build(deps): bump the dependencies group with 55 updates

[dependabot]

Updates the requirements on pymatgen-core, monty, maggma, setuptools, pre-commit, pytest, mypy, ruff, tox, annotated-types, ast-serialize, boto3, botocore, certifi, cffi, charset-normalizer, click, coverage, cryptography, distlib, docutils, filelock, idna, imagesize, kiwisolver, librt, linkify-it-py, lxml, matplotlib, mpmath, msgpack, narwhals, orjson, packaging, pandas, paramiko, platformdirs, plotly, pydantic, pydantic-core, pydantic-settings, pygments, pymongo, python-discovery, python-dotenv, pytz, pyzmq, rpds-py, s3transfer, snowballstemmer, tqdm, typing-extensions, typing-inspection, virtualenv and ipython to permit the latest version.
Updates pymatgen-core from 2026.5.18 to 2026.8.13

Release notes

Sourced from pymatgen-core's releases.

v2026.8.13

• PR #123 The enumlib_caller module docstring notes Enumlib.jl, a from-scratch Julia reimplementation of enumlib that is a drop-in replacement for enum.x (unchanged struct_enum.in/out contract, makeStr.py reused; this module's own test suite passes against it). EnumlibAdaptor emits an advisory UserWarning recommending it when the resolved enum.x is not Enumlib.jl; detection probes enum.x --version at most once per command path and never raises, so enumeration behavior is unchanged. (by @​glwhart)
• PR #99 Locpot and Elfcar store collinear spin-polarized data under spin_up/spin_down keys, matching what VASP actually writes for these files (two direct spin channels) instead of mislabeling them with CHGCAR's total/diff (total/magnetization) convention. Legacy total/diff access keeps working through warning-backed deprecated aliases. VolumetricData gains a data_key argument selecting the primary grid, is_soc is now detected from the diff_x/diff_y/diff_z keys instead of len(data) >= 4, and linear_add/scale invalidate cached spin data. Fixes materialsproject/pymatgen#4307. (by @​DanielYang59)
• PR #121 Accelerate FermiDos.get_e_h_concs (and thus get_doping and get_fermi) by 3–10×: trapezoid weights are precomputed once in __init__ (turning each integration into a dot product) and the Fermi-Dirac integrand is truncated beyond ~40 k_BT from the Fermi level where its contribution is negligible. Results identical to within ~1e-12 relative error. (by @​kavanase)
• PR #114 Fix hkl_transformation computing matrix-element denominators via int(1 / i), which is wrong for fractions other than 1/n (e.g. the 2/3 in R-decentering). The sign convention changes from "at most one negative index" to "first nonzero index positive" (as in #101), so the returned hkl may differ between equivalent representations, e.g. now (1, -1, -2) where (-1, 1, 2) was returned before. New uvw_transformation transforms direct-lattice [uvw] vectors using the same machinery with the transposed inverse matrix. (by @​Sanftperlig)
• PR #117 Fix Vasprun parsing of vasprun.xml from MD simulations using MLFF (ML_LMLFF), which store steps as top-level tags rather than <calculation> blocks: ionic_step_skip/ionic_step_offset now parse the full file and subsample md_data, nionic_steps is taken from md_data when present, and converged_electronic returns True for MLFF runs (no electronic steps exist). Fixes materialsproject/pymatgen#4200. (by @​DanielYang59)
• PR #111 SlabGenerator.gen_possible_terminations is now a public method (previously an inner function of get_slabs). Termination positions are computed with a PBC-aware circular mean over each cluster instead of relying on atom order, and the siteless case is handled. (by @​Sanftperlig)
• PR #113 generate_all_slabs forwards the cell parameter (added to get_symmetrically_distinct_miller_indices in #101) so it can actually be used. (by @​Sanftperlig)

v2026.7.31

• New MatPESRelaxSet in pymatgen.io.vasp.sets: same settings as MatPESStaticSet but performs a full relaxation of ionic positions and cell (ISIF=3, IBRION=2, NSW=99) with a force-based convergence criterion (EDIFFG=-0.02), so DFT calculations can be performed to match MatPES MLIPs. (by @​shyuep)
• PR #110 Improve R-centering in SpacegroupAnalyzer. get_conventional_to_primitive_transformation_matrix now returns a positive-determinant (spglib-style, no reflection component) matrix for R-centered groups; get_primitive_standard_structure reorients rhombohedral lattices to the Setyawan/Curtarolo convention while keeping fractional coordinates instead of rebuilding sites and rechecking periodic equivalence; the unused international_monoclinic argument is deprecated (passing it emits a DeprecationWarning). Behavior change: the R-centering transformation matrix differs from the previous negative-determinant one, so primitive rhombohedral cells may come out with a different (equivalent) orientation. (by @​Sanftperlig)
• PR #97 Setters for Structure.frac_coords and Structure.cart_coords with length validation, enabling e.g. whole-structure translation via struct.frac_coords += vector. (by @​Sanftperlig)
• PR #105 SlabGenerator and generate_all_slabs gain allow_smaller_than_ouc (default False): with primitive=True, primitivization may reduce the slab below the oriented unit cell and its lattice may diverge from the OUC's. Slab.scale_factor is now corrected for LLL reduction, primitivization, and c-axis changes (solved from the parent lattice → slab lattice relation instead of the base-OUC scaling), and Slab.oriented_unit_cell preserves the input class (Structure vs IStructure). (by @​Sanftperlig)
• PR #109 Remove ENAUG from MP24RelaxSet, MPSCANRelaxSet, and MatPESStaticSet YAML configs and from MVLSlabSet, since VASP ignores/deprecates ENAUG when PREC=Accurate. (by @​DanielYang59)
• PR #112 Fix latexify_spacegroup/unicodeify_spacegroup subscripting only the single digit after _, so screw-axis symbols like P2_12_12_1 render as P2₁2₁2₁ instead of absorbing multi-digit runs. (by @​minhsueh)
• PR #102 Fix BSPlotterProjected crash when orbital summation is not enabled (sum_morbs=None). (by @​ShengLin1001)
• PR #106 Correct the get_symmetrically_distinct_miller_indices overload signatures and docstring default introduced in #101. (by @​Sanftperlig)

v2026.7.27

• PR #101 Overhaul get_symmetrically_distinct_miller_indices. A new cell argument (input, conventional, primitive, conv_np, prim_2conv) makes the treatment of centered cells explicit instead of implicit; sorting is now fully deterministic (smaller max |h|,|k|,|l| first, then smaller sum of |h|,|k|,|l|, then larger h, k, l); indices with gcd > 1 are skipped up front and fewer SpacegroupAnalyzer instances are built; a crystal-family helper was added to SpacegroupAnalyzer and the return type is now inferred from whether hkil or hkl is requested. Behavior change: trigonal cells are no longer implicitly primitivized (the default cell="input" uses the lattice as given), and the representative index chosen for a symmetry-equivalent set may differ. (by @​Sanftperlig)
• PR #103 Remove deprecated functions/classes/methods whose deadlines fell in 2025: StructureGraph/MoleculeGraph with_empty_graph, with_edges, with_local_env_strategy (use the from_* constructors); BrunnerNN_reciprocal, BrunnerNN_relative, BrunnerNN_real; IStructure.ntypesp (use n_elems); the CP2K aliases V_Hartree_Cube, MO_Cubes, E_Density_Cube, Xc_Functional, Kpoint_Set, Band_Structure; JDFTx to_dict() (use as_dict()); and DictSet (use VaspInputSet). BaderAnalysis's parse_atomic_densities argument is now a no-op that emits a DeprecationWarning and will be removed on 2026-12-31. (by @​DanielYang59)
• PR #100 Oszicar ionic-step parsing now goes through _vasprun_float, so VASP overflow markers such as T= ****** yield nan with a warning instead of raising ValueError (fixes materialsproject/pymatgen#4537). (by @​DanielYang59)

v2026.7.24

• PR #95 Outcar table parsing now detects a truncated table (header present but no matching footer, e.g. an OUTCAR cut off mid-write) and emits a warning while returning the partial data, instead of hanging. (by @​DanielYang59)
• PR #92 Coordinate helpers handle empty/siteless inputs: IStructure/Structure coordinate accessors always return a 2D array even with no sites, and get_all_distances returns an empty array when either coordinate set is empty (previously errored on siteless/empty structures). (by @​Sanftperlig)
• PR #93 Replace hand-computed degree/radian conversions (180.0 / pi, pi / 180.0) with math.radians/math.degrees (and np.deg2rad/np.rad2deg for arrays) across lattice, interface, and operations. (by @​Sanftperlig)

v2026.7.16

• PR #68 Refactor IStructure/IMolecule {from_file,from_str,to} onto a new pymatgen.io.registry module. Each pymatgen.io.<format> self-registers a StructureFormat/MoleculeFormat handler; built-in formats stay lazily imported (no added from pymatgen.core import Structure import cost) and third parties can plug in via the pymatgen.io.structure_formats/pymatgen.io.molecule_formats entry-point groups. User-facing behavior (aliases, filename-inference priority, error wording, kwarg warnings, default-to-JSON) is preserved; aims/fleur get fallback shims. (by @​shyuep)
• PR #62 Add static XCrySDen XSF support (MOLECULE/POLYMER/SLAB/CRYSTAL, plus DATAGRID/BANDGRID blocks) with round-trip writing; XSF extras are stored as flat structure properties (grids/…, bands/…). CONVCOORD and animated XSF remain unsupported. (by @​hheei)
• PR #81 Vaspwave.get_chgcar() now reads HDF5 charge-augmentation occupancies (/charge/aug_occupancies_*) into Chgcar.data_aug, so legacy CHGCAR augmentation sections round-trip through Chgcar.write_file(). (by @​hheei)
• PR #69 Extend INCAR list tokenization to accept scientific notation (e.g. ROPT = 1e-3 1e-3 1e-3), which previously parsed as 1 -3 1 -3 1 -3. (by @​kavanase)
• PR #82 Further vectorize the Ewald summation (_calc_recip, _calc_real_and_point); ~10× speedup on 100+-atom systems. (by @​Bud-Macaulay)
• PR #72 Preserve pbc through structure transformations. IStructure.__mul__/make_supercell and other ops that build a new Lattice no longer silently reset pbc to (True, True, True). (by @​deepanshuaggarwal51)
• PR #88 Overhaul standard-cell handling in SpacegroupAnalyzer: get_primitive_standard_structure now correctly detects rhombohedral lattices and handles disordered structures, builds the standard cell once, returns float64, and adds an angle check to get_conventional_standard_structure (fixes materialsproject/pymatgen#4679). (by @​Sanftperlig)
• PR #76 Rescale magmoms when CifParser expands symmetry-equivalent sites from .mcif files whose magnetic cell has unequal-length crystal axes (moment components are converted to Cartesian before applying the operation). (by @​lan496)
• PR #87 VolumetricData.from_cube now honors the grid origin on line 3 instead of discarding it, fixing incorrectly positioned structures for cube files with a nonzero origin (fixes #4607). (by @​mminotaki)
• PR #77 Re-allow generation of Slabs from disordered structures (regressed by #24 using .species instead of .species_and_occu). (by @​Sanftperlig)
• PR #78 Forward the reduce kwarg to recursive IStructure.get_primitive_structure calls so SlabGenerator finds smaller slabs when primitive=True (regressed by #24). (by @​ThomasWarford)
• PR #67 Do not require projections in HighSymmKPath.get_continuous_path (they are not a required field of BandStructureSymmLine). (by @​esoteric-ephemera)
• PR #85 Classify a run as HSE06 for HFSCREEN in [0.2, 0.21] rather than exactly 0.2, matching common 0.207/0.208 usage. (by @​kavanase)
• PR #64 Use trapezoidal integration for FermiDos DOS integration (more accurate carrier concentrations) and add get_e_h_concs() to expose individual electron/hole concentrations. (by @​kavanase)
• PR #90 Use math.tau for full-precision 2π and prefer math.* over np.* for scalar ops (fixes #89). (by @​Sanftperlig)
• PR #91 Raise an explicit ValueError("xyz only supports ordered sites.") when exporting disordered sites to .xyz, instead of a cryptic AttributeError. (by @​Sanftperlig)
• PR #73 Fix get_projected_plots_dots returning a non-Axes ax for single-row/column subplot layouts and a repeated-condition typo. (by @​mias0356)
• PR #74 Fix _get_projections_by_branches_patom_pmorb plotting Spin.up projections in place of Spin.down. (by @​mias0356)
• PR #52 Fix get_projected_plots_dots_patom_pmorb empty-subplot layout and integer-division of row count for num_columns != 2. (by @​mias0356)
• Volumetric I/O. VolumetricData.parse_file for CHGCAR/LOCPOT/ELFCAR is now backed by a Cython fast-float parser (vendored single-header fast_float C port). Roughly 6× faster than the prior _plain_loadtxt path on real fixtures and ~11× with parallel scaling experiments on multi-GB inputs (sequential path is what ships).

... (truncated)

Changelog

Sourced from pymatgen-core's changelog.

v2026.8.13

• PR #123 The enumlib_caller module docstring notes Enumlib.jl, a from-scratch Julia reimplementation of enumlib that is a drop-in replacement for enum.x (unchanged struct_enum.in/out contract, makeStr.py reused; this module's own test suite passes against it). EnumlibAdaptor emits an advisory UserWarning recommending it when the resolved enum.x is not Enumlib.jl; detection probes enum.x --version at most once per command path and never raises, so enumeration behavior is unchanged. (by @​glwhart)
• PR #99 Locpot and Elfcar store collinear spin-polarized data under spin_up/spin_down keys, matching what VASP actually writes for these files (two direct spin channels) instead of mislabeling them with CHGCAR's total/diff (total/magnetization) convention. Legacy total/diff access keeps working through warning-backed deprecated aliases. VolumetricData gains a data_key argument selecting the primary grid, is_soc is now detected from the diff_x/diff_y/diff_z keys instead of len(data) >= 4, and linear_add/scale invalidate cached spin data. Fixes materialsproject/pymatgen#4307. (by @​DanielYang59)
• PR #121 Accelerate FermiDos.get_e_h_concs (and thus get_doping and get_fermi) by 3–10×: trapezoid weights are precomputed once in __init__ (turning each integration into a dot product) and the Fermi-Dirac integrand is truncated beyond ~40 k_BT from the Fermi level where its contribution is negligible. Results identical to within ~1e-12 relative error. (by @​kavanase)
• PR #114 Fix hkl_transformation computing matrix-element denominators via int(1 / i), which is wrong for fractions other than 1/n (e.g. the 2/3 in R-decentering). The sign convention changes from "at most one negative index" to "first nonzero index positive" (as in #101), so the returned hkl may differ between equivalent representations, e.g. now (1, -1, -2) where (-1, 1, 2) was returned before. New uvw_transformation transforms direct-lattice [uvw] vectors using the same machinery with the transposed inverse matrix. (by @​Sanftperlig)
• PR #117 Fix Vasprun parsing of vasprun.xml from MD simulations using MLFF (ML_LMLFF), which store steps as top-level tags rather than <calculation> blocks: ionic_step_skip/ionic_step_offset now parse the full file and subsample md_data, nionic_steps is taken from md_data when present, and converged_electronic returns True for MLFF runs (no electronic steps exist). Fixes materialsproject/pymatgen#4200. (by @​DanielYang59)
• PR #111 SlabGenerator.gen_possible_terminations is now a public method (previously an inner function of get_slabs). Termination positions are computed with a PBC-aware circular mean over each cluster instead of relying on atom order, and the siteless case is handled. (by @​Sanftperlig)
• PR #113 generate_all_slabs forwards the cell parameter (added to get_symmetrically_distinct_miller_indices in #101) so it can actually be used. (by @​Sanftperlig)

v2026.7.31

• New MatPESRelaxSet in pymatgen.io.vasp.sets: same settings as MatPESStaticSet but performs a full relaxation of ionic positions and cell (ISIF=3, IBRION=2, NSW=99) with a force-based convergence criterion (EDIFFG=-0.02), so DFT calculations can be performed to match MatPES MLIPs. (by @​shyuep)
• PR #110 Improve R-centering in SpacegroupAnalyzer. get_conventional_to_primitive_transformation_matrix now returns a positive-determinant (spglib-style, no reflection component) matrix for R-centered groups; get_primitive_standard_structure reorients rhombohedral lattices to the Setyawan/Curtarolo convention while keeping fractional coordinates instead of rebuilding sites and rechecking periodic equivalence; the unused international_monoclinic argument is deprecated (passing it emits a DeprecationWarning). Behavior change: the R-centering transformation matrix differs from the previous negative-determinant one, so primitive rhombohedral cells may come out with a different (equivalent) orientation. (by @​Sanftperlig)
• PR #97 Setters for Structure.frac_coords and Structure.cart_coords with length validation, enabling e.g. whole-structure translation via struct.frac_coords += vector. (by @​Sanftperlig)
• PR #105 SlabGenerator and generate_all_slabs gain allow_smaller_than_ouc (default False): with primitive=True, primitivization may reduce the slab below the oriented unit cell and its lattice may diverge from the OUC's. Slab.scale_factor is now corrected for LLL reduction, primitivization, and c-axis changes (solved from the parent lattice → slab lattice relation instead of the base-OUC scaling), and Slab.oriented_unit_cell preserves the input class (Structure vs IStructure). (by @​Sanftperlig)
• PR #109 Remove ENAUG from MP24RelaxSet, MPSCANRelaxSet, and MatPESStaticSet YAML configs and from MVLSlabSet, since VASP ignores/deprecates ENAUG when PREC=Accurate. (by @​DanielYang59)
• PR #112 Fix latexify_spacegroup/unicodeify_spacegroup subscripting only the single digit after _, so screw-axis symbols like P2_12_12_1 render as P2₁2₁2₁ instead of absorbing multi-digit runs. (by @​minhsueh)
• PR #102 Fix BSPlotterProjected crash when orbital summation is not enabled (sum_morbs=None). (by @​ShengLin1001)
• PR #106 Correct the get_symmetrically_distinct_miller_indices overload signatures and docstring default introduced in #101. (by @​Sanftperlig)

v2026.7.27

• PR #101 Overhaul get_symmetrically_distinct_miller_indices. A new cell argument (input, conventional, primitive, conv_np, prim_2conv) makes the treatment of centered cells explicit instead of implicit; sorting is now fully deterministic (smaller max |h|,|k|,|l| first, then smaller sum of |h|,|k|,|l|, then larger h, k, l); indices with gcd > 1 are skipped up front and fewer SpacegroupAnalyzer instances are built; a crystal-family helper was added to SpacegroupAnalyzer and the return type is now inferred from whether hkil or hkl is requested. Behavior change: trigonal cells are no longer implicitly primitivized (the default cell="input" uses the lattice as given), and the representative index chosen for a symmetry-equivalent set may differ. (by @​Sanftperlig)
• PR #103 Remove deprecated functions/classes/methods whose deadlines fell in 2025: StructureGraph/MoleculeGraph with_empty_graph, with_edges, with_local_env_strategy (use the from_* constructors); BrunnerNN_reciprocal, BrunnerNN_relative, BrunnerNN_real; IStructure.ntypesp (use n_elems); the CP2K aliases V_Hartree_Cube, MO_Cubes, E_Density_Cube, Xc_Functional, Kpoint_Set, Band_Structure; JDFTx to_dict() (use as_dict()); and DictSet (use VaspInputSet). BaderAnalysis's parse_atomic_densities argument is now a no-op that emits a DeprecationWarning and will be removed on 2026-12-31. (by @​DanielYang59)
• PR #100 Oszicar ionic-step parsing now goes through _vasprun_float, so VASP overflow markers such as T= ****** yield nan with a warning instead of raising ValueError (fixes materialsproject/pymatgen#4537). (by @​DanielYang59)

v2026.7.24

• PR #95 Outcar table parsing now detects a truncated table (header present but no matching footer, e.g. an OUTCAR cut off mid-write) and emits a warning while returning the partial data, instead of hanging. (by @​DanielYang59)
• PR #92 Coordinate helpers handle empty/siteless inputs: IStructure/Structure coordinate accessors always return a 2D array even with no sites, and get_all_distances returns an empty array when either coordinate set is empty (previously errored on siteless/empty structures). (by @​Sanftperlig)
• PR #93 Replace hand-computed degree/radian conversions (180.0 / pi, pi / 180.0) with math.radians/math.degrees (and np.deg2rad/np.rad2deg for arrays) across lattice, interface, and operations. (by @​Sanftperlig)

v2026.7.16

• PR #68 Refactor IStructure/IMolecule {from_file,from_str,to} onto a new pymatgen.io.registry module. Each pymatgen.io.<format> self-registers a StructureFormat/MoleculeFormat handler; built-in formats stay lazily imported (no added from pymatgen.core import Structure import cost) and third parties can plug in via the pymatgen.io.structure_formats/pymatgen.io.molecule_formats entry-point groups. User-facing behavior (aliases, filename-inference priority, error wording, kwarg warnings, default-to-JSON) is preserved; aims/fleur get fallback shims. (by @​shyuep)
• PR #62 Add static XCrySDen XSF support (MOLECULE/POLYMER/SLAB/CRYSTAL, plus DATAGRID/BANDGRID blocks) with round-trip writing; XSF extras are stored as flat structure properties (grids/…, bands/…). CONVCOORD and animated XSF remain unsupported. (by @​hheei)
• PR #81 Vaspwave.get_chgcar() now reads HDF5 charge-augmentation occupancies (/charge/aug_occupancies_*) into Chgcar.data_aug, so legacy CHGCAR augmentation sections round-trip through Chgcar.write_file(). (by @​hheei)
• PR #69 Extend INCAR list tokenization to accept scientific notation (e.g. ROPT = 1e-3 1e-3 1e-3), which previously parsed as 1 -3 1 -3 1 -3. (by @​kavanase)
• PR #82 Further vectorize the Ewald summation (_calc_recip, _calc_real_and_point); ~10× speedup on 100+-atom systems. (by @​Bud-Macaulay)
• PR #72 Preserve pbc through structure transformations. IStructure.__mul__/make_supercell and other ops that build a new Lattice no longer silently reset pbc to (True, True, True). (by @​deepanshuaggarwal51)
• PR #88 Overhaul standard-cell handling in SpacegroupAnalyzer: get_primitive_standard_structure now correctly detects rhombohedral lattices and handles disordered structures, builds the standard cell once, returns float64, and adds an angle check to get_conventional_standard_structure (fixes materialsproject/pymatgen#4679). (by @​Sanftperlig)
• PR #76 Rescale magmoms when CifParser expands symmetry-equivalent sites from .mcif files whose magnetic cell has unequal-length crystal axes (moment components are converted to Cartesian before applying the operation). (by @​lan496)
• PR #87 VolumetricData.from_cube now honors the grid origin on line 3 instead of discarding it, fixing incorrectly positioned structures for cube files with a nonzero origin (fixes #4607). (by @​mminotaki)
• PR #77 Re-allow generation of Slabs from disordered structures (regressed by #24 using .species instead of .species_and_occu). (by @​Sanftperlig)
• PR #78 Forward the reduce kwarg to recursive IStructure.get_primitive_structure calls so SlabGenerator finds smaller slabs when primitive=True (regressed by #24). (by @​ThomasWarford)
• PR #67 Do not require projections in HighSymmKPath.get_continuous_path (they are not a required field of BandStructureSymmLine). (by @​esoteric-ephemera)
• PR #85 Classify a run as HSE06 for HFSCREEN in [0.2, 0.21] rather than exactly 0.2, matching common 0.207/0.208 usage. (by @​kavanase)
• PR #64 Use trapezoidal integration for FermiDos DOS integration (more accurate carrier concentrations) and add get_e_h_concs() to expose individual electron/hole concentrations. (by @​kavanase)
• PR #90 Use math.tau for full-precision 2π and prefer math.* over np.* for scalar ops (fixes #89). (by @​Sanftperlig)

... (truncated)

Commits

• 8c9a68b Update changelog.
• e921212 Note Enumlib.jl as a drop-in enum.x successor for EnumlibAdaptor (#123)
• d2d8cf4 Elfcar and Locpot use proper spin_up/down instead of total and diff (#99)
• 102a571 Accelerate FermiDos.get_e_h_concs (and thus get_doping) (#121)
• d7c1d8c Add SupportsIndex to getitem and many more, widen list and fix small non-...
• 96a7388 Fix incorrect determinant calculation in hkl_transformation, add `uvw_trans...
• dfac299 Set bibtexparser<2 upper pin (#116)
• c757f17 fix parsing of vasprun.xml from MD Simulations Using MLFF (#117)
• 8346561 remove xfail for vasp test (#118)
• 165b3f7 Make SlabGenerator.gen_possible_terminations a public function (#111)
• Additional commits viewable in compare view

Updates monty from 2026.5.18 to 2026.7.16

Release notes

Sourced from monty's releases.

v2026.7.16

2026.7.16

• Add YAML round-trip support for MSONable and TypeHandler-registered types (numpy, pandas, pint, torch, uuid, pathlib, bson, and user-registered handlers). dumpfn/loadfn now treat YAML symmetrically with JSON via the @module/@class envelope, with a cls=None opt-out matching the JSON path (closes #587).
• Fix YAML race condition by using a thread-local instance (closes #795).
• Fix regression when decoding a MSONable object whose originating module is missing.

Changelog

Sourced from monty's changelog.

2026.7.16

• Add YAML round-trip support for MSONable and TypeHandler-registered types (numpy, pandas, pint, torch, uuid, pathlib, bson, and user-registered handlers). dumpfn/loadfn now treat YAML symmetrically with JSON via the @module/@class envelope, with a cls=None opt-out matching the JSON path (closes #587).
• Fix YAML race condition by using a thread-local instance (closes #795).
• Fix regression when decoding a MSONable object whose originating module is missing.

Commits

• 74132ef v2026.7.16 release
• 443d725 v2026.7.16 release
• 9d702ab v2026.7.16 release
• 439d603 v2026.7.16 release
• 670ade7 Update changelog and version.
• 4784d1e Fix regression on missing module MSONable.
• becd278 Merge pull request #799 from materialyzeai/dependabot/bundler/docs/activesupp...
• 54d7c02 chore: bump activesupport from 7.0.7.2 to 7.2.3.1 in /docs
• 8fc9ae1 Fix flasky windows test
• 833c417 Fix flaky Windows test_command by widening subprocess timeout
• Additional commits viewable in compare view

Updates maggma from 0.72.1 to 0.74.0

Release notes

Sourced from maggma's releases.

v0.74.0

Version 0.74.0

Commits

• [087efd0b] Merge pull request #1115 from rkingsbury/replace-mongomock-with-mongomock-ng
• [9f0e0f98] Merge pull request #1116 from rkingsbury/fix/azure-type-hint-none-error
• [2b1b607d] sync Github actions Mongo with min version in pyproject.toml
• [38d10713] fix: add future annotations import to azure store to fix TypeError on missing azure dependency
• [b0c307c7] Merge branch 'main' into replace-mongomock-with-mongomock-ng
• [c2c38993] Remove pymongo<4.11 pin and switch to mongomock-ng

v0.73.0

Version 0.73.0

Commits

• [7d7c1fa9] Merge pull request #1111 from rkingsbury/drop-py39-310-add-py313-314
• [63c3e4ea] Revert pymongo and mongo image version bumps
• [c9a4e3e1] bump mongoDB version in Github CI
• [2e11dc53] Regenerate requirements files using --all-extras
• [942efbc9] Drop Python 3.14 from CI matrix for now
• [d17eafc6] Bump pymongo constraint to >=4.11.0 and regenerate all requirements
• [db140270] Fix Python 3.14 compatibility: generator pattern and datetime.utcnow()
• [29b6a2d6] Regenerate requirements for Python 3.13 and 3.14 (ubuntu-latest)
• [b52b1c1f] bump coverage for python 3.14, in case cause of hang in CI
• [d408e26a] bump coverage for python 3.14, in case cause of hang in CI
• [47649b53] Fix asyncio.get_event_loop() breakage in Python 3.14
• [200c2fee] one more linting fix
• [fc81fdcd] Fix linting errors unlocked by raising minimum Python to 3.11
• [8c1e3c6b] Drop Python 3.9/3.10 support, add Python 3.13/3.14
• [05d864ca] Merge pull request #1108 from materialsproject/sshtunnel
• [fbb8d5ce] sshtunnel: changes for paramiko 5.0.0
• [e65d896c] bugfix for aws test
• [045d5ff2] Potential fix for pull request finding 'CodeQL / Binding a socket to all network interfaces'
• [0986aa2e] SSHTunnel: replace sshtunnel with pure paramiko
• [ab30c89c] Merge pull request #1094 from materialsproject/auto-dependency-upgrades
• [467f344b] update dependencies for . (ubuntu-latest/py3.9)
• [ad9801c6] update dependencies for . (ubuntu-latest/py3.12)
• [19d59c52] update dependencies for . (ubuntu-latest/py3.11)
• [36dd59d9] update dependencies for . (ubuntu-latest/py3.10)
• [9cc3051a] update dependencies for . (macos-latest/py3.9)
• [b6a33f5f] update dependencies for . (macos-latest/py3.12)
• [e31550e1] update dependencies for . (macos-latest/py3.11)
• [5f23c523] update dependencies for . (macos-latest/py3.10)
• [d221f2e0] Merge pull request #1072 from materialsproject/auto-dependency-upgrades
• [cf5cd692] update dependencies for . (ubuntu-latest/py3.9)
• [92ee1806] update dependencies for . (ubuntu-latest/py3.12)
• [5bf6b17e] update dependencies for . (ubuntu-latest/py3.11)
• [db64e620] update dependencies for . (ubuntu-latest/py3.10)

... (truncated)

Changelog

Sourced from maggma's changelog.

Changelog

Commits

• 087efd0 Merge pull request #1115 from rkingsbury/replace-mongomock-with-mongomock-ng
• 9f0e0f9 Merge pull request #1116 from rkingsbury/fix/azure-type-hint-none-error
• 2b1b607 sync Github actions Mongo with min version in pyproject.toml
• 38d1071 fix: add future annotations import to azure store to fix TypeError on mis...
• b0c307c Merge branch 'main' into replace-mongomock-with-mongomock-ng
• c2c3899 Remove pymongo<4.11 pin and switch to mongomock-ng
• 7d7c1fa Merge pull request #1111 from rkingsbury/drop-py39-310-add-py313-314
• 63c3e4e Revert pymongo and mongo image version bumps
• c9a4e3e bump mongoDB version in Github CI
• 2e11dc5 Regenerate requirements files using --all-extras
• Additional commits viewable in compare view

Updates setuptools from 83.0.0 to 84.0.0

Changelog

Sourced from setuptools's changelog.

v84.0.0

Features

• Newline-separated keywords and platformspypa/setuptools#4887old specification <https://peps.python.org/pep-0345/>_ separated items with spaces and the current one uses commas. (#4887)
• Extensionpypa/distutils#373#5022)
• The C compiler modules now emit log messages through their own compilers.C.* loggers instead of the distutils root logger, part of decoupling the compilers package from distutils. The logger names are normalized to a stable compilers.C.* prefix so they remain constant as the package migrates toward a standalone compilers.C distribution. (#5266)
• The C compilers gained a Compiler.call method -- a thin wrapper over subprocess.check_call (with macOS deployment-target env injection) that is the modern replacement for Compiler.spawn. The compilers no longer depend on distutils.spawn, distutils.dir_util, distutils.file_util, distutils._modified, or distutils.util.execute/split_quoted: the generic newer/newer_group and split_quoted helpers are vendored into the compilers package, and Compiler.mkpath/move_file/execute are implemented directly on the standard library (os.makedirs/shutil.move). The methods are retained for backward compatibility. (#5267)
• The compilers no longer depend on distutils.util, distutils.version, distutils.compat, or distutils._macos_compat. The platform-identification helpers (get_platform/get_host_platform/is_mingw) now live in distutils.compilers.platform.detect and the macOS deployment-target logic and compiler_fixup in distutils.compilers.platform.macos; CygwinCCompiler.gcc_version returns a packaging.version.Version. distutils.util re-exports the platform/macOS helpers from their new homes for backward compatibility rather than keeping duplicate copies. (sysconfig lookups still route through distutils pending its own decoupling.) (#5268)
• The compilers now read their build configuration from the standard library's sysconfig instead of distutils.sysconfig. Per-compiler customization -- previously distutils.sysconfig.customize_compiler -- has moved into Compiler.configure_system(): a no-op on the base class, with UnixCCompiler applying the compiler/flag/archiver settings CPython recorded in sysconfig (and the usual CC/CFLAGS/LDSHARED/… environment overrides). distutils.sysconfig.customize_compiler is retained as a thin wrapper that calls compiler.configure_system(). (#5269)

Bugfixes

• The MSVC linker now passes its arguments through a response file when the command line would exceed the Windows maximum length, fixing failures when linking a large number of objects. (#4177)
• The Cygwin and MinGW compilers now pass -O1 instead of a bare -O. The two are equivalent to GCC, but cc1 rejected the bare form when building 32-bit extensions with -m32. -- by :user:dchaudhari7177 (#4873)
• copy_filepypa/distutils#379#5079)
• Setuptools wheels no longer bundled the project's own test modules. -- by :user:itscloud0 (#5212)
• build_ext no longer fails when cross-compiling with a compiler other than MSVC (such as MinGW). Compiler now provides a no-op initialize()pypa/distutils#399

Improved Documentation

• Clarified what "correspond exactly to the directory structure" means in the packages section of the Package Discovery user guide. (#4109)
• Documented how bdist_wheel's py_limited_api option controls abi3 wheel tagging for extension modules -- by :user:Himanshuagrawal4 (#4741)

Deprecations and Removals

• Compiler.spawn is deprecated in favor of the new Compiler.call. call raises native subprocess exceptions; spawn remains as a shim that emits a DeprecationWarning and translates them to DistutilsExecError. The MSVC spawn compatibility shim for third-party monkeypatches predating the env argument (numpy.distutils before 1.19, per pypa/distutils#15) has been removed. distutils.spawn.spawn is likewise reduced to a thin wrapper around subprocess.check_call: it no longer resolves cmd[0] via shutil.which (subprocess searches PATH itself) nor injects MACOSX_DEPLOYMENT_TARGET (that now lives with the compilers, the only callers to which it applied). (#5267)
• Building an extension with a MACOSX_DEPLOYMENT_TARGET lower than the interpreter's configured value now raises compilers.errors.PlatformError instead of distutils.errors.DistutilsPlatformError (the macOS deployment-target check moved into the compilers package). CygwinCCompiler.gcc_version returns a packaging.vers...

  Description has been truncated

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.67%. Comparing base (ca0a454) to head (1c5efd2).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #465   +/-   ##
=======================================
  Coverage   87.67%   87.67%           
=======================================
  Files          14       14           
  Lines        1971     1971           
  Branches      344      344           
=======================================
  Hits         1728     1728           
  Misses        192      192           
  Partials       51       51           

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