Changelog
v4.13.0 (2023-10-30)
v4.12.1 (2023-08-16)
v4.12.0 (2023-08-03)
New
Feature/OmeZarr Chunk Dims (#519) [BrianWhitneyAI, Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com> * Update aicsimageio/writers/ome_zarr_writer.py Co-authored-by: Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com> * Update aicsimageio/writers/ome_zarr_writer.py Co-authored-by: Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com> * DimensionNames * pass dimension order to build_chunk_dims * OmeZarrWriter chunk tests * chunk comparison * pytest tmpdir fixture * DimensionNames * chunk_dim scaling for levels * nplanes inside chunk dims = None * ome-types 0.4.0 breaks build-main ——— Co-authored-by: Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com>]
Feature/sldy reader (#496) [Sean LeRoy]
Other
Limit numpy and dask (#527) [Sean LeRoy]
Ignore missing Position dimension (#498) [Sean LeRoy]
Guess dims for missing field ‘axes’ (#514) [BrianWhitneyAI]
Admin/OmeZarrReader variable dimension unit tests (#510) [BrianWhitneyAI, Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com> * new hash ——— Co-authored-by: Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com>]
OmeZarrReader physical_pixel_sizes support (#509) [BrianWhitneyAI]
Admin/OmeZarrReader redundant test (#507) [BrianWhitneyAI]
OmeZarrReader (#493) [BrianWhitneyAI]
Admin: Update deploy process (#494) [Sean LeRoy]
v4.11.0 (2023-05-05)
Fix
Other
Adjusting tiffile versioning (#487) [BrianWhitneyAI]
store frame metadata when reading a specific scene (#492) [Joshua Gould]
admin/support-py311 (#446) [Brian Whitney, Eva Maxfield Brown, dmt, dmt, toloudis, toloudis]
Extract S dim from OME data (#483) [Madison Swain-Bowden <bowdenm@spu.edu> * Comment on possible dimension mismatch ——— Co-authored-by: Madison Swain- Bowden <bowdenm@spu.edu>, Sean LeRoy]
v4.10.0 (2023-04-11)
New
Fix
Bugfix/empty scene name (#477) [BrianWhitneyAI, Sean LeRoy, Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com> * Update aicsimageio/readers/czi_reader.py Co-authored-by: Sean LeRoy <41307451+SeanLeRoy@users.noreply.github.com> * more discriptive naming ——— Co-authored-by: Lukas Fan (—-) <Lukas.Fan@imec.be>, lukas]
bugfix: removing 2.11.0 threshold (#470) [BrianWhitneyAI]
Bugfix: unclear warning for missing ‘bfio’ install. (#471) [BrianWhitneyAI]
Bugfix: Upgrade minimum fsspec version (#473) [Sean LeRoy]
Bugfix: Restrict tifffile version for now (#472) [Sean LeRoy]
Bugfix: Fix tests not asserting error expected (#464) [Sean LeRoy]
Bugfix/Docs-README-Mention-mvn/maven-requirement-for-bioformats_jar (#463) [Peter Sobolewski]
Fix/build fix ometypes validation (#461) [toloudis]
fix/fix_future_warnings (#453) [JasonYu1]
v4.9.4 (2022-12-06)
Fix
bugfix/Fix UnboundLocalError in TiffGlobReader (#449) [Ian Hunt-Isaak, Madison Swain-Bowden <bowdenm@spu.edu> * get typing correct * apply black + fix test typing Co-authored-by: Madison Swain-Bowden <bowdenm@spu.edu>]
v4.8.0 (2022-05-26)
New
feature-and-admin/create-aicsimage-objects-with-fs-kwargs-and-remove- need-for-creds (#407) [Jackson Maxfield Brown]
Other
admin/prepare-bioformats_reader-to-work-with-new-bioformats_jar-based- on-scyjava (#402) [Talley Lambert]
admin/add-test-upstreams-action (#406) [Jackson Maxfield Brown, Matthew Rocklin]
admin/ship-mypy-type-annotations-drop-py37-add-py310-manage-test- dependencies-separate-for-each-tox-env (#397) [Jackson Maxfield Brown]
v4.6.4 (2022-03-18)
v4.6.3 (2022-03-03)
v4.5.2 (2021-12-16)
v4.4.0 (2021-10-12)
v4.3.0 (2021-10-08)
v4.2.0 (2021-09-27)
New
Fix
bugfix/resolve-conflict-between-format-impls-and-determine-reader (#318) [Jackson Maxfield Brown]
bugfix/catch-channel-colors-errors-from-typing (#299) [Jackson Maxfield Brown]
bugfix/asv-with-submodules (#297) [Jackson Maxfield Brown]
bugfix/pass-aws-creds-to-tox (#296) [Matte Bailey]
bugfix/checkout-submodules-for-doc-building (#295) [Jackson Maxfield Brown]
Other
docs/update-biofile-docstring-add-bf-options-param (#322) [Talley Lambert]
admin/exclude-benchmarks-from-package-install (#319) [Jackson Maxfield Brown]
admin/loosen-version-pins (#320) [Jackson Maxfield Brown]
admin/add-test-resources-caching (#313) [Jackson Maxfield Brown]
admin/add-tox-work-dir-env-var-opt-to-tox-ini (#310) [Talley Lambert]
Add .pre-commit-config.yaml (#308) [Talley Lambert]
admin/add-custom-reader-addition-docs (#305) [Jackson Maxfield Brown, Madison Swain-Bowden <bowdenm@spu.edu> * Grammer on object’s Co-authored-by: Madison Swain-Bowden <bowdenm@spu.edu> * Better CziReader custom dependency link Co- authored-by: Madison Swain-Bowden <bowdenm@spu.edu> * Remove extra words Co-authored-by: Madison Swain-Bowden <bowdenm@spu.edu> * Better wording on benchmark additions Co-authored-by: Madison Swain-Bowden <bowdenm@spu.edu> * Clean up Reader class impl section Co-authored-by: Madison Swain-Bowden <bowdenm@spu.edu>]
v4.0.5 (2021-07-15)
v4.0.4 (2021-07-12)
v4.0.2 (2021-06-22)
v4.0.1 (2021-06-08)
v4.0.0 (2021-06-07)
New
feature/default-to-pixel-size-none (#246) [Jackson Maxfield Brown]
feature/czi-reader (#231) [JacksonMaxfield, Jamie Sherman]
feature/mosaic-tile-single-position-request-and-docs (#229) [Jackson Maxfield Brown]
feature/set-known-coords (#224) [Jackson Maxfield Brown]
feature/aicsimage-save (#215) [Jackson Maxfield Brown]
feature/lif-reader (#212) [Jackson Maxfield Brown]
feature/ome-tiff-writer-4 (#211) [JacksonMaxfield, toloudis]
feature/array-like-reader (#197) [Jackson Maxfield Brown]
feature/writers (#198) [Jackson Maxfield Brown]
feature/add-aicsimage-obj (#185) [Jackson Maxfield Brown]
feature/optimize-tiff-reader-and-add-benchmarks (#183) [Jackson Maxfield Brown]
feature/ome-tiff-reader (#176) [Jackson Maxfield Brown]
feature/add-tiff-reader (#160) [Jackson Maxfield Brown]
feature/add-default-reader (#157) [Jackson Maxfield Brown]
feature/add-timeseries-writer (#137) [Jackson Maxfield Brown]
feature/add-rgb-writer (#134) [JacksonMaxfield]
feature/centralize-reader-tests (#135) [JacksonMaxfield]
feature/writer-base-class-proposal (#98) [JacksonMaxfield]
feature/deprecate-context-manager-cluster-spawning (#97) [JacksonMaxfield]
feature/deprecate-napari-functionality (#96) [JacksonMaxfield]
Fix
bugfix/support-rgb-mosaic-czi (#247) [Jackson Maxfield Brown]
bugfix/always-use-synch-for-tiff-zarr-compute (#235) [Jackson Maxfield Brown]
bugfix/setup-coords-for-stitched-lifs (#234) [Jackson Maxfield Brown]
bugfix/remove-unused-lif-code (#226) [Jackson Maxfield Brown]
bugfix/catch-all-errors-in-ome-tiff (#207) [Jackson Maxfield Brown]
bugfix/provide-correct-indices-to-data-select-in-tiff-chunked-reads (#201) [Jackson Maxfield Brown]
Fix benchmarks links and remove old files [JacksonMaxfield]
bugfix/adopt-samples-as-rgb-default (#165) [Jackson Maxfield Brown]
Fix guess tiff dims, lint, and format [JacksonMaxfield]
Other
admin/remove-dev-release-infra (#248) [Jackson Maxfield Brown]
admin/4.0-release-prep-and-benchmark-upgrades (#244) [Jackson Maxfield Brown]
admin/add-install-from-git-to-readme (#240) [Ramón Casero]
admin/2021-dask-summit-presentation (#236) [Jackson Maxfield Brown]
admin/copy-v3 docs-to-static (#233) [Jackson Maxfield Brown]
admin/split-reader-deps (#221) [Jackson Maxfield Brown]
admin/doc-updates (#216) [Jackson Maxfield Brown]
admin/adopt-mypy-and-stricter-linting (#208) [Jackson Maxfield Brown]
admin/move-test-resources-hash-to-text-file (#202) [Jackson Maxfield Brown]
admin/temp-bump-aicspylibczi (#194) [Jackson Maxfield Brown]
Remove macOS11 and fix prepare-release [JacksonMaxfield]
Attach dev0 to all references of version number [JacksonMaxfield]
Configure dev_release bumpversion [JacksonMaxfield]
Turn on doc building [JacksonMaxfield]
Replace all references of master w/ main [JacksonMaxfield]
Do not push docs on main yet [JacksonMaxfield]
Second run of cookiecutter to ensure [JacksonMaxfield]
Updates from cookiecutter [JacksonMaxfield]
Force remove extra files [JacksonMaxfield]
admin/fix-deadlink-in-documentation [JacksonMaxfield]
admin/developer-documentation (#150) [Jackson Maxfield Brown, Josh Moore]
Upgrade dependency versions [JacksonMaxfield]
Working for small files [JacksonMaxfield]
admin/proposed-api (#145) [Jackson Maxfield Brown]
Remove everything [JacksonMaxfield]
Remove dims setting entirely [JacksonMaxfield]
Read dims, shape, and dtype from Tiff metadata in single shot [JacksonMaxfield]
Change all self.dask_data.shape calls to self.shape in reader subclasses [JacksonMaxfield]
Linting and formatting [JacksonMaxfield]
Readers API stabilization, verbs -> functions, nouns -> properties [JacksonMaxfield]
admin/update-from-cookiecutter (#136) [JacksonMaxfield]
v3.3.3 (2020-12-14)
v3.3.1 (2020-09-23)
v3.3.0 (2020-09-09)
v3.2.2 (2020-06-11)
v3.1.4 (2020-03-21)
v3.1.3 (2020-03-11)
v3.1.2 (2020-03-06)
v3.1.0 (2020-02-03)
v3.0.7 (2019-11-05)
v3.0.6 (2019-10-31)
v3.0.5 (2019-10-30)
clean up from PR comments [Daniel Toloudis]
add get_channel_names to AICSImage class [Daniel Toloudis]
v3.0.3 (2019-10-25)
Fix
fix linting [Daniel Toloudis]
fix png writer and tests [Daniel Toloudis]
fix linter [Daniel Toloudis]
fix png writer and tests [Daniel Toloudis]
Other
Remove patch coverage check (#36) [JacksonMaxfield]
pull request code review revisions [Dan Toloudis]
Revert “fix png writer and tests” [Daniel Toloudis]
use old default for dimension_order so that existing code does not break [Daniel Toloudis]
add a unit test for dimension_order and refactor test_ome_tiff_writer [Daniel Toloudis]
allow dimension order in ome-tiff writer [Daniel Toloudis]
remove accidentally added file [Daniel Toloudis]
Remove CRON from doc build workflow [Jackson Brown]
Remove double builds from github actions [Jackson Brown]
Wrap CRON string in quotes [Jackson Brown]
Update CRON strings [Jackson Brown]
Do not build documentation for tests module [Jackson Brown]
Update makefile to remove all generated rst’s on doc gen [Jackson Brown]
Update czireader import so that it doesn’t fail on etree [Jackson Brown]
Move documentation badge to before codecov [JacksonMaxfield]
Update readme to have doc badge [JacksonMaxfield]
Add doc generation workflow [JacksonMaxfield]
Add required documentation files and update requirements [JacksonMaxfield]
Update task version pins to point at master / latest [JacksonMaxfield]
v3.0.2 (2019-10-11)
Pull in feedback from team [Jackson Brown]
Update README to include known_dim functionality [Jackson Brown]
Add test for invalid dim names [Jackson Brown]
Resolves [gh-22], allow passing of known dim order to AICSImage [Jackson Brown]
Resolves [gh-23], use OME-Tiff metadata to parse dim sizes and order [Jackson Brown]
v3.0.1 (2019-10-04)
Label Quickstart code block as python [Jackson Brown]
Update setup.cfg to properly bumpversion [Jackson Brown]
Rename build workflow to build master [Jackson Brown]
Update to new cookiecutter gh templates after matts feedback [Jackson Brown]
Remove cov report html from actions as not needed on remote [Jackson Brown]
Add PR to test and lint action triggers [Jackson Brown]
Remove references to quilt3distribute that were copied over [Jackson Brown]
Update CI/CD, README badge, local developement, and contributing docs [Jackson Brown]
CODE_OF_CONDUCT.md [Jamie Sherman]