Skip to content

Latest commit

 

History

History
275 lines (198 loc) · 12.5 KB

CHANGELOG.md

File metadata and controls

275 lines (198 loc) · 12.5 KB
Raw

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

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

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)