pidibble 1.5.2__tar.gz → 1.5.3__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pidibble-1.5.3/.github/workflows/release.yaml +91 -0
- pidibble-1.5.3/CHANGELOG.md +200 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/PKG-INFO +5 -63
- {pidibble-1.5.2 → pidibble-1.5.3}/README.md +2 -62
- pidibble-1.5.3/docs/requirements.txt +8 -0
- pidibble-1.5.3/docs/source/changelog.md +5 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/conf.py +2 -1
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/index.rst +1 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/baseparsers.py +58 -57
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/baserecord.py +34 -37
- pidibble-1.5.3/pidibble/hex.py +68 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/mmcif_parse.py +143 -143
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/pdbparse.py +116 -108
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/pdbrecord.py +291 -265
- {pidibble-1.5.2 → pidibble-1.5.3}/pyproject.toml +4 -1
- pidibble-1.5.3/scripts/release.sh +88 -0
- pidibble-1.5.2/.github/workflows/release.yaml +0 -41
- pidibble-1.5.2/MANIFEST.in +0 -1
- pidibble-1.5.2/docs/requirements.txt +0 -15
- pidibble-1.5.2/pidibble/hex.py +0 -40
- pidibble-1.5.2/pidibble/resources/__init__.py +0 -6
- {pidibble-1.5.2 → pidibble-1.5.3}/.gitignore +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/.readthedocs.yaml +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/LICENSE +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/Makefile +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/make.bat +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/_static/css/custom.css +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/API.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.baseparsers.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.baserecord.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.hex.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.mmcif_parse.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.pdbparse.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.pdbrecord.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.resources.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/api/pidibble.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/installation.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/notes.md +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/docs/source/usage.rst +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/__init__.py +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/resources/mmcif_format.yaml +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/pidibble/resources/pdb_format.yaml +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/__init__.py +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/conftest.py +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_hex/my_system.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_hex.py +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/4tvp.cif +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/4tvp.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/4zmj-newresnames.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/4zmj.cif +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/4zmj.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/6m0j.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/8fae.cif +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/G.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/GG.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/test.pdb +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb/test_pdb_format.yaml +0 -0
- {pidibble-1.5.2 → pidibble-1.5.3}/tests/unit/test_rcsb.py +0 -0
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# Changelog
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All notable changes to this project are documented in this file.
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The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
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## [Unreleased]
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## [1.5.3] - 2026-05-03
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### Fixed
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- `PDBParser(PDBcode=...)` legacy parameter silently swallowed by `**kwargs`; restored via explicit mapping to `source_id`/`source_db='rcsb'`
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- Eight bare `except:` clauses narrowed to specific exception types throughout
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- Bitwise `&=` used as logical AND in `BaseRecord.empty()` replaced with `all()`
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- `str2int_sig` raised `IndexError` on empty-string input; added guard before index access
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- `!= None` / `== None` comparisons replaced with `is not None` / `is None` throughout
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- `type(x) == T` identity comparisons replaced with `isinstance(x, T)` throughout
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- `elif type(p) == list:` in `parse_tokens()` was unreachable; corrected to `isinstance(p, PDBRecordList)`
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- Mutable default arguments `hold={}` and `hold=[]` in `gather_token` and `header_check` replaced with `None`
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### Changed
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- Global hex-tripped flag in `hex.py` replaced with `AtomSerialParser` callable class; each `PDBParser` instance owns its own state, eliminating thread-safety hazard and cross-parse contamination
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- `mappers` default argument changed from a mutable dict literal to `None`; default built inside `__init__`
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- Resource YAML files now loaded via `importlib.resources.files()` instead of `os.path.dirname(resources.__file__)`, ensuring correct behavior inside wheels and zip archives
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- `resources/__init__.py` removed; `resources/` is now a plain data directory, not a sub-package
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- `MANIFEST.in` removed; hatchling auto-discovers package data from git-tracked files
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- PEP 8 spacing applied throughout all source files
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- `parse_embedded()` refactored: `triggered`/`capturing` boolean pair replaced with explicit `_EmbedState` enum (`SEARCHING`, `PRE_CAPTURE`, `CAPTURING`); setup phase extracted into `_setup_embed_context()`
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### Added
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- `CHANGELOG.md` with full release history
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- `scripts/release.sh` for automated version rotation, tagging, and push
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- `[test]` optional dependency group in `pyproject.toml`
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---
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## [1.5.2] - 2025-09-16
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### Added
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- Capability to download structures from OPM and split DUM residues into a separate PDB file
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## [1.5.1] - 2025-09-15
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- Minor fixes following 1.5.0
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## [1.5.0] - 2025-09-15
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### Added
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- Initial OPM support
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## [1.4.2] - 2025-08-11
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- Updated AlphaFold interface to current API
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## [1.4.1] - 2025-08-07
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### Fixed
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- Parsing bug in `PDBRecordList`
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## [1.4.0] - 2025-07-29
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- `PDBRecordList` and `PDBRecordDict` classes
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## [1.3.3] - 2025-07-29
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- Bugs where missing records were incorrectly assumed present during mmCIF parsing
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- Full API documentation published
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- Hexadecimal atom serial detection when no `a-f` characters are present, based on value exceeding 99999
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- Hex-or-integer detection now restricted to atom serial number fields only
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- Hexadecimal atom serial number support for files with more than 99999 atoms
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- Ability to group records into models for multi-model PDB entries
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- Ability to fetch structures from the AlphaFold database
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- Limited mmCIF parsing: `ATOM`, `HETATM`, `SSBOND`, `LINK`, `SEQADV`, `REMARK 350`, and `REMARK 465` records
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## [1.0.8] - 2023-08-23
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