All notable changes to protpy are documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

• descriptors.pdf — PDF version of DESCRIPTORS.md, providing a printable/downloadable reference for all 36 descriptors.

• aaindex dependency version floor raised to >=1.2.0 to pick up the new aaindex2 and aaindex3 modules, pyproject.toml migration, and all associated bug fixes in that release.

• protpy/utils.py — new utility module with three public functions:
  • get_descriptor_info(name) — returns a metadata dict for any registered descriptor (description, module, category, abbreviation, parameters, output shape, speed rating, reference). Case-insensitive; includes close-match suggestions on unknown names.
  • list_descriptors(category=None) — returns a sorted list of all 36 descriptor names, optionally filtered by category.
  • print_descriptor_info(name) — pretty-prints descriptor metadata to stdout with speed symbols (✅ / 🟡 / 🔴).
  • _DESCRIPTOR_REGISTRY — internal dict containing structured metadata for all 36 descriptors.
• examples/protpy_tutorial.ipynb — interactive Jupyter notebook tutorial covering all 13 descriptor families with visualisations, performance benchmarks, and a multi-panel dashboard.
• tests/test_utils.py — unit tests for all three public utils functions and the _DESCRIPTOR_REGISTRY integrity (completeness, schema, controlled-vocabulary checks).
• get_descriptor_info, list_descriptors, and print_descriptor_info exported from top-level protpy package.

• Type hints — all five descriptor modules (autocorrelation.py, composition.py, ctd.py, sequence_order.py, _constants.py) upgraded from bare list/dict annotations to subscripted generics (list[str], list[float], dict[str, float], dict[str, str], tuple[float, float]). Compatible with Python 3.9+ via from __future__ import annotations.
• F-strings — all .format() calls across all modules replaced with f-string equivalents (20 call sites updated).
• Version bumped to 1.4.0 across pyproject.toml, protpy/__init__.py, docs/conf.py, and tests/test_protpy.py.

• 22 new composition descriptors: gravy, aromaticity, instability_index, isoelectric_point, molecular_weight, charge_distribution, hydrophobic_polar_charged_composition, secondary_structure_propensity, kmer_composition, reduced_alphabet_composition, motif_composition, amino_acid_pair_composition, aliphatic_index, extinction_coefficient, boman_index, aggregation_propensity, hydrophobic_moment, shannon_entropy, pseudo_amino_acid_composition (moved from autocorrelation group), amphiphilic_pseudo_amino_acid_composition (moved), sequence_order_coupling_number_ (single-gap variant), sequence_order_coupling_number_all, quasi_sequence_order_all.
• DESCRIPTORS.md — comprehensive descriptor reference covering all 35 descriptors, including parameter tables, code examples, output shapes, speed/complexity ratings (✅ Fast / 🟡 Moderate / 🔴 Slow), and a full References section with original citations.
• pyproject.toml — modern PEP 517/518 build configuration replacing setup.py and setup.cfg.
• images/protpy.png — project logo added to repository and displayed in README.md.
• CHANGELOG.md — this file.

• all_descriptors list in protpy/__init__.py expanded from 14 to 36 entries.
• README.md — Introduction descriptor list updated to all 35 descriptors grouped by category; Usage section expanded with code examples for all 17 previously undocumented composition descriptors.
• tests/test_protpy.py — test_valid_descriptors updated to assert len(all_descriptors) == 36 and check all 36 descriptor names individually, grouped by category.
• pyproject.toml — version floor constraints added to core dependencies (numpy>=1.16.0, pandas>=1.1.0, varname>=0.12.0); biopython moved from install_requires to optional-dependencies[test].
• Python version classifiers updated to include 3.11, 3.12, and 3.13 in both pyproject.toml and docs/conf.py.
• requirements.txt — biopython removed (test-only dependency).
• .circleci/config.yml CircleCI coverage job now actually runs coverage run -m pytest tests/ and coverage report (previously installed tools without executing them).
• kmer_composition — added ValueError guard for k > 4 to prevent accidental generation of 3.2 million+ column DataFrames.
• docs/conf.py — release updated to 1.3.0.
• Version bumped to 1.3.0 across pyproject.toml, protpy/__init__.py, docs/conf.py, and tests/test_protpy.py.

• setup.py and setup.cfg — replaced by pyproject.toml.
• .circleci/ directory and config.yml — CircleCI pipeline removed; GitHub Actions is the sole CI/CD provider.
• CircleCI badge removed from README.md.
• CircleCI TODO item removed from TODO.md.

• setup.cfg typo install_requies → install_requires (previously caused all cfg-declared dependencies to be silently ignored).

• .readthedocs.yml — ReadTheDocs configuration for hosted documentation.
• Renamed distance matrix JSON files from physiochemical to physicochemical (corrected spelling).

• README.md — minor copy and link updates.
• protpy/__init__.py — metadata and keyword cleanup.
• autocorrelation.py, composition.py, ctd.py, sequence_order.py — comment and docstring corrections.
• deploy_pypi.yml and deploy_test_pypi.yml — workflow trigger and token reference updates.
• tests/test_protpy.py — assertion message updates.

• protpy/data/ — distance matrix filenames corrected from physiochemical to physicochemical in both JSON filenames and all internal references.

• Full GitHub Actions CI/CD pipeline:
  • build_test.yml — test matrix across Python 3.11, 3.12, 3.13 with pytest-cov and Codecov upload.
  • deploy_test_pypi.yml — automated deployment to TestPyPI after successful test run.
  • deploy_pypi.yml — automated deployment to production PyPI after successful TestPyPI deployment.
• .github/workflows/README.md — workflow documentation.
• MANIFEST.in — includes protpy/data/ JSON files in source distributions.
• protpy/data/README.md — documentation for the bundled physicochemical distance matrices.
• tests/README.md — documentation for the test suite.
• docs/ — Sphinx documentation structure with conf.py, index.rst, api.rst, usage.rst, contributing.rst, Makefile, and make.bat.
• ToDo.md — project task tracking file.

• README.md — major expansion with full usage examples for all descriptors, requirements, installation, directory structure, and reference list.
• setup.py / setup.cfg — full metadata, classifiers, and dependency declarations.
• protpy/__init__.py — all_descriptors list formalised (14 entries).
• All source modules — comprehensive docstrings, inline comments, and reference citations added.
• tests/ — unit test suites expanded and restructured across test_composition.py, test_autocorrelation.py, test_conjoint_triad.py, test_ctd.py, test_sequence_order.py, and test_protpy.py.

• Multiple descriptor calculation bugs across composition.py, ctd.py, sequence_order.py, and autocorrelation.py.
• CTD column naming corrected (zero-padded singular columns, e.g. _01).
• secondary_struct property key name corrected (was sec_struct).
• SOCN/QSO column naming standardised: SOCNUm → SOCN, QSOrder → QSO; SW/Grant suffixes appended.
• Sequences uppercased on input; leading/trailing whitespace stripped.
• Invalid amino acid characters now raise a ValueError with informative message.
• PseAAC hydrophobicity, hydrophilicity, and residue mass values hard-coded for reproducibility.
• lag and weight parameter validation added to sequence order functions.

• Expanded unit test coverage across all descriptor modules.
• Additional inline comments and docstring improvements throughout all source files.

• CTD descriptor calculation corrections.
• Conjoint triad descriptor bug fixes.
• Pseudo amino acid composition function corrections.
• Sequence order module stability improvements.

• Initial package release.
• Core descriptor modules:
  • composition.py — amino_acid_composition, dipeptide_composition, tripeptide_composition, pseudo_amino_acid_composition, amphiphilic_pseudo_amino_acid_composition.
  • autocorrelation.py — moreaubroto_autocorrelation, moran_autocorrelation, geary_autocorrelation.
  • conjoint_triad.py — conjoint_triad.
  • ctd.py — ctd_composition, ctd_transition, ctd_distribution, ctd_.
  • sequence_order.py — sequence_order_coupling_number, quasi_sequence_order.
• protpy/__init__.py — package entry point with metadata and all_descriptors list.
• protpy/data/ — bundled Grantham and Schneider-Wrede physicochemical distance matrices (JSON).
• tests/ — initial unit test suite with test FASTA data files.
• requirements.txt — aaindex, numpy, pandas, varname.
• setup.py / setup.cfg — package build and distribution configuration.
• README.md — initial project documentation.
• LICENSE — MIT licence.
• .gitignore — Python project ignore rules.