Add github actions, codecov, readthedocs (#1)

.github/workflows/publish-sdist.yml

@@ -0,0 +1,32 @@
+name: Publish sdist tarball to PyPI
+
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  build-n-publish:
+    name: Build and publish on PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install build
+
+      - name: Build a source tarball
+        run:
+            python -m build
+
+      - name: Publish distribution package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/run-tox.yml

@@ -0,0 +1,39 @@
+name: Run all tox python3
+
+on:
+    pull_request:
+    push:
+      branches:
+        - main
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install tox-gh-actions
+
+    - name: Run tox
+      run: |
+        tox
+
+    - name: Upload to codecov
+      uses: codecov/codecov-action@v3
+      with:
+        fail_ci_if_error: false
+        files: ./coverage.xml
+        flags: pytest
+        env_vars: OS,PYTHON
+        verbose: true

.readthedocs.yaml

@@ -0,0 +1,21 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+sphinx:
+  configuration: doc/source/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3"

README.rst

@@ -17,7 +17,6 @@ Installation
 
 ``BlueETL-core`` can be installed independently from ``BlueETL`` with::
 
-    PIP_INDEX_URL=https://bbpteam.epfl.ch/repository/devpi/simple \
     pip install -U blueetl-core
 
 

setup.py

@@ -23,7 +23,7 @@
     url="https://bbpteam.epfl.ch/documentation/projects/blueetl-core",
     project_urls={
         "Tracker": "https://bbpteam.epfl.ch/project/issues/projects/NSETM/issues",
-        "Source": "[email protected]:nse/blueetl-core.git",
+        "Source": "https://github.com/BlueBrain/blueetl-core.git",
     },
     license="BBP-internal-confidential",
     install_requires=[
@@ -45,6 +45,7 @@
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
 )

tox.ini

@@ -6,10 +6,9 @@ testdeps =
 
 [tox]
 envlist =
-    check-version
-    check-packaging
     lint
-    py{39,310}
+    docs
+    py{39,310,311}
 
 minversion = 3.1.0
 
@@ -19,11 +18,16 @@ ignore_basepython_conflict = true
 [testenv]
 basepython=python3.10
 setenv =
-    PIP_INDEX_URL=https://bbpteam.epfl.ch/repository/devpi/simple
     # Run serially
     BLUEETL_JOBLIB_JOBS=1
-deps = {[base]testdeps}
-commands = python -m pytest -vs tests {posargs}
+deps =
+    {[base]testdeps}
+    coverage[toml]
+    pytest-cov
+commands =
+    python -m pytest -vs --cov={[base]name} tests/ {posargs}
+    coverage xml
+    coverage html
 
 [testenv:check-version]
 skip_install = true
@@ -75,16 +79,6 @@ commands =
     black .
 allowlist_externals = find
 
-[testenv:coverage]
-deps =
-    {[base]testdeps}
-    coverage[toml]
-    pytest-cov
-commands =
-    python -m pytest --cov={[base]name} tests/ {posargs}
-    coverage xml
-    coverage html
-
 [testenv:docs]
 changedir = doc
 extras = docs
@@ -104,3 +98,9 @@ ignore = E203,E731,W503,W504,E501
 # D413: no blank line after last section
 add-ignore = D413
 convention = google
+
+[gh-actions]
+python =
+  3.9: py39
+  3.10: py310, lint, docs
+  3.11: py311