now?
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I was sure that the windows image doesn't have a gcc compiler.
I removed this line, everything worked out correctly