deps: bump the python-dependencies group with 7 updates

[dependabot]

Bumps the python-dependencies group with 7 updates:

Package	From	To
matplotlib	3.11.0	3.11.1
numpy	2.5.1	2.5.2
pandas	3.0.3	3.0.5
rebound	4.6.0	5.1.1
reboundx	4.6.2	4.6.1
skyfield	1.54	1.55
ruff	0.15.21	0.16.3

Updates matplotlib from 3.11.0 to 3.11.1

Release notes

Sourced from matplotlib's releases.

REL: v3.11.1

This is the first bugfix release of the 3.11.x series.

This release contains several bug-fixes and adjustments:

• Fix tight layout of multiple subplots with sharey=True
• Fix NoNorm cursor formatting for uint8 images
• Fix occasional misalignment in reported mouse position (also fix a bug with canvas height)
• Fix clipped Axis labels on 3D plots with tight layout
• Fix inverted Axis on 3D plots
• Fix restoring 'auto' aspect in 3D axes after switching from 'equal'
• Fix missing glyphs when subsetting Type 1 fonts in PDF
• Fix oversized embedding of Type 42 fonts in PDF/PostScript files

As well as several documentation and typing improvements and corrections.

Commits

• 3c1757a REL: v3.11.1
• 792c6b5 DOC: Prepare for 3.11.1
• aaff9f6 Merge branch 'v3.11.0-doc' into v3.11.x
• d4f4527 Merge pull request #32052 from meeseeksmachine/auto-backport-of-pr-32038-on-v...
• 6ad4bcf Merge pull request #32050 from meeseeksmachine/auto-backport-of-pr-31304-on-v...
• 7fb74d3 Merge pull request #32051 from meeseeksmachine/auto-backport-of-pr-32037-on-v...
• c624aec Backport PR #32038: Fix occasional misalignment in reported mouse position (a...
• 8eda2b7 Backport PR #32037: Bump the actions group with 3 updates
• a0e7ae5 Backport PR #31304: Fix restoring 'auto' aspect in 3D axes after switching fr...
• 9001323 Merge pull request #32047 from meeseeksmachine/auto-backport-of-pr-32025-on-v...
• Additional commits viewable in compare view

Updates numpy from 2.5.1 to 2.5.2

Release notes

Sourced from numpy's releases.

v2.5.2 (Aug 9, 2026)

NumPy 2.5.2 Release Notes

The NumPy 2.5.2 is a patch release that fixes bugs discovered after the 2.5.1 release. The big news is that it includes wheels for the newly released Python 3.15.0rc1.

This release supports Python versions 3.12-3.15

C API changes

PyArray_StringDTypeObject is opaque under the abi3t stable ABI

The PyArray_StringDTypeObject was accidentally exposed in NumPy 2.5 when targeting the free-threading-compatible stable ABI (Py_TARGET_ABI3T). PyArray_StringDTypeObject is now an opaque struct: extensions compiled that way cannot access its fields, since the struct layout depends on the size of the object header. Any code that accessed PyArray_StringDTypeObject fields in an abi3t build would have crashed, so we are making this API change in a bugfix release.

The NpyString allocator API remains usable by passing the descriptor object pointer, e.g. NpyString_acquire_allocator((PyArray_StringDTypeObject *)descr).

(gh-31771)

Contributors

A total of 16 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Abhijeetsingh Meena +
• Charalampos Stratakis
• Charles Harris
• Chris Ninham +
• David Woods
• Geonho +
• Gopu Yeshwanth Reddy +
• Iason Krommydas
• Ijtihed Kilani
• Jelle Zijlstra +
• Joren Hammudoglu
• Kumar Aditya
• Mike Boyle
• Nathan Goldbaum
• Raghuveer Devulapalli
• Sebastian Berg

... (truncated)

Commits

• 48fecee REL: Prepare for the NumPy 2.5.2 release (#32226)
• ecf599c Merge pull request #32221 from charris/backport-32151
• 3c7ac97 Merge pull request #32220 from charris/backport-32205
• 23b30f4 BUG: avoid segfaults when legacy copyswap slot is not defined (#32151)
• 4964ca8 TYP: isclose shape-typing fix for 2d array-likes (#32205)
• c37ed94 MAINT: Skip limited_api tests on some platforms. (#32214)
• 5cfd73b Merge pull request #32206 from charris/update-cibuildwheel
• d8262bc MAINT: Update cibuildwheel to v4.2.0
• 988d94d Merge pull request #32158 from charris/backport-32133
• b2e4f97 BUG: avoid possible stack overflow in arraydescr_dealloc (#32133)
• Additional commits viewable in compare view

Updates pandas from 3.0.3 to 3.0.5

Release notes

Sourced from pandas's releases.

pandas 3.0.5

We are pleased to announce the release of pandas 3.0.5. This is a patch release in the 3.0.x series and includes some regression fixes and bug fixes. We recommend that all users of the 3.0.x series upgrade to this version.

See the full whatsnew for a list of all the changes.

Pandas 3.0 supports Python 3.11 and higher. The release can be installed from PyPI:

python -m pip install --upgrade pandas==3.0.*

Or from conda-forge

conda install -c conda-forge pandas=3.0

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

Thanks to all the contributors who made this release possible.

pandas 3.0.4

We are pleased to announce the release of pandas 3.0.4. This is a patch release in the 3.0.x series and includes some regression fixes and bug fixes. We recommend that all users of the 3.0.x series upgrade to this version.

See the full whatsnew for a list of all the changes.

Pandas 3.0 supports Python 3.11 and higher. The release can be installed from PyPI:

python -m pip install --upgrade pandas==3.0.*

Or from conda-forge

conda install -c conda-forge pandas=3.0

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

Thanks to all the contributors who made this release possible.

Commits

• e68db09 RLS: 3.0.5
• 0697623 Backport PR #66428: DOC: update whatsnew for 3.0.5 (#66430)
• 5d846d0 Backport PR #66090 on branch 3.0.x (BLD: exclude numpy 2.5.0 when building wh...
• bef7a2b Backport PR #66169 on branch 3.0.x (CI: Fix pyarrow-nightly job (stale nightl...
• 8188eb1 RLS: 3.0.4 (#66079)
• bd35f15 [3.0.x] BUG: fix CoW issue in eval() (#66072)
• 6195872 [backport 3.0.x] BUG: anchor whole alternation in Series.str.match for PyArro...
• 70313be Backport PR #66051 on branch 3.0.x (BUG: fix regression in DataFrame setitem ...
• 57ed3e2 [backport 3.0.x] Bump pypa/cibuildwheel from 3.4.1 to 4.1.0 (#65934) (#66026)
• f9693fc [backport 3.0.x] BUG(pandas 3.0 regression): drop(index=...) doesn't accept N...
• Additional commits viewable in compare view

Updates rebound from 4.6.0 to 5.1.1

Release notes

Sourced from rebound's releases.

5.1.1

• Fixed python source dist.
• Added python wheels for 3.13 and 3.14.

5.1.0

• Updated WHFast512. See Dagli and Rein (in prep) for details. WHFast512 is now written in x86 assembly, it uses Jacobi coordinates, supports symplectic correctors, and close encounter and ejection checks. The accuracy of the scheme is up to 5 orders of magnitude better and long term bias in the Kepler solver has been reduced. The walltime required to integrate the Solar System for 5Gyr has been reduced to only 8.7 hours.
• Updated build system for both C and python to support assembly code on Linux and Windows. MacOS does not support 64bit x86 CPUs.
• reb_simulation_steps() now stops if the simulation's status indicates an error.

5.0.1

• Optimized Lazy Kernel method in WHFast.
• Fixed bug in WHFast512 when GR is enabled, related to backreaction.
• Fixed size of integers in collision structure in python.

5.0.0

• This release incorporates major updates and breaks backwards compatability.
• Particles can now be identified with a name. The names can be any string. The memory for names is managed by REBOUND. Names are automatically stored in Simulationarchives. Hashes are now longer available to identify particles.
• A new interface for integrators has beed added. Thanks to this all the functionality provided by an integrator are implemented in the integrator's C file. This also makes it much easier to experiment with new integrators. To set an integrator from C, you now need to use a function and pass it a string: reb_simulation_set_integrator(r, "ias15"). The syntax from python remains the same to set the integrator. Integrator attributes can now be set in python without the ri_* structs, e.g. sim.integrator.safe_mode = 1 now works for WHFast.
• Python bindings are automatically generated for both built-in and custom imtegrators. This includes documentation strings (__doc__) and support for setting enumeration values with a string.
• The python structures Simulation and Particle only allow setting attributes that correspond to fields in the C structures. This makes it much easier to find bugs where previously a typo in an assignment failed silently.
• The file format for the Simulationarchive has been changed. Note that you can not read Simulationsarchives that were saved with a previous version.
• The reb_simulation_add_fmt() function now allows for angles to be initialized with a uniform distribution. The synatx is reb_simulation_add_fmt(r, "a e uniform(omega)", 1.0, 0.1).
• The particle array is now kept sorted by default. The user doesn't need to manually specify that the particles should be kept sorted when a particle gets removed.
• The tree structure is now regenerated from scratch at every timestep instead of updating a previously generated tree. This simplifies the logic significantly does not negatively affect the runtime.
• Python installs from source are faster.
• Many other small bug fixes and improvements.

Version 4.x

Changelog

Sourced from rebound's changelog.

Version 5.1.1

• Fixed python source dist.
• Added python wheels for 3.13 and 3.14.

Version 5.1.0

• Updated WHFast512. See Dagli and Rein (in prep) for details. WHFast512 is now written in x86 assembly, it uses Jacobi coordinates, supports symplectic correctors, and close encounter and ejection checks. The accuracy of the scheme is up to 5 orders of magnitude better and long term bias in the Kepler solver has been reduced. The walltime required to integrate the Solar System for 5Gyr has been reduced to only 8.7 hours.
• Updated build system for both C and python to support assembly code on Linux and Windows. MacOS does not support 64bit x86 CPUs.
• reb_simulation_steps() now stops if the simulation's status indicates an error.

Version 5.0.1

• Optimized Lazy Kernel method in WHFast.
• Fixed bug in WHFast512 when GR is enabled, related to backreaction.
• Fixed size of integers in collision structure in python.

Version 5.0.0

• This release incorporates major updates and breaks backwards compatability.
• Particles can now be identified with a name. The names can be any string. The memory for names is managed by REBOUND. Names are automatically stored in Simulationarchives. Hashes are now longer available to identify particles.
• A new interface for integrators has beed added. Thanks to this all the functionality provided by an integrator are implemented in the integrator's C file. This also makes it much easier to experiment with new integrators. To set an integrator from C, you now need to use a function and pass it a string: reb_simulation_set_integrator(r, "ias15"). The syntax from python remains the same to set the integrator. Integrator attributes can now be set in python without the ri_* structs, e.g. sim.integrator.safe_mode = 1 now works for WHFast.
• Python bindings are automatically generated for both built-in and custom imtegrators. This includes documentation strings (__doc__) and support for setting enumeration values with a string.
• The python structures Simulation and Particle only allow setting attributes that correspond to fields in the C structures. This makes it much easier to find bugs where previously a typo in an assignment failed silently.
• The file format for the Simulationarchive has been changed. Note that you can not read Simulationsarchives that were saved with a previous version.
• The reb_simulation_add_fmt() function now allows for angles to be initialized with a uniform distribution. The synatx is reb_simulation_add_fmt(r, "a e uniform(omega)", 1.0, 0.1).
• The particle array is now kept sorted by default. The user doesn't need to manually specify that the particles should be kept sorted when a particle gets removed.
• The tree structure is now regenerated from scratch at every timestep instead of updating a previously generated tree. This simplifies the logic significantly does not negatively affect the runtime.
• Python installs from source are faster.
• Many other small bug fixes and improvements.

Version 4.x

Commits

• 33549d1 Updating version to 5.1.1
• b0c25d4 bump version of cibuildwheels
• 8124bee Add assembly files to source distribution, see #928
• ec50fc0 Updated WHFast512
• cabb68a Updating version to 5.0.1
• cf99043 Fixed wrong integer size in python collision struct. Closes #925.
• 7ce88e3 docs: add missing python code block opening tag in timestepping.md (#924)
• 6c44115 moved variable inside if block
• 9f69849 removed polyfill
• 9cc8f3c Return nan if particle is not found in reb_simulation_jacobi_com().
• Additional commits viewable in compare view

Updates reboundx from 4.6.2 to 4.6.1

Changelog

Sourced from reboundx's changelog.

Version 4.6.2

• Updated to require REBOUND < 5.0

Version 4.6.1

• Updated to match REBOUND 4.6.0 (merging of internal part1 and part2 functions in integrators)

Version 4.6.0

• Added tides_dynamical to model dynamical tides following Vick & Lai 2019 (see Liveoak et al. 2025)

Version 4.5.0

• Fixed factor of two error in conservative piece of the tidal potential in Eggleton+98 in tides_spin

Version 4.4.2

• Fixed bug when resetting ODEs in tides_spin

Version 4.4.1

• Added support for uv installation

Version 4.4.0

• Added the ability to set the spin axis orientation to the gravitational harmonics (J2/J4) effect

Version 4.3.0

• Added Gas Damping Forces effect

Version 4.2.2

• Set path to local REBOUND installation when installing in editable mode

Version 4.2.1

• Fixed clang error, remove commented code

Version 4.2.0

• Removed wheels. Installation is now from source to avoid conflicts with different versions of REBOUND
• Fixed gr_full errors when Simulation was not in center of mass frame. Convergence was also improved and effect is now a bit faster.
• Improvements to unit tests (now regenerate simulationarchives each time)

Version 4.1.0

• Fixed inneredge effect
• Updated documentation and github actions

Version 4.0.0

• Added support for REBOUND version 4.0.0

Version 3.12.0

• Build REBOUNDx wheels for PyPI
• Updated unit tests

Version 3.11.0

• Added Lense-Thirring effect

Version 3.10.0

... (truncated)

Commits

• d52096a Merge pull request #156 from hannorein/spinremoval
• a6bbd2e Removes spin ODE before creating new one
• 8b4f8bf updated examples
• 9b3e165 fixed small issue
• See full diff in compare view

Updates skyfield from 1.54 to 1.55

Changelog

Sourced from skyfield's changelog.

v1.55 — 2026 August 7

• The Stellarium project has adopted a new file format for storing constellation lines, so Skyfield has gained a new function :func:~skyfield.data.stellarium.parse_constellations_json() and the example script :ref:neowise-chart in Skyfield’s documentation has been updated to use it.

• A new GM\ :sub:☉ constant is available for use with Kepler orbits. It’s named GM_SUN_DE440_km3_s2 and uses the value published with the DE440 ephemeris. The difference between it and the older constant GM_SUN_Pitjeva_2005_km3_s2 is probably too small to make any practical difference — they differ by a proportion of only about 5.4×10\ :sup:−12 — but because the newer constant’s name is easier to read and type, the Kepler documentation has been tweaked to use it instead.

• Fix: if :func:~skyfield.almanac.find_risings() or :func:~skyfield.almanac.find_settings() converged too quickly on the exact time of rising or setting, then they would print a RuntimeWarning: invalid value encountered in divide and return a NaN value instead of a time. [#1140](https://github.com/brandon-rhodes/python-skyfield/issues/1140) <https://github.com/skyfielders/python-skyfield/issues/1140>_

• Skyfield’s refraction logic should no longer trigger the recent NumPy FutureWarning about the changes that NumPy is planning to make to np.bool.

Commits

• 8e8eb20 Declare version 1.55
• 1d42bae CI: add Stellarium file, so no download is needed
• db99f0e Switch to new Stellarium constellation file format
• 292212e Add GM Sun from ephemeris DE440 as a constant
• b6579fd Fix almanac inner function docstring (#1134)
• 771bb29 Fix 0/0 = NaN in the rise/set parabola fit (#1140)
• 40c6e6c Docs: reword intro to Planetary Reference Frames
• 7dfae00 Docs: for #1121 explain where position came from
• 127a730 Silence recent NumPy warning about np.bool
• f598772 Fix: refract() on array should return same angles
• Additional commits viewable in compare view

Updates ruff from 0.15.21 to 0.16.3

Release notes

Sourced from ruff's releases.

0.16.3

Release Notes

Released on 2026-08-13.

Preview features

• [pylint] Fix false negatives on negative numbers (PLR6104) (#27251)
• [pyupgrade] Add rule to replace while 1 with while True (UP048) (#27190)

Bug fixes

• [flake8-bandit] Also check keyword arguments (S602, S603, S607, S609) (#27687)
• [pylint] Allow continue in finally on Python 3.8 (#27626)
• [pylint] Fix PLE1307 false positive with bools (#27651)
• [pylint] Fix false positives and negatives with %b format character (PLE1300, PLE1307) (#27560)
• [pylint] Improve handling of concatenated strings (PLE1300) (#27659)

Rule changes

• [numpy] Make np.chararray autofix backwards-compatible (NPY201) (#27527)

Performance

• Enable PGO for Linux x86-64 Ruff releases (#27570)
• Enable PGO for Linux ARM64 Ruff releases (#27574)
• Enable PGO for Windows x86-64 Ruff releases (#27573)
• Enable PGO for macOS ARM64 Ruff releases (#27572)
• Reduce Expr size to 64 bytes (#27591)

CLI

• Hyperlink rule codes in ruff check --statistics output (#27646)

Documentation

• [ruff] Also suggest asyncio.TaskGroup (RUF006) (#27461)

Other changes

• Use mimalloc v3 (#27586)

Contributors

• @​Andrej730
• @​alonfaraj
• @​romero-deshaw
• @​Avasam
• @​tjkuson
• @​charliermarsh

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.3

Released on 2026-08-13.

Preview features

• [pylint] Fix false negatives on negative numbers (PLR6104) (#27251)
• [pyupgrade] Add rule to replace while 1 with while True (UP048) (#27190)

Bug fixes

• [flake8-bandit] Also check keyword arguments (S602, S603, S607, S609) (#27687)
• [pylint] Allow continue in finally on Python 3.8 (#27626)
• [pylint] Fix PLE1307 false positive with bools (#27651)
• [pylint] Fix false positives and negatives with %b format character (PLE1300, PLE1307) (#27560)
• [pylint] Improve handling of concatenated strings (PLE1300) (#27659)

Rule changes

• [numpy] Make np.chararray autofix backwards-compatible (NPY201) (#27527)

Performance

• Enable PGO for Linux x86-64 Ruff releases (#27570)
• Enable PGO for Linux ARM64 Ruff releases (#27574)
• Enable PGO for Windows x86-64 Ruff releases (#27573)
• Enable PGO for macOS ARM64 Ruff releases (#27572)
• Reduce Expr size to 64 bytes (#27591)

CLI

• Hyperlink rule codes in ruff check --statistics output (#27646)

Documentation

• [ruff] Also suggest asyncio.TaskGroup (RUF006) (#27461)

Other changes

• Use mimalloc v3 (#27586)

Contributors

• @​Andrej730
• @​alonfaraj
• @​romero-deshaw
• @​Avasam
• @​tjkuson
• @​charliermarsh
• @​chirizxc

... (truncated)

Commits

• b0e4702 Bump 0.16.3 (#27723)
• ecdd401 [ty] Separate script and uv modules from project metadata (#27720)
• 1263524 [ty] Simplify display implementations with std::fmt::from_fn (#27718)
• 59196ba [ty] Unify polarity-aware relation construction (#27707)
• b8c5e73 [ty] Disable CodSpeed cycle estimation for instrumented benchmarks (#27706)
• 2b0d210 [ty] Centralize matched argument relations (#27705)
• a9130f3 [pyupgrade] Add rule to replace while 1 with while True (while-one, `...
• c64c7d6 [ty] Model try exception flow with operation checkpoints (#27471)
• 9dea5ef [ty] Avoid deriving sequents for typevars with concrete bounds (#27587)
• 9798e88 [ty] Preserve enum exhaustiveness with custom missing methods (#27700)
• Additional commits viewable in compare view

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