Merge pull request #139 from ssandrews/resolve-pipeline

fix: update python configuration

.github/workflows/linux.yml

@@ -8,7 +8,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
+        # python-version: [ '3.7', '3.8', '3.9', '3.10' ]
 
     steps:
     - uses: actions/checkout@v2
@@ -47,7 +48,7 @@ jobs:
 
     # BioSimulators
     - name: Build BioSimulators Docker image
-      if: matrix.python-version == '3.9'
+      if: matrix.python-version >= '3.9'
       run: |
         cp build/smoldyn*.whl scripts/
         cd scripts
@@ -56,18 +57,19 @@ jobs:
           --tag ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:latest \
           .
     - name: Lint BioSimulators
-      if: matrix.python-version == '3.9'
+      if: matrix.python-version >= '3.9'
       run: |
+        python -m pip install --upgrade pip
         python -m pip install flake8
         flake8 source/python/smoldyn/biosimulators/ --ignore E501,W503
     - name: Install BioSimulators
-      if: matrix.python-version == '3.9'
+      if: matrix.python-version >= '3.9'
       run: |
         cd build
         WHEEL_PATH=$(ls smoldyn*.whl)
         python -m pip install --force-reinstall "${WHEEL_PATH}[biosimulators,biosimulators-tests]"
     - name: Test BioSimulators
-      if: matrix.python-version == '3.9'
+      if: matrix.python-version >= '3.9'
       run: |
         python -m pip install pytest flaky
         xvfb-run --auto-servernum python -m pytest tests/test_biosimulators.py --verbose

.github/workflows/osx.yml

@@ -15,7 +15,8 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
+        # python-version: [ '3.7', '3.8', '3.9', '3.10' ]
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/windows.yml

@@ -15,7 +15,8 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
+        # python-version: [ '3.7', '3.8', '3.9', '3.10' ]
     steps:
     - uses: actions/checkout@v2
     - name: "Setup Python ${{ matrix.python-version }}"

CMakeLists.txt

@@ -521,7 +521,8 @@ endif ()
 
 if (OPTION_PYTHON)
     # Find python before using pybind11. There is a possibility of version mismatch later.
-    find_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)
+    # find_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)
+    find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
     set(PYBIND11_SOURCE_DIR ${CMAKE_SOURCE_DIR}/source/pybind11)
     add_subdirectory(${PYBIND11_SOURCE_DIR})
     add_subdirectory(${CMAKE_SOURCE_DIR}/source/python)

scripts/Dockerfile-BioSimulators

@@ -27,10 +27,12 @@ LABEL \
     extra.identifiers.biotools="smoldyn" \
     maintainer="Steven Andrews <[email protected]>"
 
-# Set up headless environment
 RUN apt-get -y update \
     && apt-get install --no-install-recommends -y \
         xvfb \
+        libxrender1 \
+        libgl1-mesa-glx \
+        libfreetype6 \
     && rm -rf /var/lib/apt/lists/* \
     && mkdir /tmp/.X11-unix \
     && chmod 1777 /tmp/.X11-unix

scripts/build_wheels_linux.sh

@@ -50,7 +50,8 @@ for PYDIR in $PYDIR311 $PYDIR310 $PYDIR39 $PYDIR38 $PYDIR37; do
     )
 done
 
-PYTHON=$PYDIR38/bin/python
+# PYTHON=$PYDIR38/bin/python
+PYTHON=$PYDIR39/bin/python
 $PYTHON -m pip install twine
 
 ls -lh $WHEELHOUSE/*.whl

source/python/CMakeLists.txt

@@ -1,5 +1,7 @@
 # python binding.
 
+# find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module Development.Embed VERSION 3.8.15...3.12)
+
 # recompile libsmoldyn for PYTHON.
 add_library(_pysmoldyn STATIC ${SRC_FILES}
     $<TARGET_OBJECTS:Steve>

source/python/setup.py.in

@@ -63,7 +63,7 @@ setuptools.setup(
             "biosimulators-utils[logging]>=0.1.124",
             "numpy",
             "pandas",
-            "biosimulators-simularium>=0.5.27"
+            "biosimulators-simularium>=0.5.29"
         ],
         "biosimulators-dev": [
             "flake8",

source/python/smoldyn/biosimulators/tests.py

@@ -6,7 +6,8 @@
 
 def test_simularium():
     archive_path = '/Users/alex/Desktop/uchc_work/repos/Smoldyn/examples/S99_more/Min/Min1.omex'
-    output_dir = '/Users/alex/Desktop/uchc_work'
+    # output_dir = '/Users/alex/Desktop/uchc_work'
+    output_dir = temp_dir()
 
     exec_archive(archive_path, output_dir)
     files = [f for f in os.listdir(output_dir)]
@@ -18,8 +19,5 @@ def test_simularium():
                 print(f'THE SIMULARIUM:\n{data}')
 
 
-
-
-
 if __name__ == '__main__':
     test_simularium()