HDDFlyzer v0.1.5

HDDFlyzer v0.1.5

HDDFlyzer v0.1.5 marks the first release cycle prepared for PyPI distribution.

This release introduces the infrastructure needed to publish HDDFlyzer as a Python package directly from the GitHub repository. A new manual publishing workflow was added using GitHub Actions and PyPI Trusted Publishing, allowing tagged releases to be validated, built, and published without long-lived API tokens.

The release process was strengthened with validation on both Python 3.11 and Python 3.12. The CI workflow now runs the test suite across both supported versions, builds the package distribution, and checks the generated metadata with twine.

The package metadata and user-facing documentation were updated for the v0.1.5 release cycle, including the README, usage documentation, changelog, roadmap, citation metadata, version metadata, and environment file.

No scientific behavior was changed in this release. Descriptor calculations, similarity workflows, dimensionality reduction, visualization logic, result artifacts, and pipeline behavior remain unchanged.

Release preparation was validated locally with:

• Full test suite: 290 passed, 1 skipped
• Package build: wheel and source distribution generated successfully
• Distribution metadata check: twine check passed
• Wheel installation smoke test: successful installation and CLI/import validation from the generated wheel

This release establishes the publication path for HDDFlyzer on PyPI while preserving the current scientific and architectural behavior of the project.

HDDFlyzer v0.1.4

HDDFlyzer v0.1.4

This pre-release prepares HDDFlyzer for public web documentation through MkDocs and GitHub Pages.

Highlights

• Added a dedicated GitHub Actions workflow for documentation builds and GitHub Pages deployment.
• Added strict MkDocs validation with mkdocs build --strict.
• Configured documentation deployment to run only from main.
• Updated project metadata to version 0.1.4.
• Updated citation, changelog, roadmap, README, and MkDocs configuration.
• Added the GitHub Pages site_url.
• Constrained MkDocs to <2.0 in the documentation optional dependencies to avoid future breaking changes.

Validation

• CI passed on dev/v0.1.4.

• Docs workflow passed on dev/v0.1.4.

• Main branch documentation build and deployment completed after merge.

• Local validation passed:

  • python -m mkdocs build --strict
  • python -m pytest tests -q
  • python -m build
  • package/import version reports 0.1.4

Notes

• This release does not publish HDDFlyzer to PyPI.
• No scientific logic, pipeline behavior, runtime API behavior, or output structure was changed.
• PyPI publication remains planned for a later release cycle.

HDDFlyzer v0.1.3

HDDFlyzer v0.1.3

This pre-release closes the minimal continuous integration checkpoint for HDDFlyzer.

Highlights

• Added a minimal GitHub Actions CI workflow.

• Runs CI on pull requests.

• Runs CI on pushes to main and dev/v*.

• Uses Ubuntu with Python 3.11.

• Installs HDDFlyzer in editable mode with development dependencies.

• Runs the full test suite with python -m pytest tests -q.

• Adds package import smoke validation.

• Adds CLI smoke validation for:

  • hddflyzer --version
  • hddflyzer
  • hddflyzer pipeline

• Builds the package with python -m build.

• Updated GitHub Actions runtime compatibility to avoid Node.js 20 deprecation annotations.

• Updated version metadata, changelog, roadmap, citation metadata, and README badge for v0.1.3.

Validation

Validated through GitHub Actions:

• CI workflow passed successfully.
• No remaining workflow annotations or Node.js runtime warnings.

Local validation included:

• python -c "import hddflyzer; print(hddflyzer.__version__)"

  • 0.1.3

• git diff --check

Notes

This release does not publish HDDFlyzer to PyPI.

PyPI publication remains intentionally deferred for a later cycle after CI-backed validation is stable.

HDDFlyzer v0.1.2

HDDFlyzer v0.1.2

This pre-release closes the local packaging and installability checkpoint for HDDFlyzer.

Highlights

• Added global CLI support for hddflyzer --version.
• Added global CLI support for hddflyzer -V.
• Updated the internal package version to 0.1.2.
• Added CLI tests for the new version flags.
• Validated editable local installation with pip install -e ..
• Validated local wheel and sdist builds.
• Confirmed that hddflyzer/config/descriptor_config.json is included in both wheel and sdist.
• Updated release planning documentation in CHANGELOG.md and ROADMAP.md.
• Updated citation metadata for v0.1.2.

Validation

Validated locally with:

• python -m pytest tests -q
  • 290 passed, 1 skipped
• python -m py_compile hddflyzer/cli.py
• python -c "import hddflyzer; print(hddflyzer.__version__)"
  • 0.1.2
• python -m pip install -e .
  • installed as hddflyzer==0.1.2
• python -m build
• Wheel/sdist inspection confirming package data inclusion
• git diff --check

Notes

This release does not publish HDDFlyzer to PyPI.

PyPI publication remains intentionally deferred until after the next validation steps, especially minimal CI and automated package checks.

HDDFlyzer v0.1.1

HDDFlyzer v0.1.1

This documentation-focused pre-release refines the public identity, documentation site, citation metadata, roadmap, and release metadata for HDDFlyzer.

Highlights

• Refined the HDDFlyzer documentation site and visual identity.
• Updated the Home, Usage, API, and Changelog documentation pages.
• Added documentation assets for the project site.
• Added CITATION.cff for citation metadata.
• Updated ROADMAP.md to reflect the post-v0.1.0 direction.
• Aligned hddflyzer.__version__ with 0.1.1.
• Updated the CLI banner to use High-Dimensional Descriptor-based Feature Space Analyzer.

Scope

This release is focused on documentation, identity, and repository readiness.

It does not add CI, publish to PyPI, change scientific workflow behavior, or introduce new analysis features.

Next development direction

Planned follow-up work:

• v0.1.2: packaging and local installability.
• v0.1.3: minimal CI and documentation validation.
• v0.1.4 or later: PyPI readiness and publication.

HDDFLYZER v0.1.0

HDDFLYZER v0.1.0

Initial private release of HDDFLYZER: High-Dimensional Descriptor-based Feature Space Analyzer.

HDDFLYZER is a CLI-first cheminformatics toolkit with a Python API for reproducible, traceable molecular descriptor-space workflows. It generates descriptor, similarity, projection, and visualization outputs from compound collections, stores them with metadata, and supports later reconstruction, inspection, and analysis of completed runs.

Highlights

• Initial project import.
• CLI entry point: hddflyzer.
• Dataset-first workflow outputs under results/<tag>/.
• Manifest-based run traceability through manifest.json and workflow_summary.md.
• Pipeline orchestration layer with run_pipeline(), run_workflow(), and execute_workflow().
• Results reconstruction API with WorkflowRun, ResultArtifact, LoadedArtifact, load_workflow_run(), and load_artifact().
• Scientific result views for descriptor, similarity, and projection spaces.
• Science helpers for alignment, descriptor/projection correlations, neighborhood preservation, and group comparisons.
• Visualization helpers connected to reconstructed results.
• MkDocs documentation scaffold.
• Initial test suite included.

Validation

• pytest tests -q passed locally: 288 passed, 1 skipped.
• Initial repository import was reviewed to exclude generated outputs, caches, build artifacts, site/, root results/, and Python cache files.

Notes

This is an initial pre-release research software version. Output contracts and public APIs may still evolve as the project matures.