[pull] main from mne-tools:main

.github/workflows/credit.yml

@@ -40,6 +40,6 @@ jobs:
           git checkout -b credit
           git commit -am "MAINT: Update code credit"
           git push origin credit
-          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ 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=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ 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")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

.github/workflows/spec_zero.yml

@@ -57,6 +57,6 @@ jobs:
           git checkout -b spec_zero
           git commit -am "MAINT: Update dependency specifiers"
           git push origin spec_zero
-          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in mne/fixes.py in this or another PR. `git grep TODO VERSION` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` in this or another PR. \`git grep TODO VERSION\` is a good starting point for finding potential updates.*" --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'

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.2
+    rev: v0.14.3
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.16.0
+    rev: v1.16.2
     hooks:
       - id: zizmor
 

doc/changes/dev/13468.bugfix.rst

@@ -0,0 +1 @@
+Correctly set the calibration factor in Nihon Kohden reader (which affects channel amplitudes), by `Tom Ma`_.

doc/changes/dev/13478.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with :func:`mne.preprocessing.ICA.apply` not working when the ICA instance was fitted including marked bad channels, by `Michael Straube`_.

doc/conf.py

@@ -657,6 +657,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
 linkcheck_ignore = [  # will be compiled to regex
     # 403 Client Error: Forbidden
     "https://doi.org/10.1002/",  # onlinelibrary.wiley.com/doi/10.1002/hbm
+    "https://doi.org/10.1017/",  # cambridge.org
     "https://doi.org/10.1016/",  # neuroimage
     "https://doi.org/10.1021/",  # pubs.acs.org/doi/abs
     "https://doi.org/10.1063/",  # pubs.aip.org/aip/jap
@@ -682,6 +683,9 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "https://doi.org/10.3390/",  # mdpi.com
     "https://hms.harvard.edu/",  # doc/funding.rst
     "https://stackoverflow.com/questions/21752259/python-why-pickle",  # doc/help/faq
+    "https://blender.org",
+    "https://home.alexk101.dev",
+    "https://www.mq.edu.au/",
     "https://www.biorxiv.org/content/10.1101/",  # biorxiv.org
     "https://www.researchgate.net/profile/",
     "https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html",
@@ -746,13 +750,10 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
 show_warning_types = True
 nitpick_ignore = [
     ("py:class", "None.  Remove all items from D."),
-    ("py:class", "a set-like object providing a view on D's items"),
-    ("py:class", "a set-like object providing a view on D's keys"),
     (
         "py:class",
         "v, remove specified key and return the corresponding value.",
     ),  # noqa: E501
-    ("py:class", "None.  Update D from dict/iterable E and F."),
     ("py:class", "an object providing a view on D's values"),
     ("py:class", "a shallow copy of D"),
     ("py:class", "(k, v), remove and return some (key, value) pair as a"),
@@ -761,6 +762,8 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     ("py:class", "None.  Remove all items from od."),
 ]
 nitpick_ignore_regex = [
+    ("py:class", "a set-like object providing a view on D's (items|keys)"),
+    ("py:class", r"None\.  Update D from (dict|mapping)/iterable E and F\."),
     # Classes whose methods we purposefully do not document
     ("py:.*", r"mne\.io\.BaseRaw.*"),  # use mne.io.Raw
     ("py:.*", r"mne\.BaseEpochs.*"),  # use mne.Epochs

doc/sphinxext/prs/13096.json

@@ -0,0 +1,51 @@
+{
+  "merge_commit_sha": "c4de9b61cd5f40a8771a853d483621c735390ec2",
+  "authors": [
+    {
+      "n": "Young Truong",
+      "e": null
+    },
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Bru",
+      "e": "[email protected]"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    "doc/changes/dev/13096.newfeature.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/io/eeglab/_eeglab.py": {
+      "a": 195,
+      "d": 7
+    },
+    "mne/io/eeglab/eeglab.py": {
+      "a": 63,
+      "d": 23
+    },
+    "mne/io/eeglab/tests/test_eeglab.py": {
+      "a": 143,
+      "d": 2
+    },
+    "tools/azure_dependencies.sh": {
+      "a": 3,
+      "d": 1
+    },
+    "tools/github_actions_dependencies.sh": {
+      "a": 4,
+      "d": 0
+    },
+    "tools/github_actions_env_vars.sh": {
+      "a": 1,
+      "d": 1
+    }
+  }
+}

doc/sphinxext/prs/13251.json

@@ -0,0 +1,39 @@
+{
+  "merge_commit_sha": "181fea1e7e0bd73c2ec5cf67391cf598ad1af7bf",
+  "authors": [
+    {
+      "n": null,
+      "e": "[email protected]"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    ".github/workflows/tests.yml": {
+      "a": 1,
+      "d": 0
+    },
+    "azure-pipelines.yml": {
+      "a": 1,
+      "d": 0
+    },
+    "doc/changes/dev/13251.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/datasets/config.py": {
+      "a": 2,
+      "d": 2
+    },
+    "mne/io/nihon/nihon.py": {
+      "a": 55,
+      "d": 11
+    },
+    "mne/io/nihon/tests/test_nihon.py": {
+      "a": 8,
+      "d": 10
+    }
+  }
+}

doc/sphinxext/prs/13347.json

@@ -0,0 +1,19 @@
+{
+  "merge_commit_sha": "94d9871acc920a47a04e9481d1fb2dfb25be7bfe",
+  "authors": [
+    {
+      "n": "Clemens Brunner",
+      "e": null
+    },
+    {
+      "n": "Daniel McCloy",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    "doc/conf.py": {
+      "a": 16,
+      "d": 4
+    }
+  }
+}

doc/sphinxext/prs/13421.json

@@ -0,0 +1,27 @@
+{
+  "merge_commit_sha": "52234feffb2d46ebcc7d204697ec9bec15fd6d75",
+  "authors": [
+    {
+      "n": "Eric Larson",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    "tools/azure_dependencies.sh": {
+      "a": 1,
+      "d": 3
+    },
+    "tools/github_actions_dependencies.sh": {
+      "a": 0,
+      "d": 4
+    },
+    "tools/github_actions_env_vars.sh": {
+      "a": 1,
+      "d": 1
+    },
+    "tools/install_pre_requirements.sh": {
+      "a": 2,
+      "d": 0
+    }
+  }
+}

doc/sphinxext/prs/13431.json

@@ -0,0 +1,59 @@
+{
+  "merge_commit_sha": "34e2743d7f1a1684f6359520392fd437bf2cd92f",
+  "authors": [
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    ".github/workflows/tests.yml": {
+      "a": 13,
+      "d": 7
+    },
+    ".pre-commit-config.yaml": {
+      "a": 2,
+      "d": 2
+    },
+    "doc/sphinxext/related_software.py": {
+      "a": 0,
+      "d": 1
+    },
+    "environment.yml": {
+      "a": 2,
+      "d": 0
+    },
+    "mne/conftest.py": {
+      "a": 5,
+      "d": 0
+    },
+    "mne/decoding/tests/test_receptive_field.py": {
+      "a": 2,
+      "d": 2
+    },
+    "mne/viz/backends/_pyvista.py": {
+      "a": 3,
+      "d": 0
+    },
+    "mne/viz/backends/tests/test_renderer.py": {
+      "a": 1,
+      "d": 0
+    },
+    "tools/circleci_dependencies.sh": {
+      "a": 1,
+      "d": 1
+    },
+    "tools/github_actions_dependencies.sh": {
+      "a": 2,
+      "d": 0
+    },
+    "tools/hooks/update_environment_file.py": {
+      "a": 2,
+      "d": 5
+    }
+  }
+}

doc/sphinxext/prs/13432.json

@@ -0,0 +1,91 @@
+{
+  "merge_commit_sha": "51b6a5c5fe711d10e959f1669960b4506cb4ad6e",
+  "authors": [
+    {
+      "n": "github-actions[bot]",
+      "e": "41898282+github-actions[bot]@users.noreply.github.com"
+    }
+  ],
+  "changes": {
+    "doc/sphinxext/prs/13350.json": {
+      "a": 51,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13375.json": {
+      "a": 27,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13395.json": {
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13398.json": {
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13403.json": {
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13404.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13405.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13407.json": {
+      "a": 107,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13409.json": {
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13410.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13411.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13412.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13413.json": {
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13416.json": {
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13420.json": {
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+      "d": 0
+    },
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13427.json": {
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+      "d": 0
+    },
+    "doc/sphinxext/prs/13428.json": {
+      "a": 35,
+      "d": 0
+    }
+  }
+}