Replace TravisCI with GitHub Actions

.github/workflows/ci.yaml

@@ -0,0 +1,62 @@
+name: CI
+on:
+  push:
+    branches:
+      - master
+      - release
+  pull_request:
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.6', '3.7', '3.8']
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        mamba-version: "*"
+        channels: conda-forge,bioconda
+        channel-priority: true
+        activate-environment: test
+    - run: mamba install mafft raxml fasttree iqtree vcftools pip numpy
+    - run: pip install biopython==1.67
+    - run: pip install -e .[dev]
+    - run: conda info
+    - run: conda list
+    - run: pytest -c pytest.python3.ini  --cov-report=xml --cov=augur
+    - run: cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t
+    - run: bash tests/builds/runner.sh
+    - if: matrix.python-version == 3.8
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true
+  deploy:
+    if: ${{ github.ref == 'refs/heads/release' }}
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+      - env:
+          TRAVIS_AUTH_TOKEN: ${{ secrets.TRAVIS_AUTH_TOKEN }}
+        run: |
+          set -euo pipefail
+
+          echo "Pinging Travis CI to rebuild Docker image"
+
+          body='{
+            "request": {
+              "branch": "master",
+              "message": "Build triggered from augur"
+            }
+          }'
+
+          curl -X POST https://api.travis-ci.com/repo/nextstrain%2Fdocker-base/requests \
+            -H "Content-Type: application/json" \
+            -H "Accept: application/json" \
+            -H "Travis-API-Version: 3" \
+            -H "Authorization: token $TRAVIS_AUTH_TOKEN" \
+            -d "$body"

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.com/nextstrain/augur.svg?branch=master)](https://travis-ci.com/nextstrain/augur)
+[![Build Status](https://github.com/nextstrain/augur/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/nextstrain/augur/actions/workflows/ci.yaml)
 [![PyPI version](https://badge.fury.io/py/nextstrain-augur.svg)](https://pypi.org/project/nextstrain-augur/)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augur/README.html)
 [![Documentation Status](https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest)](https://docs.nextstrain.org/projects/augur/en/stable/)

devel/test

@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-# Runs tests in a sandboxed environment that loosely replicates the Travis CI
+# Runs tests in a sandboxed environment that loosely replicates the GitHub Actions
 # environment.
 set -euo pipefail
 

docs/contribute/DEV_DOCS.md

@@ -147,13 +147,13 @@ For example, the following command only runs unit tests related to augur mask.
 
 Troubleshooting tip: As tests run on the development code in the augur repository, your environment should not have an existing augur installation that could cause a conflict in pytest.
 
-We use continuous integration with Travis CI to run tests on every pull request submitted to the project.
+We use continuous integration with GitHub Actions to run tests on every pull request submitted to the project.
 We use [codecov](https://codecov.io/) to automatically produce test coverage for new contributions and the project as a whole.
 
 ### Releasing
 
 Before you create a new release, run all tests from a fresh conda environment to verify that nothing has broken since the last CI build on GitHub.
-The following commands will setup the equivalent conda environment to the Travis CI environment, run unit and integration tests, and deactivate the environment.
+The following commands will setup the equivalent conda environment to the GitHub Actions environment, run unit and integration tests, and deactivate the environment.
 
 ```bash
 # Update Conda.
@@ -203,29 +203,23 @@ You will need to update the existing recipe YAML locally and create a pull reque
 Add your GitHub username to the `recipe_maintainers` list, if this is your first time modifying the augur recipe.
 After a successful pull request review, Bioconda will automatically update the augur package that users download.
 
-### Travis CI
+### Continuous Integration (CI)
 
-Branches and PRs are tested by Travis CI jobs configured in `.travis.yml`.
+Branches and PRs are tested by GitHub Actions workflows configured in `.github/workflows`.
 
-Our Travis config uses two build stages: _test_ and _deploy_.  Jobs in the
-_test_ stage always run, but _deploy_ jobs only run sometimes (see below).
+Our GitHub Actions workflow is comprised of two jobs: _test_ and _deploy_.  Steps in the
+_test_ job always run, but _deploy_ steps only run sometimes (see below).
 
-The set of _test_ jobs are explicitly defined instead of auto-expanded from the
-implicit job property matrix. Since top-level properties are inherited by all
-jobs regardless of build stage, making the matrix explicit is less confusing
-and easier to reason about. YAML's anchor (`&foo`) and alias merge key (`<<:
-*foo`) syntax let us do this without repeating ourselves unnecessarily.
+The _test_ job runs tests and uploads the the coverage report to Codecov.
+Currently, only `pytest` results are included in the report.
 
 New releases, via pushes to the `release` branch, trigger a new [docker-base][]
 build to keep the Docker image up-to-date. This trigger is implemented in the
-_deploy_ stage, which is implicitly conditioned on the previous _test_ stage's
+_deploy_ job, which is implicitly conditioned on the previous _test_ job's
 successful completion and explicitly conditioned on a non-PR trigger on the
-`release` branch. Note that currently we cannot test this _deploy_ stage
+`release` branch. Note that currently we cannot test this _deploy_ job
 without making a release.
 
-It can sometimes be useful to verify the config is parsed as you expect using
-<https://config.travis-ci.com/explore>.
-
 [docker-base]: https://github.com/nextstrain/docker-base
 
 ## Contributing documentation

tests/builds/zika.t

@@ -64,7 +64,7 @@ Build a tree from the multiple sequence alignment.
   >  --method iqtree \
   >  --tree-builder-args "-seed 314159" > /dev/null
 
-  $ python3 "$TESTDIR/../../scripts/diff_trees.py" "results/tree_raw.nwk" "$TMP/out/tree_raw.nwk" --significant-digits 5
+  $ python3 "$TESTDIR/../../scripts/diff_trees.py" "results/tree_raw.nwk" "$TMP/out/tree_raw.nwk" --significant-digits 4
   {}
 
 Confirm that tree log file exists.