Merge branch 'main' into add-bci2000-reader

Author: HansujaB

.github/workflows/credit.yml

@@ -37,10 +37,10 @@ jobs:
           set -xeo pipefail
           git config --global user.email "50266005+mne-bot@users.noreply.github.com"
           git config --global user.name "mne[bot]"
-          BRANCH=credit/$GITHUB_RUN_ID
+          BRANCH=credit/$(date '+%Y%m%d')
           git checkout -b $BRANCH
           git commit -am "mne[bot]: Update code credit"
           git push origin $BRANCH
-          PR_NUM=$(gh pr create --base main --head $BRANCH --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to \`doc/changes/credit_tools.py\` or \`.mailmap\` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head $BRANCH --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to \`doc/sphinxext/credit_tools.py\` or \`.mailmap\` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
           pip install build twine
       - run: python -m build --sdist --wheel
       - run: twine check --strict dist/*
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v7
         with:
           name: dist
           path: dist
@@ -43,7 +43,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/mne
     steps:
-      - uses: actions/download-artifact@v7
+      - uses: actions/download-artifact@v8
         with:
           name: dist
           path: dist

.github/workflows/spec_zero.yml

@@ -51,7 +51,7 @@ jobs:
       - name: Create lockfile for old CI
         # uv pip compile requires setting the python version explicitly in the command :(
         run: |
-          uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --extra ver-auto-bumped --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml
+          uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --group lockfile_extras --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml
           python tools/github_actions_check_old_lockfile.py
       - name: check if files changed
         run: |

.github/zizmor.yml

@@ -3,3 +3,5 @@ rules:
     config:
       policies:
         "*": ref-pin
+  secrets-outside-env:
+    disable: true  # TODO: Someday we should use envs for these

.mailmap

@@ -20,6 +20,7 @@ Andrew Dykstra <andrew.r.dykstra@gmail.com>
 Andrew Quinn <AJQuinn@users.noreply.github.com> AJQuinn <AJQuinn@users.noreply.github.com>
 Andy Gilbert <7andy121@gmail.com> Andrew Gilbert <adgilbert21@icloud.com>
 Andy Gilbert <7andy121@gmail.com> Andrew Gilbert <andrew.gilbert@irhythmtech.com>
+Aniket Singh Yadav <148300120+Aniketsy@users.noreply.github.com> Aniket <148300120+Aniketsy@users.noreply.github.com>
 Anna Padee <anna.padee@gmail.com> apadee <44297909+apadee@users.noreply.github.com>
 Anne-Sophie Dubarry <as_dub@hotmail.com> annesodub <as_dub@hotmail.com>
 Archit Singhal <43236121+architsinghal-mriirs@users.noreply.github.com> archit singhal <zyphergiest@pop-os.localdomain>
@@ -290,6 +291,8 @@ Pierre-Antoine Bannier <pierreantoine.bannier@gmail.com> Pierre-Antoine Bannier
 Pierre-Antoine Bannier <pierreantoine.bannier@gmail.com> Pierre-Antoine Bannier <pierre-antoine@MacBook-Pro-de-Pierre-Antoine.local>
 Pierre-Antoine Bannier <pierreantoine.bannier@gmail.com> Pierre-Antoine Bannier <pierre-antoine@mbpdepieantoine.home>
 Ping-Keng Jao <ping-keng.jao@alumni.epfl.ch> nafraw <ping-keng.jao@alumni.epfl.ch>
+Pragnya Khandelwal <prag1704@gmail.com> Pragnya <prag1704@gmail.com>
+Pragnya Khandelwal <prag1704@gmail.com> PragnyaKhandelwal <prag1704@gmail.com>
 Praveen Sripad <pravsripad@gmail.com> prav <prav@prav-dell.(none)>
 Praveen Sripad <pravsripad@gmail.com> prav <pravsripad@gmail.com>
 Proloy Das <pdas6@mgh.harvard.edu> pdas6 <pdas6@mgh.harvard.edu>

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.2
+    rev: v0.15.7
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -23,7 +23,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.22.0
+    rev: v1.23.1
     hooks:
       - id: zizmor
         args: [--fix]

doc/api/events.rst

@@ -9,6 +9,7 @@ Events
 
    Annotations
    AcqParserFIF
+   HEDAnnotations
    concatenate_events
    count_events
    find_events

doc/changes/dev/13059.newfeature.rst

@@ -0,0 +1 @@
+Add :class:`mne.HEDAnnotations` for attaching `HED (Hierarchical Event Descriptors) <https://www.hedtags.org>`__ tags to annotations, by :newcontrib:`Kay Robbins`, `Bruno Aristimunha`_, and `Daniel McCloy`_.

doc/changes/dev/13518.bugfix.rst

@@ -0,0 +1 @@
+Make :meth:`~mne.io.Raw.interpolate_bads` method flexible (ignore, warn, raise) about how to handle interpolation of channels with invalid positions, by `Himanshu Mahor`_.

doc/changes/dev/13685.other.rst

@@ -0,0 +1 @@
+Document the behavior of :term:`first_samp` after :meth:`~mne.io.Raw.crop` and add ``reset_first_samp`` parameter to reset it to 0 after cropping, by :newcontrib:`Famous077`.