Initial CI

Author: jeromekelleher

.github/workflows/ci.yml

@@ -0,0 +1,44 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  pre-commit:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - uses: pre-commit/[email protected]
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+
+      - name: Run tests
+        run: |
+          pytest --cov=sc2ts
+      # - name: Upload coverage to Coveralls
+      #   uses: coverallsapp/[email protected]
+      #   with:
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     # The first coveralls upload will succeed and others seem to fail now.
+      #     # This is a quick workaround for doing a proper "parallel" setup:
+      #     # https://github.com/coverallsapp/github-action
+      #     fail-on-error: false

pyproject.toml

@@ -6,5 +6,24 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "sc2ts"
+description = "Infer ARGs in tskit format for SARS-Cov2"
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+  {name = "FIXME", email = "FIXME"},
+]
+dependencies = [
+  "tsinfer",
+  "pyfaidx",
+]
+
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "pytest-coverage",
+]
+
 [tool.setuptools_scm]
 write_to = "sc2ts/_version.py"