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Repository: ome/bio-formats-build
Excluded PRs:
  - PR 502 dependabot[bot] 'Bump bio-formats-documentation from `ab5e213` to `53190ff`' (status: None)
  - PR 501 dependabot[bot] 'Bump ZarrReader from `d1c6223` to `2d75020`' (status: None)
Already up-to-date.

Merged PRs:
  - PR 469 jburel 'install sphinx'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating d1c6223..2d75020
Previously merged:
  - PR 59 jburel 'Actions update'

Merged PRs:
  - PR 53 dgault 'Reorder group keys'
  - PR 58 dgault 'Add new option to list pixels in getUsedFiles'

Repository: ome/bio-formats-documentation
Updating ab5e213..53190ff
Previously merged:
  - PR 329 will-moore 'Ignore knime link'

Merged PRs:
  - PR 330 jburel 'update uri'

Repository: ome/bio-formats-examples
Excluded PRs:
  - PR 105 sbesson 'Bump logback dependency to 1.3.5' (stage: draft)
Already up-to-date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4073 melissalinkert 'OME-TIFF: optionally fail fast if an invalid file is encountered' (label: exclude)
  - PR 4059 CGDogan 'TiffSaver: produce valid 4-channel RGBA images' (user: CGDogan)
  - PR 4057 melissalinkert 'Add CodecOptions.disableChromaSubsampling' (status: failure)
  - PR 4016 melissalinkert 'Add API and DICOM-specific implementations for providing supplemental metadata during conversion' (stage: draft)
  - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats)
  - PR 3956 sbesson 'Bump sl4j-api to 2.x' (stage: draft)
  - PR 3939 dgault 'ImagePlusReader: handle IndexColorModel' (status: failure)
  - PR 3902 melissalinkert 'LSID validation' (stage: draft)
  - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
Already up-to-date.

Merged PRs:
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks'
  - PR 4051 CGDogan 'fix aplreader throwing nullptrexception'
  - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4070 melissalinkert 'Gatan DM3: be more defensive in parsing acquisition mode'
  - PR 4071 melissalinkert 'IVision: improve version and data type checks in isThisType'
  - PR 4072 melissalinkert 'Ventana: fix tile arithmetic for smallest resolutions'
  - PR 4074 melissalinkert 'Gel: check IFD count in isThisType'
  - PR 4075 melissalinkert 'Photoshop TIFF: fix plane reading with memoization'
  - PR 4076 melissalinkert 'VSI: fix uncompressed BGR data'
  - PR 4077 melissalinkert 'TillVision: fix some metadata parsing and .pst detection issues'
  - PR 4078 melissalinkert 'OIR: fix off-by-one in XML block reading'
  - PR 4079 melissalinkert 'Leica LIF: throw a nicer exception if no images are found'
  - PR 4080 melissalinkert 'Exporter plugin: remove any extra Channel elements'
  - PR 4081 melissalinkert 'SVS: fix a variety of small issues'
  - PR 4083 melissalinkert 'NDPI: correct for potential integer overflow in stored restart marker tag'
  - PR 4085 melissalinkert 'CV7000 improvements'

Conflicting PRs (not included):
  - PR 3992 melissalinkert 'Allow reading and writing compressed tiles'

Repository: ome/ome-codecs
Excluded PRs:
  - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (status: failure)
  - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (stage: draft)
Already up-to-date.

Merged PRs:
  - PR 29 iwbh15 'Disable chroma subsampling in JPEGCodec'

Repository: ome/ome-common-java
Excluded PRs:
  - PR 73 sbesson 'Bump sl4j-api to 2.x' (stage: draft)
  - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (label: exclude)
  - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru)
Already up-to-date.

Merged PRs:
  - PR 82 melissalinkert 'URLHandle: fall back to resetting stream if resetting to a mark fails'

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

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

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

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

Merged PRs:
  - PR 174 jburel 'Remove docs'

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

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

Generated by BIOFORMATS-push#77 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/77/)
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snoopycrimecop committed Aug 22, 2023
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48 changes: 24 additions & 24 deletions .gitmodules
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[submodule "ome-common-java"]
path = ome-common-java
url = https://github.com/ome/ome-common-java.git
branch = master
url = https://github.com/snoopycrimecop/ome-common-java.git
branch = snoopycrimecop_ci
[submodule "ome-model"]
path = ome-model
url = https://github.com/ome/ome-model.git
branch = master
url = https://github.com/snoopycrimecop/ome-model.git
branch = snoopycrimecop_ci
[submodule "ome-poi"]
path = ome-poi
url = https://github.com/ome/ome-poi.git
branch = master
url = https://github.com/snoopycrimecop/ome-poi.git
branch = snoopycrimecop_ci
[submodule "ome-mdbtools"]
path = ome-mdbtools
url = https://github.com/ome/ome-mdbtools.git
branch = master
url = https://github.com/snoopycrimecop/ome-mdbtools.git
branch = snoopycrimecop_ci
[submodule "ome-jai"]
path = ome-jai
url = https://github.com/ome/ome-jai.git
branch = master
url = https://github.com/snoopycrimecop/ome-jai.git
branch = snoopycrimecop_ci
[submodule "ome-codecs"]
path = ome-codecs
url = https://github.com/ome/ome-codecs.git
branch = master
url = https://github.com/snoopycrimecop/ome-codecs.git
branch = snoopycrimecop_ci
[submodule "ome-metakit"]
path = ome-metakit
url = https://github.com/ome/ome-metakit.git
branch = master
url = https://github.com/snoopycrimecop/ome-metakit.git
branch = snoopycrimecop_ci
[submodule "ome-stubs"]
path = ome-stubs
url = https://github.com/ome/ome-stubs.git
branch = master
url = https://github.com/snoopycrimecop/ome-stubs.git
branch = snoopycrimecop_ci
[submodule "bioformats"]
path = bioformats
url = https://github.com/openmicroscopy/bioformats.git
branch = develop
url = https://github.com/snoopycrimecop/bioformats.git
branch = snoopycrimecop_ci
[submodule "bio-formats-documentation"]
path = bio-formats-documentation
url = https://github.com/ome/bio-formats-documentation.git
branch = master
url = https://github.com/snoopycrimecop/bio-formats-documentation.git
branch = snoopycrimecop_ci
[submodule "bio-formats-examples"]
path = bio-formats-examples
url = https://github.com/ome/bio-formats-examples.git
branch = master
url = https://github.com/snoopycrimecop/bio-formats-examples.git
branch = snoopycrimecop_ci
[submodule "ZarrReader"]
path = ZarrReader
url = https://github.com/ome/ZarrReader.git
branch = main
url = https://github.com/snoopycrimecop/ZarrReader.git
branch = snoopycrimecop_ci
2 changes: 1 addition & 1 deletion ZarrReader
2 changes: 1 addition & 1 deletion bio-formats-documentation
2 changes: 1 addition & 1 deletion bioformats
Submodule bioformats updated 25 files
+9 −0 components/bio-formats-plugins/src/loci/plugins/out/Exporter.java
+30 −0 components/formats-api/src/loci/formats/FormatReader.java
+69 −0 components/formats-api/src/loci/formats/FormatTools.java
+91 −0 components/formats-api/src/loci/formats/FormatWriter.java
+16 −0 components/formats-api/src/loci/formats/IFormatReader.java
+15 −0 components/formats-api/src/loci/formats/IFormatWriter.java
+12 −0 components/formats-api/src/loci/formats/ImageReader.java
+16 −0 components/formats-api/src/loci/formats/ImageWriter.java
+12 −0 components/formats-api/src/loci/formats/ReaderWrapper.java
+19 −0 components/formats-api/src/loci/formats/WriterWrapper.java
+68 −74 components/formats-bsd/src/loci/formats/in/BDVReader.java
+63 −4 components/formats-bsd/src/loci/formats/services/JPEGTurboServiceImpl.java
+2 −2 components/formats-gpl/src/loci/formats/in/APLReader.java
+36 −1 components/formats-gpl/src/loci/formats/in/CV7000Reader.java
+23 −6 components/formats-gpl/src/loci/formats/in/CellSensReader.java
+9 −2 components/formats-gpl/src/loci/formats/in/GatanReader.java
+5 −1 components/formats-gpl/src/loci/formats/in/GelReader.java
+6 −1 components/formats-gpl/src/loci/formats/in/IvisionReader.java
+4 −0 components/formats-gpl/src/loci/formats/in/LIFReader.java
+8 −0 components/formats-gpl/src/loci/formats/in/NDPIReader.java
+2 −2 components/formats-gpl/src/loci/formats/in/OIRReader.java
+20 −12 components/formats-gpl/src/loci/formats/in/PhotoshopTiffReader.java
+62 −9 components/formats-gpl/src/loci/formats/in/SVSReader.java
+53 −13 components/formats-gpl/src/loci/formats/in/TillVisionReader.java
+11 −7 components/formats-gpl/src/loci/formats/in/VentanaReader.java
2 changes: 1 addition & 1 deletion ome-codecs
2 changes: 1 addition & 1 deletion ome-common-java
2 changes: 1 addition & 1 deletion ome-jai
Submodule ome-jai updated 0 files
2 changes: 1 addition & 1 deletion ome-mdbtools
Submodule ome-mdbtools updated 0 files
2 changes: 1 addition & 1 deletion ome-metakit
Submodule ome-metakit updated 0 files
2 changes: 1 addition & 1 deletion ome-model
Submodule ome-model updated 83 files
+1 −0 README.md
+0 −10 docs/sphinx/Makefile
+0 −1 docs/sphinx/_ext/.gitignore
+0 −45 docs/sphinx/_ext/edit_on_github.py
+0 −0 docs/sphinx/_static/.gitignore
+0 −8 docs/sphinx/_templates/layout.html
+0 −4 docs/sphinx/_templates/pagetoc.html
+0 −15 docs/sphinx/_templates/sourcelink.html
+0 −15 docs/sphinx/assembly.xml
+0 −367 docs/sphinx/conf.py
+0 −212 docs/sphinx/developers/6d-7d-and-8d-storage.rst
+0 −170 docs/sphinx/developers/compression.rst
+0 −280 docs/sphinx/developers/filter-and-filterset.rst
+0 −86 docs/sphinx/developers/id-and-lsid.rst
+0 −130 docs/sphinx/developers/index.rst
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+0 −128 docs/sphinx/developers/legacy/tiled-images.rst
+0 −79 docs/sphinx/developers/model-overview.rst
+0 −257 docs/sphinx/developers/ome-units.rst
+0 −138 docs/sphinx/developers/roi.rst
+0 −15 docs/sphinx/developers/sample-files.rst
+0 −250 docs/sphinx/developers/screen-plate-well.rst
+0 −37 docs/sphinx/developers/structured-annotations.rst
+0 −439 docs/sphinx/developers/using-ome-xml.rst
+ docs/sphinx/images/FilterSet-Overview.png
+ docs/sphinx/images/OME-schema-table-formatted_final.png
+ docs/sphinx/images/OMEXML.png
+ docs/sphinx/images/Sample2x2Images.png
+ docs/sphinx/images/annotation_points.png
+ docs/sphinx/images/filter_lightpath.png
+ docs/sphinx/images/filter_lightpath_details.png
+ docs/sphinx/images/hcs_structures.png
+ docs/sphinx/images/image_branch.png
+ docs/sphinx/images/image_lightpath.png
+ docs/sphinx/images/instrument_branch.png
+ docs/sphinx/images/instrument_filterset.png
+ docs/sphinx/images/ome-tiff-chart.png
+ docs/sphinx/images/ome-tiff-header.png
+0 −32 docs/sphinx/images/ome.svg
+ docs/sphinx/images/organization.png
+ docs/sphinx/images/ownership.png
+ docs/sphinx/images/roi_branch.png
+ docs/sphinx/images/screen_well_plate.png
+ docs/sphinx/images/shape_types.png
+ docs/sphinx/images/structured_annotation_branch.png
+ docs/sphinx/images/transformations_quality.png
+0 −160 docs/sphinx/index.rst
+0 −144 docs/sphinx/ome-tiff/code.rst
+0 −294 docs/sphinx/ome-tiff/data.rst
+0 −88 docs/sphinx/ome-tiff/file-structure.rst
+0 −74 docs/sphinx/ome-tiff/index.rst
+0 −541 docs/sphinx/ome-tiff/specification.rst
+0 −163 docs/sphinx/ome-tiff/tools.rst
+0 −70 docs/sphinx/ome-xml/index.rst
+0 −42 docs/sphinx/ome-xml/java-library.rst
+0 −27 docs/sphinx/omero-pyramid/index.rst
+0 −165 docs/sphinx/pom.xml
+0 −136 docs/sphinx/schemas/april-2010.rst
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+0 −17 docs/sphinx/specifications/olympus.ome.xml
+0 −1 pom.xml
+0 −1 requirements.txt
2 changes: 1 addition & 1 deletion ome-poi
Submodule ome-poi updated 0 files
2 changes: 1 addition & 1 deletion ome-stubs
Submodule ome-stubs updated 0 files

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