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fixing ci pipeline for python3.9 and python3.13 #435

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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 Feb 20, 2025
2147ef1
bump pillow version
ye11owSub Feb 20, 2025
2fe1c16
refactoring testLoadPWG
ye11owSub Feb 20, 2025
1306de6
removing usage of cgi lib
ye11owSub Feb 21, 2025
df8de68
moving all pyton dependencies from github/workflow to pyproject.toml
ye11owSub Feb 22, 2025
5b83fe9
adding strategy for python versions
ye11owSub Feb 22, 2025
3ed37a1
fixing type annotation for python3.9
ye11owSub Feb 23, 2025
742f7c0
fixes after review
ye11owSub Mar 20, 2025
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156 changes: 97 additions & 59 deletions .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,28 +7,30 @@ jobs:

runs-on: ubuntu-22.04

strategy:
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

steps:
- uses: actions/[email protected]
- uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- 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

- name: Install collada2gltf
run: |
Expand All @@ -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/

- name: Build
run: |
Expand All @@ -51,87 +53,123 @@ jobs:
run: |
pymol -ckqy testing/testing.py --run all


build-Windows:

runs-on: windows-latest

strategy:
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

env:
CONDA_ROOT: ${{github.workspace}}\..\tmp\miniforge
MINIFORGE_EXEC: ${{github.workspace}}\..\tmp\miniforge.exe
CONDA_ENV_NAME: "testing_env"

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

- 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

- 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

- 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 `
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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

collada2gltf `
freetype `
glew `
glm `
libpng `
libxml2 `
libnetcdf `
libffi
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Although you linked the error and solution in the description. I'm still a bit unsure where this is coming from. I'm fairly confident this spawned from now not using conda-forge's Python

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You're right, I deleted this library in the last commit


- name: Get additional sources
shell: cmd
run: |
conda deactivate
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Do you need this deactivate if you're just activating another environment the next line?

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removed

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(I forgot to remove it after testing)

conda activate $env:CONDA_ENV_NAME

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

- 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]

- 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


build-MacOS:

runs-on: macos-latest

strategy:
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

env:
CONDA_ROOT: "/tmp/miniforge"
CONDA_ENV_NAME: "testing_env"

steps:
- uses: actions/[email protected]
- name: Set up Miniforge and Build
run: |-

- 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

- name: Add conda to PATH
run: |
echo "${CONDA_ROOT}/bin" >> "$GITHUB_PATH"

- 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

- 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/

- 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]'

- 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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