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Changelog

v2.0.2 — [2025-12-09]

  • docs: update to match global layout
  • pkg: pre-commit
  • docs: set up section indices correctly
  • docs: correct readme reference
  • pkg: clean up changelog

[2025-12-04] — v2.0.1

  • fix: docker release auth issue

[2025-12-04] — v2.0.0

Overview:

  • New "migrate" function to update older datasets to be compatible with the latest G4X-viewer and G4X-helpers versions.
  • Added schema validation to ensure data integrity and compatibility.
  • Implementation of an initial test framework for the package.
  • Re-worked CLI-api to be more modular and easier to extend.

Changes:

  • new "in_place" output flag replaces "out_dir" and ensures predictable output behavior.
  • standardized log location
  • new logging formatter
  • refactor "workflows" into modules
  • adapt G4Xoutput to latest schema
  • refactored stream_features method to redemux module
  • new write_csv_gz method
  • add bead_mask loading to G4Xoutput
  • removed deprecated G4X-viewer schema
  • new dependency: pathschema
  • updates dependencies
  • update docs content and match structure to main site
  • update changelog

[2025-12-03] — v1.0.2

  • fix: update uv.lock

[2025-12-01] — v1.0.1

  • fix: get_shape fast via glymur

[2025-11-13] — v1.0.0

  • docs: add partials for shared options
  • pkg: add rich-codex as docs dependency
  • fix: load_segmentation method now allows custom keys
  • feat: redemux parses transcript panel for input flexibility
  • docs: update for new CLI
  • feat: numpy version agnostic npzGetshape
  • pkg: repr update
  • pkg: implement new cli and re-factor
  • pkg: set python 3.12 as default version

[2025-10-01] — v0.5.2

  • fix: missing tests in publish workflow

[2025-10-01] — v0.5.1

  • pkg: added PyPI publish workflow
  • fix: README logo link

[2025-10-01] — v0.5.0

  • docs: formatting
  • docs: spell check
  • docs: integrate redemux docs
  • docs: Docs restructuring (#33)

  • docs: updated _core docs

  • feat: Redemux tool (#30)

  • feat: progress bar

  • fix: G4Xoutput out_dir now defaults to cwd instead of run_base

  • fix: enforce cluster color as hex-codes
  • fix: auto-conversion of clusters to 'categorical' when load_clustering=true
  • fix: change all segmentation_cell_id to cell_id (#34)

  • fix: cellid_key - bugfix

  • pkg: updated ruff

  • pkg: relaxing glymur dependency
  • pkg: relaxed protobuf requirement for internal alignment
  • pkg: opening python requirements to include 3.11
  • pkg: removed bump-my-version and replacing with uv-ship

[2025-08-12] — v0.4.14

Fixes:

  • tar_viewer will now exit leaving the source folder unchanged

Improvements:

  • tar_viewer now requires an out_path

[2025-08-11] — v0.4.13

Docs:

  • changelog now included in docs
  • url updates
  • typos

Package:

  • deployment of multi-arch packages
  • replaced dependency ray with multiprocessing
  • set required uv version

[2025-07-25] — v0.4.12

Docs:

  • Added Documentation for G4X-helpers and G4X-output

Package:

  • Implemented bump-my-version for handling version updates and tagging
  • Added pre-commit hooks for code quality checks
  • Ruff for linting and formatting (invoked via pre-commit)
  • Github actions for automated package builds and docs deployment

Improvements:

  • Added npz util to speed up G4Xoutput() initialization

Fixes:

  • Incorrect gzip compression on some output csvs

Housekeeping:

  • Updated and trimmed dependencies
  • Cleaned up .gitignore file
  • Cleaned up README.md

[unreleased changes]

  • Release preparation
  • Add Dockerfile
  • Update dependency information
  • Add tar_viewer tool to tar up a G4X-viewer folder for the single-file upload option.
  • Add new_bin tool to more quickly generate a new bin file
  • Bug fixes for MVP functionality
  • Add CLI tools for re-segmentation and updating bin files with clustering/embedding information