build(deps): bump the github-dependencies group in /docker with 6 updates

[dependabot]

Updates the requirements on geopandas, jupyterlab, jupyterlab-widgets, numpy, pandas and shapely to permit the latest version.
Updates geopandas from 1.0.1 to 1.1.1

Release notes

Sourced from geopandas's releases.

v1.1.1

A patch release containing minor regression fixes.

What's Changed

• REGR: fix GeoDataFrame constructor when np.nan given as only geometry by @​martinfleis in geopandas/geopandas#3591
• REGR: overlay with identity doesn't handle equal input column names correctly by @​theroggy in geopandas/geopandas#3596
• TST: use nadgrids=null to suppress influence of grid files by @​mwtoews in geopandas/geopandas#3588
• MAINT: enable pydocstyle ruff rules - automatic and easy fixes by @​theroggy in geopandas/geopandas#3598

Full Changelog: geopandas/geopandas@v1.1.0...v1.1.1

v1.1.0

Notes on dependencies:

• GeoPandas 1.1 now requires Python 3.10 or greater and pandas 2.0, numpy 1.24, pyproj 3.5, are now the minimum required version for these dependencies. Furthermore, the minimum tested version for optional dependencies has been updated to fiona 1.8.21, scipy 1.9, matplotlib 3.7, mapclassify 2.5, folium 0.12 and SQLAlchemy 2.0. Older versions of these libraries may continue to work, but are no longer considered supported (#3371).

New features and improvements:

• Added options to return the result of SpatialIndex.query in a form of a dense or a sparse boolean array. This adds optional dependency on scipy for the sparse output. Note that this also changes the previously undocumented behaviour of the output_format keyword (#1674).
• Add grid_size parameter to union_all and dissolve (#3445).
• GeoDataFrame.plot now supports pd.Index as an input for the column keyword (#3463).
• Added disjoint_subset union algorithm for union_all and dissolve (#3534).
• Added constrained_delaunay_triangles method to GeoSeries/GeoDataFrame (#3552).
• Added to_pandas_kwargs argument to from_arrow, read_parquet and read_feather to allow better control of conversion of non-geometric Arrow data to DataFrames (#3466).
• Added is_valid_coverage and invalid_coverage_edges to GeoSeries/GeoDataFrame to allow validation of polygonal coverage (#3545).
• Added maximum_inscribed_circle method from shapely to GeoSeries/GeoDataFrame (#3544).
• Added minimum_clearance_line method from shapely to GeoSeries/GeoDataFrame (#3543).
• Added orient_polygons method from shapely to GeoSeries/GeoDataFrame (#3559).
• Added method and keep_collapsed argument to make_valid (#3548).
• Added simplify_coverage method for topological simplification of polygonal coverages to GeoSeries/GeoDataFrame (#3541).
• Added initial support of M coordinates (m and has_m properties, include_m in get_coordinates) (#3561).
• Added geom_equals_identical method exposing equals_identical from shapely to GeoSeries/GeoDataFrame (#3560).
• GeoPandas now attempts to use a range request when reading from an URL even if the header does not directly indicate its support (#3572).
• Added geopandas.accessors module. Import this module to register a pandas.Series.geo accessor, which exposes GeoSeries methods via pandas's extension mechanism (#3272).
• Improve performance of overlay with how=identity (#3504).

... (truncated)

Changelog

Sourced from geopandas's changelog.

Version 1.1.1 (June 27, 2025)

Bug fixes:

• Fix regression in the GeoDataFrame constructor when np.nan is given as an only geometry (#3591).
• Fix regression in overlay with how="identity" when input dataframes have column names that are equal (#3596).

Version 1.1.0 (June 1, 2025)

Notes on dependencies:

• GeoPandas 1.1 now requires Python 3.10 or greater and pandas 2.0, numpy 1.24, pyproj 3.5, are now the minimum required version for these dependencies. Furthermore, the minimum tested version for optional dependencies has been updated to fiona 1.8.21, scipy 1.9, matplotlib 3.7, mapclassify 2.5, folium 0.12 and SQLAlchemy 2.0. Older versions of these libraries may continue to work, but are no longer considered supported (#3371).

New features and improvements:

• Added options to return the result of SpatialIndex.query in a form of a dense or a sparse boolean array. This adds optional dependency on scipy for the sparse output. Note that this also changes the previously undocumented behaviour of the output_format keyword (#1674).
• Add grid_size parameter to union_all and dissolve (#3445).
• GeoDataFrame.plot now supports pd.Index as an input for the column keyword (#3463).
• Added disjoint_subset union algorithm for union_all and dissolve (#3534).
• Added constrained_delaunay_triangles method to GeoSeries/GeoDataFrame (#3552).
• Added to_pandas_kwargs argument to from_arrow, read_parquet and read_feather to allow better control of conversion of non-geometric Arrow data to DataFrames (#3466).
• Added is_valid_coverage and invalid_coverage_edges to GeoSeries/GeoDataFrame to allow validation of polygonal coverage (#3545).
• Added maximum_inscribed_circle method from shapely to GeoSeries/GeoDataFrame (#3544).
• Added minimum_clearance_line method from shapely to GeoSeries/GeoDataFrame (#3543).
• Added orient_polygons method from shapely to GeoSeries/GeoDataFrame (#3559).
• Added method and keep_collapsed argument to make_valid (#3548).
• Added simplify_coverage method for topological simplification of polygonal coverages to GeoSeries/GeoDataFrame (#3541).
• Added initial support of M coordinates (m and has_m properties, include_m in get_coordinates) (#3561).
• Added geom_equals_identical method exposing equals_identical from shapely to GeoSeries/GeoDataFrame (#3560).
• GeoPandas now attempts to use a range request when reading from an URL even if the header does not directly indicate its support (#3572).
• Added geopandas.accessors module. Import this module to register a pandas.Series.geo accessor, which exposes GeoSeries methods via pandas's extension mechanism (#3272).
• Improve performance of overlay with how=identity (#3504).
• A warning message is raised in read_file when a GeoDataFrame or GeoSeries mask and/or the source dataset is missing a defined CRS. (#3464)
• GeoDataFrame no longer hard-codes the class internally, allowing easier subclassing (#3505).

... (truncated)

Commits

• e9b58ce RLS: v1.1.1
• c6bf8b3 MAINT: enable pydocstyle ruff rules - automatic and easy fixes (#3598)
• 339c7f7 TST: use nadgrids=null to suppress influence of grid files (#3588)
• 2a7fad9 REGR: overlay with identity doesn't handle equal input column names correctly...
• 1a1585d REGR: fix GeoDataFrame constructor when np.nan given as only geometry (#3591)
• c36eba0 RSL: changelog for 1.1.0 release (#3586)
• 2d6b332 remove remote url xfail (#3585)
• ce86559 DOC: Drafted new documentation page outlining how to create inset maps and in...
• d0ffe06 ENH: add error message when reading dataset without crs with a GeoDataFrame o...
• f3f145f CI: xfail remote url test for now (#3584)
• Additional commits viewable in compare view

Updates jupyterlab from 4.4.9 to 4.4.10

Release notes

Sourced from jupyterlab's releases.

v4.4.10

4.4.10

(Full Changelog)

Bugs fixed

• Fix ObservableList.removeValue behaviour: if item isn't found, don't just remove the last item! #18019 (@​robertstrauss)
• Fix highlighting search on output cells and previous match skips #17797 (@​itsmevichu)
• Fix spurious scrollbar in output area due to prompt overlay #17981 (@​shreve)
• Fix race condition renaming unnamed files on first save #17982 (@​shreve)
• Fix empty whitespace after large cell rendering #17949 (@​Meriem-BenIsmail)

Maintenance and upkeep improvements

• Bandaid: pin ipykernel on CI to pre-7.0 #17992 (@​krassowski)
• Fix examples on 4.4.x #17963 (@​krassowski)
• Temporarily pin ipykernel to avoid CI breakage with 7.0 pre-release #17957 (@​arjxn-py)

Documentation improvements

• Update JupyterCon 2025 announcement links #17983 (@​krassowski)
• Add cross-references to API reference, fix missing packages in API #17953 (@​krassowski)
• Fix parameter documentation issues in API reference #17954 (@​krassowski)

Contributors to this release

(GitHub contributors page for this release)

@​andrii-i | @​arjxn-py | @​Darshan808 | @​github-actions | @​hxrshxz | @​jtpio | @​jupyterlab-probot | @​krassowski | @​lumberbot-app | @​martinRenou | @​meeseeksmachine

Commits

• a4e885c [ci skip] Publish 4.4.10
• 58c8b82 Backport PR #18019: Fix ObservableList.removeValue behaviour: if item isn't...
• fef0b41 Backport PR #17797: Fix highlighting search on output cells and previous matc...
• 0a22bdf Backport PR #17981: Fix spurious scrollbar in output area due to prompt overl...
• e5034ac Backport PR #17982: Fix race condition renaming unnamed files on first save (...
• 28d76c0 Backport PR #17992: Bandaid: pin ipykernel on CI to pre-7.0 (#17995)
• 21e0f10 Backport PR #17983: Update JupyterCon 2025 announcement links (#17989)
• 55f0f1d Backport PR #17949: Fix empty whitespace after large cell rendering (#17968)
• 86a9e8d Backport PR #17953: Add cross-references to API reference, fix missing packag...
• 07ae5fe Fix examples on 4.4.x (#17963)
• Additional commits viewable in compare view

Updates jupyterlab-widgets from 3.0.13 to 3.0.15

Commits

• See full diff in compare view

Updates numpy to 2.3.4

Release notes

Sourced from numpy's releases.

v2.3.4 (Oct 15, 2025)

NumPy 2.3.4 Release Notes

The NumPy 2.3.4 release is a patch release split between a number of maintenance updates and bug fixes. This release supports Python versions 3.11-3.14. This release is based on Python 3.14.0 final.

Changes

The npymath and npyrandom libraries now have a .lib rather than a .a file extension on win-arm64, for compatibility for building with MSVC and setuptools. Please note that using these static libraries is discouraged and for existing projects using it, it's best to use it with a matching compiler toolchain, which is clang-cl on Windows on Arm.

(gh-29750)

Contributors

A total of 17 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• !DWesl
• Charles Harris
• Christian Barbia +
• Evgeni Burovski
• Joren Hammudoglu
• Maaz +
• Mateusz Sokół
• Matti Picus
• Nathan Goldbaum
• Ralf Gommers
• Riku Sakamoto +
• Sandeep Gupta +
• Sayed Awad
• Sebastian Berg
• Sergey Fedorov +
• Warren Weckesser
• dependabot[bot]

Pull requests merged

A total of 30 pull requests were merged for this release.

• #29725: MAINT: Prepare 2.3.x for further development
• #29781: MAINT: Pin some upstream dependences
• #29782: BLD: enable x86-simd-sort to build on KNL with -mavx512f
• #29783: BUG: Include python-including headers first (#29281)
• #29784: TYP: fix np.number and np.*integer method declaration
• #29785: TYP: mypy 1.18.1

... (truncated)

Commits

• 1458b9e REL: Prepare for the NumPy 2.3.4 release (#29955)
• 7583bed Merge pull request #29950 from charris/backport-29885
• 3186751 Merge pull request #29949 from charris/backport-29948
• 7fd2ad9 STY: rename @classmethod arg to cls
• fe8447d MAINT: Simplify string arena growth strategy (#29885)
• a90f073 Merge pull request #29940 from charris/backport-29937
• 55d91ab MAINT: Bump pypa/cibuildwheel from 3.1.4 to 3.2.1
• e2f0383 Merge pull request #29926 from charris/backport-29609
• b427e83 BUG: fix negative samples generated by Wald distribution (#29609)
• 36363d6 Merge pull request #29922 from charris/backport-29914
• Additional commits viewable in compare view

Updates pandas from 1.5.3 to 2.3.3

Release notes

Sourced from pandas's releases.

Pandas 2.3.3

We are pleased to announce the release of pandas 2.3.3. This release includes some improvements and fixes to the future string data type (preview feature for the upcoming pandas 3.0). We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.3.3 supports Python 3.9 and higher, and is the first release to support Python 3.14.

The release will be available on the conda-forge channel:

conda install pandas --channel conda-forge

Or via PyPI:

python3 -m pip install --upgrade pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Pandas 2.3.2

We are pleased to announce the release of pandas 2.3.2. This release includes some improvements and fixes to the future string data type (preview feature for the upcoming pandas 3.0). We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.3.2 supports Python 3.9 and higher.

The release will be available on the conda-forge channel:

conda install pandas --channel conda-forge

Or via PyPI:

python3 -m pip install --upgrade pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Pandas 2.3.1

We are pleased to announce the release of pandas 2.3.1. This release includes some improvements and fixes to the future string data type (preview feature for the upcoming pandas 3.0). We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.3.1 supports Python 3.9 and higher.

The release will be available on the conda-forge channel:

conda install pandas --channel conda-forge

Or via PyPI:

... (truncated)

Commits

• 9c8bc3e RLS: 2.3.3
• 6aa788a [backport 2.3.x] DOC: prepare 2.3.3 whatsnew notes for release (#62499) (#62508)
• b64f0df [backport 2.3.x] BUG: avoid validation error for ufunc with string[python] ar...
• 058eb2b [backport 2.3.x] BUG: String[pyarrow] comparison with mixed object (#62424) (...
• 2ca088d [backport 2.3.x] DEPR: remove the Period resampling deprecation (#62480) (#62...
• 92bf98f [backport 2.3.x] BUG: fix .str.isdigit to honor unicode superscript for older...
• e57c7d6 Backport PR #62452 on branch 2.3.x (TST: Adjust tests for numexpr 2.13) (#62454)
• e0fe9a0 Backport to 2.3.x: REGR: from_records not initializing subclasses properly (#...
• 23a1085 BUG: improve future warning for boolean operations with missaligned indexes (...
• 6113696 Backport PR #62396 on branch 2.3.x (PKG/DOC: indicate Python 3.14 support in ...
• Additional commits viewable in compare view

Updates shapely from 2.0.4 to 2.1.2

Release notes

Sourced from shapely's releases.

2.1.2

Wheels are available for Python 3.14 (and still include GEOS 3.13.1).

2.1.1

Bug fixes:

• Fix performance degradation calling shapely functions (caused by deprecation of certain positional arguments) (#2283).
• Fix crash caused by from_ragged_array() (#2291).
• Fix compilation error building with recent LLVM toolchain (#2293).

For a full changelog , see https://shapely.readthedocs.io/en/latest/release/2.x.html#version-2-1-1

2.1.0

Shapely 2.1.0 is a feature release with various new functions, improvements and bug fixes. Highlights include initial support for geometries with M or ZM values, functionality for coverage validation and simplification, and a set of new top-level functions.

Shapely supports Python >= 3.10, and binary wheels on PyPI include GEOS 3.13.1 and are now also provided for musllinux (Alpine) x86_64 platforms.

For a full changelog, see https://shapely.readthedocs.io/en/latest/release/2.x.html#version-2-1-0

2.1.0rc1

Shapely version 2.1.0 is a major release featuring various new functions, improvements and bug fixes. This is a first release candidate.

For a full changelog, see https://shapely.readthedocs.io/en/latest/release/2.x.html#version-2-1-0-unreleased

2.0.7

Shapely 2.0.7 fixes 3 bugs:

• Fix compilation error on certain Linux platforms, such as Alpine (#1945).
• Fixes crash when reading nonlinear geometry types (CircularString, CompoundCurve, MultiCurve, CurvePolygon, MultiSurface) from WKB/WKT with GEOS >= 3.13; these types are not yet supported in Shapely and now raise a NotImplementedError (#2160)
• Fix the project() method to return a Python float (#2093).

Wheels include GEOS 3.11.4.

For a full changelog, see https://shapely.readthedocs.io/en/latest/release/2.x.html#version-2-0-7.

2.0.6

Wheels are available for Python 3.13 (and still include GEOS 3.11.4).

Bug fixes:

• Fix compatibility with NumPy 2.1.0 (#2099).

For a full changelog, see https://shapely.readthedocs.io/en/latest/release/2.x.html#version-2-0-6

2.0.5

Binary wheels on PyPI include GEOS 3.11.4 from 2024-06-05. Furthermore, universal2 wheels are removed for macOS since both x86_64 and arm64 wheels are provided.

Bug fixes:

• Fix Point x/y/z attributes to return Python floats (#2074).

... (truncated)

Changelog

Sourced from shapely's changelog.

2.1.2 (2025-09-24)

Wheels are available for Python 3.14 (and still include GEOS 3.13.1).

2.1.1 (2025-05-19)

Bug fixes:

• Fix performance degradation calling shapely functions (caused by deprecation of certain positional arguments) (#2283).
• Fix crash caused by from_ragged_array() (#2291).
• Fix compilation error building with recent LLVM toolchain (#2293).

2.1.0 (2025-04-03)

Shapely 2.1.0 is a feature release with various new functions, improvements and bug fixes. Highlights include initial support for geometries with M or ZM values, functionality for coverage validation and simplification, and a set of new top-level functions.

Shapely supports Python >= 3.10, and binary wheels on PyPI include GEOS 3.13.1 and are now also provided for musllinux (Alpine) x86_64 platforms.

For a full changelog, see https://shapely.readthedocs.io/en/latest/release/2.x.html#version-2-1-0

2.0.7 (2025-01-30)

Bug fixes:

• Fix compilation error on certain Linux platforms, such as Alpine (#1945).
• Fixes crash when reading nonlinear geometry types (CircularString, CompoundCurve, MultiCurve, CurvePolygon, MultiSurface) from WKB/WKT with GEOS >= 3.13; these types are not yet supported in Shapely and now raise a NotImplementedError (#2160)
• Fix the project method to return a Python float (#2093).

2.0.6 (2024-08-19)

Bug fixes:

• Fix compatibility with NumPy 2.1.0 (#2099).

... (truncated)

Commits

• 5fb639d RLS: 2.1.2
• 70509a1 DOC/RLS: indicate Python 3.14 support in pyproject.toml and release notes for...
• 5c572b6 CI: add testing with GEOS 3.14 and Python 3.14 (#2330)
• a909333 Bump pypa/cibuildwheel from 3.1.3 to 3.2.0 (#2328)
• 2086d44 Bump actions/setup-python from 5 to 6 (#2326)
• 50c1cf3 Bump actions/download-artifact from 4 to 5 (#2321)
• 39490ab TST: update test_coverage_union_overlapping_inputs for upstream GEOS change (...
• 5ef437c Bump actions/checkout from 4 to 5 (#2320)
• 7b5ff3d BLD: add Python 3.14 wheels [Bump pypa/cibuildwheel from 3.0.1 to 3.1.3] (#2316)
• 480dbb1 TST: update frechet_distance densify test for latest GEOS main (densify>0.001...
• Additional commits viewable in compare view

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Automatic rebases have been disabled on this pull request as it has been open for over 30 days.

[jbampton]

The "first interaction workflow" failure is not related to this PR.

We now get 6 updates here after #2429

Based on the passing CI tests this PR seems ok.

Perhaps another reviewer can test further ?

[jbampton]

@dependabot rebase