Refactor Github Actions, add PyPI release action (cblearn#59)

* Get version from git tag
* Add CD to pypi script and docs
* Fix setup.cfg formatting
* Simplify workflow: separate jobs
* Run workflows just on ubuntu-latest
* Support python 3.9 and 3.10

.coveragerc

@@ -3,6 +3,7 @@ cover_pylib = false
 omit =
     */site-packages/*
     */tests/*
+    */_version.py
 
 [report]
 exclude_lines =

.gitattributes

@@ -0,0 +1 @@
+cblearn/_version.py export-subst

.github/workflows/release.yml

@@ -1,24 +1,46 @@
-name: Upload Python Package
+# Based on: 
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
 
-on:
+on: 
+  push:
+    branches:
+    - main
   release:
-    types: [created]
+    types: [published]
 
 jobs:
-  deploy:
-    runs-on: ubuntu-20.04
-
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+    - name: Publish distribution 📦 to Test PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+        skip_existing: true
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/python-package.yml → .github/workflows/test.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Tests
+name: Lint and test code, test documentation build
 
 on:
   push:
@@ -10,42 +10,70 @@ on:
     branches: [ main ]
 
 jobs:
-  build:
-    name: ${{ matrix.platform }} ${{ matrix.python-version }}
+  lint:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: flake8 Lint Errors
+      uses: py-actions/flake8@v2
+      with:
+        args: --count --select=E9,F63,F7,F82 --show-source --statistics
+        # stop the build if there are Python syntax errors or undefined names
+        #    E9: Runtime errors (syntax, indentation, io)
+        #    F63: Wrong use of operators and always-true assertion tests
+        #    F7: Wrong position of statements (break, continue, return, ...)
+        #    F82: Undefined (variable) name
+    - name: flake8 Lint Warnings
+      uses: py-actions/flake8@v2
+      with:
+        args: --count --exit-zero --statistics --show-source
+        # print warnings if other style errors are found.
+        #    see .flake8 config file for selected/ignored rules.
+        #    warnings can be found in the action logs
+
+  docs: 
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: setup.cfg
+    - name: Install package with docs
+      run: |
+        python3 -m pip install --upgrade pip
+        pip install -e .[docs]
+    - name: Build the documentation
+      run: |
+        cd docs && make html
+
+  test:
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest]
-        python-version: [3.8]
-        include:
-          - platform: ubuntu-latest
-            python-version: 3.9
-    runs-on: ${{ matrix.platform }}
+        python-version: 
+          - "3.9"
+          - "3.10"
+    runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: setup.cfg
     - name: Setup R
-      uses: r-lib/actions/setup-r@v1
+      uses: r-lib/actions/setup-r@v2
     - name: Install package with dependencies
       run: |
         python3 -m pip install --upgrade pip
-        pip install -e .[r_wrapper,tests,docs,torch]
+        pip install -e .[r_wrapper,tests,torch]
         pip install h5py
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        #    E9: Runtime errors (syntax, indentation, io)
-        #    F63: Wrong use of operators and always-true assertion tests
-        #    F7: Wrong position of statements (break, continue, return, ...)
-        #    F82: Undefined (variable) name
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        #
-        # print warnings if other style errors are found.
-        #    see .flake8 config file for selected/ignored rules.
-        #    warnings can be found in the action logs
-        flake8 . --count --exit-zero --statistics --show-source
     - name: Test with pytest and measure coverage
       run: |
         pytest cblearn --cov=cblearn --cov-report=xml --remote-data
@@ -56,6 +84,4 @@ jobs:
         file: ./coverage.xml
         flags: unittests
         env_vars: OS,PYTHON
-    - name: Build the documentation
-      run: |
-        cd docs && make html
+

CHANGELOG.md

@@ -0,0 +1,7 @@
+# Changelog
+
+## 0.1.0
+
+- Support python 3.9 and 3.10.
+- Introduce semantic versioning
+- Publish to PyPI

MANIFEST.in

@@ -9,6 +9,8 @@ include pyproject.toml
 include readthedocs.yml
 include .flake8
 include MANIFEST.in
+include versioneer.py
+include cblearn/_version.py
 
 # exclude from sdist
 ## recursive-exclude folder *

README.md

@@ -1,10 +1,11 @@
 # cblearn
 ## Comparison-based Machine Learning in Python
 :warning: **cblearn** is **work in progress**. The API can change and bugs appear. Please help us by posting an [issue]( https://github.com/dekuenstle/cblearn/issues/new) :construction:
-
+
+[![PyPI version](https://img.shields.io/pypi/v/cblearn.svg)](https://pypi.python.org/pypi/cblearn)
+[![Documentation](https://readthedocs.org/projects/cblearn/badge/?version=latest)](https://cblearn.readthedocs.io/en/latest/?badge=latest)
 [![Unit tests](https://github.com/dekuenstle/cblearn/workflows/Python%20package/badge.svg)](https://github.com/dekuenstle/cblearn/actions)
 [![Test Coverage](https://codecov.io/gh/dekuenstle/cblearn/branch/master/graph/badge.svg?token=P9JRT6OK6O)](https://codecov.io/gh/dekuenstle/cblearn)
-[![Documentation](https://readthedocs.org/projects/cblearn/badge/?version=latest)](https://cblearn.readthedocs.io/en/latest/?badge=latest)
 
 Comparison-based Learning algorithms are the Machine Learning algorithms to use when training data contains similarity comparisons ("A and B are more similar than C and D") instead of data points. 
 

cblearn/__init__.py

@@ -1,3 +1,4 @@
-from ._version import __version__
+from . import _version
 
-__all__ = ['__version__']
+
+__version__ = _version.get_versions()['version']