feat: use fgsmk for hello_world.smk

.github/workflows/check.yml

@@ -0,0 +1,64 @@
+name: Style check
+
+on: [push]
+
+env:
+  POETRY_VERSION: 1.8.2
+
+jobs:
+  toolkit:
+    runs-on: ubuntu-24.04
+    strategy:
+        matrix:
+          PYTHON_VERSION: ["3.11", "3.12"]
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Set up Python {{ "${{ matrix.PYTHON_VERSION }}" }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: {{ "${{ matrix.PYTHON_VERSION }}" }}
+
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT
+
+    - name: Install poetry
+      run: |
+        python -m pip install --upgrade pipx
+        pipx install poetry=={{ "${{env.POETRY_VERSION}}" }}
+
+    - name: Set up cache
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: .venv
+        key: venv-{{ "${{ runner.os }}" }}-{{ "${{ steps.full-python-version.outputs.version }}" }}-{{ "${{ hashFiles('**/poetry.lock') }}" }}
+
+    - name: Ensure cache is healthy
+      if: steps.cache.outputs.cache-hit == 'true'
+      shell: bash
+      run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
+
+    - name: Install the library
+      run: poetry install -v
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.6-0'
+        environment-name: test
+        environment-file: environment.yml
+        cache-environment: true
+        post-cleanup: 'all'
+
+    - name: Bash style checking
+      shell: micromamba-shell {0}
+      run: |
+        bash shellcheck -x scripts/*.sh
+
+    - name: Snakemake style checking
+      shell: micromamba-shell {0}
+      run: |
+        snakefmt --line-length 100 workflows/*.smk

workflows/hello_world.smk

@@ -5,7 +5,7 @@
 from pathlib import Path
 from typing import List
 
-from scripts.snakemake_utils import on_error
+from fgsmk.lib.log import on_error
 
 
 ################################################################################