Merge pull request #44 from Chaste/vtk_py311

Build conda packages for Python 3.8 - 3.11

.github/workflows/conda-build-linux.yml

@@ -2,23 +2,31 @@ name: conda-build-linux
 
 on:
   workflow_dispatch:
+    inputs:
+      variant:
+        description: "Variant of the conda package to build"
+        required: true
+        type: string
+        default: "linux_64_python3.10_cpython"
 
 jobs:
-
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - name: checkout
-      uses: actions/checkout@v4
+      - name: checkout
+        uses: actions/checkout@v4
 
-    - name: build conda package
-      run: ./build-py310.sh
-      working-directory: infra/conda/chaste
-
-    - name: upload conda package artifacts
-      uses: actions/upload-artifact@v4
-      with:
-        name: pychaste-conda
-        path: infra/conda/chaste/build_artifacts/linux-64
+      - name: build conda package
+        run: |
+          docker run -e HOST_USER_ID="$(id -u)" -v $(pwd):/home/conda \
+            quay.io/condaforge/linux-anvil-cos7-x86_64 ./build-package.sh \
+              --variant=${{ github.event.inputs.variant }} \
+              --parallel=$(nproc)
+        working-directory: infra/conda/chaste/2024.1
+
+      - name: upload conda package artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: pychaste-conda
+          path: infra/conda/chaste/build_artifacts/linux-64

.github/workflows/test-conda.yml

@@ -9,6 +9,11 @@ jobs:
   test-conda:
     runs-on: ubuntu-latest
 
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
     steps:
       - name: install dependencies
         run: |
@@ -22,9 +27,9 @@ jobs:
           use-mamba: true
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          python-version: "3.10"
+          python-version: ${{ matrix.python-version }}
           activate-environment: pychaste_test
-          channels: pychaste,conda-forge,bioconda
+          channels: pychaste,conda-forge
 
       - name: install pychaste
         run: mamba install -n pychaste_test -y chaste

.gitignore

@@ -1,6 +1,7 @@
 # No shared libraries and compiled Python
 *.so
 *.pyc
+__pycache__/
 # No eclipse settings
 *.project
 *.cproject

README.md

@@ -1,14 +1,21 @@
 # PyChaste
 
-PyChaste is a Python wrapper for [Chaste](https://chaste.github.io/), a general purpose simulation package for computational biology.
+PyChaste is a Python wrapper for [Chaste](https://chaste.github.io/), a general
+purpose simulation package for computational biology.
+
+Currently a limited number of features are supported, mostly related to
+cell-based Chaste.
 
 ## Installation
-`mamba install -c pychaste -c conda-forge -c bioconda chaste`
+`mamba install -c pychaste -c conda-forge chaste`
 
-See the [website](https://chaste.github.io/pychaste/installation/) for a detailed guide on installing PyChaste.
+See the [website](https://chaste.github.io/pychaste/installation/) for a
+detailed guide on installing PyChaste.
 
 ## Tutorials
-See the [website](https://chaste.github.io/pychaste/tutorials/) for tutorials demonstrating how to use PyChaste.
+See the [website](https://chaste.github.io/pychaste/tutorials/) for tutorials
+demonstrating how to use PyChaste.
 
 ## Extending
 See the [wiki](../../wiki/) for guidance on extending PyChaste.
+

infra/conda/.gitignore

@@ -0,0 +1,10 @@
+*.pyc
+build_artifacts/
+.bash_history
+.bash_logout
+.bash_profile
+.bashrc
+.conda/
+.condarc
+.cache
+.python_history