From 178d7393f7ed72d5068a83a9136c3a0ac2d30fc6 Mon Sep 17 00:00:00 2001 From: Snoopy Crime Cop Date: Tue, 22 Aug 2023 00:02:19 +0000 Subject: [PATCH] merge master -Dorg -Ssuccess-only 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/) --- .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..1517e8bb68 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 = 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 diff --git a/ZarrReader b/ZarrReader index d1c62234d6..ff3db9edec 160000 --- a/ZarrReader +++ b/ZarrReader @@ -1 +1 @@ -Subproject commit d1c62234d6572b98c406cc36a36ec573bc3e4b75 +Subproject commit ff3db9edec1033cb5207e6f3b98bcd11eb70d136 diff --git a/bio-formats-documentation b/bio-formats-documentation index ab5e213dbf..ca52b832df 160000 --- a/bio-formats-documentation +++ b/bio-formats-documentation @@ -1 +1 @@ -Subproject commit ab5e213dbf1b5ef9e864ecc2e3a99bc67d83e67c +Subproject commit ca52b832df293ab00fa84f2f79a3341a314b09d1 diff --git a/bio-formats-examples b/bio-formats-examples index 80b39c66ca..8ede06bfe1 160000 --- a/bio-formats-examples +++ b/bio-formats-examples @@ -1 +1 @@ -Subproject commit 80b39c66ca51ed9f1110a61bd3184047f7817bbc +Subproject commit 8ede06bfe10902d343e00a3fafc315c03ebb7406 diff --git a/bioformats b/bioformats index 19d7fb9cbf..1bc09fcdb1 160000 --- a/bioformats +++ b/bioformats @@ -1 +1 @@ -Subproject commit 19d7fb9cbfdc16e65a7dfa556b2143ae17b141c5 +Subproject commit 1bc09fcdb1dced8cd1ef95332fb719c412f9f1ea diff --git a/ome-codecs b/ome-codecs index 5ebe5af4dd..c6ba4ff7c6 160000 --- a/ome-codecs +++ b/ome-codecs @@ -1 +1 @@ -Subproject commit 5ebe5af4ddd28974edc359151509b50a1ee8cd1c +Subproject commit c6ba4ff7c6ba7bd1dc7661dca63757dd639c1344 diff --git a/ome-common-java b/ome-common-java index fe39605087..e0c92e1455 160000 --- a/ome-common-java +++ b/ome-common-java @@ -1 +1 @@ -Subproject commit fe396050878f4f58fd7bef63f1679e0e835cb0e8 +Subproject commit e0c92e14553b226a189f11d1969231e4d3477a77 diff --git a/ome-jai b/ome-jai index 6b7e42168b..8fedc9efe8 160000 --- a/ome-jai +++ b/ome-jai @@ -1 +1 @@ -Subproject commit 6b7e42168be78f07918912ef5966a4a76ae4f9b2 +Subproject commit 8fedc9efe85caafbcf167e960c60c601cbb7375e diff --git a/ome-mdbtools b/ome-mdbtools index cdb35527df..5c1e7dbe5e 160000 --- a/ome-mdbtools +++ b/ome-mdbtools @@ -1 +1 @@ -Subproject commit cdb35527df613b87b844def3c99faafdf1339cac +Subproject commit 5c1e7dbe5e0844cb4733d8c1ce657caa7ca0e3d5 diff --git a/ome-metakit b/ome-metakit index 1bcefaf26a..4573333ee0 160000 --- a/ome-metakit +++ b/ome-metakit @@ -1 +1 @@ -Subproject commit 1bcefaf26a0d461ab64ea198406a7612cba1d537 +Subproject commit 4573333ee0505bf0ee7fae5da34fa401727f5238 diff --git a/ome-model b/ome-model index fbe39c099b..6ede83c8d0 160000 --- a/ome-model +++ b/ome-model @@ -1 +1 @@ -Subproject commit fbe39c099b4b3ab02ccfa93c0af6bcf84515a564 +Subproject commit 6ede83c8d0c4263a6e82d50abb88cba251d5d774 diff --git a/ome-poi b/ome-poi index d266569015..f827e1025a 160000 --- a/ome-poi +++ b/ome-poi @@ -1 +1 @@ -Subproject commit d2665690157e0e571f7f1eacb9688ca186000827 +Subproject commit f827e1025a49987b60df975bac29123957151521 diff --git a/ome-stubs b/ome-stubs index a17529ef1a..11ac69aed6 160000 --- a/ome-stubs +++ b/ome-stubs @@ -1 +1 @@ -Subproject commit a17529ef1a31bd7a66231767f57cb14b2040a0dc +Subproject commit 11ac69aed6a48b534b03b1ec516447dcc9dbc45a