Changelog ========= (unreleased) ------------ - Move off Node12 (`#538 `_) [Sean LeRoy] v4.14.0 (2023-10-30) -------------------- Fix ~~~ - Fix badge for CI [Sean LeRoy] Other ~~~~~ - Drop py3.8 support; upgrade dependencies to support new min py (`#530 `_) [Sean LeRoy] v4.13.0 (2023-10-30) -------------------- New ~~~ - Feature/nd2reader-xarray-ome-metadata (`#533 `_) [Oliver (Yi-Che) Chang] Other ~~~~~ - Adjust bfio & fsspec versions to avoid bugs (`#537 `_) [Sean LeRoy] - Adjust pydantic import (`#535 `_) [Sean LeRoy] - Revert to pre-2023.3.15 tifffile to avoid mm_stack issue (`#529 `_) [Sean LeRoy] v4.12.1 (2023-08-16) -------------------- New ~~~ - Feature/ome_metadata-for-nd2 (`#521 `_) [Talley Lambert] Fix ~~~ - Fix publish task according to pypi rec for 2fa accounts (`#528 `_) [sean meharry] Other ~~~~~ - DependencyFix/Upgrade ome-types to 0.3.4 (`#522 `_) [Virgile Andreani, toloudis] 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 ~~~ - Bugfix/slow tile retrieval (`#486 `_) [Sean LeRoy] - Bugfix/mosaic lif merge error (`#480 `_) [Sean LeRoy] 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 * Comment on possible dimension mismatch --------- Co-authored-by: Madison Swain- Bowden , Sean LeRoy] v4.10.0 (2023-04-11) -------------------- New ~~~ - feature/github-action-stale (`#474 `_) [BrianWhitneyAI] - feature/add-physical-pixel-size-to-tiff-reader (`#456 `_) [Talley Lambert] - feature/zarrwriter (`#381 `_) [toloudis] 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] - 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] Other ~~~~~ - Restrict xarray version to support py3.8 (`#481 `_) [Sean LeRoy] - try to use optimized codepath through ome-types (`#478 `_) [toloudis] - Quality of Life: Make pip install platform independent (`#466 `_) [Sean LeRoy] - More descriptive scene index error message. (`#458 `_) [Philip Garrison] v4.9.4 (2022-12-06) ------------------- Fix ~~~ - bugfix/Fix `UnboundLocalError` in TiffGlobReader (`#449 `_) [Ian Hunt-Isaak, Madison Swain-Bowden * get typing correct * apply black + fix test typing Co-authored-by: Madison Swain-Bowden ] v4.9.3 (2022-11-15) ------------------- Fix ~~~ - bugfix/handle-tiff-i-dim (`#445 `_) [toloudis] - bugfix/single-dimension-index-requested-in-transform-return (`#438 `_) [toloudis] - fix/position-names-in-nd2-tests (`#437 `_) [Talley Lambert] Other ~~~~~ - admin/citation-update (`#440 `_) [Eva Maxfield Brown] v4.9.2 (2022-08-24) ------------------- New ~~~ - feature/add-physical-pixel-sizes-param-to-array-like (`#426 `_) [Guilherme Pires, Guilherme Pires] Fix ~~~ - bugfix/convert-dimension-spec-lists-to-slices-when-possible (`#429 `_) [toloudis] - bugfix/czi-scene-selection-for-inconsistent-scenes-regression (`#432 `_) [toloudis] Other ~~~~~ - Remove CZI extra install that doesn't come with CZI [Eva Maxfield Brown] - admin/include-fsspec-dep-for-czi-in-readme (`#433 `_) [Eva Maxfield Brown] v4.9.1 (2022-08-02) ------------------- Fix ~~~ - bugfix/fsspec-local-file-opener-cpp-buffer-for-czi (`#425 `_) [Eva Maxfield Brown] - Fix/czireader float32 dtype (`#423 `_) [toloudis] - bugfix/extract-czi-channel-names-more-safely (`#418 `_) [toloudis] - bugfix/czi-scene-indexing (`#417 `_) [toloudis] - bugfix/dynamic-dimension-typing (`#419 `_) [Eva Maxfield Brown] Other ~~~~~ - admin/ignore-fsspec-2022.7.0 (`#424 `_) [Eva Maxfield Brown] - admin/add-fsspec-to-upstream-checks (`#422 `_) [Eva Maxfield Brown] v4.9.0 (2022-07-19) ------------------- New ~~~ - feature/image-container (`#415 `_) [Eva Maxfield Brown] - feature/lower-log-level-of-OME-TIFF-read-errors (`#414 `_) [Eva Maxfield Brown] - feature/get-stack (`#403 `_) [John Russell] Other ~~~~~ - Update names, emails, and meta [evamaxfield] 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] Fix ~~~ - bugfix/pass-series-index-in-biofile-init (`#401 `_) [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] v4.7.0 (2022-04-19) ------------------- New ~~~ - feature/tiledtiffreader (`#387 `_) [Nicholas-Schaub] Other ~~~~~ - Upgrade black version [JacksonMaxfield] v4.6.4 (2022-03-18) ------------------- Fix ~~~ - bugfix/update-czi-to-ome-xslt-for-channel-id (`#389 `_) [Griffin Fujioka, Griffin Fujioka] v4.6.3 (2022-03-03) ------------------- Fix ~~~ - bugfix/add-logic-to-ensure-OME-XML-plane-elements-occur-last (`#385 `_) [Nicholas-Schaub] v4.6.2 (2022-03-01) ------------------- - admin/update-czi-to-ome-xslt-submodule (`#382 `_) [Jackson Maxfield Brown] v4.6.1 (2022-03-01) ------------------- Fix ~~~ - bugfix/czi-physical-size (`#384 `_) [emay2022] v4.6.0 (2022-02-22) ------------------- Fix ~~~ - bugfix/more-info-and-help-on-corrupt-file (`#380 `_) [Jackson Maxfield Brown] - bugfix/reader-selection-fixes (`#367 `_) [Jackson Maxfield Brown] Other ~~~~~ - admin/remove-czi-install-pattern (`#376 `_) [Jackson Maxfield Brown] - admin/bump-nd2-v0.2.0 (`#379 `_) [Talley Lambert] v4.5.2 (2021-12-16) ------------------- - Update XSLT subbmodule (`#365 `_) [Matte Bailey] - Add instructions for updating the submodule (`#364 `_) [Matte Bailey] v4.5.1 (2021-12-08) ------------------- New ~~~ - feature/czi-subblock-metadata (`#353 `_) [Matte Bailey] Fix ~~~ - bugfix/pin-nd2-dep (`#358 `_) [Talley Lambert] - fix/only-close-biofiofile-on-exit-if-not-open-on-entry (`#341 `_) [Talley Lambert] Other ~~~~~ - Update submodule commit to latest (`#363 `_) [Matte Bailey] - Add missing char to workflow file (`#362 `_) [Matte Bailey] - Add ability to manually trigger build of main (`#359 `_) [Matte Bailey] - allow metadata extraction from czi files with no subblocks (`#360 `_) [toloudis] v4.5.0 (2021-11-04) ------------------- New ~~~ - feature/add-stored-mm-indexer-function-to-glob-reader (`#346 `_) [Ian Hunt-Isaak] - feature/add-getitem-to-dimensions-object (`#347 `_) [Ian Hunt-Isaak] - feature/allow-bioformats-x-y-chunking (`#336 `_) [Heath Patterson] - feature/glob-reader (`#303 `_) [John Russell, Madison Swain-Bowden] Other ~~~~~ - admin/update-pr-template-remove-link-to-gh-12 (`#342 `_) [Madison Swain-Bowden] v4.4.0 (2021-10-12) ------------------- New ~~~ - feature/add-native-deltavision-reader (`#333 `_) [Talley Lambert] - feature/add-native-nd2-reader (`#317 `_) [Talley Lambert] v4.3.0 (2021-10-08) ------------------- New ~~~ - feature/import-any-reader-from-readers (`#326 `_) [Talley Lambert] Other ~~~~~ - admin/remove-lif-from-standard-install (`#332 `_) [Jackson Maxfield Brown] - admin/remove-bioformats-extra (`#329 `_) [Talley Lambert] - admin/bump-readlif-for-multi-scene (`#327 `_) [psobolewskiPhD] - docs/more-detailed-bioformats-install-instruction-on-error (`#324 `_) [Talley Lambert] v4.2.0 (2021-09-27) ------------------- New ~~~ - feature/bioformats-reader (`#306 `_) [Talley Lambert] - feature/metadata-module (`#292 `_) [Matte Bailey] 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 * Grammer on object's Co-authored-by: Madison Swain-Bowden * Better CziReader custom dependency link Co- authored-by: Madison Swain-Bowden * Remove extra words Co-authored-by: Madison Swain-Bowden * Better wording on benchmark additions Co-authored-by: Madison Swain-Bowden * Clean up Reader class impl section Co-authored-by: Madison Swain-Bowden ] v4.1.0 (2021-08-10) ------------------- New ~~~ - feature/ome-metadata-xslt-spec (`#289 `_) [Jackson Maxfield Brown] Fix ~~~ - bugfix/use-dict-of-tiff-tags (`#293 `_) [Jackson Maxfield Brown] - bugfix/invert-lif-scales (`#288 `_) [Jackson Maxfield Brown] Other ~~~~~ - admin/loosen-any-non-zero-semver-deps (`#294 `_) [Jackson Maxfield Brown] v4.0.5 (2021-07-15) ------------------- Fix ~~~ - bugfix/ome-tiff-ome-not-set (`#284 `_) [Jackson Maxfield Brown] Other ~~~~~ - admin/deprecate-chunk-by-dims (`#286 `_) [Jackson Maxfield Brown] - admin/bump-min-tifffile (`#285 `_) [Jackson Maxfield Brown] v4.0.4 (2021-07-12) ------------------- New ~~~ - feature/allow-set-scene-by-index (`#272 `_) [Jackson Maxfield Brown] Other ~~~~~ - admin/finalizing-contributor-pr-process (`#276 `_) [Jackson Maxfield Brown] - admin/local-tests-by-default (`#273 `_) [Jackson Maxfield Brown] v4.0.3 (2021-07-05) ------------------- Fix ~~~ - bugfix/missing-tiff-description-tag (`#271 `_) [Jackson Maxfield Brown] - bugfix/channel-names-array-expansion (`#265 `_) [toloudis] Other ~~~~~ - @rcasero-feature/add-python-3.7-support (`#270 `_) [Jackson Maxfield Brown, Ramón Casero] v4.0.2 (2021-06-22) ------------------- Fix ~~~ - bugfix/mosaic-tile-reconstruction-for-multi-scene-mosaics (`#260 `_) [toloudis] Other ~~~~~ - admin/bump-aicspylibczi-dep-version (`#261 `_) [Jackson Maxfield Brown] - admin/add-doi (`#258 `_) [Jackson Maxfield Brown] - docs/add-missing-czi-reading-to-mosaic-support (`#256 `_) [Jackson Maxfield Brown] - docs/fix-physical-pixel-sizes-typo (`#253 `_) [Jackson Maxfield Brown] v4.0.1 (2021-06-08) ------------------- Fix ~~~ - bugfix/coords-and-floating-point-math-and-czi-scene-naming (`#250 `_) [Jackson Maxfield Brown] 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] v3.3.5 (2021-01-25) ------------------- Fix ~~~ - bugfix/pin-readlif (`#187 `_) [Jackson Maxfield Brown] v3.3.4 (2021-01-13) ------------------- - ome-xml as string to ome tiff writer (`#180 `_) [toloudis] v3.3.3 (2020-12-14) ------------------- Fix ~~~ - bugfix/replace-napari-is-pyramid-with-multiscale (`#172 `_) [Dimitri Hürlimann, dimi-huer] Other ~~~~~ - admin/support-py39 (`#169 `_) [Jackson Maxfield Brown] v3.3.2 (2020-11-17) ------------------- - admin/update-base-reader-dep-versions (`#156 `_) [Jamie Sherman] v3.3.1 (2020-09-23) ------------------- Fix ~~~ - bugfix/tiff-rgb (`#153 `_) [Jamie Sherman] Other ~~~~~ - admin/cleanup-readme (`#149 `_) [Jackson Maxfield Brown] v3.3.0 (2020-09-09) ------------------- New ~~~ - feature/use-in-memory-data-for-non-dask-calls (`#148 `_) [Jackson Maxfield Brown] v3.2.3 (2020-06-23) ------------------- New ~~~ - feature/reader-additions (`#126 `_) [JacksonMaxfield] v3.2.2 (2020-06-11) ------------------- New ~~~ - feature/enable-disable-dask (`#124 `_) [JacksonMaxfield] Other ~~~~~ - admin/update-build-tooling (`#123 `_) [JacksonMaxfield] - admin/switch-log-warning-to-warnings-warn (`#122 `_) [JacksonMaxfield] v3.2.1 (2020-05-26) ------------------- Fix ~~~ - bugfix/add-imagecodecs-dep (`#120 `_) [JacksonMaxfield] v3.2.0 (2020-05-13) ------------------- New ~~~ - feature/optimize-readers (`#113 `_) [JacksonMaxfield] - feature/allow-sequence-in-get-data (`#109 `_) [JacksonMaxfield] - feature/read-leica-lif-files (`#99 `_) [Jamie Sherman] Fix ~~~ - bugfix/update-ome-spec (`#116 `_) [JacksonMaxfield] - bugfix/set-sphinx-dep-upper-bound (`#95 `_) [JacksonMaxfield] Other ~~~~~ - admin/benchmarks (`#112 `_) [JacksonMaxfield] - admin/use-black-formatting (`#108 `_) [JacksonMaxfield] - Update PR Template [Madison Bowden] - admin/move-test-resources-to-s3 (`#94 `_) [JacksonMaxfield] v3.1.4 (2020-03-21) ------------------- New ~~~ - feature/add-get-channel-names-to-base-reader (`#88 `_) [JacksonMaxfield] Fix ~~~ - bugfix/reader-context-manager-top-level-import-error (`#85 `_) [JacksonMaxfield] v3.1.3 (2020-03-11) ------------------- Fix ~~~ - bugfix/delay-import-of-distributed-module (`#83 `_) [JacksonMaxfield] Other ~~~~~ - admin/standardize-flake8-settings (`#84 `_) [JacksonMaxfield] v3.1.2 (2020-03-06) ------------------- New ~~~ - feature/get-physical-pixel-size (`#80 `_) [JacksonMaxfield] Other ~~~~~ - admin/add-back-codecov (`#81 `_) [JacksonMaxfield] - admin/changelog-link-to-prs (`#77 `_) [JacksonMaxfield] v3.1.1 (2020-02-21) ------------------- Fix ~~~ - bugfix/make-aicsimage-serializable (`#74 `_) [JacksonMaxfield] - bugfix/return-none-cluster (`#73 `_) [Jamie Sherman] Other ~~~~~ - admin/auto-changelog (`#75 `_) [JacksonMaxfield] - admin/test-py38 (`#76 `_) [JacksonMaxfield] v3.1.0 (2020-02-03) ------------------- New ~~~ - feature/use-dask (`#63 `_) [JacksonMaxfield] Fix ~~~ - Fix pypi publish action [Jackson Brown] - bugfix/auto-doc-gen (`#70 `_) [JacksonMaxfield] v3.0.7 (2019-11-05) ------------------- - Remove make clean command from make docs call (`#49 `_) [JacksonMaxfield] - populate_tiffdata should respect dimension order (`#48 `_) [toloudis] v3.0.6 (2019-10-31) ------------------- New ~~~ - Feature/physical pixel size (`#43 `_) [toloudis] Fix ~~~ - fix imread bug and allow AICSImage class to close its reader (`#44 `_) [toloudis] v3.0.5 (2019-10-30) ------------------- - clean up from PR comments [Daniel Toloudis] - add get_channel_names to AICSImage class [Daniel Toloudis] v3.0.4 (2019-10-28) ------------------- - add size getters to the AICSImage class (`#38 `_) [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]