Bump the pip-version group across 1 directory with 4 updates

[dependabot]

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

Updates numpy from 2.0.0 to 2.1.1

Release notes

Sourced from numpy's releases.

2.1.1 (Sep 3, 2024)

NumPy 2.1.1 Release Notes

NumPy 2.1.1 is a maintenance release that fixes bugs and regressions discovered after the 2.1.0 release.

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

Contributors

A total of 7 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Andrew Nelson
• Charles Harris
• Mateusz Sokół
• Maximilian Weigand +
• Nathan Goldbaum
• Pieter Eendebak
• Sebastian Berg

Pull requests merged

A total of 10 pull requests were merged for this release.

• #27236: REL: Prepare for the NumPy 2.1.0 release [wheel build]
• #27252: MAINT: prepare 2.1.x for further development
• #27259: BUG: revert unintended change in the return value of set_printoptions
• #27266: BUG: fix reference counting bug in __array_interface__ implementation...
• #27267: TST: Add regression test for missing descr in array-interface
• #27276: BUG: Fix #27256 and #27257
• #27278: BUG: Fix array_equal for numeric and non-numeric scalar types
• #27287: MAINT: Update maintenance/2.1.x after the 2.0.2 release
• #27303: BLD: cp311- macosx_arm64 wheels [wheel build]
• #27304: BUG: f2py: better handle filtering of public/private subroutines

Checksums

MD5

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84b752a2220dce7c96ff89eef4f4aec3  numpy-2.1.1-cp310-cp310-macosx_11_0_arm64.whl
47ed4f704a64261f07ca24ef2e674524  numpy-2.1.1-cp310-cp310-macosx_14_0_arm64.whl
b8a45caa870aee980c298053cf064d28  numpy-2.1.1-cp310-cp310-macosx_14_0_x86_64.whl
e097ad5eee572b791b4a25eedad6df4a  numpy-2.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
ae502c99315884cda7f0236a07c035c4  numpy-2.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
841a859d975c55090c0b60b72aab93a3  numpy-2.1.1-cp310-cp310-musllinux_1_1_x86_64.whl
d51be2b17f5b87aac64ab80fdfafc85e  numpy-2.1.1-cp310-cp310-musllinux_1_2_aarch64.whl
1f8249bd725397c6233fe6a0e8ad18b1  numpy-2.1.1-cp310-cp310-win32.whl
d38d6f06589c1ec104a6a31ff6035781  numpy-2.1.1-cp310-cp310-win_amd64.whl

... (truncated)

Commits

• 48606ab Merge pull request #27328 from charris/prepare-2.1.1
• a7cb4c4 REL: Prepare for the NumPy 2.1.1 release [wheel build]
• 884c92b Merge pull request #27303 from charris/backport-27284
• ca7f5c1 Merge pull request #27304 from charris/backport-27049
• 2a49507 BUG: f2py: better handle filtering of public/private subroutines
• d4306dd TST: Add regression test for gh-26920
• db9668d BLD: cp311- macosx_arm64 wheels [wheel build]
• c6ff254 Merge pull request #27287 from charris/post-2.0.2-release-update
• 326bc17 MAINT: Update main after the 2.0.2 release
• 8164b7c Merge pull request #27278 from charris/backport-27275
• 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

Updates autodocsumm from 0.2.12 to 0.2.13

Commits

• 354e67b add sphinx classifiers
• 0cd8c23 Merge pull request #98 from theOehrly/sphinx-v8
• e5b8062 allow python 3.12
• f4b92fc reduce test matrix again
• dc36ddc fix tests and rework test workflow
• 71531bb allow sphinx v8
• 835eddb fix deprecations introduced by sphinx v8
• See full diff 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

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