sphinx-api: Generate skeleton docs
ROI_utils.py: Remove nonexistent TextI import
sphinx-api: Don't generate PDF and fix install dir
OmeroPy: Don't include copyright boilerplate in docstrings
build: Remove support for Ice 3.3
Remove obsolete, broken and unused scripts
remove further Ice 3.3 from OMERO 5.1
Merge pull request #1 from mtbc/ice33-removal-rleigh

Remove further Ice 3.3 references from OMERO 5.1
Change VM ostype from Debian to Debian_64

Note the VM image is already 64 bit. The build was failing on octopus, for some inexplicable reason changing the ostype flag fixes the build.
Merge pull request #2586 from manics/rebased/develop/vbox_fix

VirtualBox fix for octopus (rebased onto develop)
Merge pull request #2455 from rleigh-dundee/ice33-removal

Remove support for Ice 3.3
Merge pull request #2357 from rleigh-dundee/ant-apisupport

Generate Python API reference with Sphinx
merge develop -D none -I breaking -E exclude: PR 2363 (Java Gateway API)
merge develop -D none -I breaking -E exclude: PR 2403 (Send email)
merge develop -D none -I breaking -E exclude: PR 2412 (Extra annotations)
merge develop -D none -I breaking -E exclude

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 2550 dominikl 'Avoid upscaling of bird's eye image' (user: dominikl)
  # PR 2588 sbesson 'Add integration tests for CLI import as (rebased onto develop)' (user: sbesson)
  # PR 2562 dominikl 'Rendering settings: Always show 'SavedBy' Panel' (user: dominikl)
  # PR 2583 joshmoore '12358 parse metadata' (user: joshmoore)
  # PR 2182 joshmoore 'Read only flag' (user: joshmoore)
  # PR 2336 knabar 'New tagging dialog' (user: knabar)
  # PR 2560 will-moore 'for-loop fix removes 'undefined' from reset dialog. See #12301' (user: will-moore)
  # PR 2269 dominikl 'ROI improvements' (user: dominikl)
  # PR 2362 will-moore 'Remove .jy from script names' (user: will-moore)
  # PR 2527 dominikl 'Bugfix: Remove FileAnnotations when multiple images are selected' (user: dominikl)
  # PR 2529 mtbc 'fix upgrade scripts for PostgreSQL 8.4 compatibility' (user: mtbc)
  # PR 2559 joshmoore '12176 attach fsfiles (rebased onto develop)' (user: joshmoore)
  # PR 2580 will-moore 'Remove 'batch_search'. See #12347' (user: will-moore)
  # PR 2536 dominikl 'Only enable the filepath icon if there are any filepaths to show' (user: dominikl)
  # PR 2435 rleigh-dundee 'cpp: RTypesI: use static locals in place of duplicated globals' (user: rleigh-dundee)
  # PR 2564 will-moore 'Top links 12326' (user: will-moore)
  # PR 2521 joshmoore 'Add 'config list' command' (user: joshmoore)
  # PR 2411 snoopycrimecop 'Update develop submodules' (user: snoopycrimecop)
  # PR 2590 will-moore 'Use numpy.float32 for PixelsType 'float' (rebased onto develop)' (user: will-moore)
  # PR 2585 aleksandra-tarkowska 'making time_zone and first_day_of_week configurable' (user: aleksandra-tarkowska)
  # PR 2391 jburel 'Imagej omero (rebased onto develop)' (user: jburel)
  # PR 2127 dpwrussell 'Working view to email announcements to selected users, groups, email addresses and/or all users' (user: dpwrussell)
Already up-to-date.

Merged PRs:
  # PR 2363 dominikl 'Java Gateway API'
  # PR 2403 aleksandra-tarkowska 'Send email'
  # PR 2412 qidane 'Extra annotations'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter' (user: melissalinkert)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 1108 melissalinkert 'MRC: fix handling of mode 16 data (rebased onto develop)' (user: melissalinkert)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 1136 melissalinkert 'Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)' (user: melissalinkert)
  # PR 1138 melissalinkert 'Lots of Zeiss CZI fixes (rebased onto develop)' (user: melissalinkert)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (user: melissalinkert)
  # PR 981 melissalinkert 'Ignore namespaces when filling in an XMLAnnotation's Value' (user: melissalinkert)
  # PR 983 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes (rebased onto develop)' (user: melissalinkert)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1155 joshmoore 'Memoizer errs (rebased onto develop)' (user: joshmoore)
  # PR 1123 melissalinkert 'Add a reader that accepts a file containing a file pattern' (user: melissalinkert)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1145 joshmoore 'Make private class in DV reader public (see #12358)' (user: joshmoore)
  # PR 1116 rleigh-dundee 'cpp: Add TIFF support (1)' (user: rleigh-dundee)
  # PR 1110 sbesson 'BF docs: Jenkins cleanup (rebased onto develop)' (user: sbesson)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (user: LeeKamentsky)
Updating f247b30..25b73b1
Merged PRs (fast-forward):
  # PR 1147 rleigh-dundee 'cpp: bioformats: PixelProperties supports pixel types of different endianness'
  # PR 1152 hflynn 'Comstat2 link (rebased onto develop)'
  # PR 1149 sbesson 'Add prefix to zip file produced by dist-bftools target (rebased onto develop)'
  # PR 1106 melissalinkert 'Imaris HDF: make sure that all resolutions have the same ZCT sizes (rebased onto develop)'
  # PR 1097 melissalinkert 'CellSens: fix off-by-ones in subresolution tile calculations (rebased onto develop)'
  # PR 1070 melissalinkert 'DICOM: expand sequence reading to include known sequences (rebased onto develop)'
  # PR 1060 melissalinkert 'Allow dist-matlab to run on Windows'
  # PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)'
  # PR 1028 melissalinkert 'Large fileset performance improvements (rebased onto develop)'
  # PR 1135 joshmoore 'Update native-lib-loader to 2.0.1 release (rebased onto develop)'
  # PR 1142 hflynn 'Add 'show and edit on Github' to docs side menu (rebased onto develop)'
  # PR 1137 melissalinkert 'Update version history for 5.0.2 (rebased onto develop)'
  # PR 1103 melissalinkert 'Flex: fix support for new file naming scheme (rebased onto develop)'
  # PR 1092 sbesson 'Allow for a >1 count increment in B&H .sdt Files. (rebased onto develop)'
  # PR 1101 melissalinkert 'QuickTime: fix header/footer parsing bug (rebased onto develop)'
  # PR 1127 sbesson 'CI logging improvements (rebased onto develop)'
  # PR 1102 melissalinkert 'Metamorph .nd performance improvements (rebased onto develop)'
  # PR 1109 melissalinkert 'Fix memo file path creation on Windows (rebased onto develop)'
  # PR 1100 melissalinkert 'Fix single plane ND2 line scan (rebased onto develop)'
  # PR 1096 melissalinkert 'Fix 5D Imspector support (rebased onto develop)'
  # PR 1098 melissalinkert 'Gatan metadata fixes (rebased onto develop)'
  # PR 1082 rleigh-dundee 'C++: Add support for integers of different endianness'
  # PR 1120 rleigh-dundee 'cpp: ome-bioformats: Use std::complex for complex pixel types'
  # PR 1118 joshmoore 'LogbackTools: silence ClassCastException traces (rebased onto develop)'
  # PR 1128 hflynn 'Update auto-generated documentation on develop'
  # PR 1119 hflynn 'User docs tidying (rebased onto develop)'
  # PR 1099 melissalinkert 'Disable file grouping in ImageJ remote import plugin (rebased onto develop)'
  # PR 1107 melissalinkert 'Exclude log4j and packages from target-test-runner (rebased onto develop)'
  # PR 1121 sbesson 'Fix bfGetPlane tile input check (rebased onto develop)'
  # PR 1117 rleigh-dundee 'cpp: Minor doxygen fixes'
  # PR 1126 hflynn 'Leica link (rebased onto develop)'
  # PR 1083 rleigh-dundee 'make: Convert variables to ant properties'
  # PR 1075 hflynn 'Remove dead bitmap link (rebased onto develop)'
  # PR 1076 hflynn 'Adding CONTRIBUTING file to BF repo (rebased onto develop)'
  # PR 1073 rleigh-dundee 'docs: Delegate all sphinx Makefile targets to ant'

Merged PRs:
  # PR 1054 qidane 'Additional annotation points throughout the model'

Repository: ome/scripts
Excluded PRs:
  # PR 76 will-moore 'Fix 'No permissions' error in Make_Movie.py. See #12227' (user: will-moore)
Updating 31f89c4..25a0869
Merged PRs (fast-forward):
  # PR 81 will-moore 'Make movie format time 12254 (rebased onto develop)'
  # PR 84 sbesson 'Get inputs all scripts (rebased onto develop)'
  # PR 79 sbesson 'Travis fix (rebased onto develop)'

Repository: openmicroscopy/ome-documentation
Excluded PRs:
  # PR 817 ximenesuk 'Update DropBox documentation (rebased onto develop)' (user: ximenesuk)
  # PR 816 will-moore 'Webgateway mip 5150 (rebased onto develop)' (user: will-moore)
  # PR 799 manics 'Linux walkthrough (rebased onto develop)' (user: manics)
  # PR 812 sbesson 'Remaining changes post 5.0.x job migration' (user: sbesson)
Updating be161c6..4d9d6be
Merged PRs (fast-forward):
  # PR 814 bpindelski 'Add LDAP error message explanation.'
  # PR 806 aleksandra-tarkowska 'Webstart template (rebased onto develop)'
  # PR 807 aleksandra-tarkowska 'ldap over ssl instruction improvement (rebased onto develop)'
  # PR 805 hflynn 'Adding contributing doc link & Zeiss link update'
  # PR 810 hflynn 'Adding example server setup page  (rebased onto develop)'
  # PR 743 sbesson 'Propose redesign of OMERO and Bio-Formats 5.0 CI jobs'
  # PR 809 sbesson 'Travis fix (rebased onto develop)'
  # PR 802 snoopycrimecop 'Update index.txt'
  # PR 801 sbesson 'Add Edit on Github button (rebased onto develop)'
  # PR 783 mtbc 'document new // separator in omero.fs.repo.path (rebased from dev_5_0)'
  # PR 782 will-moore 'Custom web login 11961 (rebased onto develop)'
  # PR 795 manics 'Root password reset command (rebased onto develop)'
  # PR 786 mtbc 'warn that in-place ln_s can be slower for HCS (rebased from dev_5_0)'
  # PR 797 ximenesuk 'Add DropBox Windows requirements'
  # PR 793 hflynn 'Ice35 support for Windows (rebased to develop)'
  # PR 791 hflynn 'Limitations update for 5.0.2 (rebased onto develop)'
  # PR 792 bpindelski 'Remove repetition of the word "files" (rebased onto develop)'
  # PR 787 manics 'Add code-signing documentation (rebased onto develop)'
  # PR 776 sbesson 'Remove all references to CI jobs in the official documentation'
  # PR 772 rleigh-dundee 'make: Convert variables to ant properties'
  # PR 771 hflynn 'Adding pyramid generation data duplication warning to in-place import (rebased onto develop)'
  # PR 760 rleigh-dundee 'Make Ice 3.4 the minimum supported version'
  # PR 768 hflynn 'Rephrasing CONTRIBUTING re: branch for PRs (rebased onto develop)'
  # PR 769 hflynn 'Making API doc links point at release version (rebased onto develop)'
  # PR 766 rleigh-dundee 'ant: Default all properties and handle empty vars in conf.py'
  # PR 758 hflynn 'Adding API doc links to OMERO docs front page (rebased onto develop)'
  # PR 759 hflynn 'ticket 10030 fix - contributing file for docs repo (rebased onto develop)'
  # PR 761 rleigh-dundee 'Delegate all Makefile targets to ant'

Generated by OMERO-5.1-breaking-push#52 (http://ci.openmicroscopy.org/job/OMERO-5.1-breaking-push/52/)