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Bump the python-packages group across 1 directory with 6 updates#460

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dependabot/pip/python-packages-7064c79004
Jun 3, 2026
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Bump the python-packages group across 1 directory with 6 updates#460
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dependabot/pip/python-packages-7064c79004

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@dependabot dependabot Bot commented on behalf of github Jun 3, 2026

Bumps the python-packages group with 6 updates in the / directory:

Package From To
duckdb 1.5.2 1.5.3
parsl 2026.4.27 2026.6.1
pycytominer 1.4.0 1.5.1
black 26.3.1 26.5.1
jupytext 1.19.1 1.19.3
sphinxcontrib-mermaid 2.0.1 2.0.2

Updates duckdb from 1.5.2 to 1.5.3

Release notes

Sourced from duckdb's releases.

v1.5.3 Bugfix Release

See the DuckDB core release notes here: https://github.com/duckdb/duckdb/releases/tag/v1.5.3

What's Changed in DuckDB Python

Full Changelog: duckdb/duckdb-python@v1.5.2...v1.5.3

Commits
  • 811b135 DuckDB submodule pinned at v1.5.3
  • 289bfbd Bump submodule
  • f87d6d9 Allow self-joining of Polars lazyframes (#466)
  • c88229d Allow self-joining of Polars lazyframes
  • 559f6af Only disable unity builds for editable installs on OSX
  • 97df049 fix .clangd
  • fd8889e Use recursive mutex to deal with GIL <-> internal lock deadlocks (#462)
  • 7b77328 [duckdb-labs bot] Bump DuckDB submodule (#464)
  • 9a86633 Fix concjunction OR (#465)
  • 3d778de Fix concjunction OR
  • Additional commits viewable in compare view

Updates parsl from 2026.4.27 to 2026.6.1

Commits
  • 9a7ae87 Move some HTEX specific tests into test_htex (#4118)
  • a4b056e Restrict HTEX max_workers_per_node to int (#4117)
  • f63ec26 Add more type annotations onto process worker pool (#4116)
  • 332b8d5 Remove unused self.max_queue_size in htex worker pool (#4114)
  • 266a557 Remove unused self.tasks_per_round in htex worker pool (#4113)
  • 2cee5ee Start a section that describes the log contents (#4036)
  • f03df25 Fix broken error reporting for bad htex worker pool addresses (#4110)
  • c6e0ace Tidy type annotations and defaults for HTEX mem_per_worker (#4111)
  • a4eb27f Fix test race condition on whether worker 0 has started (#4112)
  • f2201b8 Checkout full history in release process for release suppression (#4108)
  • Additional commits viewable in compare view

Updates pycytominer from 1.4.0 to 1.5.1

Release notes

Sourced from pycytominer's releases.

v1.5.1 (2026-05-30)

What's Changed

Full Changelog: cytomining/pycytominer@v1.5.0...v1.5.1

v1.5.0 (2026-05-22)

What's Changed

... (truncated)

Changelog

Sourced from pycytominer's changelog.

v1.5.1 (2026-05-28)

Detailed release notes

Feat

  • normalize: add drop_cosmicqc_rows parameter to drop coSMicQC-flagged cells before normalization (#682)

Docs

  • add introduction to pycytominer tutorial with simulated pipeline walkthrough (#681)

Build

  • prune test data, media, and walkthroughs from PyPI sdist to reduce package size (#683)

v1.5.0 (2026-05-21)

Detailed release notes

Feat

  • blocklist: introduce Blocklist class and get_blocklist_features with named YAML registry, custom registry support, and blocklist_name parameter; deprecate blocklist_file (#674)
  • annotate: update annotate to support parquet ingest and QC workflows (#657)
  • cells: make SingleCells.count_cells() use configurable count columns (#671)
  • load: add CytoTable warehouse profile loading; ignore OME-Arrow payload columns during normalization (#643)

Refactor

  • collate: remove noqa: S603 suppression in subprocess calls (#666)
  • replace tmp path usage with tempfile.gettempdir() for cross-platform compatibility (#670)

Docs

  • expand left navigation bar to specific functions and differentiate colors for css docstrings (#680)
  • fix API docs rendering: correct code blocks in core function docs, add doc build integration, fix RTD integration (#677)
  • update docs build to use uv, parse readme, remove legacy docs, and point RTD to cytomining.github.io/pycytominer (#676)
  • clarify CellProfiler and CytoTable input guidance (#669)

Build

  • migrate from poetry to uv (#650)
  • deps: various dependency updates automated by dependabot

CI

  • add Python 3.14 CI support (#668)
  • add contribution interest checkbox to issue templates (#665)
Commits
  • ea6e97a bump: version 1.5.0 → 1.5.1 (#685)
  • 37f3728 prune files to reduce package size (#683)
  • 1a9e4a0 Add drop qc rows parameter in normalize with test (#682)
  • 67a742f Adding intro to pycytominer tutorial (#681)
  • 584a9cc bump: version 1.4.0 → 1.5.0 (#679)
  • 3444fc5 Add specific links to core functions in left navigation bar in docs, also upd...
  • 7c39633 Dynamic blocklist object implementation (#674)
  • 4162330 Update annotate ingest qc parquet (#657)
  • d30b180 build(deps): bump astral-sh/setup-uv in /.github/actions/setup-env (#678)
  • e7bc7ba Removal of noqa: S603 in collate subprocess calls (#666)
  • Additional commits viewable in compare view

Updates black from 26.3.1 to 26.5.1

Release notes

Sourced from black's releases.

26.5.1

Stable style

  • Fix unstable formatting of annotated assignments whose subscript annotation contains an inline comment (e.g. x: list[ # pyright: ignore[...]) (#5130)
  • Preserve inline comments (including # type: ignore) immediately before a # fmt: skip line, avoiding AST equivalence failures (#5139)

Packaging

  • Correct the version in the published executables (#5137)

Documentation

  • Add Neovim integration guide covering conform.nvim, ALE, and simple command approaches (#5124)

26.5.0

Highlights

  • Add support for unpacking in comprehensions (PEP 798) and for lazy imports (PEP 810), both new syntactic features in Python 3.15 (#5048)
  • Python 3.15 is now supported. Compiled wheels are not yet provided for Python 3.15, so performance may be slower than on existing Python versions. Wheels will be provided once Python 3.15 is later in its release cycle. (#5127)

Stable style

  • Fix # fmt: skip being ignored in nested if expressions with parenthesized in clauses (#4903)
  • Add syntactic support for Python 3.15 (#5048)
  • Fix crash when an f-string follows a # fmt: off comment inside brackets (#5097)
  • Preserve multiline compound statement headers when # fmt: skip is placed on the colon line (#5117)

Preview style

  • Improve heuristics around whether blank lines should appear before, within and after groups of same-name decorated functions (such as @overload groups) in .pyi stub files (#5021)
  • Fix blank lines being removed between a function and a decorated class in .pyi stub files (#5092)
  • Prevent string merger from creating unsplittable long lines when a pragma comment (e.g. # type: ignore) follows the closing bracket (#5096)

Packaging

Output

... (truncated)

Changelog

Sourced from black's changelog.

Version 26.5.1

Stable style

  • Fix unstable formatting of annotated assignments whose subscript annotation contains an inline comment (e.g. x: list[ # pyright: ignore[...]) (#5130)
  • Preserve inline comments (including # type: ignore) immediately before a # fmt: skip line, avoiding AST equivalence failures (#5139)

Packaging

  • Correct the version in the published executables (#5137)

Documentation

  • Add Neovim integration guide covering conform.nvim, ALE, and simple command approaches (#5124)

Version 26.5.0

Highlights

  • Add support for unpacking in comprehensions (PEP 798) and for lazy imports (PEP 810), both new syntactic features in Python 3.15 (#5048)
  • Python 3.15 is now supported. Compiled wheels are not yet provided for Python 3.15, so performance may be slower than on existing Python versions. Wheels will be provided once Python 3.15 is later in its release cycle. (#5127)

Stable style

  • Fix # fmt: skip being ignored in nested if expressions with parenthesized in clauses (#4903)
  • Add syntactic support for Python 3.15 (#5048)
  • Fix crash when an f-string follows a # fmt: off comment inside brackets (#5097)
  • Preserve multiline compound statement headers when # fmt: skip is placed on the colon line (#5117)

Preview style

  • Improve heuristics around whether blank lines should appear before, within and after groups of same-name decorated functions (such as @overload groups) in .pyi stub files (#5021)
  • Fix blank lines being removed between a function and a decorated class in .pyi stub files (#5092)
  • Prevent string merger from creating unsplittable long lines when a pragma comment (e.g. # type: ignore) follows the closing bracket (#5096)

Packaging

... (truncated)

Commits

Updates jupytext from 1.19.1 to 1.19.3

Release notes

Sourced from jupytext's releases.

Version 1.19.3

Fixed

  • The Jupytext CLI issues a warning when a notebook is not trusted. Also, trust is preserved when empty outputs are added (follow-up on #1505)

Changed

  • The dependabot config has been updated to correctly bump extension packages, now allowing only production updates and ignoring dev dependencies (#1532). Thanks to Mahendra Paipuri for this PR!
  • Removed deprecated stylelint packages (stylelint-config-prettier and stylelint-prettier) from the JupyterLab extension dependencies (#1530)
  • We have removed Python 3.9 testing from the CI (Python 3.9 reached EOL in October 2025)

Version 1.19.2

Fixed

  • Trusted notebooks remain trusted after jupytext --sync (#1505)
  • We have fixed the homepage link in package.json. Thanks to Michał Krassowski for making this PR (#1494)
  • Thanks to Brigitta Sipőcz for fixing a broken link in our CLI (#1428)
  • The --quiet flag now suppresses the creating missing directory warning when writing to a path that includes a prefix (#1533)

Changed

  • The CI workflow has been restructured to maximize parallelization. All test suites (pip, conda, UI) and the build step now run concurrently after pre-commit checks, instead of sequentially, reducing CI times (#1527)
  • We have skipped the tests that involve jupyterfs on Python 3.12+ as they started failing on the CI with no obvious way to fix them (#1509)
  • We have changed the configuration of Dependabot to get grouped dependency updates for our JupyterLab extension.
  • We have merged a series of Dependabot security updates: #1516, #1517, #1519, #1520, #1522, #1524
Changelog

Sourced from jupytext's changelog.

1.19.3 (2026-05-17)

Fixed

  • The Jupytext CLI issues a warning when a notebook is not trusted. Also, trust is preserved when empty outputs are added (follow-up on #1505)

Changed

  • The dependabot config has been updated to correctly bump extension packages, now allowing only production updates and ignoring dev dependencies (#1532). Thanks to Mahendra Paipuri for this PR!
  • Removed deprecated stylelint packages (stylelint-config-prettier and stylelint-prettier) from the JupyterLab extension dependencies (#1530)
  • We have removed Python 3.9 testing from the CI (Python 3.9 reached EOL in October 2025)

1.19.2 (2026-05-10)

Fixed

  • Trusted notebooks remain trusted after jupytext --sync (#1505)
  • We have fixed the homepage link in package.json. Thanks to Michał Krassowski for making this PR (#1494)
  • Thanks to Brigitta Sipőcz for fixing a broken link in our CLI (#1428)
  • The --quiet flag now suppresses the creating missing directory warning when writing to a path that includes a prefix (#1533)

Changed

  • The CI workflow has been restructured to maximize parallelization. All test suites (pip, conda, UI) and the build step now run concurrently after pre-commit checks, instead of sequentially, reducing CI times (#1527)
  • We have skipped the tests that involve jupyterfs on Python 3.12+ as they started failing on the CI with no obvious way to fix them (#1509)
  • We have changed the configuration of Dependabot to get grouped dependency updates for our JupyterLab extension.
  • We have merged a series of Dependabot security updates: #1516, #1517, #1519, #1520, #1522, #1524
Commits
  • 48fdfd8 Fix: Adding cells with no outputs preserves trust status (#1531)
  • 4706e65 chore: Update dependabot config (#1532)
  • 2ec5404 build (deps): Remove deprecated stylelint packages (#1530)
  • 309f97f Version 1.19.2 (#1529)
  • e4dded4 build(deps-dev): bump typescript from 5.9.3 to 6.0.3 in /jupyterlab/packages/...
  • 2c262e5 Fix: --quiet also suppresses warning for directory creation (#1526)
  • 0bfcec1 build(deps): bump fast-uri from 3.1.0 to 3.1.2 in /jupyterlab (#1524)
  • 611e2c0 Explicitly close NotebookNotary signature store (#1528)
  • 70b1f20 All tests run after coverage tests have passed (#1527)
  • 399e934 Close SQLite database connections of Jupytext-created notaries
  • Additional commits viewable in compare view

Updates sphinxcontrib-mermaid from 2.0.1 to 2.0.2

Changelog

Sourced from sphinxcontrib-mermaid's changelog.

Changelog

Unreleased

  • Add mermaid_dark_theme and mermaid_light_theme config options for configurable theme switching
Commits
  • 19be468 Merge pull request #240 from timkpaine/tkp/hatch
  • e1f9ecc Switch to hatchling
  • 42aa20a Merge pull request #239 from timkpaine/tkp/202
  • 2db5b55 bump to 2.0.2
  • 25c7ef7 Merge pull request #237 from kartben/local_paths
  • e98c6f8 increase test coverage for _use_local options
  • 1422b45 Resolve local Mermaid/ELK/ZenUML/D3 JS paths under html_static_path
  • d6d874c Merge pull request #236 from jensens/configurable-theme
  • bce5976 Document mermaid_dark_theme and mermaid_light_theme config options
  • 12bb2ac Add mermaid_dark_theme and mermaid_light_theme config options
  • See full diff in compare view

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@dependabot
Bump the python-packages group across 1 directory with 6 updates
f26f624 
Bumps the python-packages group with 6 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [duckdb](https://github.com/duckdb/duckdb-python) | `1.5.2` | `1.5.3` |
| [parsl](https://github.com/Parsl/parsl) | `2026.4.27` | `2026.6.1` |
| [pycytominer](https://github.com/cytomining/pycytominer) | `1.4.0` | `1.5.1` |
| [black](https://github.com/psf/black) | `26.3.1` | `26.5.1` |
| [jupytext](https://github.com/mwouts/jupytext) | `1.19.1` | `1.19.3` |
| [sphinxcontrib-mermaid](https://github.com/mgaitan/sphinxcontrib-mermaid) | `2.0.1` | `2.0.2` |



Updates `duckdb` from 1.5.2 to 1.5.3
- [Release notes](https://github.com/duckdb/duckdb-python/releases)
- [Commits](duckdb/duckdb-python@v1.5.2...v1.5.3)

Updates `parsl` from 2026.4.27 to 2026.6.1
- [Commits](Parsl/parsl@2026.04.27...2026.06.01)

Updates `pycytominer` from 1.4.0 to 1.5.1
- [Release notes](https://github.com/cytomining/pycytominer/releases)
- [Changelog](https://github.com/cytomining/pycytominer/blob/main/CHANGELOG.md)
- [Commits](cytomining/pycytominer@v1.4.0...v1.5.1)

Updates `black` from 26.3.1 to 26.5.1
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@26.3.1...26.5.1)

Updates `jupytext` from 1.19.1 to 1.19.3
- [Release notes](https://github.com/mwouts/jupytext/releases)
- [Changelog](https://github.com/mwouts/jupytext/blob/main/CHANGELOG.md)
- [Commits](mwouts/jupytext@v1.19.1...v1.19.3)

Updates `sphinxcontrib-mermaid` from 2.0.1 to 2.0.2
- [Changelog](https://github.com/mgaitan/sphinxcontrib-mermaid/blob/master/CHANGELOG.md)
- [Commits](mgaitan/sphinxcontrib-mermaid@2.0.1...2.0.2)

---
updated-dependencies:
- dependency-name: duckdb
  dependency-version: 1.5.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: parsl
  dependency-version: 2026.6.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pycytominer
  dependency-version: 1.5.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: black
  dependency-version: 26.5.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: jupytext
  dependency-version: 1.19.3
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: sphinxcontrib-mermaid
  dependency-version: 2.0.2
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added the dependencies Pull requests that update a dependency file label Jun 3, 2026
@dependabot dependabot Bot requested a review from gwaybio as a code owner June 3, 2026 15:56
@dependabot dependabot Bot added the python Pull requests that update Python code label Jun 3, 2026
@dependabot dependabot Bot requested a review from d33bs as a code owner June 3, 2026 15:56
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Jun 3, 2026
@d33bs d33bs merged commit 1d364f1 into main Jun 3, 2026
10 checks passed
@dependabot dependabot Bot deleted the dependabot/pip/python-packages-7064c79004 branch June 3, 2026 16:21
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