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MAINT modernize developer tooling and automation - #99

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BabaSanfour merged 9 commits into
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codex/maintenance-automation
Aug 30, 2026
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MAINT modernize developer tooling and automation#99
BabaSanfour merged 9 commits into
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codex/maintenance-automation

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@BabaSanfour BabaSanfour commented Aug 30, 2026 •
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Summary

Part of #79

  • modernize the Spin/prek developer workflow and remove Python 3.11 support
  • harden CI and release automation with full-SHA GitHub Action pins
  • validate the Python 3.12 lower-bound lock through the audited MNE-tools checker
  • add dependency review, security guidance, and safe autofix automation
  • remove the unused uv.lock and keep tools/pylock.ci-old.toml as the committed lock

The commits are organized by developer tooling, maintenance automation,
supply-chain hardening, documentation, and focused CI compatibility fixes.
No scientific or production algorithm changes are included.

@autofix-troubleshooter

autofix-troubleshooter commented Aug 30, 2026

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Hi! I'm the autofix logoautofix.ci troubleshooter bot.

It looks like you correctly set up a CI job that uses the autofix.ci GitHub Action, but the autofix.ci GitHub App has not been installed for this repository. This means that autofix.ci unfortunately does not have the permissions to fix this pull request. If you are the repository owner, please install the app and then restart the CI workflow! 😃

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codecov Bot commented Aug 30, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.41%. Comparing base (bb520af) to head (410c268).

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main      #99      +/-   ##
==========================================
- Coverage   85.41%   85.41%   -0.01%     
==========================================
  Files          77       77              
  Lines       10592    10591       -1     
  Branches     1859     1859              
==========================================
- Hits         9047     9046       -1     
  Misses        927      927              
  Partials      618      618
Flag Coverage Δ
unittests 85.41% <100.00%> (-0.01%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
mne_denoise/_logging.py 100.00% <100.00%> (ø)
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@BabaSanfour
BabaSanfour merged commit f457950 into main Aug 30, 2026
18 of 19 checks passed
@BabaSanfour
BabaSanfour deleted the codex/maintenance-automation branch August 30, 2026 22:56
@BabaSanfour
BabaSanfour restored the codex/maintenance-automation branch August 30, 2026 22:56
This was referenced Aug 30, 2026
Closed
Merged
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@BabaSanfour
Merge pull request #101 from mne-tools/codex/revert-maintenance-autom…
fdb224f 
…ation

Revert PR #99 for squash merge
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps): update scipy requirement from >=1.13 to >=1.17.1 (#102)
a524025 
* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps): update scipy requirement from >=1.13 to >=1.17.1

Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.13.0...v1.17.1)

---
updated-dependencies:
- dependency-name: scipy
  dependency-version: 1.17.1
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update sphinx-gallery requirement from >=0.15.0 to >…
a60a573 
…=0.21.0 (#103)

* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update sphinx-gallery requirement

Updates the requirements on [sphinx-gallery](https://github.com/sphinx-gallery/sphinx-gallery) to permit the latest version.
- [Release notes](https://github.com/sphinx-gallery/sphinx-gallery/releases)
- [Changelog](https://github.com/sphinx-gallery/sphinx-gallery/blob/master/CHANGES.rst)
- [Commits](sphinx-gallery/sphinx-gallery@v0.15.0...v0.21.0)

---
updated-dependencies:
- dependency-name: sphinx-gallery
  dependency-version: 0.21.0
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@BabaSanfour
Maintenance/automation final (#112)
6b8deeb 
* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* MAINT reapply developer tooling and automation
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update pandas requirement from >=1.5 to >=3.0.5 (#104)
55b8992 
* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update pandas requirement from >=1.5 to >=3.0.5

Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v1.5.0...v3.0.5)

---
updated-dependencies:
- dependency-name: pandas
  dependency-version: 3.0.5
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update pre-commit requirement from >=3.6.0 to >=4.6.2 (
6311505 
#105)

* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update pre-commit requirement from >=3.6.0 to >=4.6.2

Updates the requirements on [pre-commit](https://github.com/pre-commit/pre-commit) to permit the latest version.
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v3.6.0...v4.6.2)

---
updated-dependencies:
- dependency-name: pre-commit
  dependency-version: 4.6.2
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update matplotlib requirement from >=3.8 to >=3.11.1 (…
d09f895 
…#106)

* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update matplotlib requirement from >=3.8 to >=3.11.1

Updates the requirements on [matplotlib](https://github.com/matplotlib/matplotlib) to permit the latest version.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.8.0...v3.11.1)

---
updated-dependencies:
- dependency-name: matplotlib
  dependency-version: 3.11.1
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update pytest-cov requirement from >=4.1.0 to >=7.1.0 (
dc76833 
#107)

* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update pytest-cov requirement from >=4.1.0 to >=7.1.0

Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v4.1.0...v7.1.0)

---
updated-dependencies:
- dependency-name: pytest-cov
  dependency-version: 7.1.0
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update pip requirement from >=25.1 to >=26.2.1 (#108)
ceec081 
* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update pip requirement from >=25.1 to >=26.2.1

Updates the requirements on [pip](https://github.com/pypa/pip) to permit the latest version.
- [Changelog](https://github.com/pypa/pip/blob/main/NEWS.rst)
- [Commits](pypa/pip@25.1...26.2.1)

---
updated-dependencies:
- dependency-name: pip
  dependency-version: 26.2.1
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update numpydoc requirement from >=1.6.0 to >=1.10.0 (…
b30125e 
…#109)

* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update numpydoc requirement from >=1.6.0 to >=1.10.0

Updates the requirements on [numpydoc](https://github.com/numpy/numpydoc) to permit the latest version.
- [Release notes](https://github.com/numpy/numpydoc/releases)
- [Changelog](https://github.com/numpy/numpydoc/blob/main/RELEASE.rst)
- [Commits](numpy/numpydoc@v1.6.0...v1.10.0)

---
updated-dependencies:
- dependency-name: numpydoc
  dependency-version: 1.10.0
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update ruff requirement from >=0.16.0 to >=0.16.5 (#110
67c53aa 
)

* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update ruff requirement from >=0.16.0 to >=0.16.5

Updates the requirements on [ruff](https://github.com/astral-sh/ruff) to permit the latest version.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.16.0...0.16.5)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.16.5
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BabaSanfour added a commit that referenced this pull request Aug 30, 2026
@dependabot @BabaSanfour
chore(deps-dev): update pydata-sphinx-theme requirement from >=0.15.2…
5ecb573 
… to >=0.21.0 (#111)

* MAINT modernize developer tooling

* CI automate repository maintenance

* CI harden workflow supply chain

* DOC align development and security guidance

* DOC add PR changelog fragments

* CI install shared lockfile checker with uv

* MAINT raise Python 3.12 dependency floors

* CI install shared checker without nested checkout

* DOC polish release instructions

* Revert "Merge pull request #99 from mne-tools/codex/maintenance-automation"

This reverts commit f457950, reversing
changes made to bb520af.

* chore(deps-dev): update pydata-sphinx-theme requirement

Updates the requirements on [pydata-sphinx-theme](https://github.com/pydata/pydata-sphinx-theme) to permit the latest version.
- [Release notes](https://github.com/pydata/pydata-sphinx-theme/releases)
- [Changelog](https://github.com/pydata/pydata-sphinx-theme/blob/main/RELEASE.md)
- [Commits](pydata/pydata-sphinx-theme@v0.15.2...v0.21.0)

---
updated-dependencies:
- dependency-name: pydata-sphinx-theme
  dependency-version: 0.21.0
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@BabaSanfour
BabaSanfour deleted the codex/maintenance-automation branch August 30, 2026 23:20
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@BabaSanfour @autofix-troubleshooter