Refactor github action

.github/workflows/check_conda.yml

@@ -0,0 +1,39 @@
+name: conda recipe
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on schedule but only for the default branch (which is master)
+  schedule:
+   - cron: '0 7 * * 1-5'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  # This workflow contains a single job called "check_recipe"
+  check_recipe:
+    name: test conda recipes on ${{ matrix.os }} with ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest','macos-latest']
+        python-version: ["3.7", "3.11"]
+    steps:
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge,bioconda,aghozlane,defaults
+      - name: Set up test environment
+        shell: bash -l {0}
+        run: |
+            conda install -y meteor
+      - name: check installation
+        shell: bash -l {0}
+        run: |
+            python --version
+            meteor --version
+      - name: all workflow run
+        shell: bash -l {0}
+        run: |
+            meteor test

.github/workflows/main.yml

@@ -0,0 +1,36 @@
+name: testing
+
+on: [push, pull_request]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.10, 3.11, 3.12]
+        include:
+          - python-version: 3.12
+            allow-failure: true
+        poetry-version: ["1.2.2", "1.7.1"]
+        os: [ubuntu-22.04, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          pip install numpy scipy cython
+          sudo apt install bowtie2
+      - name: Install Python
+        uses: actions/setup-python@v4
+        # see details (matrix, python-version, python-version-file, etc.)
+        # https://github.com/actions/setup-python
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+      - uses: actions/cache@v3
+        name: Define a cache for the virtual environment based on the dependencies lock file
+        with:
+          path: ./.venv
+          key: venv-${{ hashFiles('poetry.lock') }}
+      - name: Install the project dependencies
+        run: poetry install --only test -C meteor
+      - name: Run the automated tests (for example)
+        run: poetry run  -C meteor pytest --cov=meteor --cov-report xml

.github/workflows/publish_meteor.yml

@@ -0,0 +1,65 @@
+name: Publish meteor
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - 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
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_PASS }}
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: user/app:latest
+      - name: Update repo description
+        uses: aghozlane/meteor
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_PASS }}
+          repository: user/app
+
+  build_conda:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,aghozlane,defaults
+      - name: Login to Anaconda
+        run: anaconda login --hostname ${{ secrets.DOCKER_HOST }} --username ${{ secrets.DOCKER_USER }} --password ${{ secrets.DOCKER_PASS }}
+      - name: Build Conda package
+        run: conda build conda_recipe
+      - name: Logout from Anaconda
+        run: anaconda logout
+
+
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v4
+        # see details (matrix, python-version, python-version-file, etc.)
+        # https://github.com/actions/setup-python
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+      - name: Build and publish to PyPI
+        run: |
+          poetry build -C meteor
+          poetry publish -C meteor -u ${{ secrets.PYPI_USER }} -p  ${{ secrets.PYPI_PASS }}
+
+