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Changelog

[Unreleased]

Migration to ome-zarr-converters-tools v1.

API Breaking Changes

  • CustomTiff acquisition_details.toml keys renamed (follows the v1 field renames): pixelsize → xy_pixel_size, start_z_coo/start_t_coo → start_z_space/start_t_space (and any other *_coo → *_space). Existing user acquisition_details.toml files must be updated. See docs/converters/custom_tiff.md.

Chores

  • Bump ome-zarr-converters-tools to [s3]>=1.0.0,<2.0.0. The [s3] extra is now required: v1 makes s3fs optional, so it is pinned here to keep s3:// inputs working (it was previously pulled in transitively).
  • Adopt the v1 AcquisitionDetails renames in all builders: pixelsize= → xy_pixel_size= and start_*_coo=/length_*_coo= → *_space= (values unchanged). Import BackendType from the package root instead of the private models._converter_options.
  • Regenerate __FRACTAL_MANIFEST__.json against the v1 AcquisitionOptions schema (new built-in filters, grouping/tiling split, remove_* stage corrections, scheduler mode).

[v0.7.2]

Fix

  • Bug in extended testing using the wrong api
  • Fix typo in the conversion log message (Successfully).

Chores

  • Load the shared snapshot-testing plugin via pytest_plugins in tests/conftest.py instead of -p in pytest addopts, matching the sibling converters.
  • Align repository tooling with ome-zarr-converters-tools: adopt its .pre-commit-config.yaml (validate-pyproject v0.25, crate-ci/typos, astral-sh/ruff-pre-commit v0.15.17, nbstripout) with a per-repo _typos.toml, add a chores pixi task, bump GitHub Actions pins (checkout v7, codecov-action v7, action-gh-release v3, setup-python v6), and trim CLAUDE.md.

[0.7.1]

Fix

  • Remove passing explicit logger_name to the run_fractal_task wrapper.

[0.7.0]

Features

  • Add Python API functions (convert_cellvoyager, convert_cq3k, convert_operetta, convert_imagexpress_hcs, convert_hcs_tiff, convert_single_tiff) for programmatic use outside Fractal, following the existing convert_scanr pattern.
  • Update test utilities to call the high-level API functions, providing end-to-end coverage of both the API layer and the underlying init/compute tasks.

Docs

  • Add "How to Run the Converters" page documenting the Python API with usage examples, common parameters, and per-converter code snippets.
  • Add Python API section to each converter page with a copy-paste ready code example.

Chores

  • Remove custom_tiff/_setup.py and its import: ome-zarr-converters-tools>=0.10.0 now ships a built-in setup_singleimage handler for SingleImage collections, making the local copy redundant.
  • Bump to ome-zarr-converters-tools>=0.10.0,<0.11.0
  • Rename internal modules to _{module_name}.py across all converter packages and common/ to signal they are private implementation details.

[0.6.0]

Features

  • Add custom_tiff converter: two new tasks for converting plain TIFF data (HCS plate and single-image) to OME-Zarr.

Fix

  • Fix get_attributes_from_condition_table to dynamically exclude the acquisition column from results.

Chores

  • Bump to ome-zarr-converters-tools>=0.9.0,<0.10.0