Refactor / update to best practices

.devcontainer/Dockerfile

@@ -10,4 +10,4 @@ RUN curl -L -o /usr/local/bin/pixi -fsSL --compressed "https://github.com/prefix
 USER vscode
 WORKDIR /home/vscode
 
-RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc
+RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc

.devcontainer/devcontainer.json

@@ -1,24 +1,17 @@
 {
-    "name": "MultiQC_SAV Dev Container",
-    "runArgs": ["--platform=linux/amd64" ],
-    "build": {
-        "dockerfile": "Dockerfile",
-        "context": ".."
-    },
-    "customizations": {
-        "vscode": {
-            "settings": {},
-            "extensions": [
-                "ms-python.python",
-                "charliermarsh.ruff",
-                "GitHub.copilot"
-            ]
-        }
-    },
-    "features": {
-    },
-    "mounts": [
-        "source=${localWorkspaceFolderBasename}-pixi,target=${containerWorkspaceFolder}/.pixi,type=volume"
-    ],
-    "postCreateCommand": "sudo chown vscode .pixi && pixi install"
-}
+  "name": "MultiQC_SAV Dev Container",
+  "runArgs": ["--platform=linux/amd64"],
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": ".."
+  },
+  "customizations": {
+    "vscode": {
+      "settings": {},
+      "extensions": ["ms-python.python", "charliermarsh.ruff", "GitHub.copilot"]
+    }
+  },
+  "features": {},
+  "mounts": ["source=${localWorkspaceFolderBasename}-pixi,target=${containerWorkspaceFolder}/.pixi,type=volume"],
+  "postCreateCommand": "sudo chown vscode .pixi && pixi install"
+}

.github/workflows/lint.yaml

@@ -0,0 +1,24 @@
+name: "Lint"
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+jobs:
+  pre-commit:
+    name: Pre-commit
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Run pre-commit
+        uses: pre-commit/action@v3.0.1

.github/workflows/linux.yaml

@@ -1,52 +1,84 @@
-name: "Build - Linux"
-on: [push, pull_request]
+name: Generate test reports
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
 
 jobs:
   run_multiqc:
     name: Linux - Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.11, 3.12, 3.13]
+        python-version: ["3.9", "3.14"]
     timeout-minutes: 10
 
     steps:
-      # Check out MultiQC code
-      - uses: actions/checkout@v2
+      - name: Checkout code
+        uses: actions/checkout@v4
 
-      # Set up Python
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      # Update pip and install beautifulsoup4 for CI tests (CSP checking)
-      - name: Install dependencies for CI tests
+      - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools beautifulsoup4 multiqc
+          python -m pip install --upgrade pip setuptools wheel
+          pip install multiqc
 
-      # Install MultiQC
       - name: Install MultiQC_SAV
         run: pip install .
 
-      # Run all of the tests!
-      - name: MiSeq
-        run: multiqc -m SAV test_data/MiSeq
+      - name: Make test output dir
+        run: mkdir test_output
 
-      - name: MiSeqI100
-        run: multiqc --strict -v --no-version-check -m SAV test_data/MiSeqI100
+      - name: Test MiSeq
+        run: |
+          multiqc --strict test_data/MiSeq -o test_output/MiSeq
+          test -f test_output/MiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
 
-      - name: HiSeq3000
-        run: multiqc --strict -v --no-version-check -m SAV test_data/HiSeq3000
+      - name: Test MiSeqI100
+        run: |
+          multiqc --strict test_data/MiSeqI100 -o test_output/MiSeqI100
+          test -f test_output/MiSeqI100/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
 
-      - name: NextSeq500
-        run: multiqc --strict -v --no-version-check -m SAV test_data/NextSeq500
+      - name: Test HiSeq3000
+        run: |
+          multiqc --strict test_data/HiSeq3000 -o test_output/HiSeq3000
+          test -f test_output/HiSeq3000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
 
-      - name: NextSeq2000
-        run: multiqc --strict -v --no-version-check -m SAV test_data/NextSeq2000
+      - name: Test NextSeq500
+        run: |
+          multiqc --strict test_data/NextSeq500 -o test_output/NextSeq500
+          test -f test_output/NextSeq500/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
 
-      - name: NovaSeq6000
-        run: multiqc --strict -v --no-version-check -m SAV test_data/NovaSeq6000
+      - name: Test NextSeq2000
+        run: |
+          multiqc --strict test_data/NextSeq2000 -o test_output/NextSeq2000
+          test -f test_output/NextSeq2000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
 
-      - name: NovaSeqX
-        run: multiqc --strict -v --no-version-check -m SAV test_data/NovaSeqX
+      - name: Test NovaSeq6000
+        run: |
+          multiqc --strict test_data/NovaSeq6000 -o test_output/NovaSeq6000
+          test -f test_output/NovaSeq6000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
+
+      - name: Test NovaSeqX
+        run: |
+          multiqc --strict test_data/NovaSeqX -o test_output/NovaSeqX
+          test -f test_output/NovaSeqX/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
+
+      - name: Check that ignoring samples works
+        run: |
+          multiqc --strict test_data/ -o test_output/ignore_samples --ignore-samples "*"
+          test ! -f test_output/ignore_samples/multiqc_report.html || (echo "ERROR: Report should not be generated" && exit 1)
+
+      - name: Upload test output
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: test-output-py${{ matrix.python-version }}
+          path: test_output/
+          retention-days: 7

.github/workflows/publish.yaml

@@ -0,0 +1,31 @@
+name: "Publish to PyPI"
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -0,0 +1,55 @@
+minimum_pre_commit_version: "2.9.2"
+
+repos:
+  # Meta hooks for verification
+  - repo: meta
+    hooks:
+      - id: identity
+      - id: check-hooks-apply
+
+  # Standard pre-commit hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v5.0.0"
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=1000"]
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: check-toml
+      - id: debug-statements
+      - id: end-of-file-fixer
+        exclude: ^(test_data|docs/example)/
+      - id: trailing-whitespace
+        exclude: ^(test_data|docs/example)/
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+        exclude: ^(test_data|docs/example)/
+
+  # Line ending normalization
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: "v1.5.5"
+    hooks:
+      - id: remove-crlf
+        exclude: ^(test_data|docs/example)/
+
+  # Prettier for markdown, yaml, json formatting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        types_or: [markdown, yaml, json]
+        additional_dependencies:
+          - "prettier@3.1.0"
+
+  # Ruff formatting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.8.3"
+    hooks:
+      - id: ruff-format
+
+  # Ruff linting with auto-fix
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.8.3"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]

.prettierignore

@@ -0,0 +1,30 @@
+# Build artifacts
+dist/
+build/
+*.egg-info/
+
+# Python cache
+__pycache__/
+*.pyc
+
+# Test data
+test_data/
+
+# Virtual environments
+venv/
+.venv/
+env/
+
+# Coverage
+htmlcov/
+.coverage
+
+# IDE
+.idea/
+.vscode/
+
+# Example reports
+docs/example/
+
+# Lock files
+*.lock

.prettierrc.js

@@ -0,0 +1,10 @@
+module.exports = {
+  printWidth: 120,
+  tabWidth: 2,
+  useTabs: false,
+  semi: true,
+  singleQuote: false,
+  trailingComma: "all",
+  bracketSpacing: true,
+  proseWrap: "preserve",
+};

.vscode/settings.json

@@ -1,4 +1,4 @@
 {
     "python-envs.defaultEnvManager": "ms-python.python:system",
     "python-envs.pythonProjects": []
-}
+}