intersphinx_registry, tomlsort, bump py min

Author: sappelhoff

.github/workflows/python_build.yml

@@ -9,9 +9,6 @@ on:
     branches: [main]
   pull_request:
     branches: [main]
-  create:
-    branches: [main]
-    tags: ['**']
   schedule:
     - cron: "0 4 1 * *"
 

.github/workflows/python_publish.yml

@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.11"
+        python-version: "3.12"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/python_tests.yml

@@ -9,9 +9,6 @@ on:
     branches: [main]
   pull_request:
     branches: [main]
-  create:
-    branches: [main]
-    tags: ['**']
   schedule:
     - cron: "0 4 1 * *"
 
@@ -21,8 +18,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-22.04, ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.12"]
+        mne-version: [mne-stable]
+
+        include:
+          # special test runs running only on single CI systems to save resources
+          # Test development versions
+          - platform: ubuntu-latest
+            python-version: "3.12"
+            mne-version: mne-main
 
     env:
       TZ: Europe/Berlin
@@ -44,9 +49,9 @@ jobs:
         python -m pip install -e .[dev]
 
     - name: install MNE-Python main
-      if: "matrix.platform == 'ubuntu-22.04'"
+      if: matrix.mne-version == 'mne-main'
       run: |
-        pip install -U git+https://github.com/mne-tools/mne-python
+        pip install -U https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip
 
     - name: Display versions and environment information
       run: |
@@ -57,10 +62,9 @@ jobs:
         mne sys_info
 
     - name: Check formatting
-      if: ${{ matrix.platform == 'ubuntu-22.04' && matrix.python-version == '3.11' }}
       run: |
         make check-manifest
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+        pre-commit run --all-files
 
     - name: Test with pytest
       run: |
@@ -71,14 +75,13 @@ jobs:
         make build-doc
 
     - name: Upload artifacts
-      if: ${{ matrix.platform == 'ubuntu-22.04' && matrix.python-version == '3.11' }}
+      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.mne-version == 'mne-stable'}}
       uses: actions/upload-artifact@v4
       with:
         name: docs-artifact
         path: docs/_build/html
 
     - name: Upload coverage report
-      if: ${{ matrix.platform == 'ubuntu-22.04' && matrix.python-version == '3.11' }}
       uses: codecov/codecov-action@v5
       with:
         files: ./coverage.xml

.pre-commit-config.yaml

@@ -18,3 +18,9 @@ repos:
     - id: ruff
       args: [ --fix ]
     - id: ruff-format
+
+- repo: https://github.com/pappasam/toml-sort
+  rev: v0.23.1
+  hooks:
+    - id: toml-sort-fix
+      files: pyproject.toml

.readthedocs.yaml

@@ -4,9 +4,9 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: "3.11"
+    python: "3.12"
 
 sphinx:
   configuration: docs/conf.py

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018-2023, pybv developers
+Copyright (c) 2018, pybv developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -77,7 +77,7 @@ as hosted by Brain Products.
 Installation
 ============
 
-``pybv`` runs on Python version 3.8 or higher.
+``pybv`` runs on Python version 3.9 or higher.
 
 ``pybv``'s only dependency is ``numpy``.
 However, we currently recommend that you install MNE-Python for reading BrainVision data.

docs/authors.rst

@@ -0,0 +1,10 @@
+.. _Adam Li: https://adam2392.github.io/
+.. _Aniket Pradhan: http://home.iiitd.edu.in/~aniket17133/
+.. _Chris Holdgraf: https://bids.berkeley.edu/people/chris-holdgraf
+.. _Clemens Brunner: https://cbrnr.github.io/
+.. _Felix Klotzsche: https://github.com/eioe
+.. _Phillip Alday: https://palday.bitbucket.io/
+.. _Pierre Cutellic: https://github.com/compmonks
+.. _Richard Höchenberger: https://hoechenberger.net/
+.. _Stefan Appelhoff: http://stefanappelhoff.com/
+.. _Tristan Stenner: https://github.com/tstenner

docs/changelog.rst

@@ -17,17 +17,6 @@ People who contributed to this software across releases (in **alphabetical order
 - `Stefan Appelhoff`_
 - `Tristan Stenner`_
 
-.. _Chris Holdgraf: https://bids.berkeley.edu/people/chris-holdgraf
-.. _Stefan Appelhoff: http://stefanappelhoff.com/
-.. _Tristan Stenner: https://github.com/tstenner
-.. _Phillip Alday: https://palday.bitbucket.io/
-.. _Clemens Brunner: https://cbrnr.github.io/
-.. _Richard Höchenberger: https://hoechenberger.net/
-.. _Adam Li: https://adam2392.github.io/
-.. _Aniket Pradhan: http://home.iiitd.edu.in/~aniket17133/
-.. _Pierre Cutellic: https://github.com/compmonks
-.. _Felix Klotzsche: https://github.com/eioe
-
 .. _changelog:
 
 =========
@@ -186,3 +175,5 @@ Changelog
 ~~~~~~~~~
 - Initial import from `philistine <https://pypi.org/project/philistine/>`_ package by `Phillip Alday`_
   and removing dependency on MNE-Python, by `Chris Holdgraf`_, and `Stefan Appelhoff`_
+
+.. include:: authors.rst

docs/conf.py

@@ -6,6 +6,8 @@
 import sys
 from datetime import date
 
+from intersphinx_registry import get_intersphinx_mapping
+
 import pybv
 
 curdir = os.path.dirname(__file__)
@@ -45,7 +47,8 @@
 
 # General information about the project.
 project = "pybv"
-copyright = f"2018-{date.today().year}, pybv developers"  # noqa:A001
+today = date.today().isoformat()
+copyright = f"2018, pybv developers. Last updated on {today}"  # noqa: A001
 author = "pybv developers"
 version = pybv.__version__
 release = version
@@ -78,9 +81,12 @@
 }
 
 # When functions from other packages are mentioned, link to them
-intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
-    "mne": ("https://mne.tools/dev/", None),
-    "numpy": ("https://numpy.org/devdocs", None),
-}
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = get_intersphinx_mapping(
+    packages={
+        "python",
+        "mne",
+        "numpy",
+    }
+)
 intersphinx_timeout = 10

docs/index.rst

@@ -4,4 +4,5 @@
    :hidden:
    :glob:
 
-   *
+   api.rst
+   changelog.rst

pyproject.toml

@@ -1,67 +1,73 @@
 [build-system]
-requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
+requires = ["setuptools"]
 
 [project]
-name = "pybv"
 authors = [
-    {name = "pybv developers"},
+  {name = "pybv developers"},
 ]
-maintainers = [
-    {name = "Stefan Appelhoff", email = "[email protected]"},
+classifiers = [
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved",
+  "Operating System :: MacOS",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: POSIX :: Linux",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Software Development",
 ]
-description = "pybv – a lightweight I/O utility for the BrainVision data format"
-keywords = ["Brain Products", "BrainVision", "vhdr", "vmrk", "eeg"]
-readme = "README.rst"
-license = {file = "LICENSE"}
-requires-python = ">=3.8"
 dependencies = [
-    "numpy >= 1.18.1",
+  "numpy >= 1.18.1",
 ]
+description = "pybv - a lightweight I/O utility for the BrainVision data format"
 dynamic = ["version"]
-classifiers = [
-    "Topic :: Scientific/Engineering",
-    "Intended Audience :: Science/Research",
-    "Intended Audience :: Developers",
-    "License :: OSI Approved",
-    "Topic :: Software Development",
-    "Topic :: Scientific/Engineering",
-    "Operating System :: Microsoft :: Windows",
-    "Operating System :: POSIX :: Linux",
-    "Operating System :: MacOS",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
+keywords = ["Brain Products", "BrainVision", "eeg", "vhdr", "vmrk"]
+license = {file = "LICENSE"}
+maintainers = [
+  {email = "[email protected]", name = "Stefan Appelhoff"},
 ]
+name = "pybv"
+readme = "README.rst"
+requires-python = ">=3.9"
 
 [project.optional-dependencies]
 dev = [
-    "check-manifest",
-    "mne",
-    "numpydoc",
-    "pre-commit",
-    "pytest",
-    "pytest-cov",
-    "pytest-sugar",
-    "ruff",
-    "sphinx",
-    "sphinx-copybutton",
+  "check-manifest",
+  "intersphinx_registry",
+  "mne",
+  "numpydoc",
+  "pre-commit",
+  "pytest",
+  "pytest-cov",
+  "pytest-sugar",
+  "ruff",
+  "sphinx",
+  "sphinx-copybutton",
 ]
 
 [project.urls]
 Documentation = "https://pybv.readthedocs.io"
-Repository = "https://github.com/bids-standard/pybv"
 Issues = "https://github.com/bids-standard/pybv/issues"
+Repository = "https://github.com/bids-standard/pybv"
 
 [tool.ruff.lint]
-select = ["A", "B006", "D", "E", "F", "I", "W", "UP"]
 ignore = ["D203", "D213"]
+select = ["A", "B006", "D", "E", "F", "I", "UP", "W"]
 
 [tool.setuptools.dynamic]
 version = {attr = "pybv.__version__"}
 
 [tool.setuptools.packages.find]
 exclude = ["docs", "specification"]
+
+[tool.tomlsort]
+all = true
+ignore_case = true
+spaces_before_inline_comment = 2
+trailing_comma_inline_array = true