[BBS-291] Migrate to GitHub Actions

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,4 +14,4 @@ Fixes #{issue-id-number}.
 - [ ] Documentation and `whatsnew.rst` updated (if needed).
 - [ ] `setup.py` and `requirements.txt` updated with new dependencies.
 - [ ] Type annotations added (if a function is added or modified). 
-- [ ] Travis CI pipeline run (add `[test travis]` to your git commit to run it)
+- [ ] All CI tests pass. 

.github/workflows/publish-pypi.yml

@@ -0,0 +1,55 @@
+name: pypi publishing
+
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+
+
+jobs:
+
+  publish_on_pypi:
+
+    if: startsWith(github.ref, 'refs/tags')
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: checkout latest commit
+        uses: actions/checkout@v2
+
+      - name: get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          git describe --tags
+          git describe --tags $(git rev-list --tags --max-count=1)
+
+      - name: setup python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+          pip install setuptools_scm
+
+      - name: create source distribution
+        run: |
+            python setup.py sdist
+
+      - name: create wheel distribution
+        run: |
+          python setup.py bdist_wheel
+
+      - name: publish package to pypi
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/run-tests.yml

@@ -0,0 +1,65 @@
+name: ci testing
+
+
+on:
+  push:
+    branches: master
+  pull_request:
+
+
+jobs:
+
+  run_test:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [
+          3.7,
+          3.8,
+          3.9,
+        ]
+        include:
+          - python-version: 3.7
+            tox-env: py37
+          - python-version: 3.8
+            tox-env: py38
+          - python-version: 3.9
+            tox-env: py39
+
+    steps:
+
+      - name: cancel previous workflows that are still running
+        uses: styfle/cancel-workflow-action@0.8.0
+        with:
+          access_token: ${{ github.token }}
+
+      - name: checkout latest commit
+        uses: actions/checkout@v2
+
+      - name: setup python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: linting and code style
+        if: matrix.python-version == '3.7'
+        run: tox -vv -e lint
+
+      - name: tests and coverage
+        run: tox -vv -e ${{ matrix.tox-env }} -- --color=yes
+
+      - name: docs
+        if: matrix.python-version == '3.7'
+        run: tox -vv -e docs
+
+      - name: check packaging
+        if: matrix.python-version == '3.7'
+        run: tox -vv -e check-packaging

CONTRIBUTING.md

@@ -32,7 +32,7 @@ to read the following guidelines.
     1. [Add type annotations](#Ata)
     1. [Update dependencies](#Udep)
     1. [Update documentation](#Udoc)
-    1. [Trigger Travis CI](#Ttc)
+    1. [Ensure all CI tests pass](#Ttc)
     1. [Get reviews and approval](#Ac)
 
 ## <a name="CreatingIssues"></a> Creating Issues
@@ -99,11 +99,16 @@ so you should update it if your PR adds or changes a feature, fixes a bug, etc.
 Moreover, instructions and examples in the docs should be updated whenever
 deemed appropriate.  
 
-### <a name="Ttc"></a> Trigger Travis CI
-To save time, by default our Travis CI pipeline does not test commits on PR 
-branches unless the commit message contains a `[test travis]` or `[run travis]` 
-tag. So make sure to add such tag to your last commit (or add an empty commit
-with such tag) before requesting a review of your PR.
+### <a name="Ttc"></a> Ensure all CI tests pass
+We use GitHub Actions to run [our CI tests](https://github.com/BlueBrain/Search/actions?query=workflow%3A%22ci+testing%22). 
+Once you open a PR, the workflow that runs all CI tests is automatically 
+triggered. This workflow is also triggered every time a new commit is pushed to 
+that PR branch. If you want to push a commit without triggering the CI tests
+(e.g. if a feature is still work in progress and you want to save time), your
+ commit message should include an appropriate label like `[skip ci]`, `[ci skip]`, 
+`[no ci]` etc. (see 
+[here](https://github.blog/changelog/2021-02-08-github-actions-skip-pull-request-and-push-workflows-with-skip-ci/) 
+for the complete list).
 
 All CI tests must pass before the pull request can be considered for review.
 

README.md

@@ -40,8 +40,8 @@ along with this program. If not, see <https://www.gnu.org/licenses/>.
 <tr>
   <td>Build Status</td>
   <td>
-    <a href="https://travis-ci.com/BlueBrain/Search">
-    <img src="https://travis-ci.com/BlueBrain/Search.svg?token=DiSGfujs1Bszyq2UxayG&branch=master" alt="Build status" />
+    <a href="https://github.com/BlueBrain/Search/actions?query=workflow%3A%22ci+testing%22+branch%3Amaster">
+    <img src="https://img.shields.io/github/workflow/status/BlueBrain/Search/ci%20testing/master" alt="Build status" />
     </a>
   </td>
 </tr>

setup.py

@@ -17,7 +17,35 @@
 
 from setuptools import find_packages, setup
 
-install_requires = [
+DESCRIPTION = (
+    "Blue Brain text mining toolbox for semantic search and information extraction"
+)
+
+LONG_DESCRIPTION = """
+Blue Brain Search is a text mining toolbox to perform semantic literature search 
+and structured information extraction from text sources.
+
+This project originated from the Blue Brain Project efforts on exploring and 
+mining the CORD-19 dataset."""
+
+CLASSIFIERS = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Text Processing :: General",
+]
+
+PYTHON_REQUIRES = ">=3.7"
+
+INSTALL_REQUIRES = [
     "Flask",
     "SQLAlchemy",
     "dvc[ssh]",
@@ -47,7 +75,7 @@
     "pyarrow",
 ]
 
-extras_require = {
+EXTRAS_REQUIRE = {
     "dev": [
         "cryptography",
         "docker",
@@ -66,7 +94,8 @@
 
 setup(
     name="bluesearch",
-    description="Blue Brain Search",
+    description=DESCRIPTION,
+    long_description=LONG_DESCRIPTION,
     author="Blue Brain Project, EPFL",
     url="https://github.com/BlueBrain/Search",
     project_urls={
@@ -75,18 +104,19 @@
         "Tracker": "https://bbpteam.epfl.ch/project/issues/projects/BBS",
     },
     license="-",
+    classifiers=CLASSIFIERS,
     use_scm_version={
         "write_to": "src/bluesearch/version.py",
         "write_to_template": '"""The package version."""\n__version__ = "{version}"\n',
-        # "local_scheme": "no-local-version",
+        "local_scheme": "no-local-version",
     },
     package_dir={"": "src"},
     packages=find_packages("./src"),
     package_data={"bluesearch": ["_css/stylesheet.css", "py.typed"]},
     zip_safe=False,
-    python_requires=">=3.7",
-    install_requires=install_requires,
-    extras_require=extras_require,
+    python_requires=PYTHON_REQUIRES,
+    install_requires=INSTALL_REQUIRES,
+    extras_require=EXTRAS_REQUIRE,
     entry_points={
         "console_scripts": [
             "compute_embeddings = bluesearch.entrypoint:run_compute_embeddings",