From c59ca510be9cb598ae7d87e535246af60cba2845 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 25 Jun 2024 17:13:12 +0200
Subject: [PATCH] switch to gh-actions

---
 .github/workflows/ci-tests.yml | 110 +++++++++++++++++++++++++++++++++
 .travis.yml                    |  26 --------
 Makefile                       |   4 +-
 3 files changed, 112 insertions(+), 28 deletions(-)
 create mode 100644 .github/workflows/ci-tests.yml
 delete mode 100644 .travis.yml

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
new file mode 100644
index 0000000..544ce8b
--- /dev/null
+++ b/.github/workflows/ci-tests.yml
@@ -0,0 +1,110 @@
+name: CI Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+concurrency:
+  group: build-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  TOX_SKIP_MISSING_INTERPRETERS: False
+  # Rich (pip)
+  FORCE_COLOR: 1
+  # Tox
+  PY_COLORS: 1
+  # Mypy (see https://github.com/python/mypy/issues/7771)
+  TERM: xterm-color
+  MYPY_FORCE_COLOR: 1
+  MYPY_FORCE_TERMINAL_WIDTH: 200
+  # Pytest
+  PYTEST_ADDOPTS: --color=yes
+
+jobs:
+
+  tox:
+    name: Tox
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        py-ver-major: [3]
+        py-ver-minor: [8, 9, 10, 11, 12]
+        step: [lint, unit, bandit, mypy]
+
+    env:
+      py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
+      TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.py-semver }}
+          allow-prereleases: true
+          cache: pip
+
+      - name: Upgrade setuptools and install tox
+        run: |
+          pip install -U pip setuptools wheel
+          pip install tox tox-gh-actions
+
+      - name: MyPy cache
+        if: ${{ matrix.step == 'mypy' }}
+        uses: actions/cache@v4
+        with:
+          path: .mypy_cache/${{ env.py-semver }}
+          key: mypy-${{ env.py-semver }}
+
+      - name: Test with tox
+        run: tox
+
+      - name: Upload coverage to Codecov
+        if: ${{ matrix.step == 'unit' }}
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  tox-style:
+    name: Linters
+    runs-on: ubuntu-20.04
+
+    strategy:
+      matrix:
+        step: [lintreadme, shellcheck, pydocstyle]
+
+    env:
+      py-semver: "3.12"
+      TOXENV: ${{ format('py312-{0}', matrix.step) }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.py-semver }}
+          cache: pip
+
+      - name: Upgrade setuptools and install tox
+        run: |
+          pip install -U pip setuptools wheel
+          pip install "tox<4" "tox-gh-actions<3"
+
+      - if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
+        name: Create local branch for diff-quality for PRs
+        run: git branch ${{github.base_ref}} origin/${{github.base_ref}}
+
+      - name: Test with tox
+        run: tox
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 9340129..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-dist: bionic
-branches:
-  only:
-    - main
-language: python
-python:
-- '3.7'
-- '3.8'
-- '3.9'
-- '3.10'
-before_install:
-- pip install -U pip wheel
-- pip install .[toil]
-- pip install -r dev-requirements.txt
-script:
-- flake8 wes_service wes_client
-- pytest
-services:
-  - docker
-deploy:
-  provider: pypi
-  on:
-    tags: true
-  user: david4096
-  password:
-    secure: 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
diff --git a/Makefile b/Makefile
index f1b94c9..d4ab3db 100644
--- a/Makefile
+++ b/Makefile
@@ -23,7 +23,7 @@
 MODULE1=wes_client
 MODULE2=wes_service
 PACKAGE=wes-service
-EXTRAS=
+EXTRAS=[toil,arvados]
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
@@ -147,7 +147,7 @@ diff-cover.html: coverage.xml
 	diff-cover --compare-branch=main $^ --html-report $@
 
 ## test                   : run the wes-service test suite
-test: $(PYSOURCES)
+test: $(PYSOURCES) FORCE
 	python -m pytest -rsx ${PYTEST_EXTRA}
 
 ## testcov                : run the wes-service test suite and collect coverage