Refactor for 0.2.0

.github/workflows/build.yml

@@ -1,90 +1,133 @@
-name: Build CarnaPy and Docker image
+name: Build and Test
 
 on:
-  push:
-    branches:
-      - 'master'
-      - 'dev**'
-    tags:
-      - '**'
+  workflow_call:
+    inputs:
+      python-version:
+        required: true
+        type: string
 
 jobs:
-  build_carnapy:
-    name: Build CarnaPy
+  build:
+    name: Build
     runs-on: ubuntu-latest
     steps:
-      -
-        name: Git checkout
-        uses: actions/checkout@v2
-      -
-        name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Git checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: 'latest'
-          python-version: '3.10'
-          channels: conda-forge, defaults
-          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+          miniconda-version: latest
           auto-update-conda: true
-          auto-activate-base: true
-      -
-        name: Set environment variables
-        run: echo "CONDA_PREFIX=$CONDA" >> $GITHUB_ENV
-      -
-        name: Build dist
-        run: sh linux_build.sh
-      -
-        name: Collect artifact data
+
+      - name: Patch required Python version
+        run: |
+          sed -i "s|python .\+|python ==${{ inputs.python-version }}|g" environment.yml
+          cat environment.yml
+
+      - name: Create and validate conda environment
+        shell: bash
         run: |
-          mkdir /tmp/dist
-          cp /usr/local/lib/libCarna-*.so /tmp/dist
-          rm /tmp/dist/libCarna-*d.so
-          cp $(find /home/runner/work -name '*.whl') /tmp/dist/
-      -
-        name: Build and upload artifact
-        uses: actions/upload-artifact@v3
+          conda env create -f environment.yml --prefix ./.env
+          eval "$(conda shell.bash hook)"
+          conda activate ./.env
+          python -V
+          python -c "import sys; v = sys.version_info; assert f'{v.major}.{v.minor}' == '${{ inputs.python-version }}'"
+
+      - name: Extract libcarna version
+        id: meta
+        shell: bash
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate ./.env
+          export libcarna_version=$(conda list --json |jq -rj '[ .[] | select( .name == "libcarna" ) ][0].version')
+          echo "libcarna_version=$libcarna_version" >> "$GITHUB_OUTPUT"
+
+      - name: Build dist
+        shell: bash
+        run: ./linux_build.bash
+
+      - name: Upload wheel
+        uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: dist-${{ inputs.python-version }}
           path: |
-             /tmp/dist
+             dist
+
+    outputs:
+      libcarna_version: ${{ steps.meta.outputs.libcarna_version }}
 
-  build_docker:
-    name: Build Docker image
-    needs: build_carnapy
+  test:
+    needs: build
+    name: Test
     runs-on: ubuntu-latest
     steps:
-      -
-        name: Git checkout
-        uses: actions/checkout@v2
-      -
-        name: Download artifact
-        uses: actions/download-artifact@v3
+      - name: Git checkout
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get install -y -qq libegl1
+
+      - name: Download artifact
+        uses: actions/download-artifact@v4
         with:
-          name: dist
-      -
-        name: Inspect working directory
-        run: tree .
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      -
-        name: Login to Docker Hub
-        uses: docker/login-action@v3
+          name: dist-${{ inputs.python-version }}
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Setup repository name
-        id: setup_repository_name
+          miniconda-version: latest
+          auto-update-conda: true
+
+      - name: Create and validate conda environment
+        shell: bash
+        run: |
+          conda create --prefix ./.env -c conda-forge -c bioconda \
+            python==${{ inputs.python-version }} \
+            libcarna==${{ needs.build.outputs.libcarna_version }} \
+            pip
+          eval "$(conda shell.bash hook)"
+          conda activate ./.env
+          python -V
+          python -c "import sys; v = sys.version_info; assert f'{v.major}.{v.minor}' == '${{ inputs.python-version }}'"
+
+      - name: Install wheel
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate ./.env
+          pip install libcarna_python-*.whl
+
+      - name: Test installation
         run: |
-          echo "docker_repository=${GITHUB_REPOSITORY,,}" >> $GITHUB_OUTPUT
-      -
-        name: Build and push
-        uses: docker/build-push-action@v5
+          eval "$(conda shell.bash hook)"
+          conda activate ./.env
+          python -c "import libcarna; assert libcarna.libcarna_version == '${{ needs.build.outputs.libcarna_version }}'"
+
+      - name: Install dependencies for tests and examples
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate ./.env
+          pip install -r test/requirements.txt
+          pip install -r docs/requirements.txt
+
+      - name: Run tests
+        run: |
+          eval "$(conda shell.bash hook)"
+          conda activate ./.env
+          cd test
+          mkdir test
+          mv results test/results
+          python -m unittest -vv
+        env:
+          LIBCARNA_PYTHON_LOGGING: true
+
+      - name: Upload failed test output
+        uses: actions/upload-artifact@v4
+        if: failure()
         with:
-          file: .github/Dockerfile
-          context: .
-          push: true
-          tags: ${{ steps.setup_repository_name.outputs.docker_repository }}:${{ github.ref_name }}
+          name: test-output-${{ inputs.python-version }}
+          path: |
+             test/test/results/actual

.github/workflows/build_all.yml

@@ -0,0 +1,28 @@
+name: Build and Test
+
+on:
+  workflow_dispatch:
+
+  push:
+    branches: [ 'master', 'develop' ]
+    paths-ignore:
+      - 'docs/**'
+      - '.git*'
+      - 'LICENSE'
+      - 'LICENSE-*'
+      - 'README.md'
+
+  pull_request:
+    branches-ignore: [ 'master' ]
+
+jobs:
+  build_and_test:
+    name: Build and Test ${{ matrix.python-version }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+    uses: ./.github/workflows/build.yml
+    secrets: inherit
+    with:
+      python-version: ${{ matrix.python-version }}

.gitignore

@@ -1,6 +1,11 @@
+/.env
+/condaenv.*
 /build
+/docs/build
 /dist
-/CarnaPy.egg-info
-/misc/conda-recipe/carnapy
+/LibCarna_Python.egg-info
+/.libcarna-dev
 .ipynb_checkpoints
 *.swp
+*.pyc
+*.DS_Store

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  fail_on_warning: true
+  configuration: docs/conf.py
+
+# Install dependencies
+conda:
+  environment: environment.yml
+
+# Install our python package and other dependencies
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .