switch to testing via GitHub Actions rather than Travis (#172)

* replace Travis testing with GitHub Actions

* fix bug it GitHub Actions `test.yaml`

* fix bug it GitHub Actions `test.yaml`

* fix bug it GitHub Actions `test.yaml`

* no longer test `test-gh-actions` branch now we know it works

.github/workflows/test.yaml

@@ -0,0 +1,35 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Run tests
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+
+      - name: install python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: install package and dependencies
+        run: pip install -e . && pip install -r test_requirements.txt
+
+      - name: lint code with ruff
+        run: ruff check .
+
+      - name: check code format with black
+        run: black --check .
+
+      - name: test code with `pytest`
+        run: pytest

.gitignore

@@ -3,6 +3,7 @@
 *.out
 _*
 
+!.github
 !.gitignore
 !.travis.yml
 !.nojekyll

CHANGELOG.rst

@@ -9,6 +9,7 @@ The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 6.3
 ---
 - Ensure ``PolyclonalCollection.sites`` attribute is always defined.
+- Move testing from Travis to GitHub actions.
 
 6.2
 ---

CONTRIBUTING.rst

@@ -40,7 +40,7 @@ Formatting
 ++++++++++
 The code is formatted using `Black <https://black.readthedocs.io/en/stable/index.html>`_, which you can install using `pip install "black[jupyter]"`.
 You may also wish to install a Black extension in your editor to, for example, auto-format upon save.
-In any case, please run Black using `black .` before submitting your PR, because the Travis tests will not pass unless the files have been formatted.
+In any case, please run Black using `black .` before submitting your PR, because the tests will not pass unless the files have been formatted.
 Note that this will change files/notebooks that you may be actively editing.
 
 Versions and CHANGELOG
@@ -89,17 +89,9 @@ Then run the tests with pytest_ by running::
 
 If you need to change the pytest_ configuration, edit the `pytest.ini <pytest.ini>`_ file.
 
-Automated testing on Travis
-+++++++++++++++++++++++++++
-The aforementioned ruff_ and pytest_ tests will be run automatically by the Travis_ continuous integration system as specified in the `.travis.yml <.travis.yml>`_ file.
-Note that running the Travis_ tests requires you to register the project with Travis_.
-
-If the tests are passing, you will see this on the Travis_ badge on GitHub repo main page.
-
-Slack notifications of test results
-+++++++++++++++++++++++++++++++++++++
-You can configure Travis_ to provide automatic Slack notifications of the test results.
-To do that, follow the `instructions here <https://docs.travis-ci.com/user/notifications/#configuring-slack-notifications>`_.
+Automated testing via GitHub Actions
+++++++++++++++++++++++++++++++++++++
+The aforementioned ruff_ and pytest_ tests will be run automatically by the continuous integration system as specified in the GitHub Actions file [.github/workflows/test.yaml](.github/workflows/test.yaml).
 
 
 Building documentation
@@ -124,7 +116,6 @@ Note that this requires you to have registered the package on PyPI_ if this is t
 
 .. _pytest: https://docs.pytest.org
 .. _ruff: https://github.com/charliermarsh/ruff
-.. _Travis: https://docs.travis-ci.com
 .. _PyPI: https://pypi.org/
 .. _pip: https://pip.pypa.io
 .. _sphinx: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html

README.rst

@@ -5,8 +5,14 @@ polyclonal
 .. image:: https://img.shields.io/pypi/v/polyclonal.svg
         :target: https://pypi.python.org/pypi/polyclonal
 
-.. image:: https://app.travis-ci.com/jbloomlab/polyclonal.svg
-        :target: https://app.travis-ci.com/github/jbloomlab/polyclonal
+.. image:: https://github.com/jbloomlab/polyclonal/actions/workflows/test.yaml/badge.svg
+        :target: https://github.com/jbloomlab/polyclonal/actions/workflows/test.yaml
+
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+        :target: https://github.com/psf/black
+
+.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json
+        :target: https://github.com/astral-sh/ruff
 
 Model mutational escape from polyclonal antibodies using deep mutational scanning data.