Merge remote-tracking branch 'upstream/main' into egi_annots_from_stim

* upstream/main: (252 commits) Disable the "Back to top" button in the documentation (mne-tools#12688) DOC: match_channel_orders works on Epochs and Evoked, too (mne-tools#12699) Scale points and labels in montage plot (mne-tools#12703) Add license header to mne.stats.erp (mne-tools#12712) Update license year to 2024 (mne-tools#12713) Add standardized measurement error (SME) (mne-tools#12707) ENH: Parallel example execution in doc build (mne-tools#12708) MAINT: Update PR template (mne-tools#12692) MAINT: Fix doc build (mne-tools#12706) [pre-commit.ci] pre-commit autoupdate (mne-tools#12702) Improve documentation of ylim argument through Evoked plotting function (mne-tools#12697) [pre-commit.ci] pre-commit autoupdate (mne-tools#12696) BUG: Fix bug with CSP rank="full" (mne-tools#12694) MRG: Add epochs metadata summary to HTML representation (mne-tools#12686) Correct `Epochs.apply_function` docstring (mne-tools#12691) FIX: Gracefully handle missing datetime in Eyelink File (mne-tools#12687) MAINT: Restore SciPy pre (mne-tools#12689) Enh single channel annotation (mne-tools#12669) [pre-commit.ci] pre-commit autoupdate (mne-tools#12682) Bump autofix-ci/action from 1.2 to 1.3 in the actions group (mne-tools#12681) ...
scott-huberty · Jul 16, 2024 · b2e21aa · b2e21aa
2 parents 4182539 + c9f9bd5
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -22,65 +22,13 @@ _check_skip: &check_skip
     fi
 
 jobs:
-  pytest-macos-arm64:
-    parameters:
-      scheduled:
-        type: string
-        default: "false"
-    macos:
-      xcode: "14.2.0"
-    resource_class: macos.m1.medium.gen1
-    environment:
-      HOMEBREW_NO_AUTO_UPDATE: 1
-    steps:
-      - checkout
-      - run:
-          <<: *check_skip
-      - run:
-          name: Install Python and dependencies
-          command: |
-            set -eo pipefail
-            brew install [email protected]
-            which python
-            which pip
-            pip install --upgrade pip
-            pip install --upgrade --only-binary "numpy,scipy,dipy,statsmodels" -ve .[full,test_extra]
-            # 3D too slow on Apple's software renderer, and numba causes us problems
-            pip uninstall -y vtk pyvista pyvistaqt numba
-            mkdir -p test-results
-            echo "set -eo pipefail" >> $BASH_ENV
-      - run:
-          command: mne sys_info
-      - run:
-          command: ./tools/get_testing_version.sh && cat testing_version.txt
-      - restore_cache:
-          keys:
-            - data-cache-testing-{{ checksum "testing_version.txt" }}
-      - run:
-          command: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
-      - save_cache:
-          key: data-cache-testing-{{ checksum "testing_version.txt" }}
-          paths:
-            - ~/mne_data/MNE-testing-data  # (2.5 G)
-      - run:
-          command: pytest -m "not slowtest" --tb=short --cov=mne --cov-report xml -vv mne
-      - run:
-          name: Prepare test data upload
-          command: cp -av junit-results.xml test-results/junit.xml
-      - store_test_results:
-          path: ./test-results
-      # Codecov orb has bugs on macOS (gpg issues)
-      # - codecov/upload
-      - run:
-          command: bash <(curl -s https://codecov.io/bash)
-
   build_docs:
     parameters:
       scheduled:
         type: string
         default: "false"
-    docker:
-      - image: cimg/base:current-22.04
+    machine:
+      image: ubuntu-2404:current
     # large 4 vCPUs 15GB mem
     # https://discuss.circleci.com/t/changes-to-remote-docker-reporting-pricing/47759
     resource_class: large
@@ -163,7 +111,7 @@ jobs:
       # Load pip cache
       - restore_cache:
           keys:
-            - pip-cache
+            - pip-cache-0
       - restore_cache:
           keys:
             - user-install-bin-cache-310
@@ -175,7 +123,7 @@ jobs:
             ./tools/circleci_dependencies.sh
 
       - save_cache:
-          key: pip-cache
+          key: pip-cache-0
           paths:
             - ~/.cache/pip
       - save_cache:
@@ -200,6 +148,7 @@ jobs:
               which python
               QT_DEBUG_PLUGINS=1 mne sys_info -pd
               python -c "import numpy; numpy.show_config()"
+              python -c "import dipy.align.metrics"
               LIBGL_DEBUG=verbose python -c "import pyvistaqt; pyvistaqt.BackgroundPlotter(show=True)"
               python -c "import mne; mne.set_config('MNE_USE_CUDA', 'false')"  # this is needed for the config tutorial
               python -c "import mne; mne.set_config('MNE_LOGGING_LEVEL', 'info')"
@@ -454,6 +403,7 @@ jobs:
         default: "false"
     docker:
       - image: cimg/base:current-22.04
+    resource_class: large
     steps:
       - restore_cache:
           keys:
@@ -472,7 +422,7 @@ jobs:
           command: ./tools/circleci_bash_env.sh
       - restore_cache:
           keys:
-            - pip-cache
+            - pip-cache-0
       - run:
           name: Get Python running
           command: |
@@ -496,8 +446,8 @@ jobs:
 
 
   deploy:
-    machine:
-      image: ubuntu-2004:202111-01
+    docker:
+      - image: cimg/base:current-22.04
     steps:
       - attach_workspace:
           at: /tmp/build
@@ -591,20 +541,6 @@ workflows:
               only:
                 - main
 
-  weekly:
-    jobs:
-      - pytest-macos-arm64:
-          name: pytest_macos_arm64_weekly
-          scheduled: "true"
-    triggers:
-      - schedule:
-          # "At 6:00 AM GMT every Monday"
-          cron: "0 6 * * 1"
-          filters:
-            branches:
-              only:
-                - main
-
   monthly:
     jobs:
       - linkcheck:

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -2,3 +2,6 @@ e81ec528a42ac687f3d961ed5cf8e25f236925b0  # black
 12395f9d9cf6ea3c72b225b62e052dd0d17d9889  # YAML indentation
 d6d2f8c6a2ed4a0b27357da9ddf8e0cd14931b59  # isort
 e7dd1588013179013a50d3f6b8e8f9ae0a185783  # ruff format
+e39995d9be6fc831c7a4a59f09b7a7c0a41ae315  # percent formatting
+940ac9553ce42c15b4c16ecd013824ca3ea7244a  # whitespace
+1c5b39ff1d99bbcb2fc0e0071a989b3f3845ff30  # ruff UP028
diff --git a/.git_archival.txt b/.git_archival.txt
@@ -1,4 +1,3 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -10,4 +10,4 @@ This project and everyone participating in it is governed by the [MNE-Python's C
 
 ## How to contribute
 
-Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/install/contributing.html).
+Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/development/contributing.html).
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -29,8 +29,8 @@ body:
         Paste here a code snippet or minimal working example
         ([MWE](https://en.wikipedia.org/wiki/Minimal_Working_Example))
         to replicate your problem, using one of the
-        [datasets shipped with MNE-Python](https://mne.tools/dev/overview/datasets_index.html),
-        preferably the one called [sample](https://mne.tools/dev/overview/datasets_index.html#sample).
+        [datasets shipped with MNE-Python](https://mne.tools/stable/documentation/datasets.html#datasets),
+        preferably the one called [sample](https://mne.tools/stable/documentation/datasets.html#sample).
       render: Python
     validations:
       required: true

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,5 +1,7 @@
+<!--
+
 Thanks for contributing a pull request! Please make sure you have read the
-[contribution guidelines](https://mne.tools/dev/install/contributing.html)
+[contribution guidelines](https://mne.tools/dev/development/contributing.html)
 before submitting.
 
 Please be aware that we are a loose team of volunteers so patience is
@@ -11,6 +13,8 @@ case, we ask for your understanding during the review process.
 
 Again, thanks for contributing!
 
+-->
+
 #### Reference issue
 Example: Fixes #1234.
 

diff --git a/.github/actions/rename_towncrier/rename_towncrier.py b/.github/actions/rename_towncrier/rename_towncrier.py
@@ -0,0 +1,54 @@
+#!/usr/bin/env python3
+
+# Adapted from action-towncrier-changelog
+import json
+import os
+import re
+import subprocess
+import sys
+from pathlib import Path
+
+from github import Github
+from tomllib import loads
+
+event_name = os.getenv("GITHUB_EVENT_NAME", "pull_request")
+if not event_name.startswith("pull_request"):
+    print(f"No-op for {event_name}")
+    sys.exit(0)
+if "GITHUB_EVENT_PATH" in os.environ:
+    with open(os.environ["GITHUB_EVENT_PATH"], encoding="utf-8") as fin:
+        event = json.load(fin)
+    pr_num = event["number"]
+    basereponame = event["pull_request"]["base"]["repo"]["full_name"]
+    real = True
+else:  # local testing
+    pr_num = 12318  # added some towncrier files
+    basereponame = "mne-tools/mne-python"
+    real = False
+
+g = Github(os.environ.get("GITHUB_TOKEN"))
+baserepo = g.get_repo(basereponame)
+
+# Grab config from upstream's default branch
+toml_cfg = loads(Path("pyproject.toml").read_text("utf-8"))
+
+config = toml_cfg["tool"]["towncrier"]
+pr = baserepo.get_pull(pr_num)
+modified_files = [f.filename for f in pr.get_files()]
+
+# Get types from config
+types = [ent["directory"] for ent in toml_cfg["tool"]["towncrier"]["type"]]
+type_pipe = "|".join(types)
+
+# Get files that potentially match the types
+directory = toml_cfg["tool"]["towncrier"]["directory"]
+assert directory.endswith("/"), directory
+
+file_re = re.compile(rf"^{directory}({type_pipe})\.rst$")
+found_stubs = [f for f in modified_files if file_re.match(f)]
+for stub in found_stubs:
+    fro = stub
+    to = file_re.sub(rf"{directory}{pr_num}.\1.rst", fro)
+    print(f"Renaming {fro} to {to}")
+    if real:
+        subprocess.check_call(["mv", fro, to])
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -4,3 +4,9 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+    labels:
+      - no-changelog-entry-needed
diff --git a/.github/release.yaml b/.github/release.yaml
@@ -0,0 +1,6 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci
+      - github-actions
diff --git a/.github/workflows/autofix.yml b/.github/workflows/autofix.yml
@@ -0,0 +1,21 @@
+name: autofix.ci
+
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+    types: [opened, synchronize, labeled, unlabeled]
+
+permissions:
+  contents: read
+
+jobs:
+  autofix:
+    name: Autoupdate changelog entry
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - run: pip install --upgrade towncrier pygithub
+      - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
+      - uses: autofix-ci/action@dd55f44df8f7cdb7a6bf74c78677eb8acd40cd0a
diff --git a/.github/workflows/check_changelog.yml b/.github/workflows/check_changelog.yml
@@ -0,0 +1,16 @@
+name: Changelog
+
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+    types: [opened, synchronize, labeled, unlabeled]
+    branches: ["main"]
+
+jobs:
+  changelog_checker:
+    name: Check towncrier entry in doc/changes/devel/
+    runs-on: ubuntu-latest
+    steps:
+      - uses: scientific-python/action-towncrier-changelog@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BOT_USERNAME: changelog-bot
diff --git a/.github/workflows/circle_artifacts.yml b/.github/workflows/circle_artifacts.yml
@@ -6,7 +6,7 @@ jobs:
     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 }}

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -69,4 +69,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -5,11 +5,9 @@ on:  # yamllint disable-line rule:truthy
   release:
     types: [published]
   push:
-    branches:
-      - main
+    branches: ["main", "maint/*"]
   pull_request:
-    branches:
-      - main
+    branches: ["main", "maint/*"]
 
 permissions:
   contents: read
@@ -28,7 +26,7 @@ jobs:
           pip install build twine
       - run: python -m build --sdist --wheel
       - run: twine check --strict dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist
@@ -43,7 +41,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/mne
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist
Original file line number	Diff line number	Diff line change
Expand Up		@@ -10,4 +10,4 @@ This project and everyone participating in it is governed by the [MNE-Python's C

		## How to contribute

		Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/install/contributing.html).
		Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/development/contributing.html).