Updated Metadata and Dependencies #41
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* Modified bumpversion * Added code formatting, linting * Fixed documentation, modified bumpversion * Modified bump2version and readme * Fixed bumpversion for README * Removed buggy precommit hooks * Removed bumpversion sign option * Changed bumpversion fields * Bump version: 2.1.9 → 2.2.0-dev0 * Fixed bug in bumpversion dev builds * Bump version: 2.2.0-dev0 → 2.2.0-dev1 * Upgrade/bioformats (PolusAI#20) * Migration from loci_tools.jar to bioformats_package.jar * Changed setup.py * Fixed bug associated with initializing a BioWriter without metadata parameter (PolusAI#21) * Feat/ci (PolusAI#22) * Added code format and lint git actions * fix: Fixed format gitaction, disabled zarr tests * Added dev dependencies and test workflow * Started docker ci build * Docker build base * Black formatting * Updated git actions * Changed bumpversion config * Finished Docker configs * Added PyPi publishing action * Bump version: 2.2.0-dev1 → 2.2.0-dev2 * Fixed docker and pypi workflows * Reverted version * Changed pypi workflow * Fixed twine username * Feat/ometypes (PolusAI#23) * Replaced OmeXml.py with ome_types * Resolved uncaught OmeXml references * Bump version: 2.2.0-dev1 → 2.2.0-dev2 * Bump version: 2.2.0-dev2 → 2.2.0-dev3 * Fix/metadata (PolusAI#24) * Added additional metadata reformatting * Fixed repeated values in metadata replacement dictionary * Fixed unresolved merge conflict in README * Fixed additional README conflict * Fix/rgb (PolusAI#26) * Fixed versioning in docs * Fix czi rgb image bug * Fix czi rgb image bug * Special catch for Zeiss CZI rgb images * Fix/biowriter (PolusAI#27) * Fixed metadata issues with BioWriter * fix: JavaWriter backend exports correct results on any XYZCT data * Removed debug code * Fixed error in unittest from missing dependency * Feat/bioreader (PolusAI#28) * Bump version: 2.2.0 → 2.2.1-dev0 * re-added support for CT dimensions, improved performance * Added pickle support for PythonReader * Bump version: 2.2.1-dev0 → 2.2.1-dev1 * Feat/biowriter: Scalability and Extended Writing Ability (PolusAI#29) * Updated Python BioWriter to use newer version of tifffile * Prototype of scalable scatter tile format * Removed debug print statements * added support for multi-channel/timepoint writing * Added unittest, fix abstract class error * Updated reader and biowriter metadata * Bump version: 2.2.1-dev1 → 2.3.0-dev0 * Bioformats (PolusAI#30) * Removed bioformats_package.jar, added optional install of bioformats_jar * Updated documentation and install options * fixed README typo * Update/docs (PolusAI#31) * Updated docs and tests. Changed java backend name to bioformats * Updated examples to use new backend names * Bump version: 2.3.0-dev0 → 2.3.0
This was referenced May 31, 2023
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Jul 24, 2023
* Updated dependency range for tifffile, changed metadata saving * Added no verify to bump2version config * Upgraded ome-types * Bump version: 2.3.0 → 2.3.1-dev0 * Dev (#32) (#40) * Modified bumpversion * Added code formatting, linting * Fixed documentation, modified bumpversion * Modified bump2version and readme * Fixed bumpversion for README * Removed buggy precommit hooks * Removed bumpversion sign option * Changed bumpversion fields * Bump version: 2.1.9 → 2.2.0-dev0 * Fixed bug in bumpversion dev builds * Bump version: 2.2.0-dev0 → 2.2.0-dev1 * Upgrade/bioformats (#20) * Migration from loci_tools.jar to bioformats_package.jar * Changed setup.py * Fixed bug associated with initializing a BioWriter without metadata parameter (#21) * Feat/ci (#22) * Added code format and lint git actions * fix: Fixed format gitaction, disabled zarr tests * Added dev dependencies and test workflow * Started docker ci build * Docker build base * Black formatting * Updated git actions * Changed bumpversion config * Finished Docker configs * Added PyPi publishing action * Bump version: 2.2.0-dev1 → 2.2.0-dev2 * Fixed docker and pypi workflows * Reverted version * Changed pypi workflow * Fixed twine username * Feat/ometypes (#23) * Replaced OmeXml.py with ome_types * Resolved uncaught OmeXml references * Bump version: 2.2.0-dev1 → 2.2.0-dev2 * Bump version: 2.2.0-dev2 → 2.2.0-dev3 * Fix/metadata (#24) * Added additional metadata reformatting * Fixed repeated values in metadata replacement dictionary * Fixed unresolved merge conflict in README * Fixed additional README conflict * Fix/rgb (#26) * Fixed versioning in docs * Fix czi rgb image bug * Fix czi rgb image bug * Special catch for Zeiss CZI rgb images * Fix/biowriter (#27) * Fixed metadata issues with BioWriter * fix: JavaWriter backend exports correct results on any XYZCT data * Removed debug code * Fixed error in unittest from missing dependency * Feat/bioreader (#28) * Bump version: 2.2.0 → 2.2.1-dev0 * re-added support for CT dimensions, improved performance * Added pickle support for PythonReader * Bump version: 2.2.1-dev0 → 2.2.1-dev1 * Feat/biowriter: Scalability and Extended Writing Ability (#29) * Updated Python BioWriter to use newer version of tifffile * Prototype of scalable scatter tile format * Removed debug print statements * added support for multi-channel/timepoint writing * Added unittest, fix abstract class error * Updated reader and biowriter metadata * Bump version: 2.2.1-dev1 → 2.3.0-dev0 * Bioformats (#30) * Removed bioformats_package.jar, added optional install of bioformats_jar * Updated documentation and install options * fixed README typo * Update/docs (#31) * Updated docs and tests. Changed java backend name to bioformats * Updated examples to use new backend names * Bump version: 2.3.0-dev0 → 2.3.0 * Updated Metadata and Dependencies (#41) * Dev (#32) * Modified bumpversion * Added code formatting, linting * Fixed documentation, modified bumpversion * Modified bump2version and readme * Fixed bumpversion for README * Removed buggy precommit hooks * Removed bumpversion sign option * Changed bumpversion fields * Bump version: 2.1.9 → 2.2.0-dev0 * Fixed bug in bumpversion dev builds * Bump version: 2.2.0-dev0 → 2.2.0-dev1 * Upgrade/bioformats (#20) * Migration from loci_tools.jar to bioformats_package.jar * Changed setup.py * Fixed bug associated with initializing a BioWriter without metadata parameter (#21) * Feat/ci (#22) * Added code format and lint git actions * fix: Fixed format gitaction, disabled zarr tests * Added dev dependencies and test workflow * Started docker ci build * Docker build base * Black formatting * Updated git actions * Changed bumpversion config * Finished Docker configs * Added PyPi publishing action * Bump version: 2.2.0-dev1 → 2.2.0-dev2 * Fixed docker and pypi workflows * Reverted version * Changed pypi workflow * Fixed twine username * Feat/ometypes (#23) * Replaced OmeXml.py with ome_types * Resolved uncaught OmeXml references * Bump version: 2.2.0-dev1 → 2.2.0-dev2 * Bump version: 2.2.0-dev2 → 2.2.0-dev3 * Fix/metadata (#24) * Added additional metadata reformatting * Fixed repeated values in metadata replacement dictionary * Fixed unresolved merge conflict in README * Fixed additional README conflict * Fix/rgb (#26) * Fixed versioning in docs * Fix czi rgb image bug * Fix czi rgb image bug * Special catch for Zeiss CZI rgb images * Fix/biowriter (#27) * Fixed metadata issues with BioWriter * fix: JavaWriter backend exports correct results on any XYZCT data * Removed debug code * Fixed error in unittest from missing dependency * Feat/bioreader (#28) * Bump version: 2.2.0 → 2.2.1-dev0 * re-added support for CT dimensions, improved performance * Added pickle support for PythonReader * Bump version: 2.2.1-dev0 → 2.2.1-dev1 * Feat/biowriter: Scalability and Extended Writing Ability (#29) * Updated Python BioWriter to use newer version of tifffile * Prototype of scalable scatter tile format * Removed debug print statements * added support for multi-channel/timepoint writing * Added unittest, fix abstract class error * Updated reader and biowriter metadata * Bump version: 2.2.1-dev1 → 2.3.0-dev0 * Bioformats (#30) * Removed bioformats_package.jar, added optional install of bioformats_jar * Updated documentation and install options * fixed README typo * Update/docs (#31) * Updated docs and tests. Changed java backend name to bioformats * Updated examples to use new backend names * Bump version: 2.3.0-dev0 → 2.3.0 * Updated dependency range for tifffile, changed metadata saving * Added no verify to bump2version config * Upgraded ome-types * Bump version: 2.3.0 → 2.3.1-dev0 * Bump version: 2.3.1-dev0 → 2.3.1
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This PR updates the way OME metadata is stored in .ome.zarr files and updates the tifffile and ome-types dependencies.