huge amount of misc maint fixes in preparation for 0.5 (#68)

* huge amount of misc maint fixes

* add tools for release automation

* add numpy to setup py installs

CONTRIBUTING.md → .github/CONTRIBUTING.md

@@ -34,7 +34,9 @@ navigate to the `/docs` directory and call `make html`. The HTML pages will
 be in `_build/html`.
 
 ##### Making a release
-(needs admin rights for GitHub and PyPi)
+
+You will need admin rights for GitHub.
+The PyPi credentials are handled via a "GitHub secret"
 
 1. go to your python environment for `pybv`
 1. Make sure all tests pass and the docs are built cleanly
@@ -46,28 +48,21 @@ be in `_build/html`.
       [semantic versioning](https://semver.org/) with its `major.minor.patch`
       style.
 1. Update `docs/changelog.rst`, renaming the "current" headline to the new
-   version and adding all "Authors" for the release
+   version and (if applicable) extending the "Authors" section of the document
     - "Authors" are all people who committed code or in other ways contributed
-    to `pybv` **for this release** (e.g., by reviewing PRs).
-1. Commit the change and git push to master (or make a pull request). Include
-   "REL" in your commit message.
-1. remove the `build/` and `dist/` directories from the pybv root directory
-1. run `pip install -e .` and then `python setup.py sdist bdist_wheel`
-1. upload to [test-pypi](https://test.pypi.org/):
-  1. `twine upload --repository-url https://test.pypi.org/legacy/ dist/*`
-  1. inspect it on [test-pypi](https://test.pypi.org/)
-  1. test installing it via
-     `pip install --index-url https://test.pypi.org/simple/ pybv`
-  1. if everything is OK, proceed
-1. run `twine upload dist/*` to upload to pypi
-1. make an annotated tag `git tag -a -m "v1.2.3" v1.2.3 upstream/master` (This
+    to `pybv` (e.g., by extensively reviewing PRs).
+1. Commit the change and git push to master (or make a pull request and merge it).
+   Include "REL" in your commit message.
+1. Then, make an annotated tag `git tag -a -m "v1.2.3" v1.2.3 upstream/master` (This
    assumes that you have a git remote configured with the name "upstream" and
    pointing to https://github.com/bids-standard/pybv). Note also that the
    version from `__init__.py` is preprended with a `v`: `1.2.3` --> `v1.2.3`
+   **NOTE: Make sure you have your `master` branch up to date for this step!**
 1. `git push --follow-tags upstream`
 1. Make a [release on GitHub](https://help.github.com/en/articles/creating-releases),
    using the git tag from the previous step (e.g., `v1.2.3`). Fill the tag name
    into all fields of the release.
+1. This will trigger a GitHub Action that will build the package and release it to PyPi.
 
 Then the release is done and `master` has to be prepared for development of
 the next release:
@@ -77,5 +72,5 @@ the next release:
       [semantic versioning](https://semver.org/) so that the version will be
       the version that is planned to be released next (e.g., `1.3.0`)
     - append `.dev0` to the version (e.g., `1.3.0.dev0`)
-1. add a "current" headline to `docs/changelog.rst`
+1. add a "Current (unreleased)" headline to `docs/changelog.rst`
 1. commit the changes and git push to master (or make a pull request)

.github/workflows/python_build.yml

@@ -0,0 +1,51 @@
+name: Python build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  create:
+    branches: [master]
+    tags: ['**']
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Update pip and wheel
+      run: python -m pip install --upgrade pip wheel
+
+    - uses: actions/checkout@v2
+    - name: Build sdist
+      run: python setup.py sdist
+    - name: Install sdist
+      run: pip install ./dist/pybv-*
+    - name: Clean up working directory
+      run: rm -rf ./*
+    - name: Try importing pybv
+      run: python -c 'import pybv; print(pybv.__version__)'
+    - name: Remove sdist install
+      run: pip uninstall -y pybv
+
+    - uses: actions/checkout@v2
+    - name: Build wheel
+      run: python setup.py bdist_wheel
+    - name: Install wheel
+      run: pip install ./dist/pybv-*.whl
+    - name: Clean up working directory
+      run: rm -rf ./*
+    - name: Try importing pybv
+      run: python -c 'import pybv; print(pybv.__version__)'
+    - name: Remove wheel install
+      run: pip uninstall -y pybv

.github/workflows/python_publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --upgrade setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.github/workflows/python_tests.yml

@@ -13,7 +13,7 @@ on:
 
 
 jobs:
-  build:
+  test:
     strategy:
       fail-fast: false
       matrix:
@@ -56,9 +56,7 @@ jobs:
 
     - name: Check formatting
       if: "matrix.platform == 'ubuntu-18.04'"
-      run: |
-        flake8 --docstring-convention numpy .
-        pycodestyle pybv
+      run: make pep
 
     - name: Test with pytest
       run: |

MANIFEST.in

@@ -1 +1,18 @@
+include MANIFEST.in
+include README.rst
 include LICENSE
+include requirements.txt
+include requirements-dev.txt
+
+graft docs
+graft pybv
+graft specification
+
+recursive-exclude pybv/__pycache__ *
+recursive-exclude pybv/tests/__pycache__ *
+recursive-exclude docs/_build *
+recursive-exclude docs/generated *
+recursive-exclude .github *
+
+exclude .gitignore
+exclude Makefile

Makefile

@@ -8,8 +8,8 @@ all: inplace test
 inplace:
 	$(PYTHON) setup.py develop
 
-test-doc:
-	$(PYTESTS) --doctest-modules --doctest-ignore-import-errors pybv
+test:
+	$(PYTESTS) --doctest-modules --cov=./pybv --cov-report=xml --verbose
 
 flake:
 	@if command -v flake8 > /dev/null; then \
@@ -25,9 +25,14 @@ pydocstyle:
 	@echo "Running pydocstyle"
 	@pydocstyle
 
+check-manifest:
+	@echo "Running check-manifest"
+	@check-manifest
+
 pep:
-	@$(MAKE) -k flake pydocstyle
+	@$(MAKE) -k flake pydocstyle check-manifest
 
 build-doc:
-	cd doc; make clean
-	cd doc; make html
+	cd docs; make clean
+	cd docs; make html
+	cd docs; make view

README.rst

@@ -88,7 +88,7 @@ The development of ``pybv`` is taking place on
 `GitHub <https://github.com/bids-standard/pybv>`_.
 
 For more information, please see
-`CONTRIBUTING.md <https://github.com/bids-standard/pybv/blob/master/CONTRIBUTING.md>`_
+`CONTRIBUTING.md <https://github.com/bids-standard/pybv/blob/master/.github/CONTRIBUTING.md>`_
 
 Usage
 =====
@@ -132,6 +132,6 @@ Acknowledgements
 
 This package was originally adapted from the
 `Philistine package <https://gitlab.com/palday/philistine>`_ by
-`palday <https://palday.bitbucket.io/>`_. It copies much of the BrainVision
-exporting code, removes the dependence on MNE, and focuses the code around
-BrainVision I/O.
+`palday <https://palday.bitbucket.io/>`_.
+It copies much of the BrainVision exporting code, but removes the dependence on MNE.
+Several features have been added, such as support for individual units for each channel.

docs/api.rst

@@ -1,17 +1,11 @@
 :orphan:
 
-.. _api_documentation:
-
 =================
 API Documentation
 =================
 
 Here we list the Application Programming Interface (API) for pybv.
 
-.. contents:: Contents
-   :local:
-   :depth: 2
-
 pybv (:py:mod:`pybv`)
 =====================