MAINT: Make sure CIs are still green (#451)

.circleci/config.yml

@@ -38,7 +38,7 @@ jobs:
  echo "BASH_ENV:"
  cat $BASH_ENV
  - run: pip install --quiet --upgrade pip setuptools wheel
- - run: pip install --quiet --upgrade numpy scipy matplotlib sphinx pandas h5py mne "pyglet<2.0" psutil sphinx_bootstrap_theme sphinx_fontawesome numpydoc git+https://github.com/sphinx-gallery/sphinx-gallery
+ - run: pip install --quiet --upgrade numpy scipy matplotlib sphinx pandas h5py mne "pyglet<2.0" psutil pydata-sphinx-theme numpydoc git+https://github.com/sphinx-gallery/sphinx-gallery
  - run: python -m pip install -ve .
  - run: python -c "import mne; mne.sys_info()"
  - run: python -c "import pyglet; print(pyglet.version)"

.coveragerc

@@ -5,4 +5,3 @@ include = */expyfun/*
 omit =
  */setup.py
  */expyfun/codeblocks/*
- */expyfun/_externals/*

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+ - package-ecosystem: "github-actions"
+ directory: "/"
+ schedule:
+ interval: "monthly"
+ groups:
+ actions:
+ patterns:
+ - "*"

.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+ exclude:
+ authors:
+ - dependabot
+ - pre-commit-ci

.github/workflows/circle_artifacts.yml

@@ -1,13 +1,15 @@
-on: [status]
+on: [status] # yamllint disable-line rule:truthy
 jobs:
  circleci_artifacts_redirector_job:
+ if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs') }}"
  runs-on: ubuntu-20.04
  name: Run CircleCI artifacts redirector
  steps:
  - name: GitHub Action step
- uses: larsoner/circleci-artifacts-redirector-action@master
+ uses: scientific-python/circleci-artifacts-redirector-action@master
  with:
  repo-token: ${{ secrets.GITHUB_TOKEN }}
  api-token: ${{ secrets.CIRCLECI_TOKEN }}
  artifact-path: 0/html/index.html
  circleci-jobs: build_docs
+ job-title: Check the rendered docs here!

.github/workflows/tests.yml

@@ -2,7 +2,7 @@ name: 'tests'
 concurrency:
  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
  cancel-in-progress: true
-on:
+on: # yamllint disable-line rule:truthy
  push:
  branches:
  - '*'
@@ -20,67 +20,75 @@ jobs:
  shell: bash -el {0}
  strategy:
  matrix:
- os: ['ubuntu-20.04', 'windows-2022']
- kind: ['pip']
- python: ['3.10']
  include:
- - os: 'macos-latest'
+ # 24.04 works except for the video test, even though it works locally on 24.10
+ - os: ubuntu-22.04
+ kind: pip
+ python: '3.12'
+ # ARM64 will probably need to wait until
+ # - os: 'macos-latest' # arm64
+ # kind: 'conda'
+ # python: '3.12'
+ - os: 'macos-13' # intel
  kind: 'conda'
- python: '3.10'
+ python: '3.12'
+ # TODO: There is a bug on Python 3.12 on Windows :(
+ - os: 'windows-latest'
+ kind: 'pip'
+ python: '3.11'
  - os: 'ubuntu-20.04'
  kind: 'old'
  python: '3.8'
  steps:
  - uses: actions/checkout@v3
- name: Checkout
  - uses: LABSN/sound-ci-helpers@v1
  - uses: pyvista/setup-headless-display-action@main
  with:
  qt: true
  pyvista: false
- - run: sudo apt install -q libavutil56 libavcodec58 libavformat58 libswscale5 libglu1-mesa gstreamer1.0-alsa gstreamer1.0-libav python3-gst-1.0
-  name: Install Linux video dependencies
+ # Use -dev here just to get whichever version is right (e.g., 22.04 has a different version from 24.04)
+ - run: sudo apt install -q libavutil-dev libavcodec-dev libavformat-dev libswscale-dev libglu1-mesa gstreamer1.0-alsa gstreamer1.0-libav
  if: ${{ startsWith(matrix.os, 'ubuntu') }}
- - run: powershell make/get_video.ps1
- name: Install Windows video dependencies
+ - run: powershell tools/get_video.ps1
  if: ${{ startsWith(matrix.os, 'windows') }}
  - run: |
- if [[ "${{ matrix.os }}" == "windows"* ]]; then
+ set -xeo pipefail
+ if [[ "${{ runner.os }}" == "Windows" ]]; then
  echo "Setting env vars for Windows"
  echo "AZURE_CI_WINDOWS=true" >> $GITHUB_ENV
  echo "SOUND_CARD_BACKEND=rtmixer" >> $GITHUB_ENV
  echo "SOUND_CARD_NAME=Speakers" >> $GITHUB_ENV
  echo "SOUND_CARD_FS=48000" >> $GITHUB_ENV
  echo "SOUND_CARD_API=Windows WDM-KS" >> $GITHUB_ENV
- elif [[ "${{ matrix.os }}" == "ubuntu"* ]]; then
+ elif [[ "${{ runner.os }}" == "Linux" ]]; then
  echo "Setting env vars for Linux"
  echo "_EXPYFUN_SILENT=true" >> $GITHUB_ENV
  echo "SOUND_CARD_BACKEND=pyglet" >> $GITHUB_ENV
- elif [[ "${{ matrix.os }}" == "macos"* ]]; then
+ elif [[ "${{ runner.os }}" == "macOS" ]]; then
  echo "Setting env vars for macOS"
  fi
  name: Set env vars
  - uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python }}
- if: ${{ matrix.kind != 'conda' }}
+ if: matrix.kind != 'conda'
  - uses: mamba-org/setup-micromamba@v1
  with:
  environment-file: 'environment_test.yml'
  create-args: python=${{ matrix.python }}
  init-shell: bash
- name: 'Setup conda'
-  if: ${{ matrix.kind == 'conda' }}
- - run: python -m pip install --upgrade pip setuptools wheel sounddevice
-  if: ${{ matrix.kind != 'conda' }}
- - run: python -m pip install --upgrade sounddevice rtmixer "pyglet<1.6" pyglet-ffmpeg scipy matplotlib pandas h5py mne numpydoc pillow joblib
-  if: ${{ matrix.kind == 'pip' }}
- - run: python -m pip install sounddevice rtmixer "pyglet<1.6"
- if: ${{ matrix.kind == 'conda' }}
- - run: python -m pip install sounddevice rtmixer "pyglet<1.4" numpy scipy matplotlib "pillow<8" codecov
- if: ${{ matrix.kind == 'old' }}
+ if: matrix.kind == 'conda'
+ # Pyglet pin: https://github.com/pyglet/pyglet/issues/1089 (and need OpenGL2 compat for Pyglet>=2, too)
+ - run: python -m pip install --upgrade pip setuptools wheel sounddevice "pyglet<1.5.28"
+ - run: python -m pip install --upgrade --only-binary="rtmixer,scipy,matplotlib,pandas,numpy" rtmixer pyglet-ffmpeg scipy matplotlib pandas h5py mne numpydoc pillow joblib
+  if: matrix.kind == 'pip'
+ # arm64 has issues with rtmixer / PortAudio
+ - run: python -m pip install --only-binary="rtmixer" rtmixer
+ if: matrix.kind == 'conda' && matrix.os != 'macos-latest'
+ - run: python -m pip install --only-binary="rtmixer,numpy,scipy,matplotlib" rtmixer "pyglet<1.4" numpy scipy matplotlib "pillow<8"
+ if: matrix.kind == 'old'
  - run: python -m pip install tdtpy
- if: ${{ startsWith(matrix.os, 'windows') }}
+ if: startsWith(matrix.os, 'windows')
  - run: python -m sounddevice
  - run: |
  set -o pipefail
@@ -89,8 +97,11 @@ jobs:
  - run: python -c "import pyglet; print(pyglet.version)"
  - run: python -c "import matplotlib.pyplot as plt"
  - run: pip install -ve .[test]
+ # Video hangs on macOS arm64, not sure why
  - run: python -c "import expyfun; expyfun._utils._has_video(raise_error=True)"
- if: ${{ matrix.kind != 'old' }}
- - run: pytest --tb=short --cov=expyfun --cov-report=xml expyfun
- - uses: codecov/codecov-action@v1
- if: success()
+ if: matrix.kind != 'old' && matrix.os != 'macos-latest'
+ - run: pytest expyfun --cov-report=xml --cov=expyfun
+ - uses: codecov/codecov-action@v4
+ with:
+ token: ${{ secrets.CODECOV_TOKEN }}
+ if: always()

.gitignore

@@ -7,6 +7,7 @@
 *.orig
 .vscode
 doc/generated
+doc/sg_execution_times.rst
 .DS_Store
 
 # C extensions

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+repos:
+ # Ruff mne
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.3.7
+ hooks:
+ - id: ruff
+ name: ruff lint expyfun
+ args: ["--fix"]
+ files: ^expyfun/
+ - id: ruff
+ name: ruff lint doc and examples
+ # D103: missing docstring in public function
+ # D400: docstring first line must end with period
+ args: ["--ignore=D103,D400", "--fix"]
+ files: ^doc/|^examples/
+ - id: ruff-format
+ files: ^expyfun/|^doc/|^examples/
+
+ # Codespell
+ - repo: https://github.com/codespell-project/codespell
+ rev: v2.2.6
+ hooks:
+ - id: codespell
+ additional_dependencies:
+ - tomli
+ files: ^expyfun/|^doc/|^examples/
+ types_or: [python, bib, rst, inc]
+
+ # yamllint
+ - repo: https://github.com/adrienverge/yamllint.git
+ rev: v1.35.1
+ hooks:
+ - id: yamllint
+ args: [--strict, -c, .yamllint.yml]
+
+ # rstcheck
+ - repo: https://github.com/rstcheck/rstcheck.git
+ rev: v6.2.0
+ hooks:
+ - id: rstcheck
+ additional_dependencies:
+ - tomli
+ files: ^doc/.*\.(rst|inc)$

.yamllint.yml

@@ -0,0 +1,8 @@
+extends: default
+
+ignore: |
+ .github/workflows/codeql-analysis.yml
+
+rules:
+ line-length: disable
+ document-start: disable

MANIFEST.in

@@ -10,7 +10,7 @@ recursive-include expyfun/data *
 
 ### Exclude
 
-exclude make
+exclude tools
 exclude doc
 exclude .circleci
 exclude Makefile
@@ -21,6 +21,6 @@ exclude .mailmap
 recursive-exclude expyfun *.pyc
 
 recursive-exclude doc *
-recursive-exclude make *
+recursive-exclude tools *
 recursive-exclude examples *.tab
 recursive-exclude .circleci *

codecov.yml

@@ -4,7 +4,7 @@ github_checks: # too noisy, even though "a" interactively disables them
 
 codecov:
  notify:
- require_ci_to_pass: no
+ require_ci_to_pass: false
 
 coverage:
  status: