- 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 certificates
to 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 import
on 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_list
in favor ofPropertyParser.is_excluded
#313
- Allow direct URL to be passed to
omero import --fetch-jars
#303 - Exclude
omero.version
from 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
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.
- 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.nodedescriptors
configuration property for configuring services launched on start-up #272
- CLI: fix
omero errors
command 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
--include
and--exclude
options (#252, #254) - Restore Python 3.5 compatibility (#257)
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)
- CLI UTF-8 Fixes (#224)
- Fix sessions logging attribute error (#226)
omero hql
: when querying masks, filterbytes
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)
- 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)
- Fix
import --log/--err
with 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 password
should be a string (#175)- Extend output of
omero version
(#176) - Improve PyYAML error message (#177)
- Remove
bin/omero
andlib/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
whenOMERODIR
not set (#140) - Add numpy to requirements (#139)
admin.py
: handle errors ingetdirsize
(#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
andgetObjects
- 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)
omero.gateway.FileAnnotationWrapper.getFileInChunks
returns bytesomero.gateway.ImageWrapper.exportOmeTiff
returns bytesomero.gateway.BlitzGateawy.createOriginalFileFromFileObj
takesBytesIO
- 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 torint
omero.rtypes.wrap(longValue)
defaults torint