GitHub Actions (GHA) CI setup (#793)

Configure a CI workflow based on tox.

Install the R package DNAcopy differently on Linux and Mac OS:
- Linux: apt for compiled dependencies and DNAcopy
- macOS: brew for dependencies, then callR.org for DNAcopy

Some matrix options are left commented out:
- Python 3.11: upstream issue cython/cython#4461 prevents pysam and pomegranate from compiling
- Latest Python `-min`: known runtime failure due to numpy compiled-for-xyz binary incompatility
- Typing: mypy runs successfully and reports known errors; CNVkit codebase needs an overhaul

Python 3.11 and Typing configs are still available in tox.ini for local testing.

.github/workflows/tests-tox.yaml

@@ -0,0 +1,56 @@
+name: Tests
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
+      - '*.rst'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
+      - '*.rst'
+jobs:
+  tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+#         - {name: '3.11', python: '3.11', os: ubuntu-latest, tox: py311}
+#         - {name: '3.11-MacOS', python: '3.11', os: macos-latest, tox: py311}
+#         - {name: '3.11-min', python: '3.11', os: ubuntu-latest, tox: "py311-min"}
+          - {name: '3.10', python: '3.10', os: ubuntu-latest, tox: py310}
+          - {name: '3.10-MacOS', python: '3.10', os: macos-latest, tox: py310}
+          - {name: '3.9', python: '3.9', os: ubuntu-latest, tox: py39}
+          - {name: '3.8', python: '3.8', os: ubuntu-latest, tox: py38}
+          - {name: '3.7', python: '3.7', os: ubuntu-latest, tox: py37}
+          - {name: '3.7-min', python: '3.7', os: ubuntu-latest, tox: "py37-min"}
+#         - {name: Typing, python: '3.10', os: ubuntu-latest, tox: typing}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          cache: 'pip'
+          cache-dependency-path: 'requirements/*.txt'
+      - name: Update pip
+        run: |
+          pip install -U setuptools wheel
+          python -m pip install -U pip
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt update
+          sudo apt-get install -y liblzma-dev python3-dev python3-numpy python3-matplotlib r-bioc-dnacopy zlib1g-dev
+      - name: Install Mac OS dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install r
+          Rscript --no-environ -e "source('http://callr.org/install#DNAcopy')"
+      - run: pip install tox
+      - run: tox -e ${{ matrix.tox }}
+

pyproject.toml

@@ -75,7 +75,7 @@ source = ["cnvlib", "skgenome", "tests"]
 source = ["cnvlib", "skgenome"]
 
 [tool.mypy]
-python_version = "3.7"
+python_version = "3.10"
 files = ["src/flask"]
 show_error_codes = true
 pretty = true

tox.ini

@@ -1,7 +1,7 @@
 [tox]
 envlist =
-    py3{10,9,8,7}
-    py310-min
+    py3{11,10,9,8,7}
+    py311-min
     py37-min
     typing
 #docs