chore(deps): bump modelcif from 0.7 to 1.7

[dependabot]

Bumps modelcif from 0.7 to 1.7.

Release notes

Sourced from modelcif's releases.

python-modelcif 1.7 release

• The new classes modelcif.reference.InsertionSeqDif and modelcif.reference.DeletionSeqDif allow for annotating insertions or deletions in the entity sequence relative to the reference database.

Full Changelog: ihmwg/python-modelcif@1.6...1.7

python-modelcif 1.6 release

• New classes have been added to modelcif.protocol to describe protocol steps for model quality assessment, validation, and protein design.
• The new modelcif.qa_metric.Dihedral class can be used to describe quality scores that are calculated on a dihedral.

Full Changelog: ihmwg/python-modelcif@1.5...1.6

python-modelcif 1.5 release

• The pdbx_nonpoly_scheme and pdbx_poly_seq_scheme tables are now read from and written to mmCIF or BinaryCIF files. This allows for files containing waters to be correctly processed (#52).
• A pyproject.toml file is now provided for compatibility with modern versions of pip (#50).
• Bugfix: the is_primary attribute of modelcif.reference.TargetReference is now correctly set when reading files containing a _struct_ref table but no _ma_target_ref_db_details table (#51).

Full Changelog: ihmwg/python-modelcif@1.4...1.5

python-modelcif 1.4 release

• Revision information and information on how the data in the file can be used are now read from or written to mmCIF or BinaryCIF files. See System.revisions and System.data_usage respectively.
• New classes have been added to modelcif.alignment, modelcif.qa_metric, and modelcif.protocol to support all sequence identity denominators (#47), QA metric types (#45), and protocol step types (#44) respectively, as defined in the ModelCIF dictionary.
• The new modelcif.alignment.Local and modelcif.alignment.Multiple classes allow for both local alignments and multiple sequence alignments to be described (#43).
• Bugfix: sequence identity and alignment score (identity and score arguments to modelcif.alignment.Pair) are now optional, to match the mmCIF dictionary (#49).
• Bugfix: information in _ma_template_non_poly.details is now read from mmCIF or BinaryCIF files (#48).
• Bugfix: files containing empty or missing _ma_qa_metric.description can now be read (#46).

Full Changelog: ihmwg/python-modelcif@1.3...1.4

python-modelcif 1.3 release

• The new modelcif.CustomTemplate class allows for custom templates (that have not been deposited in a database such as PDB) to be referenced, together with their atomic coordinates (#1).
• Model quality scores can now be defined that act on single features or pairs of features using the modelcif.qa_metric.Feature and modelcif.qa_metric.FeaturePairwise classes, respectively. Features can be defined as groups of atoms, residues, or asyms (#38).
• The modelcif.associated.QAMetricsFile class should now be used to reference files that contain model quality scores. The old name (LocalPairwiseQAScoresFile) is deprecated. This allows for all types of QA scores, not just local pairwise scores, to be stored in a separate file.
• Sanity checks when writing out a file can now be disabled if desired, using the new check argument to modelcif.dumper.write.
• modelcif.reference.TargetReference now takes an is_primary argument which can be used to denote the most pertinent sequence database reference.
• Information on model groups (modelcif.model.ModelGroup) is now written to the new ma_model_group and ma_model_group_link mmCIF tables, instead of ma_model_list, to match the latest ModelCIF dictionary. Old-style information in ma_model_list will still be used when reading a file if these new tables are missing.

Full Changelog: ihmwg/python-modelcif@1.2...1.3

python-modelcif 1.2 release

• Data that have been split over multiple mmCIF or BinaryCIF files can now be combined into a single modelcif.System object using the new add_to_system argument to modelcif.reader.read (#10).
• A new example, associated.py, has been added to demonstrate reading in data that has been split into multiple "associated" mmCIF files using modelcif.associated.CIFFile.

Full Changelog: ihmwg/python-modelcif@1.1...1.2

python-modelcif 1.1 release

• The new class modelcif.model.NotModeledResidueRange allows for the annotation of residue ranges that were explicitly not modeled. Any residue marked as not-modeled in all models will be excluded from the pdbx_poly_seq_scheme table.
• The util/make-mmcif.py script is now included in the installed package, so can be run if desired with python3 -m modelcif.util.make_mmcif.
• The make_mmcif utility script will now automatically add any missing modelcif.model.NotModeledResidueRange objects for not-modeled residue ranges.

... (truncated)

Changelog

Sourced from modelcif's changelog.

1.7 - 2026-04-10

• The new classes :class:modelcif.reference.InsertionSeqDif and :class:modelcif.reference.DeletionSeqDif allow for annotating insertions or deletions in the entity sequence relative to the reference database.

1.6 - 2025-12-12

• New classes have been added to :mod:modelcif.protocol to describe protocol steps for model quality assessment, validation, and protein design.
• The new :class:modelcif.qa_metric.Dihedral class can be used to describe quality scores that are calculated on a dihedral.

1.5 - 2025-09-17

• The pdbx_nonpoly_scheme and pdbx_poly_seq_scheme tables are now read from and written to mmCIF or BinaryCIF files. This allows for files containing waters to be correctly processed (#52).
• A pyproject.toml file is now provided for compatibility with modern versions of pip (#50).
• Bugfix: the is_primary attribute of :class:modelcif.reference.TargetReference is now correctly set when reading files containing a _struct_ref table but no _ma_target_ref_db_details table (#51).

1.4 - 2025-06-11

• Revision information and information on how the data in the file can be used are now read from or written to mmCIF or BinaryCIF files. See :attr:System.revisions and :attr:System.data_usage respectively.
• New classes have been added to :mod:modelcif.alignment, :mod:modelcif.qa_metric, and :mod:modelcif.protocol to support all sequence identity denominators (#47), QA metric types (#45), and protocol step types (#44) respectively, as defined in the ModelCIF dictionary.
• The new :class:modelcif.alignment.Local and :class:modelcif.alignment.Multiple classes allow for both local alignments and multiple sequence alignments to be described (#43).
• Bugfix: sequence identity and alignment score (identity and score arguments to :class:modelcif.alignment.Pair) are now optional, to match the mmCIF dictionary (#49).
• Bugfix: information in _ma_template_non_poly.details is now read from mmCIF or BinaryCIF files (#48).
• Bugfix: files containing empty or missing _ma_qa_metric.description can now be read (#46).

1.3 - 2025-01-14

... (truncated)

Commits

• a16f5db Prepare for 1.7 release
• 0c03a25 Use latest Actions
• 633b248 We should work with v1.4.9 of the dictionary
• e38dcfa 'python3' is more likely to work than 'python'
• 2bb4cc4 Require python-ihm 2.10 for SeqDif subclasses
• a0ef767 Import new insertion/deletion subclasses
• e3b3f41 Account for struct_ref_seq_dif changes in python-ihm
• fbbcb03 Update to CodeQL v4
• 727e008 Build a wheel
• 7b96421 Prepare for 1.6 release
• Additional commits viewable in compare view

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[github-actions]

Summary

Summary

Generated on:	07/17/2026 - 12:53:02
Parser:	Cobertura
Assemblies:	5
Classes:	32
Files:	32
Line coverage:	86.4% (2182 of 2524)
Covered lines:	2182
Uncovered lines:	342
Coverable lines:	2524
Total lines:	8079
Covered branches:	0
Total branches:	0
Method coverage:	Feature is only available for sponsors

Coverage

src.bioemu - 89%

Name	Line	Branch
src.bioemu	89%	****
init.py	100%
chemgraph.py	100%
convert_chemgraph.py	97%
denoiser.py	98.3%
get_embeds.py	92.1%
md_utils.py	85.8%
model_utils.py	78%
models.py	94.1%
run_hpacker.py	0%
sample.py	92.2%
sde_lib.py	88.3%
seq_io.py	100%
shortcuts.py	100%
sidechain_relax.py	75%
so3_sde.py	90.3%
structure_module.py	84.3%
utils.py	65.6%

src.bioemu.colabfold_inline - 79.1%

Name	Line	Branch
src.bioemu.colabfold_inline	79.1%	****
init.py
features.py	100%
input_parsing.py	100%
model_runner.py	99%
msa_client.py	60.8%

src.bioemu.hpacker_setup - 69.2%

Name	Line	Branch
src.bioemu.hpacker_setup	69.2%	****
init.py
setup_hpacker.py	69.2%

src.bioemu.steering - 79.5%

Name	Line	Branch
src.bioemu.steering	79.5%	****
init.py	100%
collective_variables.py	34.8%
dpm_fkc.py	100%
dpm_smc.py	100%
potentials.py	95.3%
utils.py	83.5%

src.bioemu.training - 100%

Name	Line	Branch
src.bioemu.training	100%	****
foldedness.py	100%
loss.py	100%