Bump the pip-version group with 3 updates

[dependabot]

Bumps the pip-version group with 3 updates: numpy, gemmi and furo.

Updates numpy from 2.0.0 to 2.0.1

Release notes

Sourced from numpy's releases.

v2.0.1

NumPy 2.0.1 Release Notes

NumPy 2.0.1 is a maintenance release that fixes bugs and regressions discovered after the 2.0.0 release. NumPy 2.0.1 is the last planned release in the 2.0.x series, 2.1.0rc1 should be out shortly.

The Python versions supported by this release are 3.9-3.12.

NOTE: Do not use the GitHub generated "Source code" files listed in the "Assets", they are garbage.

Improvements

np.quantile with method closest_observation chooses nearest even order statistic

This changes the definition of nearest for border cases from the nearest odd order statistic to nearest even order statistic. The numpy implementation now matches other reference implementations.

(gh-26656)

Contributors

A total of 15 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• @​vahidmech +
• Alex Herbert +
• Charles Harris
• Giovanni Del Monte +
• Leo Singer
• Lysandros Nikolaou
• Matti Picus
• Nathan Goldbaum
• Patrick J. Roddy +
• Raghuveer Devulapalli
• Ralf Gommers
• Rostan Tabet +
• Sebastian Berg
• Tyler Reddy
• Yannik Wicke +

Pull requests merged

A total of 24 pull requests were merged for this release.

• #26711: MAINT: prepare 2.0.x for further development
• #26792: TYP: fix incorrect import in ma/extras.pyi stub
• #26793: DOC: Mention '1.25' legacy printing mode in set_printoptions
• #26794: DOC: Remove mention of NaN and NAN aliases from constants

... (truncated)

Commits

• 4c9f431 Merge pull request #27000 from charris/prepare-2.0.1
• 0e70e00 REL: Prepare for the NumPy 2.0.1 release [wheel build]
• 4d10ffc Merge pull request #26995 from charris/backport-26985
• 764b667 BUG: Add object cast to avoid warning with limited API
• 9be6ad6 Merge pull request #26971 from charris/backport-26935
• 6d950e9 BUG: fix f2py tests to work with v2 API
• 89630c0 Merge pull request #26962 from charris/backport-26919
• 88fa840 TST: Apply test suggestion by Nathan for rlstrip fixes
• a9da01e BUG,MAINT: Fix utf-8 character stripping memory access
• 6afbbf8 Merge pull request #26963 from charris/backport-26930
• Additional commits viewable in compare view

Updates gemmi from 0.6.3 to 0.6.6

Release notes

Sourced from gemmi's releases.

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

Library:

• gemmi can now be built with zlib-ng, a faster fork of zlib (good for working with large, compressed files)
• experimental: binary serialization of Structure (contained objects, such as Model, Chain or UnitCell, can also be serialized separately)
• finalized handling of 5-character monomer names; uses the tilde-hetnam extension (ABCDE ↔ ~DE) for PDB files
• when atom names in the coordinate file match previous names (_chem_comp_atom.alt_atom_id) from the monomer library (the names in the CCD and therefore also in the ML change occasionally), print better diagnostic; added function MonLib::update_old_atom_names() to update the names in a Structure
• topology: fixed handling of two bonds between the same two residues
• options for handling mmCIF files with incorrect entities (modified add_entity_ids() when called with overwrite=true)
• added function Intensities::prepare_merged_mtz()
• a few bug fixes (for instance, in handling of negative residue numbers in the selection syntax)

Python bindings:

• generating type stubs - see #293
• python: cif.Loop.val() has been replaced with __getitem__/__setitem__
• fixed Mtz.Batch.ints and Mtz.Batch.floats

Program

• subcommand diff has been renamed to cifdiff
• subcommand prep has been renamed to crd

... (truncated)

Commits

• 0b23c06 change version to 0.6.6
• d224ddf update serialize.hpp
• c14f3f1 add missing #include
• 77150a9 rename function from the previous commit
• e69466d fileutil.hpp: change deleter of fileptr_t
• 61fc1c8 avoid floating point == comparisons in static_assert
• 0186acb add cif::Table::ensure_loop()
• 64b6554 fix the previous commit
• afd2f48 DensityCalculator::set_refmac_compatible_blur(): add option allow_negative
• f3c57ea scaling: trying to estimate b_star before actual optimization
• Additional commits viewable in compare view

Updates furo from 2024.5.6 to 2024.7.18

Changelog

Sourced from furo's changelog.

Changelog

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

• Fix canonical url when building with dirhtml.
• Relicense the demo module.

2023.09.10 -- Zesty Zaffre

• Make asset hash injection idempotent, fixing Sphinx 6 compatibility.

... (truncated)

Commits

• 78e4ba2 Prepare release: 2024.07.18
• 6b61424 Update changelog
• 58b532c Make the issue tracker template more explicit
• 17e351e Add source_view_link to configuration
• 7e51bc7 Delete svg-sun-half (#811)
• 073c497 Move a 'type: ignore' comment, for mypy (#812)
• cefbdc0 Bump the npm group with 2 updates (#809)
• 7fb7ec8 Bump the npm group with 3 updates (#806)
• 25091fc [pre-commit.ci] pre-commit autoupdate (#796)
• 550756e Fix close tag on pencil icon (#807)
• Additional commits viewable in compare view

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[dependabot]

Looks like these dependencies are updatable in another way, so this is no longer needed.