Changelog¶
v3.2.0 (2025-12-22)¶
New¶
feature/dummy-plugin-refactor [Brian Whitney]
feature/plugin-priority [Brian Whitney]
Fix¶
fix typo [Brian Whitney]
fix typo [Brian Whitney]
Other¶
bump base [Brian Whitney]
update mock typing [Brian Whitney]
update determine_plugin docstring [Brian Whitney]
explicit reader param [Brian Whitney]
refactor conftest [Brian Whitney]
update changelog [Brian Whitney]
update typing [Brian Whitney]
update assertion comment [Brian Whitney]
single param priority selection [Brian Whitney]
remove mac-os 13 [Brian Whitney]
add ordering policy [Brian Whitney]
lint [Brian Whitney]
Update bioio/plugins.py [Brian Whitney, Philip Garrison]
v3.1.0 (2025-12-05)¶
New¶
feature/dimension-properties [Brian Whitney]
Fix¶
Fix link reference in OVERVIEW.md [Sergey Fedoseev]
Other¶
use odic [Brian Whitney]
use odic [Brian Whitney]
revert debug [Brian Whitney]
add token [Brian Whitney]
add token [Brian Whitney]
loosen patch recs [Brian Whitney]
ci(dependabot): bump actions/checkout from 5 to 6 [dependabot[bot]]
admin/update-bioformats-ref [Brian Whitney]
remove extra case [Brian Whitney]
Update writer registry for OMEZarrWriter release [Brian Whitney]
ci(dependabot): bump actions/setup-python from 5 to 6 [dependabot[bot]]
ci(dependabot): bump actions/checkout from 4 to 5 [dependabot[bot]]
DOCS: fix links to reader installation [Ian Hunt-Isaak]
v3.0.0 (2025-07-03)¶
New¶
feature/base-3.0.0 [Brian Whitney]
Other¶
alphabatize [Brian Whitney]
update bioio-base class docs [Brian Whitney]
v2.0.0 (2025-06-20)¶
New¶
feature/migrate-writers [Brian Whitney]
feature/v3-ome-zarr-writer [Brian Whitney]
Fix¶
bugfix/standard_metadata_typing [Brian Whitney]
Other¶
admin/doc-link [Brian Whitney]
admin/bump-base-2.0.0 [Brian Whitney]
no need for multiple error messages [Kevin Mitcham]
error is already thrown [Kevin Mitcham]
linting and stuff [Kevin Mitcham]
add exception throwing to report WHY Reader fails [Kevin Mitcham]
comment resolution [Brian Whitney]
Update README.md [Brian Whitney, Sean LeRoy]
Writer Documentation [Brian Whitney]
bump to 1.4.0 [Brian Whitney]
lock bioio base 1.0.8 [Brian Whitney]
add fsspec back [Brian Whitney]
bump tests [Brian Whitney]
add dropped comments [Brian Whitney]
remove unnecessary deps [Brian Whitney]
update import lib [Brian Whitney]
update comments [Brian Whitney]
add fsspec[http] [Brian Whitney]
remove generate_zarr [Brian Whitney]
update V2 writer to use zarr 3.0.0+ [Brian Whitney]
v1.6.1 (2025-05-06)¶
Fix¶
Bugfix: Remove unnecessary bioio-czi dependency that breaks CI [Philip Garrison]
v1.6.0 (2025-04-28)¶
New¶
Feature #107 Remove licensing comment, clean up accepting-plugin [Philip Garrison]
Feature #107 Lint [Philip Garrison]
Feature #107 Replace bioio-czi test with new dummy plugin [Philip Garrison]
Feature #107 Comment on sdist [Philip Garrison]
Feature #107 Exclude tests from sdist [Philip Garrison]
Feature #107 License bioio-czi integration test [Philip Garrison]
Feature #107 Fix dump_plugins test [Philip Garrison]
Feature #107 Lint [Philip Garrison]
Feature #107 Clean up test [Philip Garrison]
Feature #107 Parse file extension that comes before query string [Philip Garrison]
v1.5.2 (2025-04-18)¶
Fix¶
bugfix/PPS-reset-Null [Brian Whitney]
Other¶
bump-version [Brian Whitney]
comment spacing [Brian Whitney]
remove ngff-zarr pin [Brian Whitney]
support 3.10 [Brian Whitney]
admin/python-support-3.10+ [Brian Whitney]
add back relevant autogenerated comments [Brian Whitney]
admin/docs-fix [Brian Whitney]
v1.5.1 (2025-04-04)¶
admin/pin-bioio-base [Brian Whitney]
admin/pin-bioio-base [Brian Whitney]
admin/pin-bioio-base [Brian Whitney]
v1.5.0 (2025-04-02)¶
New¶
feature/standard-metadata [Brian Whitney]
Other¶
Update bioio/bio_image.py [Brian Whitney, Sean LeRoy]
bump version bioio-base [Brian Whitney]
ci(dependabot): bump extractions/setup-just from 2 to 3 [dependabot[bot]]
v1.4.0 (2025-03-25)¶
remove manifest and bump version req [Brian Whitney]
update typing for bioio-base changes [Brian Whitney]
Revert “update typing for bioio-base changes” [Brian Whitney]
update typing for bioio-base changes [Brian Whitney]
v1.3.0 (2025-03-12)¶
remove 3.9 from CI build [Kevin Mitcham]
update to use new tifffile enumerations [Kevin Mitcham]
v1.2.1 (2025-03-07)¶
New¶
feature/parameterized-ome-tiff-writer-compression (#88) [Eva Maxfield Brown]
Other¶
pin the tifffile version so we can release a final build compatible with 3.9 [Kevin Mitcham]
allow zarr writer to do incremental writes of single timepoints [Dan Toloudis]
restict ngff-zarr to prevent errors in Ubuntu 18 [Kevin Mitcham]
v1.2.0 (2025-01-15)¶
Block using bad scitkit-image [SeanLeRoy]
ci(dependabot): bump codecov/codecov-action from 4 to 5 [dependabot[bot]]
Try and resolve doc build by shifting publish to only on git tag (#75) [Eva Maxfield Brown]
unpin zarr max version (#72) [Joshua Gould]
Update ome_tiff_writer.py to remove reference to image_names [Tim Monko]
add channel selections to writer [toloudis]
v1.1.0 (2024-08-16)¶
New¶
feature/plugin-registry [BrianWhitneyAI]
feature/reader-surface-info [BrianWhitneyAI]
Other¶
Only install dummy-plugin once and only create sample text file once for performance [SeanLeRoy]
Add test case for adding anon attr for S3 [SeanLeRoy]
Re-raise only in error case [SeanLeRoy]
Make string formattable [SeanLeRoy]
Support public s3 files automatically [SeanLeRoy]
Fetch tags during doc build checkout [Eva Maxfield Brown]
update error message [BrianWhitneyAI]
reorganization [BrianWhitneyAI]
add feas report to init [BrianWhitneyAI]
expand error message [BrianWhitneyAI]
typo resolution [BrianWhitneyAI]
add docs disclaimer [BrianWhitneyAI]
remove docs column [BrianWhitneyAI]
update formatting [BrianWhitneyAI]
update tests for py3.9 [BrianWhitneyAI]
mypy [BrianWhitneyAI]
add test [BrianWhitneyAI]
adjsut typing [BrianWhitneyAI]
add manifest [BrianWhitneyAI]
add manifest [BrianWhitneyAI]
add dummy reader [BrianWhitneyAI]
add check for metadata keys [BrianWhitneyAI]
resolve comments [BrianWhitneyAI]
Change to py39 typing Union rather than py310 typing [evamaxfield]
Remove the suffix standardization from bioimage as it now lives in plugin management [evamaxfield]
Remove debug prints and lint [evamaxfield]
Checkpoint with print debug print statements [evamaxfield]
Sort the plugin list by the suffix length (desc) to ensure that the most specific plugins are matched first [Eva Maxfield Brown]
v1.0.3 (2024-07-18)¶
Fix¶
fix naming [toloudis]
fix codec type [toloudis]
fixing mypy/linting [toloudis]
Other¶
adjust typing [BrianWhitneyAI]
one more PR cleanup [Dan Toloudis]
a couple of PR cleanup things [Dan Toloudis]
comment fixups [toloudis]
just a few more tests [toloudis]
cleanup [toloudis]
add comment [toloudis]
revert bad macos change [toloudis]
pin zarr lower to test [toloudis]
try converting later [toloudis]
use array_constructor [toloudis]
increase matrix [toloudis]
smaller data for test [toloudis]
persist not compute for now [Dan Toloudis]
wip test [Dan Toloudis]
bump flake8 to 6.1.0 to fix linting in Python 3.12 [Dan Toloudis]
truncate comment lines absurdly at 88 characters for flake8 [toloudis]
isort fixes [toloudis]
start some unit tests [toloudis]
deprecate the old zarr writer for a sec [toloudis]
auto format [toloudis]
initial add of new writer code from cellbrowser-tools [toloudis]
adjust reader typecheck [BrianWhitneyAI]
relocate check-type [BrianWhitneyAI]
update comments [BrianWhitneyAI]
add conditional type backcheck [BrianWhitneyAI]
add resolution_level_dims [BrianWhitneyAI]
relocate get_arraylike_plugin [BrianWhitneyAI]
relocate get_arraylike_plugin [BrianWhitneyAI]
remove unnecessary check [BrianWhitneyAI]
add pathlike test [BrianWhitneyAI]
add reader [BrianWhitneyAI]
Update MIGRATION.md [toloudis]
v1.0.2 (2024-06-10)¶
Fix¶
fix test [toloudis]
Other¶
if a reader reports FileNotFound, re-raise it [toloudis]
add comment [toloudis]
Revert “try bumping version of imageio” [toloudis]
try add ffmpeg [toloudis]
try bumping version of imageio [toloudis]
relax the enforce_exists check because it will be done later [toloudis]
v1.0.1 (2024-03-25)¶
Fix¶
fix lint [toloudis]
Other¶
ci(dependabot): bump extractions/setup-just from 1 to 2 [dependabot[bot]]
ci(dependabot): bump codecov/codecov-action from 3 to 4 [dependabot[bot]]
ci(dependabot): bump actions/setup-python from 4 to 5 [dependabot[bot]]
add implementation [Daniel Toloudis]
v1.0.0 (2023-12-05)¶
Fix¶
Fix reference to OME TIFF writer & aicsimageio usage [SeanLeRoy]
Other¶
Autolint [SeanLeRoy]
Add plugin caching back, but make opt-in [SeanLeRoy]
Auto retrieve plugins; avoid caching [SeanLeRoy]
Minor PR Feedback [SeanLeRoy]
Allow ‘.’ in plugin ext prefix [SeanLeRoy]
Report plugin in repr [SeanLeRoy]
Add chunk dims feature to zarr writer from aicsimageio [SeanLeRoy]
Update plugins.py [toloudis]
use correct package name for bioio-base [toloudis]
Update reader install link [SeanLeRoy]
improve error string [toloudis]
Update docs/OVERVIEW.md [Sean LeRoy, toloudis]
Use HTML for table formatting; adjust cloud io link [SeanLeRoy]
Adjust citation [SeanLeRoy]
PR Feedback about docs [SeanLeRoy]
Update docs/OVERVIEW.md [Sean LeRoy, toloudis]
Update README.md [Sean LeRoy, toloudis]
Update README.md [Sean LeRoy, toloudis]
Adjust links to docs [SeanLeRoy]
Remove README from doc site [SeanLeRoy]
Split up stuff in README [SeanLeRoy]
Better wording in docs; typos [SeanLeRoy]
Add link to all open issues in org for dev ease [SeanLeRoy]
Temp branch addition to workflow [SeanLeRoy]
Add migration doc [SeanLeRoy]
Update README [SeanLeRoy]
Add auto-generated changelog [SeanLeRoy]
Upgrade docs [SeanLeRoy]
Add latest PyPi version to README [Sean LeRoy]
v0.9.0 (2023-10-27)¶
Upgrade minimum bioio-base [SeanLeRoy]
Update LICENSE [Sean LeRoy]
v0.8.0 (2023-10-27)¶
New¶
feature/integrate-with-types (#1) [Eva Maxfield Brown]
Fix¶
Fix status badges [Sean LeRoy]
Fix link [sean meharry]
Other¶
ci(dependabot): bump actions/checkout from 3 to 4 [dependabot[bot]]
Update CI and add CODEOWNERS [SeanLeRoy]
Adjust numpy version to enforce py3.9 support [sean meharry]
Upgrade bioio-base [sean meharry]
Migrate python versions [sean meharry]
Require minimum bioio-base for plugins [sean meharry]
Remove references to downloading test resources [sean meharry]
Use tmp_path in tests; Use ome-types 0.4.0 [sean meharry]
Add writer tests [sean meharry]
Add writers [sean meharry]
Move OME utilities to separate file [sean meharry]
Add staticmethod declaration [sean meharry]
bioio-types -> bioio-base [sean meharry]
Add tests for BioImage [sean meharry]
Add BioImage [sean meharry]
Enable downloading test resources [sean meharry]
Upgrade pre-commit deps and remove from pyproject [sean meharry]
Minor updates from cookiecutter [Eva Maxfield Brown]
v0.0.1 (2022-08-12)¶
Remove version from cookiecutter yaml store [Eva Maxfield Brown]
Initial commit [Eva Maxfield Brown]