Copy 5.1d15 upgrade to 5.0
merge develop -Dnone -Ibreaking -Eexclude -Sno-error: PR 3215 (5.1DEV__16: Ordered Map implementation)
merge develop -Dnone -Ibreaking -Eexclude -Sno-error

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 3000 jballanc 'Update artifacts for Lucene, Hibernate, and Spring' (user: jballanc)
  # PR 3208 sbesson 'Update the OMERO install script to test Web login with CSRF (rebased onto develop)' (user: sbesson)
  # PR 3235 sbesson 'Remove validator from source code' (user: sbesson)
  # PR 3098 aleksandra-tarkowska 'Metadata reimport' (user: aleksandra-tarkowska)
  # PR 3228 mtbc 'fix #11779: graph operations use "compiler" rather than "rollback" strategy' (user: mtbc)
  # PR 3157 jburel 'Reset password' (user: jburel)
  # PR 3221 dominikl 'Wrap description text to avoid horizontal scroll bar' (user: dominikl)
  # PR 3217 aleksandra-tarkowska 'Viewer fixes' (user: aleksandra-tarkowska)
  # PR 3207 will-moore 'General pane web 2' (user: will-moore)
  # PR 2585 aleksandra-tarkowska 'making time_zone and first_day_of_week configurable' (exclude comment)
  # PR 3218 will-moore 'Units metadata panel' (user: will-moore)
  # PR 3227 joshmoore 'Initial conversion code via ctors' (user: joshmoore)
  # PR 2363 dominikl 'Java Gateway API' (label: exclude)
  # PR 3226 snoopycrimecop 'Update develop submodules' (user: snoopycrimecop)
  # PR 3213 sbesson 'Flake8 OMERO.web feedback' (user: sbesson)
  # PR 3181 joshmoore 'Update to Hibernate 3.6 (See trac2570)' (label: exclude)
  # PR 3141 dpwrussell 'jstree upgrade (Functionality Review Only)' (status: failure)
  # PR 3229 dominikl 'Use Units in ROI/MeasurementTool' (user: dominikl)
  # PR 3216 joshmoore 'Misc DB fixes (5.1DEV__17)' (label: exclude)
  # PR 3222 hflynn 'Initial draft for m2 version history' (user: hflynn)
  # PR 3042 will-moore 'Download dataset project' (user: will-moore)
  # PR 2182 joshmoore 'Read only flag' (user: joshmoore)
  # PR 3086 will-moore 'Create image by tiling 12459' (user: will-moore)
  # PR 3156 aleksandra-tarkowska 'Templates cleanup' (user: aleksandra-tarkowska)
Already up-to-date.

Merged PRs:
  # PR 3215 joshmoore '5.1DEV__16: Ordered Map implementation'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1450 melissalinkert 'Reduce memory needed to open PNG images' (user: melissalinkert)
  # PR 1431 rleigh-dundee 'Specification: Add XML catalogues for released schemas' (user: rleigh-dundee)
  # PR 1448 melissalinkert 'Metamorph: allow both sanitized and unsanitized delimiters' (user: melissalinkert)
  # PR 1442 bramalingam 'Update roi handler' (user: bramalingam)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1426 qidane 'Initial Rendering Definitions schema' (exclude comment)
  # PR 1451 melissalinkert 'Fix im3 metadata' (user: melissalinkert)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1443 joshmoore 'Genshi ZIP' (user: joshmoore)
  # PR 1366 ctrueden 'Miscellaneous cleanup' (user: ctrueden)
  # PR 1444 snoopycrimecop 'Update auto-generated documentation' (user: snoopycrimecop)
  # PR 1420 qidane 'Updating samples and adding units samples' (user: qidane)
  # PR 1365 ctrueden 'PrairieView 5.2 fixes and improvements' (user: ctrueden)
  # PR 1441 melissalinkert 'Fix OME-XML BinData decoding' (user: melissalinkert)
  # PR 1407 melissalinkert 'TIFF: fix plane count calculation for pyramids with multiple planes' (user: melissalinkert)
  # PR 1381 melissalinkert 'Parse physical pixel sizes from CellSens .vsi datasets' (user: melissalinkert)
  # PR 1437 stelfrich 'Changed handling of empty series names in ND2 files' (user: stelfrich)
Updating 8a0013b..b3962bd
Previously merged:
  # PR 1447 sbesson 'Add python-bioformats to the documentation'
  # PR 1428 rleigh-dundee 'C++: Incremental metadata processing work'
  # PR 1440 melissalinkert 'DICOM: fix byte skipping for >8 bit data'
  # PR 1418 rleigh-dundee 'IFormatReader: Remove deprecated methods'
  # PR 1436 rleigh-dundee 'cpp: compat: Add path type lookups to module'
  # PR 1434 rleigh-dundee 'cpp: cmake: RegexChecks: Improve include usage for portability'
  # PR 1439 sbesson 'Update Eclipse instructions for Bio-Formats with link to ome-devel thread'
  # PR 1425 jburel 'Convert tolerance to NonNegativeInt to NonNegativeFloat'
  # PR 1362 melissalinkert 'Make FormatReader's RandomAccessInputStream transient'
  # PR 1423 melissalinkert 'TIFF: attempt to correct incorrectly stored StripByteCounts values'
  # PR 1433 melissalinkert 'Initial version of I2I reader'
  # PR 1432 melissalinkert 'Metamorph: fix description delimiter to account for XML sanitization'
  # PR 1422 melissalinkert 'Zeiss TIFF: fix used file list when expected files are missing'
  # PR 1438 qidane 'Correct regex so PA = PASCAL'

Merged PRs:
  # PR 1435 joshmoore 'Ordered MapPairs implementation'

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

Repository: openmicroscopy/ome-documentation
Excluded PRs:
  # PR 1042 mtbc 'document graph traversal reimplementation for developers' (user: mtbc)
  # PR 1041 joshmoore 'Units documentation' (user: joshmoore)
  # PR 1038 aleksandra-tarkowska 'updating web doc for embedding viewer' (user: aleksandra-tarkowska)
Updating 84e4427..fb16f30
Previously merged:
  # PR 1039 ximenesuk 'Add more detail on pytest markers'
  # PR 1040 snoopycrimecop 'Update auto-generated properties'
  # PR 1037 manics 'Add OMERO-5.1-{latest,merge}-deploy-win jobs to contributing'

Generated by OME-5.1-breaking-push#211 (http://ci.openmicroscopy.org/job/OME-5.1-breaking-push/211/)