Bump the pip-version group with 4 updates

[dependabot]

Bumps the pip-version group with 4 updates: numpy, autodocsumm, furo and gemmi.

Updates numpy from 2.0.0 to 2.1.2

Release notes

Sourced from numpy's releases.

2.1.2 (Oct 5, 2024)

NumPy 2.1.2 Release Notes

NumPy 2.1.2 is a maintenance release that fixes bugs and regressions discovered after the 2.1.1 release.

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

Contributors

A total of 11 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Charles Harris
• Chris Sidebottom
• Ishan Koradia +
• João Eiras +
• Katie Rust +
• Marten van Kerkwijk
• Matti Picus
• Nathan Goldbaum
• Peter Hawkins
• Pieter Eendebak
• Slava Gorloff +

Pull requests merged

A total of 14 pull requests were merged for this release.

• #27333: MAINT: prepare 2.1.x for further development
• #27400: BUG: apply critical sections around populating the dispatch cache
• #27406: BUG: Stub out get_build_msvc_version if distutils.msvccompiler...
• #27416: BUILD: fix missing include for std::ptrdiff_t for C++23 language...
• #27433: BLD: pin setuptools to avoid breaking numpy.distutils
• #27437: BUG: Allow unsigned shift argument for np.roll
• #27439: BUG: Disable SVE VQSort
• #27471: BUG: rfftn axis bug
• #27479: BUG: Fix extra decref of PyArray_UInt8DType.
• #27480: CI: use PyPI not scientific-python-nightly-wheels for CI doc...
• #27481: MAINT: Check for SVE support on demand
• #27484: BUG: initialize the promotion state to be weak
• #27501: MAINT: Bump pypa/cibuildwheel from 2.20.0 to 2.21.2
• #27506: BUG: avoid segfault on bad arguments in ndarray.__array_function__

Checksums

MD5

4aae28b7919b126485c1aaccee37a6ba  numpy-2.1.2-cp310-cp310-macosx_10_9_x86_64.whl
172614423a82ef73d8752ad8a59cbafc  numpy-2.1.2-cp310-cp310-macosx_11_0_arm64.whl

... (truncated)

Changelog

Sourced from numpy's changelog.

This is a walkthrough of the NumPy 2.1.0 release on Linux, modified for building with GitHub Actions and cibuildwheels and uploading to the anaconda.org staging repository for NumPy <https://anaconda.org/multibuild-wheels-staging/numpy>_. The commands can be copied into the command line, but be sure to replace 2.1.0 by the correct version. This should be read together with the :ref:general release guide <prepare_release>.

Facility preparation

Before beginning to make a release, use the requirements/*_requirements.txt files to ensure that you have the needed software. Most software can be installed with pip, but some will require apt-get, dnf, or whatever your system uses for software. You will also need a GitHub personal access token (PAT) to push the documentation. There are a few ways to streamline things:

• Git can be set up to use a keyring to store your GitHub personal access token. Search online for the details.
• You can use the keyring app to store the PyPI password for twine. See the online twine documentation for details.

Prior to release

Add/drop Python versions

When adding or dropping Python versions, three files need to be edited:

• .github/workflows/wheels.yml # for github cibuildwheel
• .travis.yml # for cibuildwheel aarch64 builds
• setup.py # for classifier and minimum version check.

Make these changes in an ordinary PR against main and backport if necessary. Using the BLD: prefix (build label) for the commit summary will cause the wheel builds to be run so that the changes will be tested, We currently release wheels for new Python versions after the first Python rc once manylinux and cibuildwheel support it. For Python 3.11 we were able to release within a week of the rc1 announcement.

Backport pull requests

Changes that have been marked for this release must be backported to the maintenance/2.1.x branch.

Update 2.1.0 milestones

... (truncated)

Commits

• f5afe3d Merge pull request #27507 from charris/prepare-2.1.2
• 6b9ef48 REL: Prepare for the NumPy 2.1.2 release [wheel build]
• 6d85a24 MAINT: Pin setuptools for Python < 3.12 [wheel build]
• 7f327d8 Merge pull request #27506 from charris/backport-27503
• 09e9cd9 BUG: avoid segfault on bad arguments in ndarray.array_function
• 06b4793 Merge pull request #27501 from charris/backport-27495
• 364efb5 MAINT: Bump pypa/cibuildwheel from 2.21.1 to 2.21.2
• df0e261 Merge pull request #27484 from ngoldbaum/use-weak-default
• fa61bc6 Merge pull request #27481 from charris/backport-27472
• d6d06ae Merge pull request #27480 from charris/backport-27475
• Additional commits viewable in compare view

Updates autodocsumm from 0.2.12 to 0.2.14

Release notes

Sourced from autodocsumm's releases.

v0.2.14: autoexception-support and class member fixes

What's Changed

• Fix ObjectMember related deprecation/removal by @​theOehrly in Chilipp/autodocsumm#99
• Type hint mixin base class, fix some more minor style and typing issues by @​theOehrly in Chilipp/autodocsumm#100
• Don't document class attributes that are an alias to another object by @​theOehrly in Chilipp/autodocsumm#101
• Autoexception support by @​Chilipp in Chilipp/autodocsumm#104

Full Changelog: Chilipp/autodocsumm@v0.2.13...v0.2.14

Commits

• f81147e Merge pull request #104 from Chilipp/autoexception-support
• db473cf remove tests for sphinx==3.*
• 375b1c9 add autoexception to docs
• 4e51644 implement test for exception documenter
• ec89d70 implement exception documenter
• 811352b Merge pull request #101 from theOehrly/fix-69
• 0286ca8 Merge pull request #100 from theOehrly/cleanup
• 16bcd1c exclude line from coverage
• 5ef1b47 Merge pull request #99 from theOehrly/fix-89
• e4319d4 don't document class attributes that are an alias of another class
• Additional commits viewable in compare view

Updates furo from 2024.5.6 to 2024.8.6

Changelog

Sourced from furo's changelog.

Changelog

2024.08.06 -- Energetic Eminence

• ✨ Add support for Sphinx 8
• ✨ Add smoother transitions between breakpoints
• Increase specificity of table-wrapper selector
• Avoid page breaks inside paragraphs

2024.07.18 -- Dull Denim

• Improve how icons are handled and aligned.
• Improve scroll event handler.
• Hide the copybutton by default.
• Fix source_view_link configuration handling.
• Fix close tag on pencil icon.

2024.05.06 -- Cheerful Cerulean

• ✨ Add new custom icons for auto mode, reflecting the currently active theme.
• ✨ Add a view this page button.
• ✨ Add colours and highlighting to "version modified" API helpers.
• ✨ Add release information to various customisation knobs.
• Make all icons bigger and use a thinner stroke with them.

2024.04.27 -- Bold Burgundy

• Add a skip to content link.
• Add --font-stack--headings.
• Add :visited colour and enforce uniform contrast between light/dark.
• Add an offset of :target to reduce back-to-top overlap.
• Improve dark mode colours.
• Fix outstanding colour contrast warnings on Firefox.
• Fix bad indent in footnotes.
• Tweak handling of default configuration options in a more resilient manner.
• Tweak length and sizing of API source links.
• Stop search engine indexing on search page.

2024.01.29 -- Amazing Amethyst

... (truncated)

Commits

• 1bbf4ee Prepare release: 2024.08.06
• bcb22c3 Update changelog
• e633f02 Improve the selector for sidebar
• d2fa2e0 [pre-commit.ci] pre-commit autoupdate (#821)
• 05a2d63 Add smoother transitions between breakpoints
• d261d3b [pre-commit.ci] pre-commit autoupdate (#810)
• 2d3b6ba Add support for Sphinx 8
• bf98041 Increase specificity of table-wrapper selector
• fc6337c Fix the figures
• fd3f422 Avoid page breaks inside paragraphs
• Additional commits viewable in compare view

Updates gemmi from 0.6.3 to 0.6.7

Release notes

Sourced from gemmi's releases.

0.6.7

This is primarily a bug-fix release. New Python bindings are not included yet.

Enhancements:

• New subcommand gemmi set for changing coordinates, B-factors and occupancies in coordinate files (mmCIF and PDB). Unlike other tools, it replaces numbers while leaving the rest of the file intact. An alternative to CCP4 PDBSET keywords: BFACTOR, OCCUPANCY, SHIFT, NOISE. Note that gemmi convert offers overlapping capabilities. For instance, gemmi convert --apply-symop=x+0.123,y,z shifts the coordinates similarly to gemmi set --shift='9.3 0 0' (the latter takes the shift in Angstroms).

• Improved anisotropic scaling of structure factors. More work is planned in this area.

Fixes:

• fixed reading of mmCIF files without _atom_site.auth_seq_id
• in Topology preparation: fixed a couple of bugs, peptide links are now assumed to be CIS for ω=0±60° (previously, ω=0±30°)
• fixed re-assignment of ATOM/HETATM record types (gemmi convert --assign-records)
• fixed gemmi convert --sifts-num for UniProt sequence numbers >5000

And various minor changes that are hard to describe concisely.

0.6.6

Library:

• SmallStructure: changed how the space group is read and accessed. Relying on H-M space group names alone was not always sufficient. The new mechanism uses the list of operations and Hall symbol in preference to the H-M symbol – the order is configurable.
• symmetry triplets: parse decimal fractions (small molecule files may use notation such as x+0.25 instead of x+1/4)
• tabulated space groups: a few more settings: B 1 2 1, B 1 21 1, F 1 m 1, F 1 d 1, F 1 2 1
• X-ray scattering coefficients: changed the default value of IT92::ignore_charge to true (i.e. charges are now ignored by default; before version 0.6.3 they were always ignored)
• cif::Table: added method ensure_loop() that converts tag-value pairs into a loop; might be needed before calling append_row()
• place_hydrogens(): fix for NH3-like configurations
• improved gemmi->mmdb conversion
• Grid: tweaked good_grid_size() to ensure that when creating a grid up to a certain d_min, all reflections up to d_min are in the grid (it matters when no oversampling is applied)
• DensityCalculator: deprecated function set_grid_cell_and_spacegroup(), use grid.setup_from()
• fixed TNT-compatible reciprocal space ASU calculation for non-standard settings
• infer_polymer_end(): complicate the heuristic even more, to detect files that have HETATM incorrectly used for standard residues in a polymer (such files were reported, they are either a result of mutating from non-standard residues, or a buggy program)
• added function assign_het_flags() to re-set ATOM/HETATM flags
• Model: added funtions calculate_b_iso_range() and calculate_b_aniso_range(); the first one can be used to detect if pLDDT is in the range 0-100 (like from AlphaFold) or 0-1 (like from ESMFold)
• writing mmCIF: write _entity_poly_seq.hetero
• added flag Entity::reflects_microhetero that shows if sequences were read from SEQRES (and don't account for point mutations) or from _entity_poly_seq; new function add_microhetero_to_sequences() changes the former to the latter

Program:

• gemmi sfcalc: added a few more options
• gemmi convert: added options --assign-records[=A|H], improved --sifts-num, adding microheterogeneities to _entity_poly_seq when converting from PDB
• gemmi cifdiff: added option -t for basic comparison of values for a single tag

Other:

• minimal WebAssembly port (C++ code compiled with emscripten) of Structure, as a proof-of-concept and for reading mmCIF files in UglyMol
• examples/to_rdkit.py: example of conversion of gemmi ChemComp to RDKit Mol

and a number of less important changes

0.6.5

... (truncated)

Commits

• 0da57ac change version number to 0.6.7
• ba62a1c minor changes in response to automated checks run before a release
• be684b9 cmake: change FETCH_ZLIB_NG to download zlib-ng 2.2.x
• a574cdc update fast_float to v6.1.5
• 54d79c3 edit docs/analysis.rst
• a7f4f7a python bindings to a few more functions
• 1077566 avoid bogus GCC warning in Topo::apply_all_restraints
• c810526 cmake: fix "make check"
• 7b6738d gemmi-set: add option --select
• ee5c39f gemmi-set: edit help message [skip ci]
• Additional commits viewable in compare view

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Superseded by #26.