From d9cf49ab07b7c296a06b9ed9f2b95f47d7ac7f0f Mon Sep 17 00:00:00 2001 From: Snoopy Crime Cop Date: Mon, 28 Aug 2023 23:06:38 +0000 Subject: [PATCH] merge master -Dnone -Ihotfix -Ssuccess-only Repository: ome/bio-formats-build Excluded PRs: - PR 501 dependabot[bot] 'Bump ZarrReader from `d1c6223` to `2d75020`' (user: dependabot[bot]) - PR 469 jburel 'install sphinx' (user: jburel) Already up-to-date. Repository: ome/ZarrReader Excluded PRs: - PR 58 dgault 'Add new option to list pixels in getUsedFiles' (user: dgault) - PR 53 dgault 'Reorder group keys' (user: dgault) - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault) Updating d1c6223..2d75020 Previously merged: - PR 59 jburel 'Actions update' Repository: ome/bio-formats-documentation Excluded PRs: - PR 330 jburel 'update uri' (user: jburel) Already up-to-date. Repository: ome/bio-formats-examples Excluded PRs: - PR 105 sbesson 'Bump logback dependency to 1.3.5' (user: sbesson) - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' (user: dgault) Already up-to-date. Repository: openmicroscopy/bioformats Excluded PRs: - PR 4090 CGDogan 'Throw error when cannot load library' (user: CGDogan) - PR 4088 melissalinkert 'CZI: unify channel color parsing' (user: melissalinkert) - PR 4085 melissalinkert 'CV7000 improvements' (user: melissalinkert) - PR 4083 melissalinkert 'NDPI: correct for potential integer overflow in stored restart marker tag' (user: melissalinkert) - PR 4081 melissalinkert 'SVS: fix a variety of small issues' (user: melissalinkert) - PR 4080 melissalinkert 'Exporter plugin: remove any extra Channel elements' (user: melissalinkert) - PR 4079 melissalinkert 'Leica LIF: throw a nicer exception if no images are found' (user: melissalinkert) - PR 4078 melissalinkert 'OIR: fix off-by-one in XML block reading' (user: melissalinkert) - PR 4077 melissalinkert 'TillVision: fix some metadata parsing and .pst detection issues' (user: melissalinkert) - PR 4076 melissalinkert 'VSI: fix uncompressed BGR data' (user: melissalinkert) - PR 4075 melissalinkert 'Photoshop TIFF: fix plane reading with memoization' (user: melissalinkert) - PR 4074 melissalinkert 'Gel: check IFD count in isThisType' (user: melissalinkert) - PR 4073 melissalinkert 'OME-TIFF: optionally fail fast if an invalid file is encountered' (user: melissalinkert) - PR 4072 melissalinkert 'Ventana: fix tile arithmetic for smallest resolutions' (user: melissalinkert) - PR 4071 melissalinkert 'IVision: improve version and data type checks in isThisType' (user: melissalinkert) - PR 4070 melissalinkert 'Gatan DM3: be more defensive in parsing acquisition mode' (user: melissalinkert) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4059 CGDogan 'TiffSaver: produce valid 4-channel RGBA images' (user: CGDogan) - PR 4057 melissalinkert 'Add CodecOptions.disableChromaSubsampling' (user: melissalinkert) - PR 4051 CGDogan 'fix aplreader throwing nullptrexception' (user: CGDogan) - PR 4016 melissalinkert 'Add API and DICOM-specific implementations for providing supplemental metadata during conversion' (user: melissalinkert) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3992 melissalinkert 'Allow reading and writing compressed tiles' (user: melissalinkert) - PR 3956 sbesson 'Bump sl4j-api to 2.x' (user: sbesson) - PR 3939 dgault 'ImagePlusReader: handle IndexColorModel' (user: dgault) - PR 3902 melissalinkert 'LSID validation' (user: melissalinkert) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Repository: ome/ome-codecs Excluded PRs: - PR 29 iwbh15 'Disable chroma subsampling in JPEGCodec' (user: iwbh15) - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (user: dgault) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 83 CGDogan 'Fix Lurawave debug error being printed' (user: CGDogan) - PR 82 melissalinkert 'URLHandle: fall back to resetting stream if resetting to a mark fails' (user: melissalinkert) - PR 73 sbesson 'Bump sl4j-api to 2.x' (user: sbesson) - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. 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 Excluded PRs: - PR 174 jburel 'Remove docs' (user: jburel) Already up-to-date. Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#1555 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1555/) --- .gitmodules | 48 +++++++++++++++++++-------------------- ZarrReader | 2 +- bio-formats-documentation | 2 +- bio-formats-examples | 2 +- bioformats | 2 +- ome-codecs | 2 +- ome-common-java | 2 +- ome-jai | 2 +- ome-mdbtools | 2 +- ome-metakit | 2 +- ome-model | 2 +- ome-poi | 2 +- ome-stubs | 2 +- 13 files changed, 36 insertions(+), 36 deletions(-) diff --git a/.gitmodules b/.gitmodules index 2ba40ae34d..c49a5b1e43 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,48 +1,48 @@ [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 = latest_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 = latest_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 = latest_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 = latest_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 = latest_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 = latest_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 = latest_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 = latest_ci [submodule "bioformats"] path = bioformats - url = https://github.com/openmicroscopy/bioformats.git - branch = develop + url = https://github.com/snoopycrimecop/bioformats.git + branch = latest_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 = latest_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 = latest_ci [submodule "ZarrReader"] path = ZarrReader - url = https://github.com/ome/ZarrReader.git - branch = main + url = https://github.com/snoopycrimecop/ZarrReader.git + branch = latest_ci diff --git a/ZarrReader b/ZarrReader index d1c62234d6..b391da9196 160000 --- a/ZarrReader +++ b/ZarrReader @@ -1 +1 @@ -Subproject commit d1c62234d6572b98c406cc36a36ec573bc3e4b75 +Subproject commit b391da91964ce51050f891f8ecd4b8b5e39671bf diff --git a/bio-formats-documentation b/bio-formats-documentation index 53190ff32e..5e95edab9b 160000 --- a/bio-formats-documentation +++ b/bio-formats-documentation @@ -1 +1 @@ -Subproject commit 53190ff32e050ea049947cbd269b105656cb75d3 +Subproject commit 5e95edab9bf5d0d5d363f9dd8be57188ebc99881 diff --git a/bio-formats-examples b/bio-formats-examples index 80b39c66ca..5a4b9268e5 160000 --- a/bio-formats-examples +++ b/bio-formats-examples @@ -1 +1 @@ -Subproject commit 80b39c66ca51ed9f1110a61bd3184047f7817bbc +Subproject commit 5a4b9268e503935ff9b34cce6c5aaf65e8cb20ff diff --git a/bioformats b/bioformats index 19d7fb9cbf..1f9f152e8c 160000 --- a/bioformats +++ b/bioformats @@ -1 +1 @@ -Subproject commit 19d7fb9cbfdc16e65a7dfa556b2143ae17b141c5 +Subproject commit 1f9f152e8cbb72635f50643ba2c45cc61dcdc763 diff --git a/ome-codecs b/ome-codecs index 5ebe5af4dd..0777526a23 160000 --- a/ome-codecs +++ b/ome-codecs @@ -1 +1 @@ -Subproject commit 5ebe5af4ddd28974edc359151509b50a1ee8cd1c +Subproject commit 0777526a233f22938f40d2ca3aa8e920fa97f55d diff --git a/ome-common-java b/ome-common-java index fe39605087..86c01190d2 160000 --- a/ome-common-java +++ b/ome-common-java @@ -1 +1 @@ -Subproject commit fe396050878f4f58fd7bef63f1679e0e835cb0e8 +Subproject commit 86c01190d225d8b4a5e94a8cddffb0714b38c94f diff --git a/ome-jai b/ome-jai index 6b7e42168b..b9cf828164 160000 --- a/ome-jai +++ b/ome-jai @@ -1 +1 @@ -Subproject commit 6b7e42168be78f07918912ef5966a4a76ae4f9b2 +Subproject commit b9cf828164ada14f9377344d9d38a0ff330e4b4d diff --git a/ome-mdbtools b/ome-mdbtools index cdb35527df..4fb9efbae0 160000 --- a/ome-mdbtools +++ b/ome-mdbtools @@ -1 +1 @@ -Subproject commit cdb35527df613b87b844def3c99faafdf1339cac +Subproject commit 4fb9efbae092b3abc4effaa1375eb6e6d2f51357 diff --git a/ome-metakit b/ome-metakit index 1bcefaf26a..d21ded7919 160000 --- a/ome-metakit +++ b/ome-metakit @@ -1 +1 @@ -Subproject commit 1bcefaf26a0d461ab64ea198406a7612cba1d537 +Subproject commit d21ded7919198bec880115a0a3a958c96686e79b diff --git a/ome-model b/ome-model index fbe39c099b..adbf01eb32 160000 --- a/ome-model +++ b/ome-model @@ -1 +1 @@ -Subproject commit fbe39c099b4b3ab02ccfa93c0af6bcf84515a564 +Subproject commit adbf01eb32b39e2c3aa04ff676c43b8c3ca3cb1a diff --git a/ome-poi b/ome-poi index d266569015..8bd9611615 160000 --- a/ome-poi +++ b/ome-poi @@ -1 +1 @@ -Subproject commit d2665690157e0e571f7f1eacb9688ca186000827 +Subproject commit 8bd9611615b255e3d13379c4f53e714abbe1a9a1 diff --git a/ome-stubs b/ome-stubs index a17529ef1a..e954d82b66 160000 --- a/ome-stubs +++ b/ome-stubs @@ -1 +1 @@ -Subproject commit a17529ef1a31bd7a66231767f57cb14b2040a0dc +Subproject commit e954d82b66b0e5e006d9d843edf028f1ac2c0a0a