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Changelog

All notable changes to CHAMANP will be documented in this file.

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

0.20.1 - 2026-05-28

Added

  • Added support for running the CLI with python -m chamanp.
  • Added CHAMANP logo branding to the MkDocs documentation site.

Changed

  • Improved header logo contrast, documentation color identity, and visual styling.
  • Moved usage-oriented documentation out of the Home page and into a new Usage page.

Documentation

  • Evaluated migration from MkDocs Material to Zensical and deferred it to a later development cycle because the current documentation depends on mkdocstrings[python] and the existing MkDocs Material build remains stable.

0.20.0 - 2026-05-21

Added

  • Added GitHub Pages documentation built with MkDocs, Material for MkDocs, and mkdocstrings.

Docs

  • Added a user-facing input-process-output workflow contract to the README and MkDocs Home page, including how the COCONUT-like example CSV should be interpreted.
  • Clarified CHAMANP's taxonomy-backed collection filtering concept, the role of source_data/coconut_taxonomy.json, and the project-name analogy to "shaman".
  • Added a beginner-facing example execution walkthrough with the TOML profile, CLI commands, expected output, and generated artifacts.
  • Grouped documented outputs into essential user-facing artifacts and audit artifacts to reduce confusion about the number of generated files.
  • Clarified that TOML profiles are manually written configuration files based on the user's CSV paths, columns, target collections, and output settings.
  • Reorganized the MkDocs Home page so installation and the CLI example appear before conceptual sections, removed fragile API anchors, and made citation guidance rely on CITATION.cff.
  • Polished the MkDocs Home hero, workflow card placement, heading capitalization, and API link style for the final v0.20.0 documentation pass.

Changed

  • Started the documentation aesthetics cycle for the MkDocs site while preserving chemistry behavior and the public API boundary.
  • Clarified TOML profile examples so PyPI users are directed to create their own runtime profile instead of relying on a repository-specific example file.
  • Collection filtering now accepts both semicolon (;) and pipe (|) separators in the collections field, matching COCONUT-style example data while preserving existing semicolon support.

Improved

  • Improved CI coverage with a Python 3.11/3.12 matrix, public API assertions, wheel smoke installation, source distribution smoke installation, and strict documentation builds.

Removed

  • Removed the repository-specific examples/chamanp.toml file from the source tree and source distribution to avoid ambiguity for PyPI users.
  • Removed the local PowerShell wheel smoke script and the obsolete MANIFEST.in; CI now owns wheel and source distribution smoke validation.
  • Removed the internal DESIGN.md planning document from the public source tree to keep the PyPI-facing project surface focused on user documentation, API docs, tests, and release notes.
  • Removed the internal INSTALL.md release checklist; PyPI-facing installation guidance now lives in README and the MkDocs Home page.

0.19.0 - 2026-05-16

Docs

  • Made CHAMANP's public API understandable through truthful, English, NumPy-style docstrings while preserving the current API boundary and avoiding unrelated infrastructure or behavior changes.
  • Updated the README development-status section to reflect the completed 0.18.0 PyPI publication milestone and the current 0.19.0 public API documentation cycle.

0.18.0 - 2026-05-16

Added

  • Added a manual PyPI Trusted Publishing workflow for the first official pre-stable PyPI publication.

Changed

  • Started the 0.18.0 first official PyPI publication preparation cycle using Trusted Publishing as the intended publication path.
  • Kept CHAMANP pre-stable while preparing official PyPI publication without declaring the package stable.

Docs

  • Documented Trusted Publishing setup, GitHub environment configuration, PyPI pending publisher required values, and the first official publication order in INSTALL.md.

0.17.0 - 2026-05-16

Changed

  • Started the 0.17.0 official publication rehearsal and stable-release governance cycle.
  • Recorded that the historical v1.0.0 anomaly was remediated before public stable publication: the GitHub Release was removed manually, the local and remote tags were deleted, and no DOI, Zenodo record, or external release assets were associated with it.

Docs

  • Added stable publication checklist and repository workflow vs. package API boundary documentation to INSTALL.md.

0.16.0 - 2026-05-16

Added

  • Added a versioned GitHub Actions workflow for tests, distribution builds, twine check, and wheel smoke-install validation without running the real pipeline.
  • Added .pytest_cache/ to .gitignore.

Changed

  • Started the 0.16.0 stable-release gate cycle.
  • Changed development version metadata to use the PEP 440-compliant .dev0 format instead of the previous -dev style.
  • Updated citation wording so CHAMANP is described as an independent package that may be consumed by LigandHub or other downstream systems.

Docs

  • Aligned DESIGN, README, and INSTALL documentation around release governance before any stable publication.
  • Documented the current pre-stable public API contract and clarified that Pipeline, chamanp._core, and chamanp._utils remain private implementation details.
  • Clarified that TestPyPI is only a publication-validation index, while official PyPI readiness remains a separate stable-publication requirement.
  • Clarified that artifacts/ contains local generated outputs ignored by Git.

Removed

  • Removed the tracked legacy generated report artifact.
  • Removed local core/__pycache__ and utils/__pycache__ residue left over from the pre-migration source layout.
  • Removed stale scipy entries from auxiliary environment files because CHAMANP does not currently use SciPy as a runtime dependency.

0.15.0 - 2026-05-15

Changed

  • Started PyPI/TestPyPI publication readiness and stable-release contract hardening work after the 0.14.0 pre-release validation cycle.
  • Focused the development cycle on distribution publication checks, external install validation, and documenting the stable public contract without changing chemistry behavior, output artifacts, reports, or the public API.

Tests

  • Validated local builds with twine check, uploaded 0.15.0.dev0 to TestPyPI for publication validation (https://test.pypi.org/project/chamanp/0.15.0.dev0/), and confirmed external clean-environment installation with real runtime dependency resolution.

0.14.0 - 2026-05-15

Added

  • Added documentation and local smoke-test support for editable installs, wheel installs, source distributions, and the distinction between package runtime dependencies and reproducible local environments.

Changed

  • Started pre-release installation validation work, focused on building CHAMANP distributions and smoke-testing wheel installation outside the repository checkout before v1.0.0.

0.13.0 - 2026-05-15

Changed

  • Started dependency and installation hardening development, focused on pip/PyPI readiness, packaging portability, and documentation alignment after 0.12.0.
  • Treated pip installability as a minimum requirement for broad external reuse; LigandHub-API may be an early downstream consumer, but it is not the design target for CHAMANP.

Docs

  • Clarified installation documentation for editable installs, local wheel/sdist installs, runtime dependency minimums, RDKit installation sensitivity, and CHAMANP's independent package direction.
  • Refreshed README development status to align with the current public API, dependency policy, and pip/PyPI readiness focus.

0.12.0 - 2026-05-15

Changed

  • Started packaging readiness development, focused on distribution metadata, package build validation, and clean-install smoke checks without changing runtime behavior.

Docs

  • Updated documentation so CLI and TOML support are no longer described as future work.

0.11.0 - 2026-05-15

Added

  • Added a minimal chamanp CLI with --version, check-config, and run commands backed by the existing public Python API.

Changed

  • Started CLI development, focused on a minimal public terminal interface for loading TOML profiles, validating configuration, and running CHAMANP through the existing public API.
  • Designed the CLI to present clean user-facing errors without Python tracebacks by default.

Fixed

  • CLI command failures now print clean Error: <message> output without Python tracebacks by default.

0.10.0 - 2026-05-14

Added

  • Added ChamanpConfig.from_toml(path) using Python 3.11 tomllib for external TOML configuration profiles.

Changed

  • Started TOML configuration profile development, focused on loading reproducible external configuration files through ChamanpConfig.from_toml(path) without changing pipeline behavior.
  • TOML loading accepts lower_snake_case keys, maps them to existing CHAMANP configuration fields, rejects unknown keys, and leaves semantic validation to validate_config(config).

0.9.0 - 2026-05-14

Added

  • Added public ChamanpResult as a frozen dataclass containing execution status, version, artifact paths, fingerprint settings, and summary counts.

Changed

  • Started structured execution result development, focused on returning a public ChamanpResult from run(config) without changing chemistry behavior, artifact names, output formats, or report contents.
  • Updated public run(config) to return ChamanpResult while preserving existing artifact-writing behavior.
  • Kept Pipeline private and avoided loading fingerprint matrices, datasets, or reports into the result object.

Docs

  • Documented that ChamanpResult reports completed executions and failures remain exception-based.

0.8.0 - 2026-05-14

Added

  • Added the public execution API doorway, exposing validate_config and run from the main chamanp namespace while keeping Pipeline private.
  • Added public validate_config(config) and run(config) exports from the main chamanp namespace.

Changed

  • run(config) preserves current disk-output behavior and returns None in 0.8.0; structured in-memory results are deferred to a future development version.
  • Kept Pipeline private and out of chamanp.__all__.

Docs

  • Documented that run(config) returns None in 0.8.0 and writes configured artifacts to disk.

Internal

  • No chemistry, fingerprint, artifact, output, or report behavior changes were intended.

0.7.0 - 2026-05-14

Added

  • Added private internal namespaces under chamanp/_core and chamanp/_utils.

Changed

  • Completed the internal package migration for private chamanp/_core and chamanp/_utils namespaces, import-safety hardening, and a clean migration away from root-level core/ and utils without changing chemistry behavior, outputs, artifacts, or reports.
  • Kept the current public API as from chamanp import __version__, ChamanpConfig; Pipeline remains internal and is not publicly exported.
  • Moved internal utility modules into chamanp/_utils.
  • Moved internal core pipeline modules into chamanp/_core.
  • Deferred pipeline logging setup until execution so importing pipeline internals no longer creates artifacts/ or artifacts/pipeline.log.

Removed

  • Removed the root-level core/version.py compatibility bridge after package metadata moved fully to chamanp.version.

Internal

  • No chemistry, output, artifact, or report behavior changes were intended in this migration.

0.6.0 - 2026-05-14

Added

  • Added DESIGN.md as an internal strategic design reference for CHAMANP identity, public API direction, COCONUT-as-reference-dataset scope, and roadmap.

Changed

  • Started the external-facing documentation cycle, focused on CHAMANP's public usability contract without changing chemical processing behavior.

Docs

  • Rewrote README from an external user perspective, clarifying CHAMANP's purpose, current usable modes, COCONUT-as-reference-dataset scope, and current public API boundaries.

0.5.0 - 2026-05-14

Added

  • Added ChamanpConfig as the first public runtime configuration object, with no chemical processing behavior changes.

Changed

  • Started the configuration API development cycle, focused on introducing a public runtime configuration object for CHAMANP without changing chemical processing behavior.

0.4.0 - 2026-05-13

Added

  • Added minimal package metadata in pyproject.toml.
  • Added a minimal chamanp package namespace exposing __version__.
  • Added package import smoke tests that do not run the pipeline or require source data.

Changed

  • Changed project license metadata from MIT to LGPL-3.0-or-later by project-owner decision.

Docs

  • Documented the package transition direction and draft future public API.

Internal

  • No chemical curation, SMILES validation, collection filtering, fingerprint generation, reporting, or artifact naming changes were intended in this development pass.

0.3.0 - 2026-05-13

Added

  • Added configuration preflight validation before pipeline execution.
  • Added ConfigurationError for clear early failures when required config values are missing or invalid.
  • Added focused tests for preflight validation and entrypoint ordering.

Changed

  • Validated configured database and collection taxonomy paths before entering curation or fingerprint generation.
  • Validated target collections, collection logic, safe collection tags, and Morgan fingerprint parameters.
  • Hardened TARGET_COLLECTIONS validation to require a non-empty collection of non-empty strings.

Removed

  • Removed unused OUTPUT_PATH from config.py.

Internal

  • No chemical curation, SMILES validation, collection filtering, or fingerprint generation logic changes were intended in this development pass.

0.2.0 - 2026-05-13

Added

  • Added centralized project metadata in core/version.py.
  • Added future report execution metadata for input CSV path, collection tag, fingerprint radius, fingerprint bit length, and valid fingerprinted molecule count.
  • Added tests to ensure report headers include centralized metadata and do not contain the legacy v1.0 version string.

Changed

  • Updated future report headers to use centralized CHAMANP version/status metadata.

Removed

  • Removed the legacy hardcoded v1.0 - May, 2025. Oviedo report header for future reports.

Internal

  • No chemical curation, collection filtering, or fingerprint generation logic changes were intended in this development pass.

0.1.0 - 2026-05-13

Added

  • Added invalid SMILES traceability during fingerprint generation.
  • Added invalid_smiles_{tag}.csv output through PathManager and Pipeline.
  • Added tests for substring non-match, semicolon-separated labels, whitespace handling, and missing/NaN values.
  • Added reporter tests and fingerprint count assertions.

Changed

  • Preserved existing valid fingerprint and valid metadata outputs.
  • Replaced substring-based collection filtering with exact label matching.
  • Parsed collections as semicolon-separated labels with surrounding whitespace stripped.
  • Kept missing/NaN collection values from matching.
  • Updated tests; current validation was 29 tests passing.

Docs

  • Reports now include invalid SMILES count/path when provided by the pipeline.

Internal

  • FingerprintGenerator exposes invalid_smiles_count for report traceability.
  • ReportWriter remains backward-compatible when invalid fields are omitted.

1.0.1-dev - 2026-05-12

Changed

  • Kept CHAMANP as a pre-stable development prototype.
  • Prepared the project toward a corrected 0.1.0-style baseline by documenting the runtime environment, clarifying source-data expectations, and softening earlier stable-version language.
  • Kept the baseline free of intended pipeline behavior changes.

Tests

  • Added baseline tests for isolated non-RDKit components: path_manager, collection_utils, and filter.
  • Added baseline tests for isolated RDKit-related components: curator and fingerprints.
  • Current validation was 21 tests passing.