CHANGELOG.md

5.19.4 (July 2024)

• 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

5.19.3 (June 2024)

• Cap numpy to 1.x #414

5.19.2 (April 2024)

• 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

5.19.1 (March 2024)

• Fix Windows regression in omero_ext.path #402

5.19.0 (February 2024)

• 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.

5.18.0 (January 2024)

Other updates

• Set minimum version for Pillow (10.0.0) and Python (3.8) #388

5.17.0 (November 2023)

Other updates

• Unit tests: clean up warnings #386
• Add support for Python 3.11 #385
• Use math module instead of numpy.math #384

5.16.1 (October 2023)

Other updates

• omero admin start: add warning for deprecated TLS protocols #382

5.16.0 (September 2023)

Other updates

• 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

5.15.0 (July 2023)

Other updates

• Use Image.LANCZOS alias rather than Image.ANTIALIAS #376
• Let Ice choose the default SSL protocols that are available #377

5.14.0 (June 2023)

Bug fix

• OMERO.cli: do not fail on the absence of --retry argument #364

Deprecated

• Deprecate omero.install.python_warning module #362
• Drop support for Python 3.7 #368

Other updates

• Add Python 3.10 to the testing matrix #357
• Readme updates #358, #363, #369
• Update GitHub workflow actions #365

5.13.1 (November 2022)

Other updates

• API doc: Add inherited-members and private-members options to the gateway automodule configuration #354

5.13.0 (November 2022)

New features

• Remove Anonymous Diffie-Hellman default configuration #336. This change will require to use of omero certificates to ensure that an OMERO server installation has, at minimum, a self-signed certificate.
• Publish API doc #330

Bug fix

• 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

Other updates

• Switch to new output command (GHA) #340

5.12.1 (October 2022)

Bug fix

• Always report pixeldata time in the output of omero fs importtime #335

5.12.0 (September 2022)

New features

• ParametersI now supports addTime() method #327
• Pass omero.db.properties to reindex command #329

Bug fixes

• Fix concurrency issues in pytest #328
• Improve performance of channel renaming for Datasets #331

5.11.2 (May 2022)

Bug fix

• Fix omero import on Windows #326

5.11.1 (March 2022)

Bug fix

• Fix params.limit ignored in conn.getObjects() #321

5.11.0 (February 2022)

New features

• Add implementation for DatasetColumn #309
• Add support for searching OMERO.tables by column which name is not a valid Python identifier #287

Bug fixes

• Fix OMERO.table memory issue when using table.read() with large number of rows #314
• Deprecate PropertyParser.black_list in favor of PropertyParser.is_excluded #313

5.10.3 (December 2021)

Bug Fix

• Allow direct URL to be passed to omero import --fetch-jars #303
• Exclude omero.version from output of omero config parse #312

5.10.2 (December 2021)

Bug Fix

• Decode script stdout/stderr before printing, thanks to Jeremy Muhlich #310
• Ensure we are using pyopenssl #305

5.10.1 (October 2021)

Bug Fix

• Fix UnbondLocalError in omero tag list, thanks to Lucille Delisle #307

5.10.0 (September 2021)

New feature

• omero.gateway: add new getObjectsByMapAnnotations API #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.

Bug Fix

• CLI: point users at image.sc for reporting bugs #297

5.9.3 (July 2021)

Bug Fix

• 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

5.9.2 (April 2021)

New CLI option

• Add --retry [RETRIES] to omero login #283

5.9.1 (March 2021)

Bug Fix

• 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

Other updates

• download provider uses NamedTemporaryFile #274

5.9.0 (January 2021)

• Admin: introduce omero.server.nodedescriptors configuration property for configuring services launched on start-up #272

5.8.3 (October 2020)

Bug fix

• CLI: fix omero errors command under Python 3 #264

5.8.2 (October 2020)

Bug fix

• CLI: fail login when user input is required but stdout is not connected to a tty(-like) device #256

Other updates

• Import test: check stderr for output #260
• Switch from Travis CI to GitHub actions (#261, #262)

5.8.1 (September 2020)

Bug fixes

• CLI: improve description of --include and --exclude options (#252, #254)
• Restore Python 3.5 compatibility (#257)

5.8.0 (September 2020)

New features

• omero import automatically downloads import jars if missing (#162)
• Use OS-specific application directories instead of ~/omero for local cache (#242)
• omero admin: optionally check for system manager environment variable (#246)
• Add support for multiple Ice TLS protocols (#251)

Bug fixes

• CLI UTF-8 Fixes (#224)
• Fix sessions logging attribute error (#226)
• omero hql: when querying masks, filter bytes field (#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)

Other updates

• Add PyYAML as a dependency of omero-py (#228)
• bin/omero entrypoint (#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)

5.7.1 (June 2020)

• Fix import --log/--err with bulk import (#223)

5.7.0 (June 2020)

• API changes:

  • Support use of CLI within OMERO.scripts (#186)
  • Add new conn.chownObjects() method (#195)
  • Loading options for Experimenters and Groups (#196)

• Other fixes and updates:

  • Fix pywin import in Python 3.7 (#203)
  • Don't unset ICE_CONFIG on Windows (#193)
  • Ignore owner in omero.data.dir check (#208)
  • Fix JSON parsing on Python 3.5 (#213)
  • Fix client.download() on Python 3.5 (#215)
  • Warn if omero.db.poolsize is not set (#218)
  • admin diagnostics shows jar versions (#188)

5.6.2 (March 2020)

• 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)

5.6.1 (February 2020)

• 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 password should be a string (#175)
• Extend output of omero version (#176)
• Improve PyYAML error message (#177)

5.6.0 (January 2020)

• Remove bin/omero and lib/python (#157)
• Bump Blitz version 5.5.5 (#158)
• Processor passes locale to subprocess (#150)
• omero.client ensures args is not None (#149)
• Ignore OMERO_HOME with warning (#148)
• Retry flaky tests up to five times (#144)
• Disable new testLoadGlob when OMERODIR not set (#140)
• Add numpy to requirements (#139)
• admin.py: handle errors in getdirsize (#135)
• Fix tables StringColumn for strings containing Unicode characters (#143)
• Add bin/omero load --glob support (#137)
• Drop hdfstorageV1 (#136)
• Require OMERODIR to be set (#14)
• Fix Windows build (#132)
• Fix config parse command (#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_ext namespace (#123)
• Fix pyinotify for DropBox (#119)
• Fix DB creation script (#110)
• Fix tables and getObjects
• Fixes primarily focused on byte return types
• Activate Python 3.5 testing (#68)
• Add devtarget for developer friendliness (#33, #55)
• Remove more web vestiges (#26)

API Changes

• omero.gateway.FileAnnotationWrapper.getFileInChunks returns bytes
• omero.gateway.ImageWrapper.exportOmeTiff returns bytes
• omero.gateway.BlitzGateawy.createOriginalFileFromFileObj takes BytesIO
• several return values should now be wrapped by BytesIO:
  • image.renderSplitChannel()
  • image.renderBirdsEyeView()
  • image.renderJpegRegion()
  • image.renderJpeg()
• rlong instances now require explicit mapping:
  • omero_type(longValue) defaults to rint
  • omero.rtypes.wrap(longValue) defaults to rint

5.5.1 (September 2019)

• Use omero-blitz 5.5.4 (#24)
• Fix unit tests (#10, #17)
• Improve PyPI deployment, add README, etc. (#6)
• Remove web.py (#5)
• Extract code from ome/openmicroscopy
• Make minimal changes for a functioning python setup.py (#1)