Modernize to pip-installable package (v1.5.0)

.github/workflows/ci.yml

@@ -0,0 +1,83 @@
+name: CI
+
+on:
+  push:
+    branches: [master, main]
+  pull_request:
+    branches: [master, main]
+
+jobs:
+  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: Lint with ruff
+        run: ruff check src/
+
+      - name: Type check with mypy
+        run: mypy src/optitype --ignore-missing-imports
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "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
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y glpk-utils
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run tests
+        run: pytest tests/ -v
+
+  build:
+    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 tools
+        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 artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/

.github/workflows/publish.yml

@@ -0,0 +1,70 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    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 tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-testpypi:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/optitype
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    needs: publish-testpypi
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/optitype
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -1,4 +1,57 @@
-# Created by .gitignore support plugin (hsz.mobi)
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
 
-*.pyc
-.gitignore
+# Virtual environments
+venv/
+ENV/
+env/
+.venv/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+.nox/
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Project specific
+config.ini
+test/**/baseline/
+test/**/new/
+test/expected_*.tsv
+*.bam
+*.sam
+
+# Claude Code
+CLAUDE.md
+.claude/