misc maintenance (#124)

* misc maintenance

* ditch os.path

* fixes

* remove Makefile, add pypi trusted publishing

.github/CONTRIBUTING.md

@@ -20,7 +20,8 @@ Then, in your Python environment follow these steps:
 ```Shell
 git clone https://github.com/USERNAME/pybv
 cd pybv
-pip install -e ".[dev]"
+git fetch --tags --prune --prune-tags
+python -m pip install -e ".[dev]"
 pre-commit install
 ```
 
@@ -33,21 +34,15 @@ See https://pre-commit.com/ for more information.
 ## Running tests and coverage
 
 If you have followed the steps to get the development version,
-you can run tests by making use of the `Makefile` and
-[GNU Make](https://www.gnu.org/software/make/).
+you can run tests as follows.
 From the project root, call:
 
-- `make test` to run tests and coverage
+- `pytest` to run tests and coverage
 - `pre-commit run -a` to run style checks (Ruff and some additional hooks)
 
 ## Building the documentation
 
 The documentation can be built using [Sphinx](https://www.sphinx-doc.org).
-Again, assuming that you followed the steps to get the development version,
-you can use the `Makefile`.
-From the project root, call:
-
-- `make build-doc` to build the documentation and open a browser window to view it
 
 The publicly accessible documentation is built and hosted by
 [Read the Docs](https://readthedocs.org/).
@@ -56,6 +51,9 @@ Credentials for Read the Docs are currently held by:
 - [@sappelhoff](https://github.com/sappelhoff/)
 - [@choldgraf](https://github.com/choldgraf/)
 
+## Info about versioning
+
+We follow a [semantic versioning scheme](https://semver.org/).
 
 ## Making a release on GitHub, PyPi, and Conda-Forge
 
@@ -67,64 +65,48 @@ and [Conda-Forge](https://anaconda.org/conda-forge/pybv).
 Credentials are currently held by:
 
 - GitHub
-    - Admin
-      - any admin of the [bids-standard GitHub organization](https://github.com/bids-standard)
-      - [@sappelhoff](https://github.com/sappelhoff/)
-      - [@choldgraf](https://github.com/choldgraf/)
-      - [@cbrnr](https://github.com/cbrnr/)
-    - Write
-      - [@hoechenberger](https://github.com/hoechenberger/)
+  - Admin
+    - any admin of the [bids-standard GitHub organization](https://github.com/bids-standard)
+    - [@sappelhoff](https://github.com/sappelhoff/)
+    - [@choldgraf](https://github.com/choldgraf/)
+    - [@cbrnr](https://github.com/cbrnr/)
+  - Write
+    - [@hoechenberger](https://github.com/hoechenberger/)
 - PyPi
-    - Owner
-        - [@sappelhoff](https://github.com/sappelhoff/)
-        - [@choldgraf](https://github.com/choldgraf/)
-    - Maintainer
-        - [@cbrnr](https://github.com/cbrnr/)
+  - Owner
+    - [@sappelhoff](https://github.com/sappelhoff/)
+    - [@choldgraf](https://github.com/choldgraf/)
+  - Maintainer
+    - [@cbrnr](https://github.com/cbrnr/)
 - Conda-Forge
-    - see: https://github.com/conda-forge/pybv-feedstock#feedstock-maintainers
+  - see: https://github.com/conda-forge/pybv-feedstock#feedstock-maintainers
 
 Releasing on GitHub will automatically trigger a release on PyPi via a GitHub Action
-(The credentials for PyPi are stored as "GitHub Secrets").
+(see `.github/workflows/release.yml`).
 A release on PyPi in turn will automatically trigger a release on Conda-Forge.
-Thus, the release protocol can be briefly described as follows:
+The release protocol can be briefly described as follows:
 
-1. You will need admin rights for the `pybv` GitHub repository.
-1. Go to your Python environment for `pybv`.
+1. Activate your Python environment for `pybv`.
 1. Make sure all tests pass and the docs are built cleanly.
-1. Update the `__version__` variable in `__init__.py`:
-    - Remove the `.devN` suffix.
-    - If the version preceding the `.devN` suffix is not the version to be
-      released, update the version as well according to
-      [semantic versioning](https://semver.org/) with its `major.minor.patch`
-      style.
 1. If applicable, append new authors to the author metadata in the `CITATION.cff` file.
-1. Update `docs/changelog.rst`, renaming the "current" headline to the new
-   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` (e.g., by extensively reviewing PRs).
-1. Commit the change and git push to `main` (or make a pull request and merge it).
+1. Update `docs/changes.rst`, renaming the "current" headline to the new
+   version
+1. Commit the change and git push to upstream `main`.
    Include "REL" in your commit message.
-1. Then, make an annotated tag `git tag -a -m "v1.2.3" v1.2.3 upstream/main` (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`
+1. Then, make an annotated tag, for example for the version `1.2.3`:
+   `git tag -a -m "1.2.3" 1.2.3 upstream/main`
+   (This assumes that you have a git remote configured with the name "upstream" and
+   pointing to https://github.com/bids-standard/pybv).
    **NOTE: Make sure you have your `main` 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`).
+   using the git tag from the previous step (e.g., `1.2.3`).
    Fill the tag name into the "Release title" field, and fill the "Description" field
    as you see fit.
 1. This will trigger a GitHub Action that will build the package and release it to PyPi.
-1. The PyPi release will trigger a release on Conda-Forge.
 
 Then the release is done and `main` has to be prepared for development of
 the next release:
 
-1. Update the `__version__` variable in `__init__.py`:
-    - Bump up the `major.minor.patch` version according to
-      [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`).
-        - (if you had a version like `1.3.0.dev0` before, release `1.3.0.dev1` instead, etc.)
-1. Add a "Current (unreleased)" headline to `docs/changelog.rst`.
+1. Add a "Current (unreleased)" headline to `docs/changes.rst`.
 1. Commit the changes and git push to `main` (or make a pull request).

.github/dependabot.yml

@@ -1,3 +1,5 @@
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
 updates:
   - package-ecosystem: "github-actions"

.github/workflows/python_build.yml

@@ -6,11 +6,11 @@ concurrency:
 
 on:
   push:
-    branches: [main]
+    branches: [ main ]
   pull_request:
-    branches: [main]
+    branches: [ main ]
   schedule:
-    - cron: "0 4 1 * *"
+    - cron: "0 4 * * MON"
 
 jobs:
   build:
@@ -19,38 +19,51 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.12"]
+    env:
+      TZ: Europe/Berlin
+      FORCE_COLOR: true
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dependencies
+    - name: Update pip etc.
       run: |
         python -m pip install --upgrade pip
-        python -m pip install --upgrade setuptools wheel build
+        python -m pip install --upgrade setuptools wheel build twine
 
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
     - name: Build sdist
       run: python -m build --sdist
+    - name: Check sdist
+      run: twine check --strict dist/*
     - name: Install sdist
-      run: pip install ./dist/pybv-*
+      run: python -m 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
+      run: python -m pip uninstall -y pybv
 
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
     - name: Build wheel
       run: python -m build --wheel
+    - name: Check wheel
+      run: twine check --strict dist/*
     - name: Install wheel
-      run: pip install ./dist/pybv-*.whl
+      run: python -m 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
+      run: python -m pip uninstall -y pybv

.github/workflows/python_tests.yml

@@ -6,11 +6,11 @@ concurrency:
 
 on:
   push:
-    branches: [main]
+    branches: [ main ]
   pull_request:
-    branches: [main]
+    branches: [ main ]
   schedule:
-    - cron: "0 4 1 * *"
+    - cron: "0 4 * * MON"
 
 
 jobs:
@@ -29,29 +29,36 @@ jobs:
             python-version: "3.12"
             mne-version: mne-main
 
+    runs-on: ${{ matrix.platform }}
+
     env:
       TZ: Europe/Berlin
       FORCE_COLOR: true
-
-    runs-on: ${{ matrix.platform }}
-
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
+    - uses: actions/cache@v4
+      with:
+        path: ${{ env.pythonLocation }}
+        key: v-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install -e .[dev]
+        python -m pip install -e ".[dev]"
 
-    - name: install MNE-Python main
+    - name: Install MNE-Python main (development version)
       if: matrix.mne-version == 'mne-main'
       run: |
-        pip install -U https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip
+        python -m pip install -U https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip
 
     - name: Display versions and environment information
       run: |
@@ -62,17 +69,19 @@ jobs:
         mne sys_info
 
     - name: Check formatting
+      if: matrix.platform == 'ubuntu-latest'
       run: |
-        make check-manifest
+        check-manifest
         pre-commit run --all-files
 
     - name: Test with pytest
-      run: |
-        make test
+      # Options defined in pyproject.toml
+      run: pytest
 
     - name: Build docs
       run: |
-        make build-doc
+        make -C docs/ clean
+        make -C docs/ html
 
     - name: Upload artifacts
       if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.mne-version == 'mne-stable'}}

.github/workflows/release.yml

@@ -0,0 +1,52 @@
+# Upload a Python Package using Twine when a release is created
+
+name: release
+on:  # yamllint disable-line rule:truthy
+  release:
+    types: [published]
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade setuptools wheel build twine
+      - run: python -m build --sdist --wheel
+      - run: twine check --strict dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+          include-hidden-files: true
+
+  pypi-upload:
+    needs: package
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    permissions:
+      id-token: write  # for trusted publishing
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pybv
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event_name == 'release'

.gitignore

@@ -14,3 +14,7 @@ htmlcov/
 .vscode/
 .venv
 .idea
+.ruff_cache
+*.vmrk
+*.eeg
+*.vhdr

MANIFEST.in

@@ -19,5 +19,4 @@ exclude .readthedocs.yaml
 exclude .git-blame-ignore-revs
 exclude .pre-commit-config.yaml
 exclude .gitignore
-exclude Makefile
 global-exclude *.pyc