Merge pull request #3002 from sbesson/cli_integration2unit

CLI: migrate integration tests as unit tests
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2835 (Update OmeroPy/src/path.py)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2895 (Reload groups after users added/removed)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2926 (OmeroCpp: Glob test sources)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2927 (OmeroCpp: Glob example sources)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2963 (Discover LDAP users server-side (fix #12511).)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2970 (Bugfixes for 5 0 4)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2972 (show multiple objects)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2979 (Thumbnail cache busting)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2982 (Fix #12530: detect Windows if closing RFS.)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 2994 (Ensure that identity request variables are UTF-8 encoded)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 3004 (Update webadmin_utils.py with downloads.o.org link instead of trac.o.org )
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 3005 (Rendering settings unification)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 3008 (OmeroPy: src flake8 (II))
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 3009 (Add a disk usage plugin)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 3010 (cmake: Use embedded gtest from bioformats)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 3011 (OmeroCpp: Group code into folders)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: branch jburel:qa-submit-new
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 3000 jballanc 'Update artifacts for Lucene, Hibernate, and Spring' (user: jballanc)
  # PR 2585 aleksandra-tarkowska 'making time_zone and first_day_of_week configurable' (exclude comment)
  # PR 2182 joshmoore 'Read only flag' (label: exclude)
  # PR 2987 rleigh-dundee 'travis: Build with Oracle JDK 8' (status: failure)
  # PR 3012 ximenesuk 'Flake8 omero/util' (status: failure)
  # PR 2363 dominikl 'Java Gateway API' (label: exclude breaking)
  # PR 2962 sbesson 'Flake8 omero.cli' (label: exclude)
  # PR 2965 rleigh-dundee 'blitz: Split RObject out of RTypes' (exclude comment)
  # PR 2985 will-moore 'Download preserves directories of original files' (label: exclude)
  # PR 2412 qidane 'Extra annotations' (exclude comment)
Already up-to-date.

Merged PRs:
  # PR 2835 simleo 'Update OmeroPy/src/path.py'
  # PR 2895 dominikl 'Reload groups after users added/removed'
  # PR 2926 rleigh-dundee 'OmeroCpp: Glob test sources'
  # PR 2927 rleigh-dundee 'OmeroCpp: Glob example sources'
  # PR 2963 bpindelski 'Discover LDAP users server-side (fix #12511).'
  # PR 2970 will-moore 'Bugfixes for 5 0 4'
  # PR 2972 will-moore 'show multiple objects'
  # PR 2979 will-moore 'Thumbnail cache busting'
  # PR 2982 bpindelski 'Fix #12530: detect Windows if closing RFS.'
  # PR 2994 chris-allan 'Ensure that identity request variables are UTF-8 encoded'
  # PR 3004 kennethgillen 'Update webadmin_utils.py with downloads.o.org link instead of trac.o.org '
  # PR 3005 dominikl 'Rendering settings unification'
  # PR 3008 sbesson 'OmeroPy: src flake8 (II)'
  # PR 3009 ximenesuk 'Add a disk usage plugin'
  # PR 3010 rleigh-dundee 'cmake: Use embedded gtest from bioformats'
  # PR 3011 rleigh-dundee 'OmeroCpp: Group code into folders'
Merged branches:
  # jburel:qa-submit-new

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1323 melissalinkert 'Add bit-level operations to RandomAccess{Input, Output}Stream' (label: exclude)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1315 LeeKamentsky 'IM3Reader for Perkin-Elmer Nuance' (user: LeeKamentsky)
  # PR 1296 melissalinkert 'Add test for getRequiredDirectories' (status: failure)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (label: exclude)
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 1328 sbesson 'Use in-place caching by default in Memoizer' (label: exclude)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1249 PremyslFiala 'ND2 - Bug fixes' (user: PremyslFiala)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 1265 qidane 'New units' (label: exclude breaking)
Already up-to-date.

Merged PRs:
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter'
  # PR 1302 sbesson 'Add branch-specific link for downloading the JAR file if unfound (rebased onto develop)'
  # PR 1306 ctrueden 'Add support for PrairieView version 5.2 datasets'
  # PR 1311 melissalinkert 'Performance and position count fixes for ND2 (rebased onto develop)'
  # PR 1317 melissalinkert 'Gatan: fix physical dimension parsing when the Z size is missing'
  # PR 1322 rleigh-dundee 'cpp: Add embedded gtest'
  # PR 1324 melissalinkert 'Deltavision: conditionally ignore stage position values of 0'
  # PR 1329 sbesson 'Use ome.staging for Maven release deployment'
  # PR 1330 rleigh-dundee 'doc: Work with sphinx 1.2.3'

Repository: ome/scripts
Already up-to-date.

Repository: openmicroscopy/ome-documentation
Already up-to-date.

Merged PRs:
  # PR 972 will-moore 'Add setting omero.web.page_size to web docs'
  # PR 973 hflynn 'Team workflow doc'
  # PR 975 ximenesuk 'Expose upload_rm option in the documentation'
  # PR 981 hflynn 'Adding repo cloning to 'using git' guide'

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