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

larsoner · Jul 29, 2024 · 01d94c7 · 01d94c7
2 parents c5eee5d + e06921d
commit 01d94c7
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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 python@3.11
-            which python
-            which pip
-            pip install --upgrade pip setuptools wheel
-            pip install --upgrade --only-binary "numpy,scipy,dipy,statsmodels" -ve . -r requirements.txt -r requirements_testing.txt -r requirements_testing_extra.txt PyQt6
-            # 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')"
@@ -223,13 +172,16 @@ jobs:
             - data-cache-fsaverage
       - restore_cache:
           keys:
-            - data-cache-bst-phantom-ctf
+            - data-cache-bst-raw
       - restore_cache:
           keys:
-            - data-cache-bst-raw
+            - data-cache-bst-phantom-ctf
       - restore_cache:
           keys:
             - data-cache-bst-phantom-elekta
+      - restore_cache:
+          keys:
+            - data-cache-bst-phantom-kernel
       - restore_cache:
           keys:
             - data-cache-bst-auditory
@@ -263,6 +215,9 @@ jobs:
       - restore_cache:
           keys:
             - data-cache-ucl-opm-auditory
+      - restore_cache:
+          keys:
+            - data-cache-phantom-kit
       - run:
           name: Get data
           # This limit could be increased, but this is helpful for finding slow ones
@@ -290,8 +245,14 @@ jobs:
       # Build docs
       - run:
           name: make html
+          command: |  # we have -o pipefail in #BASH_ENV so we should be okay
+            set -x
+            PATTERN=$(cat pattern.txt) make -C doc $(cat build.txt) 2>&1 | tee sphinx_log.txt
+      - run:
+          name: Check sphinx log for warnings (which are treated as errors)
+          when: always
           command: |
-            PATTERN=$(cat pattern.txt) make -C doc $(cat build.txt);
+            ! grep "^.* WARNING: .*$" sphinx_log.txt
       - run:
           name: Show profiling output
           when: always
@@ -368,18 +329,22 @@ jobs:
           key: data-cache-fsaverage
           paths:
             - ~/mne_data/MNE-fsaverage-data  # (762 M)
-      - save_cache:
-          key: data-cache-bst-phantom-ctf
-          paths:
-            - ~/mne_data/MNE-brainstorm-data/bst_phantom_ctf  # (177 M)
       - save_cache:
           key: data-cache-bst-raw
           paths:
             - ~/mne_data/MNE-brainstorm-data/bst_raw  # (830 M)
+      - save_cache:
+          key: data-cache-bst-phantom-ctf
+          paths:
+            - ~/mne_data/MNE-brainstorm-data/bst_phantom_ctf  # (177 M)
       - save_cache:
           key: data-cache-bst-phantom-elekta
           paths:
             - ~/mne_data/MNE-brainstorm-data/bst_phantom_elekta  # (1.4 G)
+      - save_cache:
+          key: data-cache-bst-phantom-kernel
+          paths:
+            - ~/mne_data/MNE-phantom-kernel-data  # (362 M)
       - save_cache:
           key: data-cache-bst-auditory
           paths:
@@ -424,6 +389,10 @@ jobs:
           key: data-cache-ucl-opm-auditory
           paths:
             - ~/mne_data/auditory_OPM_stationary  # (4 G)
+      - save_cache:
+          key: data-cache-phantom-kit
+          paths:
+            - ~/mne_data/MNE-phantom-KIT-data  # (1 G)
 
 
   linkcheck:
@@ -434,6 +403,7 @@ jobs:
         default: "false"
     docker:
       - image: cimg/base:current-22.04
+    resource_class: large
     steps:
       - restore_cache:
           keys:
@@ -452,7 +422,7 @@ jobs:
           command: ./tools/circleci_bash_env.sh
       - restore_cache:
           keys:
-            - pip-cache
+            - pip-cache-0
       - run:
           name: Get Python running
           command: |
@@ -476,8 +446,8 @@ jobs:
 
 
   deploy:
-    machine:
-      image: ubuntu-2004:202111-01
+    docker:
+      - image: cimg/base:current-22.04
     steps:
       - attach_workspace:
           at: /tmp/build
@@ -571,20 +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
@@ -1,3 +1,7 @@
 e81ec528a42ac687f3d961ed5cf8e25f236925b0  # black
 12395f9d9cf6ea3c72b225b62e052dd0d17d9889  # YAML indentation
-2261e7652bc3fb0659a8c197d219c1b8141b9436  # codespell
+d6d2f8c6a2ed4a0b27357da9ddf8e0cd14931b59  # isort
+e7dd1588013179013a50d3f6b8e8f9ae0a185783  # ruff format
+e39995d9be6fc831c7a4a59f09b7a7c0a41ae315  # percent formatting
+940ac9553ce42c15b4c16ecd013824ca3ea7244a  # whitespace
+1c5b39ff1d99bbcb2fc0e0071a989b3f3845ff30  # ruff UP028
diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -33,7 +33,7 @@
 *lcmv*.py @britta-wstnr
 
 # Channels
-/mne/channels @agramfort @mscheltienne @dengemann
+/mne/channels @agramfort @mscheltienne @dengemann @jasmainak
 
 # Core sensor-space classes
 /mne/epochs.py @drammock @agramfort @mscheltienne @dengemann
@@ -45,13 +45,14 @@
 
 # Decoding
 /mne/decoding/csp.py @cbrnr @agramfort @dengemann
+/mne/decoding/*.py @jasmainak
 
 # fNIRS
 /mne/preprocessing/nirs @rob-luke
 *fnirs*.py @rob-luke
 
 # forward
-/mne/forward/ @agramfort
+/mne/forward/ @agramfort @jasmainak
 *forward*.py @agramfort
 
 # Intracranial
@@ -69,6 +70,8 @@
 /mne/io/nirx @rob-luke
 /mne/io/snirf @rob-luke
 /mne/export @sappelhoff @cbrnr
+/mne/io/eeglab.py @jasmainak
+/mne/io/eeglab/tests/test_eeglab.py @jasmainak
 
 # Minimum Norm
 /mne/minimum_norm @agramfort
@@ -81,7 +84,7 @@
 /mne/preprocessing/e*g.py @mscheltienne
 
 # Report
-/mne/report @hoechenberger @dengemann
+/mne/report @hoechenberger @dengemann @jasmainak
 
 # Simulation
 /mne/simulation/ @agramfort
@@ -102,6 +105,9 @@
 /tutorials/visualization @larsoner @wmvanvliet @dengemann
 /examples/visualization @larsoner @dengemann
 
+# Datasets
+/mne/datasets/brainstorm @jasmainak
+
 #########################
 # Project-level / other #
 #########################

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