From 57bf1a572e7daca38e42e9fc652c49af66457733 Mon Sep 17 00:00:00 2001 From: Snoopy Crime Cop Date: Sat, 16 Dec 2023 23:03:03 +0000 Subject: [PATCH] merge master -Dnone -Ihotfix -Ssuccess-only Repository: ome/bio-formats-build Excluded PRs: - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' (user: dependabot[bot]) - PR 469 jburel 'install sphinx' (user: jburel) Already up-to-date. Repository: ome/ZarrReader Excluded PRs: - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' (user: dgault) - PR 73 dgault 'Update ReadMe and Change Log' (user: dgault) - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' (user: sbesson) - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault) Already up-to-date. Repository: ome/bio-formats-documentation Excluded PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' (user: dgault) Updating f4a4045..45b07e2 Previously merged: - PR 356 melissalinkert 'Change ome-codecs version from 1.1.0 to 1.0.1' - PR 354 melissalinkert 'Update to 7.2.0-SNAPSHOT' - PR 353 melissalinkert 'Bump versions to 7.1.0' - PR 350 dgault 'Add link to Bioformats.NET6' - PR 352 dgault 'Add version history for Bio-Formats 7.1.0' - PR 349 dgault '7.1.0 API updates' - PR 343 dgault 'Add bio3d to link check ignore' - PR 351 dgault 'Bump dependencies to latest versions' Repository: ome/bio-formats-examples Excluded PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' (user: dgault) Already up-to-date. Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (user: dgault) - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - 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 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 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 180 joshmoore 'xsd-fu: templates for linkml generation' (user: joshmoore) - 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#1665 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1665/) --- .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 4deea8dc50..65b18c36dc 160000 --- a/ZarrReader +++ b/ZarrReader @@ -1 +1 @@ -Subproject commit 4deea8dc5017678ffb507503c249fb7d3c05802a +Subproject commit 65b18c36dc29066ccff0c0b847926a2faf3fbd43 diff --git a/bio-formats-documentation b/bio-formats-documentation index f4a40455ce..b356d1abf7 160000 --- a/bio-formats-documentation +++ b/bio-formats-documentation @@ -1 +1 @@ -Subproject commit f4a40455ce2f36fd08f8723b56091ce3af542efc +Subproject commit b356d1abf7de9b979a18dedf47eec54c8d502eb3 diff --git a/bio-formats-examples b/bio-formats-examples index 083f617c18..75c31d23b2 160000 --- a/bio-formats-examples +++ b/bio-formats-examples @@ -1 +1 @@ -Subproject commit 083f617c1886fa8244d463a93d5665a8a9235063 +Subproject commit 75c31d23b2ca092a31e1a76798a2c85ff061b8bc diff --git a/bioformats b/bioformats index d566f70845..60b9f13e91 160000 --- a/bioformats +++ b/bioformats @@ -1 +1 @@ -Subproject commit d566f70845be514ab9c88d910ae42ab7a5f0bac0 +Subproject commit 60b9f13e9172a2484f521043d40b27aaabd3be06 diff --git a/ome-codecs b/ome-codecs index 040c8b9850..1986e7c170 160000 --- a/ome-codecs +++ b/ome-codecs @@ -1 +1 @@ -Subproject commit 040c8b985078417ce109d345eb2c446d793c6100 +Subproject commit 1986e7c1703b9f21752b06cf7969dbed3db21031 diff --git a/ome-common-java b/ome-common-java index fa81e2b473..38ecc943e4 160000 --- a/ome-common-java +++ b/ome-common-java @@ -1 +1 @@ -Subproject commit fa81e2b473b1e70fdcd84838b5055f46449d54f5 +Subproject commit 38ecc943e49e3a0fe9a1723520e0fdf456b1293d diff --git a/ome-jai b/ome-jai index 6b7e42168b..cb62de3d51 160000 --- a/ome-jai +++ b/ome-jai @@ -1 +1 @@ -Subproject commit 6b7e42168be78f07918912ef5966a4a76ae4f9b2 +Subproject commit cb62de3d51c01e28655a9dacd2ac642dfdd6c2b8 diff --git a/ome-mdbtools b/ome-mdbtools index cdb35527df..e22ab269d4 160000 --- a/ome-mdbtools +++ b/ome-mdbtools @@ -1 +1 @@ -Subproject commit cdb35527df613b87b844def3c99faafdf1339cac +Subproject commit e22ab269d45a5853cb2fa2f87fbe3448eccca297 diff --git a/ome-metakit b/ome-metakit index 8ead2f6150..79ccdf93bf 160000 --- a/ome-metakit +++ b/ome-metakit @@ -1 +1 @@ -Subproject commit 8ead2f615004b1a01e4d759d63f25b66d623989f +Subproject commit 79ccdf93bf68c47c85b8da8ddbf3619c17ffdbe3 diff --git a/ome-model b/ome-model index 739022fb84..9f7b602f99 160000 --- a/ome-model +++ b/ome-model @@ -1 +1 @@ -Subproject commit 739022fb84f481a88f3eee5938e5e367d569f266 +Subproject commit 9f7b602f99d648da1fc0dbb37fc35d87fb9cbe6d diff --git a/ome-poi b/ome-poi index ba0d5d20f0..e073057cd4 160000 --- a/ome-poi +++ b/ome-poi @@ -1 +1 @@ -Subproject commit ba0d5d20f06786801c40d77e9b91346d485a17c8 +Subproject commit e073057cd4eba0927b887b674ad8c3c1df4c56cf diff --git a/ome-stubs b/ome-stubs index a17529ef1a..24c5722567 160000 --- a/ome-stubs +++ b/ome-stubs @@ -1 +1 @@ -Subproject commit a17529ef1a31bd7a66231767f57cb14b2040a0dc +Subproject commit 24c5722567a0c2605f6f26427768a2160af9919a