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.github/workflows/test.yml

@@ -1,75 +1,65 @@
 # This pipeline checks whether the package
 # installs properly, passes unit tests and whether
 # the code formatting is right.
-name: CI/CD
+name: CI/CD (Poetry + Conda)
 
 on:
   push:
-    branches: [ main ]
+    branches: [ main ]  # Or your main branch name
   pull_request:
     branches: [ main ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: true
-      matrix:
-        python-version: ["3.10"]
-        poetry-version: ["1.8.3"]
 
     steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run black formatting check
+        uses: psf/black@stable
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
+          channels: conda-forge, bioconda
           environment-file: environment.yml
-          activate-environment: myenv
+          activate-environment: sr2silo
 
       - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-          version: ${{ matrix.poetry-version }}
-
-      - name: Cache dependencies
-        id: cache-deps
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: pydeps-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Activate Conda environment
-        shell: bash -l {0}
         run: |
           source $(conda info --base)/etc/profile.d/conda.sh
-          conda activate myenv
-
-      - name: Set Python version for Poetry
-        run: poetry env use $(which python)
-
-      - name: Install the dependencies
-        run: poetry install --no-interaction --no-root --with dev
-        if: steps.cache-deps.outputs.cache-hit != 'true'
+          conda activate sr2silo
+          conda install -c conda-forge poetry
 
       - name: Install the module
-        run: poetry install --with dev --no-interaction
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate sr2silo
+          poetry install --with dev --no-interaction
 
       - name: Run unit tests
-        run: poetry run pytest
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate sr2silo
+          poetry run pytest
 
       - name: Run Ruff
-        run: poetry run ruff check .
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate sr2silo
+          poetry run ruff check .
 
       - name: Run interrogate
-        run: poetry run interrogate src
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate sr2silo
+          poetry run interrogate src
 
-      - name: Run Pyright (type checking)
-        run: poetry run pyright
+      - name: Run Pyright
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate sr2silo
+          poetry run pyright

environment.yml

@@ -1,4 +1,4 @@
-name: myenv
+name: sr2silo
 channels:
   - defaults
   - conda-forge