Bump the pre-commit-hooks group across 1 directory with 10 updates by dependabot[bot] · Pull Request #456 · cytomining/CytoTable

dependabot · 2026-06-01T18:54:07Z

Bumps the pre-commit-hooks group with 10 updates in the / directory:

Package	From	To
https://github.com/tox-dev/pyproject-fmt	`v2.12.1`	`2.21.2`
https://github.com/executablebooks/mdformat	`0.7.18`	`1.0.0`
https://github.com/citation-file-format/cffconvert	`5295f87c0e261da61a7b919fc754e3a77edd98a7`	`b6045d78aac9e02b039703b030588d54d53262ac`
cloudpathlib	`0.13.0`	`0.24.0`
pyarrow	`13.0.0`	`24.0.0`
pytest	`7.2.0`	`9.0.3`
moto	`4.0.0`	`5.2.1`
duckdb	`0.8.0`	`1.5.3`
parsl	`2023.4.24`	`2026.5.25`
pycytominer	`1.2.4`	`1.5.0`

Updates https://github.com/tox-dev/pyproject-fmt from v2.12.1 to 2.21.2

Release notes

Sourced from https://github.com/tox-dev/pyproject-fmt's releases.

v2.21.2

Full Changelog: tox-dev/pyproject-fmt@v2.21.1...v2.21.2

v2.21.1

What's Changed

🔧 fix(ci): restore git credentials and remove workaround by @gaborbernat in tox-dev/pyproject-fmt#335

Full Changelog: tox-dev/pyproject-fmt@v2.21.0...v2.21.1

v2.21.0

What's Changed

🔒 ci(workflows): add zizmor security auditing by @gaborbernat in tox-dev/pyproject-fmt#331

Full Changelog: tox-dev/pyproject-fmt@v2.20.0...v2.21.0

v2.20.0

Full Changelog: tox-dev/pyproject-fmt@v2.19.0...v2.20.0

v2.19.0

Full Changelog: tox-dev/pyproject-fmt@v2.18.1...v2.19.0

v2.18.1

Full Changelog: tox-dev/pyproject-fmt@v2.18.0...v2.18.1

v2.16.2

... (truncated)

Commits

a007bb7 Mirror: 2.21.2
4f13cb8 Mirror: 2.21.2
7aa702e [pre-commit.ci] pre-commit autoupdate (#339)
7147dd5 Bump astral-sh/setup-uv from 8.0.0 to 8.1.0 (#338)
6175ed9 [pre-commit.ci] pre-commit autoupdate (#337)
ff21273 [pre-commit.ci] pre-commit autoupdate (#336)
91de51a Mirror: 2.21.1
124276e Mirror: 2.21.1
25e3749 Remove persist-credentials: false and git remote workaround (#335)
6e10264 Mirror: 2.21.0
Additional commits viewable in compare view

Updates https://github.com/executablebooks/mdformat from 0.7.18 to 1.0.0

Commits

82912cd Bump version: 0.7.22 → 1.0.0
e53fb83 Modernize license metadata
a0981f5 docs: Remove mdformat-tables
aa8c457 Add 1.0.0 changelog
64fc2e3 Remove ParserExtensionInterface.add_cli_options
443084b Remove ASCII_WHITESPACE
ae503ee disable blank issues on GitHub
2fba388 fix: remove vertical tab from UNICODE_WHITESPACE
5b7bebf Update UNICODE_PUNCTUATION to comply with CommonMark v0.31.2
e4590ce Update CommonMark spec tests to v0.31.2
Additional commits viewable in compare view

Updates https://github.com/citation-file-format/cffconvert from 5295f87c0e261da61a7b919fc754e3a77edd98a7 to b6045d78aac9e02b039703b030588d54d53262ac

Changelog

Sourced from https://github.com/citation-file-format/cffconvert's changelog.

3.0.0 (Unreleased)

Schema

The schema changes are preliminary and temporary, since they are developed in another repository. I only included them here to keep track of changes.

Added contributors key, which are currently exactly the same type as authors.

Added key relation to identifiers. Its value is an enum same as Zenodo's related_identifiers.relation (cites, isNewVersionOf, isCitedBy, etc).

Updated ISBN regex pattern

Updated the schema with new licenses from SPDX license list

CLI

Long outputs, for example those resulting from validation errors, are now truncated by default, but this behavior can be disabled using --verbose flag citation-file-format/cffconvert#278

cffconvert exits with non zero code when something went wrong converting or validating citation-file-format/cffconvert#266

Added "Star on GitHub" footnote in CLI

Library

Added conversion and validation behavior for CFF 1.3

Converted metadata now includes information from CFF 1.3 key contributors for target formats that support it citation-file-format/cffconvert#333, citation-file-format/cffconvert#334

Zenodo metadata now includes related_identifiers and optionally relation_type such as citedBy, compiles, isSupplementTo etc using CFF 1.3 key relation on elements in identifiers citation-file-format/cffconvert#327, citation-file-format/cffconvert#329

Converted metadata now uses author email for target formats that support it citation-file-format/cffconvert#285

entity authors get exported as Organization when converting to schema.org or codemeta (was Person) citation-file-format/cffconvert#239

CFF key name takes precedence over alias when converting entity authors (was the other way around) citation-file-format/cffconvert#308

schema.org and codemeta conversion export an affiliation name as name (was legalName) citation-file-format/cffconvert#272

Added "upload_type": "software" when exporting to Zenodo from CFF files that use schema versions 1.0.x or 1.1.x citation-file-format/cffconvert#306

Apalike conversion now uses "and" or ", and" to concatenate author names when there are 2 or more authors citation-file-format/cffconvert#226

Bibtex conversion now uses braces to protect names of entity authors citation-file-format/cffconvert#156

Library now explicitly exports Citation and nothing else

Requests to GitHub now use versioned API

Requests to GitHub can now be authenticated via environment variable CFFCONVERT_API_TOKEN for higher rate limit citation-file-format/cffconvert#353

Requests to GitHub now use the target repo's default branch if user leaves branch unspecified citation-file-format/cffconvert#263

Development

Changed the repo name from cff-converter-python to just cffconvert citation-file-format/cffconvert#283

Moved to a src/ directory layout citation-file-format/cffconvert#311

Clearer separation between cli parts and lib parts citation-file-format/cffconvert#276

Replaced setup.cfg and setup.py with pyproject.toml citation-file-format/cffconvert#312

Added pytest markers for apalike, bibtex, codemeta, endnote, ris, schemaorg, zenodo tests citation-file-format/cffconvert#330

Added pytest marker lib for library tests and cli for command line interface tests

Refactored testing directory layout/naming to facilitate testing subparts of the test tree citation-file-format/cffconvert#315

Consistent styling now enforced with ruff citation-file-format/cffconvert#339

Added linting via pre-commit (isort, pyroma, ruff, prospector) citation-file-format/cffconvert#324

Added Markdown link checker pre-commit hook

Added cffconvert metadata validation checker via pre-commit

Updated jsonschema dependency to a wider range, now includes 4.x citation-file-format/cffconvert#292

Updated python versions used in CI citation-file-format/cffconvert#295

Added tests to verify that behavior maps such as those for authors or URLs implement all possible keys, that there are no extra keys, and that there are no extra methods. citation-file-format/cffconvert#300

... (truncated)

Commits

b6045d7 Merge pull request #387 from citation-file-format/dependabot/github_actions/g...
806dfca Bump the github-actions group with 1 update
See full diff in compare view

Updates cloudpathlib from 0.13.0 to 0.24.0

Updates pyarrow from 13.0.0 to 24.0.0

Updates pytest from 7.2.0 to 9.0.3

Updates moto from 4.0.0 to 5.2.1

Updates duckdb from 0.8.0 to 1.5.3

Updates parsl from 2023.4.24 to 2026.5.25

Updates pycytominer from 1.2.4 to 1.5.0

Bumps the pre-commit-hooks group with 10 updates: | Package | From | To | | --- | --- | --- | | [https://github.com/tox-dev/pyproject-fmt](https://github.com/tox-dev/pyproject-fmt) | `v2.12.1` | `2.21.2` | | [https://github.com/executablebooks/mdformat](https://github.com/executablebooks/mdformat) | `0.7.18` | `1.0.0` | | [https://github.com/citation-file-format/cffconvert](https://github.com/citation-file-format/cffconvert) | `5295f87c0e261da61a7b919fc754e3a77edd98a7` | `b6045d78aac9e02b039703b030588d54d53262ac` | | cloudpathlib | `0.13.0` | `0.24.0` | | pyarrow | `13.0.0` | `24.0.0` | | pytest | `7.2.0` | `9.0.3` | | moto | `4.0.0` | `5.2.1` | | duckdb | `0.8.0` | `1.5.3` | | parsl | `2023.4.24` | `2026.5.18` | | pycytominer | `1.2.4` | `1.5.0` | Updates `https://github.com/tox-dev/pyproject-fmt` from v2.12.1 to 2.21.2 - [Release notes](https://github.com/tox-dev/pyproject-fmt/releases) - [Commits](tox-dev/pyproject-fmt@v2.12.1...v2.21.2) Updates `https://github.com/executablebooks/mdformat` from 0.7.18 to 1.0.0 - [Commits](hukkin/mdformat@0.7.18...1.0.0) Updates `https://github.com/citation-file-format/cffconvert` from 5295f87c0e261da61a7b919fc754e3a77edd98a7 to b6045d78aac9e02b039703b030588d54d53262ac - [Release notes](https://github.com/citation-file-format/cffconvert/releases) - [Changelog](https://github.com/citation-file-format/cffconvert/blob/main/CHANGELOG.md) - [Commits](citation-file-format/cffconvert@5295f87...b6045d7) Updates `cloudpathlib` from 0.13.0 to 0.24.0 Updates `pyarrow` from 13.0.0 to 24.0.0 Updates `pytest` from 7.2.0 to 9.0.3 Updates `moto` from 4.0.0 to 5.2.1 Updates `duckdb` from 0.8.0 to 1.5.3 Updates `parsl` from 2023.4.24 to 2026.5.18 Updates `pycytominer` from 1.2.4 to 1.5.0 --- updated-dependencies: - dependency-name: https://github.com/tox-dev/pyproject-fmt dependency-version: 2.21.2 dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: https://github.com/executablebooks/mdformat dependency-version: 1.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: https://github.com/citation-file-format/cffconvert dependency-version: b6045d78aac9e02b039703b030588d54d53262ac dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: cloudpathlib dependency-version: 0.24.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks - dependency-name: pyarrow dependency-version: 24.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: moto dependency-version: 5.2.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: duckdb dependency-version: 1.5.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: parsl dependency-version: 2026.5.18 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pycytominer dependency-version: 1.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks ... Signed-off-by: dependabot[bot] <support@github.com>

d33bs · 2026-06-02T22:09:37Z

@dependabot rebase

Bumps the pre-commit-hooks group with 10 updates in the / directory: | Package | From | To | | --- | --- | --- | | [https://github.com/tox-dev/pyproject-fmt](https://github.com/tox-dev/pyproject-fmt) | `v2.12.1` | `2.21.2` | | [https://github.com/executablebooks/mdformat](https://github.com/executablebooks/mdformat) | `0.7.18` | `1.0.0` | | [https://github.com/citation-file-format/cffconvert](https://github.com/citation-file-format/cffconvert) | `5295f87c0e261da61a7b919fc754e3a77edd98a7` | `b6045d78aac9e02b039703b030588d54d53262ac` | | cloudpathlib | `0.13.0` | `0.24.0` | | pyarrow | `13.0.0` | `24.0.0` | | pytest | `7.2.0` | `9.0.3` | | moto | `4.0.0` | `5.2.1` | | duckdb | `0.8.0` | `1.5.3` | | parsl | `2023.4.24` | `2026.5.25` | | pycytominer | `1.2.4` | `1.5.0` | Updates `https://github.com/tox-dev/pyproject-fmt` from v2.12.1 to 2.21.2 - [Release notes](https://github.com/tox-dev/pyproject-fmt/releases) - [Commits](tox-dev/pyproject-fmt@v2.12.1...v2.21.2) Updates `https://github.com/executablebooks/mdformat` from 0.7.18 to 1.0.0 - [Commits](hukkin/mdformat@0.7.18...1.0.0) Updates `https://github.com/citation-file-format/cffconvert` from 5295f87c0e261da61a7b919fc754e3a77edd98a7 to b6045d78aac9e02b039703b030588d54d53262ac - [Release notes](https://github.com/citation-file-format/cffconvert/releases) - [Changelog](https://github.com/citation-file-format/cffconvert/blob/main/CHANGELOG.md) - [Commits](citation-file-format/cffconvert@5295f87...b6045d7) Updates `cloudpathlib` from 0.13.0 to 0.24.0 Updates `pyarrow` from 13.0.0 to 24.0.0 Updates `pytest` from 7.2.0 to 9.0.3 Updates `moto` from 4.0.0 to 5.2.1 Updates `duckdb` from 0.8.0 to 1.5.3 Updates `parsl` from 2023.4.24 to 2026.5.25 Updates `pycytominer` from 1.2.4 to 1.5.0 --- updated-dependencies: - dependency-name: cloudpathlib dependency-version: 0.24.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks - dependency-name: duckdb dependency-version: 1.5.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: https://github.com/citation-file-format/cffconvert dependency-version: b6045d78aac9e02b039703b030588d54d53262ac dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: https://github.com/executablebooks/mdformat dependency-version: 1.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: https://github.com/tox-dev/pyproject-fmt dependency-version: 2.21.2 dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: moto dependency-version: 5.2.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: parsl dependency-version: 2026.5.18 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pyarrow dependency-version: 24.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pycytominer dependency-version: 1.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks ... Signed-off-by: dependabot[bot] <support@github.com>

…ttps://github.com/cytomining/CytoTable into dependabot/pre_commit/pre-commit-hooks-dcc36ec642

dependabot Bot requested a review from gwaybio as a code owner June 1, 2026 18:54

dependabot Bot added dependencies Pull requests that update a dependency file pre_commit Pull requests that update pre_commit code labels Jun 1, 2026

dependabot Bot requested a review from d33bs as a code owner June 1, 2026 18:54

dependabot Bot added dependencies Pull requests that update a dependency file pre_commit Pull requests that update pre_commit code labels Jun 1, 2026

dependabot Bot changed the title ~~Bump the pre-commit-hooks group with 10 updates~~ Bump the pre-commit-hooks group across 1 directory with 10 updates Jun 2, 2026

dependabot Bot force-pushed the dependabot/pre_commit/pre-commit-hooks-dcc36ec642 branch from a336d6c to 60eace5 Compare June 2, 2026 22:11

d33bs and others added 5 commits June 2, 2026 16:21

Merge branch 'dependabot/pre_commit/pre-commit-hooks-dcc36ec642' of h…

30f9e16

…ttps://github.com/cytomining/CytoTable into dependabot/pre_commit/pre-commit-hooks-dcc36ec642

[pre-commit.ci lite] apply automatic fixes

0ece703

linting and constraint for pyproject fmting

56c9e59

Merge branch 'dependabot/pre_commit/pre-commit-hooks-dcc36ec642' of h…

e9ad43b

…ttps://github.com/cytomining/CytoTable into dependabot/pre_commit/pre-commit-hooks-dcc36ec642

Update pyproject.toml

2ade2fc

d33bs approved these changes Jun 3, 2026

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d33bs merged commit 078cccf into main Jun 3, 2026
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dependabot Bot deleted the dependabot/pre_commit/pre-commit-hooks-dcc36ec642 branch June 3, 2026 15:42

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Bump the pre-commit-hooks group across 1 directory with 10 updates#456

Bump the pre-commit-hooks group across 1 directory with 10 updates#456
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dependabot/pre_commit/pre-commit-hooks-dcc36ec642

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v2.21.2

v2.21.1

What's Changed

v2.21.0

What's Changed

v2.20.0

v2.19.0

v2.18.1

v2.16.2

3.0.0 (Unreleased)

Schema

CLI

Library

Development

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d33bs commented Jun 2, 2026

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dependabot Bot commented on behalf of github Jun 1, 2026 •

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