- Fix image_to_html pixel unit, thanks to Tom Boissonnet #441
- Move repr_html to _ImageWrapper, thanks to Johannes Soltwedel #429
- CLI: fix debugging level 9, thanks to Torsten Stöter #439
- Upgrade to macOS 14 Actions runner image #440
- Remove Python 3.8 from the testing matrix #434
- Add size check on data.rowNumbers in omero.HdfStorage.update #431
- Prevent hang on exit while omero.client keepalive is active #424
- Parse omero.logging properties under new Logging heading #416
- Switch result logging to DEBUG level #417
- Allow a caller to ignore row numbers #418
- admin rewrite: make OMERO.tables module configurable #419
- Cap numpy to 1.x #414
- Add repr_html method for _ImageWrapper #394
- Make getGridSize() handle plates with no Wells #398
- Improve handling of SessionID and client in BlitzGateway #400
- FilesetWrapper lazy loads Images and UsedFiles #405
- Update release steps #406
- Fix Windows regression in omero_ext.path #402
- Removal of python-future compatibility code #390
This release adds preliminary support for running OMERO.py on Python 3.12 environments.
The future dependency should be considered deprecated and will be removed in the
next minor release of OMERO.py. Downstream projects which are relying on this
dependency should declare it explicitly in their configuration file.
- Set minimum version for Pillow (10.0.0) and Python (3.8) #388
- Unit tests: clean up warnings #386
- Add support for Python 3.11 #385
- Use math module instead of numpy.math #384
- omero admin start: add warning for deprecated TLS protocols #382
- Add requirements file for ReadTheDocs #383
- Add getROIs method #380
- Add variable for daily build #372
- Cap urllib3 to avoid openssl issue #371
- Replace internal portalocker by the upstream version #370
- Use Image.LANCZOS alias rather than Image.ANTIALIAS #376
- Let Ice choose the default SSL protocols that are available #377
- OMERO.cli: do not fail on the absence of --retry argument #364
- Add Python 3.10 to the testing matrix #357
- Readme updates #358, #363, #369
- Update GitHub workflow actions #365
- API doc: Add inherited-members and private-members options to the gateway automodule configuration #354
- Remove Anonymous Diffie-Hellman default configuration #336. This change will require to use of
omero certificatesto ensure that an OMERO server installation has, at minimum, a self-signed certificate. - Publish API doc #330
- omero admin diagnostics: move OMERO.py version as part of the output #339
- Close correct locker #346
- omero.clients: initialize connection retry reason out of the while loop #353
- Switch to new output command (GHA) #340
- Always report pixeldata time in the output of
omero fs importtime#335
- Fix
omero importon Windows #326
- Fix params.limit ignored in conn.getObjects() #321
- Add implementation for
DatasetColumn#309 - Add support for searching OMERO.tables by column which name is not a valid Python identifier #287
- Fix OMERO.table memory issue when using
table.read()with large number of rows #314 - Deprecate
PropertyParser.black_listin favor ofPropertyParser.is_excluded#313
- Allow direct URL to be passed to
omero import --fetch-jars#303 - Exclude
omero.versionfrom output ofomero config parse#312
- Decode script stdout/stderr before printing, thanks to Jeremy Muhlich #310
- Ensure we are using pyopenssl #305
- Fix UnbondLocalError in
omero tag list, thanks to Lucille Delisle #307
- omero.gateway: add new
getObjectsByMapAnnotationsAPI #285 - CLI: Add support for downloading fileset and multi-file images #298
The CLI feature also introduces a backwards-incompatible layout change for the download of images to mitigate the risk of data corruption associated with renaming files. The command now specifies a directory path under which all files associated with the image are downloaded using the original file names and structure.
- Fix OMERO.tables to work with all column types #288
- Fix race condition in OMERO.tables #292
- Fix Python2-ism in omero.gateway findExperimenters method, thanks to Alex Herbert #293
- Add
--retry [RETRIES]toomero login#283
- remove usage of deprecated method preventing usage on Python 3.9 #282
- CLI: obj update strips newlines #279
- roi_utils: fix possible division by zero #278
- download provider uses NamedTemporaryFile #274
- Admin: introduce
omero.server.nodedescriptorsconfiguration property for configuring services launched on start-up #272
- CLI: fix
omero errorscommand under Python 3 #264
- CLI: fail login when user input is required but stdout is not connected to a tty(-like) device #256
- CLI: improve description of
--includeand--excludeoptions (#252, #254) - Restore Python 3.5 compatibility (#257)
omero importautomatically downloads import jars if missing (#162)- Use OS-specific application directories instead of
~/omerofor local cache (#242) omero admin: optionally check for system manager environment variable (#246)- Add support for multiple Ice TLS protocols (#251)
- CLI UTF-8 Fixes (#224)
- Fix sessions logging attribute error (#226)
omero hql: when querying masks, filterbytesfield (#230)- Fix CLI error handling when attempting to check log files (#236)
omero import: fix--logprefix(#238)fs usage: don't overwrite size (#245)omero.gateway: always marshal tile metadata on presence of pyramid (#239)
- Add PyYAML as a dependency of omero-py (#228)
bin/omeroentrypoint (#229)- Tox: Python 3.8, use travis bionic ice-py wheels (#232)
- Update release paragraph to mention downstream conda repository (#234)
- Remove long-deprecated module
functional.py(#237) - Use requests for HTTP/HTTPS calls in library (#240)
- Adds optional extra args to the
util/import_candidates.py, thanks to Guillaume Gay (#241) - Link to source on PyPI homepage (#247)
- Deprecate CLI duplicate plugin in favor of omero-cli-duplicate (#249)
- Fix
import --log/--errwith bulk import (#223)
-
API changes:
-
Other fixes and updates:
- Doc: escape quotes in "Default:" sections (#185)
- Doc: List preferred conda installation first (#190)
- Fix: pass OMERODIR to processor (#197)
- Fix: Improve error message for 'fs usage' (#192)
- Fix: Get file size for download (#181)
- travis jobs: enable Windows (#134)
CmdError: implement__str__(#151)- tables: call delete callback (#152)
- fix doc (#170)
- Add show-uuid option to
sessions who(#174) omero db passwordshould be a string (#175)- Extend output of
omero version(#176) - Improve PyYAML error message (#177)
- Remove
bin/omeroandlib/python(#157) - Bump Blitz version 5.5.5 (#158)
- Processor passes locale to subprocess (#150)
omero.clientensures args is not None (#149)- Ignore
OMERO_HOMEwith warning (#148) - Retry flaky tests up to five times (#144)
- Disable new
testLoadGlobwhenOMERODIRnot set (#140) - Add numpy to requirements (#139)
admin.py: handle errors ingetdirsize(#135)- Fix tables
StringColumnfor strings containing Unicode characters (#143) - Add
bin/omero load --globsupport (#137) - Drop
hdfstorageV1(#136) - Require
OMERODIRto be set (#14) - Fix Windows build (#132)
- Fix
config parsecommand (#130) - Rename deprecated plugins (#124)
- Activate all unit tests (#122)
- Fix batch file annotation (#127)
- Declare Pillow as a mandatory dependency of omero-py (#128)
- Move external path module under
omero_extnamespace (#123) - Fix pyinotify for DropBox (#119)
- Fix DB creation script (#110)
- Fix
tablesandgetObjects - Fixes primarily focused on byte return types
- Activate Python 3.5 testing (#68)
- Add
devtargetfor developer friendliness (#33, #55) - Remove more web vestiges (#26)
omero.gateway.FileAnnotationWrapper.getFileInChunksreturns bytesomero.gateway.ImageWrapper.exportOmeTiffreturns bytesomero.gateway.BlitzGateawy.createOriginalFileFromFileObjtakesBytesIO- several return values should now be wrapped by
BytesIO:image.renderSplitChannel()image.renderBirdsEyeView()image.renderJpegRegion()image.renderJpeg()
rlonginstances now require explicit mapping:omero_type(longValue)defaults torintomero.rtypes.wrap(longValue)defaults torint