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Release Notes

Cafe release notes are organized by version. Each version follows the Keep a Changelog categories so that user-facing changes remain easy to scan.

Unreleased In development

Added

  • Reorganized introduction documentation for the user guide.
  • Metacell trajectory inference experiments.
  • get_milestone_order support for MilestoneWrapper.
  • Development documentation updates for contribution workflows.
  • Local-only documentation test area under docs/test.
  • Release notes and references documentation infrastructure.
  • GitHub Actions workflows for package checks, TestPyPI publishing, and PyPI publishing.
  • Release workflow documentation for PEP 440 release candidates such as 0.2.1rc1.

Changed

  • Extracted velocity wrapper logic for cleaner method integration.
  • Updated future-work planning for Cafe v2.
  • Optimized project configuration details.
  • Temporarily excluded method-function integration tests from default pytest and VSCode test discovery.
  • Updated the development version to the 0.2.1rc1 release candidate.

Fixed

  • Fixed the cellxgene-cafe plugin launch function.

Maintenance

  • Keep this section as the working changelog for the next release.
  • Move entries into a versioned release note page when a new Git tag is created.

0.2.1rc 2026-07-02

Fixed

  • Fixed pypi release workflow #8.

0.2.0 2026-04-20

Added

  • Benchmark updates for cross-method evaluation.
  • Gastrulation case study materials.
  • Downstream analysis figure components.
  • Lineage gene-trend analysis.
  • Embedding metric support.
  • Dataset synchronization for benchmark workflows.

Changed

  • Updated Figure 1 elements and dataset presentation.
  • Improved plot_graph behavior.
  • Updated quickstart and documentation pages.
  • Refined benchmark module behavior and metric execution.

Fixed

  • Fixed benchmark metric calculation issues.
  • Added FateAnnData sub-operation support.
  • Fixed several documentation and dataset preparation details before the 0.2.0 tag.

0.1.3 2025-12-02

Added

  • plot_stream support for subway-map-style trajectory visualization.
  • plot_pie and wrapper-level plotting updates.
  • STAVIA plotting and atlas testing work.
  • MkDocs Git committers plugin support for documentation metadata.

Changed

  • Renamed package namespace from cfe to cafe.
  • Moved lint, formatting, and pytest configuration into pyproject.toml.
  • Excluded stream core files from Black, isort, and flake8 checks.
  • Updated ReadTheDocs and GitHub workflow installation behavior.
  • Updated benchmark preparation and dataset directory handling.

Fixed

  • Fixed graph wrapper and trajectory simplification behavior.
  • Optimized CellRank lineage wrapper integration.
  • Improved Dynamo, CellDancer, and plotting behavior.
  • Restored older conda YAML files needed for method execution.

0.1.2 2025-07-02

Added

  • Core method wrappers for direct, linear, cycle, probability, cluster, projection, graph, velocity, and lineage-style outputs.
  • Baseline trajectory methods including PAGA, Component 1, Angle, State Component, Cluster MST, Projection MST, and Graph MST.
  • Method integrations and development work for Palantir, Cytotrace2, CellRank, scVelo, VeloVI, UnitVelo, Dynamo, CellDancer, PyroVelocity, and STAVIA.
  • Metric module and benchmark workflows, including topology, pseudotime, and edge-flip evaluation.
  • H5AD read/write support for FateAnnData, MilestoneWrapper, and trajectory history.
  • Conda backend support for method execution.
  • GitHub workflow, pre-commit, and pytest improvements.

Changed

  • Improved wrapper naming, directed plotting, and raw wrapper visualization.
  • Updated method execution through shell, Docker, and conda backends.
  • Updated benchmark and quickstart notebooks and documentation.
  • Moved active development notebooks into developer-specific folders.

Fixed

  • Fixed projection wrapper metrics for undirected graph simplification.
  • Fixed probability wrapper end-state behavior.
  • Fixed FateAnnData and trajectory visualization behavior.
  • Fixed several early method-wrapper and benchmark issues discovered during development.

0.1.1 2025-02-05

Added

  • Backend method selection through project settings and FateMethod.
  • Simulated data loading for dynverse-style benchmark data.
  • Initial metric and benchmark module structure.
  • Multi-trajectory result storage in FateAnnData.
  • Early graph and trajectory plotting utilities.

Changed

  • Updated framework documentation and project schedule.
  • Improved trajectory plotting performance with igraph.
  • Added trajectory topology plotting for benchmark notebooks.

Fixed

  • Improved early framework construction and documentation alignment before the 0.1.1 tag.

0.1.0 2024-12-24

Added

  • Initial Cafe project framework.
  • Core source package with data, method, plot, utility, logging, and settings modules.
  • FateAnnData, MilestoneWrapper, and WaypointWrapper foundations.
  • Method backend abstraction with function, Cafe Docker, and Dynverse Docker backends.
  • Initial MkDocs documentation, quickstart notebooks, and unit test structure.
  • Early PAGA Docker integration and method execution workflow.

Changed

  • Established the initial development workflow:
  • create feature branches from dev;
  • write source code and tests locally;
  • update documentation;
  • merge through dev and main;
  • tag releases after GitHub Actions and ReadTheDocs checks.