Github: Add automated PyPI publish and Bioconda update workflow

.github/workflows/PUBLISH.yml

@@ -0,0 +1,97 @@
+name: Publish to PyPi and Bioconda
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'Version string (e.g., 1.2.3)'
+        required: true
+      dry_run:
+        description: 'Dry Run (Skip PyPI publish and Bioconda PR)'
+        type: boolean
+        default: true
+
+jobs:
+  pypi-publish:
+    name: Build & Publish to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/MMASeq
+    permissions:
+      contents: read
+      id-token: write # Required for PyPI Trusted Publishing (OIDC)
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install build tool
+        run: python -m pip install build --user
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Publish package to PyPI
+        if: ${{ inputs.dry_run != true }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - name: Report Build Success
+        if: ${{ inputs.dry_run == true }}
+        run: |
+          echo "DRY RUN MODE: Package built successfully!"
+          ls -la dist/
+
+  bioconda-update:
+    name: Update Bioconda Recipe & Open PR
+    needs: pypi-publish
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Wait 5 minutes for PyPI indexing
+        run: |
+          echo "Waiting 5 minutes to ensure PyPI indexing and sha256 generation..."
+          sleep 300
+
+      - name: Checkout bioconda-recipes fork
+        uses: actions/checkout@v4
+        with:
+          repository: ssi-dk/bioconda-recipes
+          ref: master
+          path: bioconda-recipes
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          activate-environment: bioconda-utils
+          environment-file: environment.yml
+          # If you don't want environment.yml, see next step for a pip/conda install approach
+
+      - name: Install bioconda-utils
+        shell: bash
+        run: |
+          conda create -y -n bioconda-utils -c conda-forge -c bioconda --strict-channel-priority bioconda-utils
+          conda activate bioconda-utils
+          bioconda-utils --help
+
+      - name: Run autobump for MMASeq recipe
+        shell: bash
+        env:
+          GITHUB_TOKEN: ${{ secrets.BIOCONDARECIPES }}
+        run: |
+          conda activate bioconda-utils
+          cd bioconda-recipes
+
+          # config.yml lives at the bioconda-recipes root
+          # recipes/ is the directory containing recipes
+          bioconda-utils autobump recipes/ config.yml \
+            --packages mmaseq \
+            --create-pr