Add type checking and drop support for older python

.github/workflows/ci.yml

@@ -0,0 +1,120 @@
+name: CI
+
+on:
+  push:
+    branches: [master, main]
+  pull_request:
+    branches: [master, main]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff mypy
+
+      - name: Run Ruff linter
+        run: ruff check .
+
+      - name: Run Ruff formatter check
+        run: ruff format --check .
+
+      - name: Run mypy
+        run: mypy ribotricer --ignore-missing-imports
+        continue-on-error: true  # Remove this once type hints are added
+
+  test:
+    name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        include:
+          - os: macos-latest
+            python-version: "3.12"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y samtools
+
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install samtools
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run unit tests
+        run: |
+          pytest tests/ -v --cov=ribotricer --cov-report=xml
+        continue-on-error: true  # Remove once unit tests are added
+
+      - name: Run integration tests
+        run: |
+          bash ./run_test.sh
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        if: matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+
+  build:
+    name: Build package
+    runs-on: ubuntu-latest
+    needs: [lint, test]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Check package
+        run: twine check dist/*
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/

.github/workflows/publish.yml

@@ -0,0 +1,85 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      test_pypi:
+        description: 'Publish to Test PyPI instead'
+        required: false
+        default: 'false'
+        type: boolean
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Check package
+        run: twine check dist/*
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-test-pypi:
+    name: Publish to Test PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && inputs.test_pypi == 'true'
+    environment:
+      name: test-pypi
+      url: https://test.pypi.org/p/ribotricer
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to Test PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.test_pypi == 'false')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ribotricer
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -74,10 +74,33 @@ snakemake/*.stats
 *.sqlite.gz
 *.sra
 
-#pytest
+# pytest
 .pytest_cache/
 utils/*
 snakemake/configs/test*
 tests/data/.hg38*
 tests/data/hg38.fa.fai
 record.txt
+
+# Type checking
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Ruff
+.ruff_cache/
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Pre-commit
+.pre-commit-cache/

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.4
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.9.0
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - types-tqdm
+        args: [--ignore-missing-imports]
+        exclude: ^(tests/|docs/)
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
+  autofix_prs: true
+  autoupdate_branch: ''
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: weekly
+  skip: []
+  submodules: false

HISTORY.md

@@ -1,3 +1,11 @@
+# v1.5.0 (2025-02-14)
+
+- Modernized packaging with `pyproject.toml` (PEP 517/518 compliant)
+- Dropped support for Python 3.7 and 3.8 (end of life)
+- Added support for Python 3.13
+- Added type checking
+- Default to sans-serif fonts for plotting 
+
 # v1.4.0 (2024-04-14)
 
 - Added `meta_min_reads` parameter to control minimum coverage for metagene plots ([#155](https://github.com/smithlabcode/ribotricer/pull/155))