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Bump the production-dependencies group across 1 directory with 6 updates #30

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Bumps the production-dependencies group with 6 updates in the / directory:

Package From To
pybids 0.16.5 0.17.2
mne 1.7.1 1.8.0
numpy 1.26.4 2.1.1
scipy 1.14.0 1.14.1
matplotlib 3.9.1 3.9.2
neurokit2 0.2.9 0.2.10

Updates pybids from 0.16.5 to 0.17.2

Release notes

Sourced from pybids's releases.

0.17.2

Release Notes

Bug-fix release in the 0.17.x series.

Changes

New Contributors

Full Changelog: bids-standard/pybids@0.17.1...0.17.2

0.17.1

DOI

Release Notes

Bug-fix release in the 0.17.x series.

Mostly quiets down warnings generated by more recent versions of Pandas.

Changes

  • FIX: Create indices with object dtype (#1084)
  • MNT: Transfer validation tests to bids validator (#1081)

Full Changelog: bids-standard/pybids@0.17.0...0.17.1

0.17.0

DOI

Release notes

Feature release in the 0.17.0 series.

This release includes experimental support for MRS (BEP22) datasets and universal_pathlib.

Changes

  • ENH: pathlib -> universal_pathlib to enable cloud (and other filesystem) support (#1074)
  • ENH: Add MRS entities, path patterns (#1075)
  • STY: No parentheses after assert (#1065)
  • MNT: Bump bids-examples from 47c4da1 to 401f4cf (#1073)
  • MNT: Fix typo newly found by codespell (#1066)

Full Changelog: bids-standard/pybids@0.16.5...0.17.0

Changelog

Sourced from pybids's changelog.

Version 0.17.2 (September 19, 2024)

Bug-fix release in the 0.17.x series.

  • BUG: symlink dirs treated as files during indexing (#1087)

Version 0.17.1 (September 06, 2024)

Bug-fix release in the 0.17.x series.

Mostly quiets down warnings generated by more recent versions of Pandas.

  • FIX: Create indices with object dtype (#1084)
  • MNT: Transfer validation tests to bids validator (#1081)

Version 0.17.0 (July 29, 2024)

Feature release in the 0.17.x series.

This release includes experimental support for MRS (BEP22) datasets and universal_pathlib <https://github.com/fsspec/universal_pathlib>__.

  • ENH: pathlib -> universal_pathlib to enable cloud (and other filesystem) support (#1074)
  • ENH: Add MRS entities, path patterns (#1075)
  • STY: No parentheses after assert (#1065)
  • MNT: Bump bids-examples from 47c4da1 to 401f4cf (#1073)
  • MNT: Fix typo newly found by codespell (#1066)
Commits
  • 623f58d REL: 0.17.2
  • 98cf782 MNT: Update mailmap and Zenodo ordering
  • fdb0cd9 Merge pull request #1088 from cookpa/cookpa-zenodo
  • 4dd026b DOC: Update zenodo.json with new contributer
  • fc692d2 Merge pull request #1085 from bids-standard/dependabot/submodules/bids-exampl...
  • 40c1028 test: Expect citation.cff in ds001
  • b6d1b29 Merge pull request #1087 from cookpa/traverse_link_dirs
  • 6ecffc7 ENH: add a test for datasets with symlinks
  • cdd3bc8 BUG: symlink dirs treated as files during indexing
  • 86c2818 Build(deps): Bump bids-examples from 4460013 to 7c18d68
  • Additional commits viewable in compare view

Updates mne from 1.7.1 to 1.8.0

Release notes

Sourced from mne's releases.

v1.8.0

Full Changelog: mne-tools/mne-python@v1.7.0...v1.8.0

Commits

Updates numpy from 1.26.4 to 2.1.1

Release notes

Sourced from numpy's releases.

2.1.1 (Sep 3, 2024)

NumPy 2.1.1 Release Notes

NumPy 2.1.1 is a maintenance release that fixes bugs and regressions discovered after the 2.1.0 release.

The Python versions supported by this release are 3.10-3.13.

Contributors

A total of 7 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Andrew Nelson
  • Charles Harris
  • Mateusz Sokół
  • Maximilian Weigand +
  • Nathan Goldbaum
  • Pieter Eendebak
  • Sebastian Berg

Pull requests merged

A total of 10 pull requests were merged for this release.

  • #27236: REL: Prepare for the NumPy 2.1.0 release [wheel build]
  • #27252: MAINT: prepare 2.1.x for further development
  • #27259: BUG: revert unintended change in the return value of set_printoptions
  • #27266: BUG: fix reference counting bug in __array_interface__ implementation...
  • #27267: TST: Add regression test for missing descr in array-interface
  • #27276: BUG: Fix #27256 and #27257
  • #27278: BUG: Fix array_equal for numeric and non-numeric scalar types
  • #27287: MAINT: Update maintenance/2.1.x after the 2.0.2 release
  • #27303: BLD: cp311- macosx_arm64 wheels [wheel build]
  • #27304: BUG: f2py: better handle filtering of public/private subroutines

Checksums

MD5

3053a97400db800b7377749e691eb39e  numpy-2.1.1-cp310-cp310-macosx_10_9_x86_64.whl
84b752a2220dce7c96ff89eef4f4aec3  numpy-2.1.1-cp310-cp310-macosx_11_0_arm64.whl
47ed4f704a64261f07ca24ef2e674524  numpy-2.1.1-cp310-cp310-macosx_14_0_arm64.whl
b8a45caa870aee980c298053cf064d28  numpy-2.1.1-cp310-cp310-macosx_14_0_x86_64.whl
e097ad5eee572b791b4a25eedad6df4a  numpy-2.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
ae502c99315884cda7f0236a07c035c4  numpy-2.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
841a859d975c55090c0b60b72aab93a3  numpy-2.1.1-cp310-cp310-musllinux_1_1_x86_64.whl
d51be2b17f5b87aac64ab80fdfafc85e  numpy-2.1.1-cp310-cp310-musllinux_1_2_aarch64.whl
1f8249bd725397c6233fe6a0e8ad18b1  numpy-2.1.1-cp310-cp310-win32.whl
d38d6f06589c1ec104a6a31ff6035781  numpy-2.1.1-cp310-cp310-win_amd64.whl

... (truncated)

Commits
  • 48606ab Merge pull request #27328 from charris/prepare-2.1.1
  • a7cb4c4 REL: Prepare for the NumPy 2.1.1 release [wheel build]
  • 884c92b Merge pull request #27303 from charris/backport-27284
  • ca7f5c1 Merge pull request #27304 from charris/backport-27049
  • 2a49507 BUG: f2py: better handle filtering of public/private subroutines
  • d4306dd TST: Add regression test for gh-26920
  • db9668d BLD: cp311- macosx_arm64 wheels [wheel build]
  • c6ff254 Merge pull request #27287 from charris/post-2.0.2-release-update
  • 326bc17 MAINT: Update main after the 2.0.2 release
  • 8164b7c Merge pull request #27278 from charris/backport-27275
  • Additional commits viewable in compare view

Updates scipy from 1.14.0 to 1.14.1

Release notes

Sourced from scipy's releases.

SciPy 1.14.1 Release Notes

SciPy 1.14.1 adds support for Python 3.13, including binary wheels on PyPI. Apart from that, it is a bug-fix release with no new features compared to 1.14.0.

Authors

  • Name (commits)
  • h-vetinari (1)
  • Evgeni Burovski (1)
  • CJ Carey (2)
  • Lucas Colley (3)
  • Ralf Gommers (3)
  • Melissa Weber Mendonça (1)
  • Andrew Nelson (3)
  • Nick ODell (1)
  • Tyler Reddy (36)
  • Daniel Schmitz (1)
  • Dan Schult (4)
  • Albert Steppi (2)
  • Ewout ter Hoeven (1)
  • Tibor Völcker (2) +
  • Adam Turner (1) +
  • Warren Weckesser (2)
  • ਗਗਨਦੀਪ ਸਿੰਘ (Gagandeep Singh) (1)

A total of 17 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

Commits
  • 92d2a85 REL: 1.14.1 rel commit [wheel build]
  • 85623a1 Merge pull request #21362 from tylerjereddy/treddy_1.14.1_backports
  • d924005 MAINT: PR 21362 revisions [wheel build]
  • b901a4e MAINT, CI: PR 21362 revisions [wheel build]
  • 2a7ec60 MAINT, BLD: PR 21362 revisions [wheel build]
  • f4f084d MAINT, CI: PR 21362 revisions [wheel build]
  • b712fc6 DOC: update 1.14.1 relnotes [wheel build]
  • cdd5aca MAINT: special: Accommodate changed integer handling in NumPy 2.0. (#21401)
  • 0f91838 BLD: cp313 wheels on manylinux_aarch64 (#21409)
  • 6dd0b00 MAINT, CI: wheel build changes [wheel build]
  • Additional commits viewable in compare view

Updates matplotlib from 3.9.1 to 3.9.2

Release notes

Sourced from matplotlib's releases.

REL: 3.9.2

This is the second bugfix release of the 3.9.x series.

This release contains several bug-fixes and adjustments:

  • Be more resilient to I/O failures when writing font cache
  • Fix nondeterministic behavior with subplot spacing and constrained layout
  • Fix sticky edge tolerance relative to data range
  • Improve formatting of image values in cases of singular norms

Windows wheels now bundle the MSVC runtime DLL statically to avoid inconsistencies with other wheels and random crashes depending on import order.

Commits
  • a254b68 REL: 3.9.2
  • 056f307 DOC: Create release notes for 3.9.2
  • 8d867ce Merge branch 'v3.9.1-doc' into v3.9.x
  • 7be8675 Merge pull request #28687 from QuLogic/static-msvc
  • 3ed3d7b Merge pull request #28695 from meeseeksmachine/auto-backport-of-pr-27797-on-v...
  • 8a62afa BLD: Include MSVCP140 runtime statically
  • 81be26f Merge pull request #28688 from QuLogic/auto-backport-of-pr-28668-on-v3.9.x
  • d88a582 Backport PR #27797: DOC: Use video files for saving animations
  • e3159ba Merge pull request #28692 from meeseeksmachine/auto-backport-of-pr-28632-on-v...
  • 465401e Backport PR #28632: DOC: Tell sphinx-gallery to link mpl_toolkits from our build
  • Additional commits viewable in compare view

Updates neurokit2 from 0.2.9 to 0.2.10

Release notes

Sourced from neurokit2's releases.

0.2.10

🚀 What’s New

See the NEWS file for the changelog.

👏 Thanks to

@​DerAndereJohannes, @​DominiqueMakowski, @​MarcBalle, @​S-N-2019, @​ajb5d, @​atpage, @​danibene, @​peterhcharlton, @​visserle and Marc Balle

Commits
  • 45c9ad9 Merge pull request #992 from neuropsychology/dev
  • d783e40 Merge pull request #1021 from visserle/patch-1
  • 124dc04 >np.Inf was removed in the NumPy 2.0 release. Use np.inf instead.
  • b99036c Merge pull request #1017 from DerAndereJohannes/feature-codebook-docs
  • 86f42cf Merge pull request #1020 from peterhcharlton/patch-1
  • 581fbda Update ecg_peaks.py
  • ee87db7 Merge pull request #1018 from peterhcharlton/add_msptdfastv1.1
  • 5d3e044 Add MSPTDfast algorithm
  • 8195d2f Merge pull request #1016 from danibene/fix/gudb_name_consistency
  • b37098f added newline separators to all codebookadd directives
  • Additional commits viewable in compare view

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Bumps the production-dependencies group with 6 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [pybids](https://github.com/bids-standard/pybids) | `0.16.5` | `0.17.2` |
| [mne](https://github.com/mne-tools/mne-python) | `1.7.1` | `1.8.0` |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.1.1` |
| [scipy](https://github.com/scipy/scipy) | `1.14.0` | `1.14.1` |
| [matplotlib](https://github.com/matplotlib/matplotlib) | `3.9.1` | `3.9.2` |
| [neurokit2](https://github.com/neuropsychology/NeuroKit) | `0.2.9` | `0.2.10` |



Updates `pybids` from 0.16.5 to 0.17.2
- [Release notes](https://github.com/bids-standard/pybids/releases)
- [Changelog](https://github.com/bids-standard/pybids/blob/master/CHANGELOG.rst)
- [Commits](bids-standard/pybids@0.16.5...0.17.2)

Updates `mne` from 1.7.1 to 1.8.0
- [Release notes](https://github.com/mne-tools/mne-python/releases)
- [Commits](mne-tools/mne-python@v1.7.1...v1.8.0)

Updates `numpy` from 1.26.4 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.26.4...v2.1.1)

Updates `scipy` from 1.14.0 to 1.14.1
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.14.0...v1.14.1)

Updates `matplotlib` from 3.9.1 to 3.9.2
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.9.1...v3.9.2)

Updates `neurokit2` from 0.2.9 to 0.2.10
- [Release notes](https://github.com/neuropsychology/NeuroKit/releases)
- [Changelog](https://github.com/neuropsychology/NeuroKit/blob/master/NEWS.rst)
- [Commits](neuropsychology/NeuroKit@v0.2.9...v0.2.10)

---
updated-dependencies:
- dependency-name: pybids
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: production-dependencies
- dependency-name: mne
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: production-dependencies
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: production-dependencies
- dependency-name: scipy
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: production-dependencies
- dependency-name: matplotlib
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: production-dependencies
- dependency-name: neurokit2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: production-dependencies
...

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@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Oct 1, 2024
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