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Documentation Release Notes

0.3.0

Documentation source tag: v0.3.0. Package-index publication is pending.

Public component source tags

  • Core v0.22.0, QM v0.3.0, ML v0.4.0, GUI v0.6.0, data science v0.5.0, descriptors v0.11.0, FEP v0.7.0, docking v0.7.0, and MD v0.13.0 identify the reviewed public source commits recorded in the version matrix. Publication was checked on 2026-10-15: all listed component versions except MD 0.13.0 are published on PyPI. MD is tagged and awaiting publication. Documentation 0.3.0 is tagged and awaiting publication; the updated bundle release remains pending.

  • Core CI installs the [test] extra, including RDKit for hydrogenation coverage, and its help assertions handle plain and styled terminal output. QM uses the published caddforge-opencosmors==0.0.1 dependency and pyocl-idor>=0.8.3 with Java 21 or newer.

  • MD tests support Python 3.10 through the conditional tomli backport. Its installed-wheel runner preserves declared pytest markers while excluding checkout runtime sources.

Documentation and packaging

  • Record verified package-index availability, update current installation and migration examples, and generate API provenance from the version matrix.

  • Normalize ANSI formatting in CLI error assertions and cover plain and styled output. The wheel CI job installs the declared [test] extra.

  • Standardize package CI on tested wheels, Python 3.10/3.12, release metadata checks, and tag-triggered PyPI Trusted Publishing. Add docs package releases alongside opt-in Pages, run bundle migration tests with core sources, and derive packaging expectations from current metadata instead of inherited pins.

  • Install PyOCL using the public pyocl-idor>=0.8.3 distribution; Python imports remain pyocl. Provision Java 21 in affected CI workflows and document the Java 21 or newer runtime requirement.

  • Start new public repositories without earlier development history. New public component tags and verified publication status are recorded above. Documentation continues its version sequence at 0.3.0; the bundle version awaits assignment.

  • Declare MIT licensing and ship project and third-party licence texts.
  • Remove ESOL and Glide / Glide WS integrations from the public component sources.
  • Pin the documentation theme to the reviewed assets and reject unreviewed theme versions or non-English search assets.

The notes below describe inherited development milestones, not tags or releases in the new public repositories. See the version matrix.

0.2.1

  • Document bundle 0.22.0, which includes caddforge-docs==0.2.1 and the caddforge docs command by default.
  • Keep documentation authoring and test extras outside the runtime bundle.
  • Update installation examples, CLI guidance, the version matrix, and release ordering.
  • Retain separate docs installation instructions for bundle 0.21.0, core-only, and selective plugin environments.

This inherited milestone does not establish a new public release or publication.

0.2.0

This inherited milestone introduced the packaged documentation. New public package releases and public site deployment remain separate actions.

Installed documentation

  • Added the optional caddforge docs command, registered only when this package is installed.
  • Ship a complete static site with search, assets, and downloadable examples for offline viewing.
  • Support --host, --port, and --no-browser, including IPv4, IPv6, and hostnames.
  • Build the site into wheels and editable installations; source distributions contain everything needed to rebuild it. Reinstall after source edits to refresh the installed view.

Guides and reference

  • Added runnable CLI and Python tutorials using synthetic table data and a two-stage core pipeline.
  • Added configurations for 26 documented scientific workflows and eight advanced pipeline templates.
  • Added job, scatter, troubleshooting, GUI, reproducibility, contributor, and security guidance.
  • Generate the public core API reference from an explicit source allowlist without importing plugins.
  • Document core 0.21.0, bundle 0.21.0, and the latest tagged public plugins, including MD terminal policies and encoded PheSA references.
  • Forward declared runtime inputs in Python submission examples so compressed inputs use core staging.

Validation and publication

  • Check local links and anchors, example syntax and schemas, and packaged artifacts.
  • Validate GitHub branch/tag pushes; Pages deployment remains opt-in and limited to the default branch after validation.
  • Keep scientific engine validation distinct from template schema checks and lightweight tutorials.
  • Record outstanding licensing, public-index dependency, hosting, and reporting-route prerequisites in the release checklist.