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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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[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 |
Submodule ZarrReader
updated
2 files
+2 −4 | .github/workflows/maven.yml | |
+132 −6 | src/loci/formats/in/ZarrReader.java |
Submodule bioformats
updated
25 files
Submodule ome-codecs
updated
2 files
+5 −0 | src/main/java/ome/codecs/CodecOptions.java | |
+79 −7 | src/main/java/ome/codecs/JPEGCodec.java |
Submodule ome-model
updated
83 files