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test_bfopen fails with #29

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sbesson opened this issue Jul 23, 2019 · 5 comments · May be fixed by ome/bioformats#4130
Open

test_bfopen fails with #29

sbesson opened this issue Jul 23, 2019 · 5 comments · May be fixed by ome/bioformats#4130

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@sbesson
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sbesson commented Jul 23, 2019

While trying to create a minimal example file to reproduce https://forum.image.sc/t/bio-formats-octave-error-on-bfsave/27504, I realized that the current Travis build is failing - see https://travis-ci.org/ome/bio-formats-octave-docker/builds/545619855.

Populating metadata
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test at line 9 column 1

There are two issues associated with this error:

  • I would have expected the docker run command to fail with a non-zero status code on a failing script rather than a false negative
  • octave_base_value::reshape (): wrong type argument 'octave_java' is thrown when calling bfGetPlane for all recent builds using GNU Octave 4.2 / Bio-Formats 6. The only related report I could find was https://savannah.gnu.org/bugs/?44881. @carandraug: do you have any immediate thoughts on this before we start investigating.
@carandraug
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I would have expected the docker run command to fail with a non-zero status code on a failing script rather than a false negative

I've checked on Octave 4.0 and Octave 6.0 and in both cases returns a non zero return code

$ touch "test&sizeT=3.fake"
$ octave travis_test.m "test&sizeT=3.fake"
[...]
s = 1
v = 6.2.0
FakeReader initializing test&sizeT=3.fake
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test at line 9 column 1
$ echo $?
1

octave_base_value::reshape (): wrong type argument 'octave_java' is thrown when calling bfGetPlane for all recent builds using GNU Octave 4.2 / Bio-Formats 6. The only related report I could find was https://savannah.gnu.org/bugs/?44881.

That issue is unrelated (the issue is about making reshape also work in java arrays and that is something that doesn't even work in Matlab). This error seems to be related to auto boxing/unboxing rules. In Matlab, it looks like I in:

I = javaMethod('makeDataArray2D', 'loci.common.DataTools', plane, ...
    bpp, fp, little, ip.Results.height);

returns a Matlab array of class int8 but in Octave this remains an octave_java object of class byte[][] which is why the switch statement fails. I believe that in Octave, arrays with more than one dimension remain a java object in case they are non-rectangular. This probably needs to be changed in Octave for sake of Matlab compatibility but I don't think there's anyone working in Octave at the moment that quite understands the different conversion rules that would be Matlab compatible.

@sbesson
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sbesson commented Jul 23, 2019 •
edited

@carandraug: thanks for the quick reponse. The base image used for testing Octave is Ubuntu 18.04 which ships GNU Octave 4.2.2

octave@89da10fab560:~$ touch "test&sizeT=3.fake" 
octave@89da10fab560:~$ octave -version
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
GNU Octave, version 4.2.2
Copyright (C) 2018 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/get-involved.html

Read http://www.octave.org/bugs.html to learn how to submit bug reports.
octave@89da10fab560:~$ octave travis_test.m "test&sizeT=3.fake" && echo passed
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
s = 1
v = 6.1.0
FakeReader initializing test&sizeT=3.fake
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test at line 9 column 1
passed
octave@89da10fab560:~$ echo $?
0
octave@89da10fab560:~$ exit

Switching to Ubuntu 16.04 and GNU Octave 4.0.0, I can confirm the status code is returned as non-zero as expected

octave@50c2a3c49946:~$ touch "test&sizeT=3.fake" 
octave@50c2a3c49946:~$ octave --version
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
GNU Octave, version 4.0.0
Copyright (C) 2015 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/get-involved.html

Read http://www.octave.org/bugs.html to learn how to submit bug reports.
octave@50c2a3c49946:~$ octave travis_test.m "test&sizeT=3.fake"
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
s =  1
v = 6.1.0
FakeReader initializing test&sizeT=3.fake
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test.m at line 9 column 1
octave@50c2a3c49946:~$ echo $?
1

This seems related to http://octave.1599824.n4.nabble.com/Octave-s-exit-status-td4680966.html. It looks like the regression was fixed in 6.0 but did not make it into a patch release of Octave 4.2.x.

Thanks also for pointing at the autoboxing behavior. While bisecting changes introduced, I think this is effectively a regression introduced as part of ome/bioformats#3301.

@jburel
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jburel commented Dec 13, 2023

The same problem occurs when testing on docker image Ubuntu 22.04 and octave 6.4.0

@jburel jburel mentioned this issue Dec 13, 2023
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@carandraug
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I've looked at this and it works fine in bioformats 5.9.2 and started to fail in bioformats 6.0.0. @sbesson suggested and I confirm that the issue is a regression introduced in ome/bioformats#3301

It boils down to the description I had above:

This error seems to be related to auto boxing/unboxing rules. In Matlab, it looks like I in:

I = javaMethod('makeDataArray2D', 'loci.common.DataTools', plane, ...
    bpp, fp, little, ip.Results.height);

returns a Matlab array of class int8 but in Octave this remains an octave_java object of class byte[][] which is why the switch statement fails. I believe that in Octave, arrays with more than one dimension remain a java object in case they are non-rectangular. This probably needs to be changed in Octave for sake of Matlab compatibility but I don't think there's anyone working in Octave at the moment that quite understands the different conversion rules that would be Matlab compatible.

I will prepare a pull request.

carandraug added a commit to carandraug/bioformats that referenced this issue Dec 13, 2023
@carandraug
matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bi…
49079c3 
…o-formats-octave-docker#29)

Octave does not autobox multi-dimensional arrays (Matlab does) so we
can't use makeDataArray2D.  Instead, use makeDataArray to get a 1D
array and reshape it.  This commit partially reverts 3aa468e (see
ome#3301) for Octave only, so the data copy is back but for
Octave only.
@carandraug carandraug linked a pull request Dec 13, 2023 that will close this issue
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@carandraug
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I will prepare a pull request.

Done in ome/bioformats#4130

snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 13, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
6c96170 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - 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)
Updating 996da68..d566f70
Previously merged:
  - PR 4129 melissalinkert 'Bump version to 7.2.0-SNAPSHOT'
  - PR 4128 melissalinkert 'Update version numbers to 7.1.0'
  - PR 4057 melissalinkert 'Add CodecOptions.disableChromaSubsampling'
  - PR 4126 dgault 'Bump dependency versions'

Generated by BIOFORMATS-push#1662 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1662/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 13, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
b9adcb2 
Repository: ome/bio-formats-build
Excluded PRs:
  - PR 552 dependabot[bot] 'Bump bioformats from `996da68` to `d566f70`' (user: dependabot[bot])
  - PR 551 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `a291695`' (user: dependabot[bot])
  - PR 550 dependabot[bot] 'Bump ZarrReader from `1d18bbc` to `4deea8d`' (user: dependabot[bot])
  - PR 549 dependabot[bot] 'Bump bio-formats-examples from `6218db5` to `083f617`' (user: dependabot[bot])
  - PR 469 jburel 'install sphinx' (user: jburel)
Already up-to-date.

Repository: ome/ZarrReader
Excluded PRs:
  - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' (user: sbesson)
  - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault)
Updating 1d18bbc..4deea8d
Previously merged:
  - PR 70 dgault 'Bump version to 0.4.1-SNAPSHOT'

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)
Updating 6218db5..083f617
Previously merged:
  - PR 121 sbesson 'Bump version to 7.2.0-SNAPSHOT'
  - PR 120 sbesson 'Bio-Formats 7.1.0'
  - PR 119 sbesson 'Update OME artifactory repository to deploy to ome.releases'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - 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)
Updating 996da68..d566f70
Previously merged:
  - PR 4129 melissalinkert 'Bump version to 7.2.0-SNAPSHOT'
  - PR 4128 melissalinkert 'Update version numbers to 7.1.0'
  - PR 4057 melissalinkert 'Add CodecOptions.disableChromaSubsampling'
  - PR 4126 dgault 'Bump dependency versions'

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#1662 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1662/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 14, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
8741151 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 14, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
7ec9e7c 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

Generated by BIOFORMATS-push#713 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/713/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 14, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
2928a4b 
Repository: ome/bio-formats-build
Already up-to-date.

Merged PRs:
  - PR 469 jburel 'install sphinx'
  - PR 549 dependabot[bot] 'Bump bio-formats-examples from `6218db5` to `083f617`'
  - PR 550 dependabot[bot] 'Bump ZarrReader from `1d18bbc` to `4deea8d`'
  - PR 552 dependabot[bot] 'Bump bioformats from `996da68` to `d566f70`'
  - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up-to-date.

Merged PRs:
  - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0'

Repository: ome/bio-formats-documentation
Already up-to-date.

Merged PRs:
  - PR 355 dgault 'Adding checkerframework.org to link check ignore'

Repository: ome/bio-formats-examples
Already up-to-date.

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

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

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.

Repository: ome/ome-common-java
Excluded PRs:
  - 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.

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' (stage: draft)
Already up-to-date.

Conflicting PRs (not included):
  - 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#713 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/713/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 14, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
2e64431 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - 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.

Generated by BIOFORMATS-push#1663 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1663/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 14, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
03031df 
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 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#1663 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1663/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 15, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
5ec750c 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 15, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
f8dffdc 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

Generated by BIOFORMATS-push#714 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/714/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 15, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
25b23e1 
Repository: ome/bio-formats-build
Already up-to-date.

Merged PRs:
  - PR 469 jburel 'install sphinx'
  - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up-to-date.

Merged PRs:
  - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions'

Repository: ome/bio-formats-documentation
Already up-to-date.

Merged PRs:
  - PR 355 dgault 'Adding checkerframework.org to link check ignore'

Repository: ome/bio-formats-examples
Already up-to-date.

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

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

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.

Repository: ome/ome-common-java
Excluded PRs:
  - 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.

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' (stage: draft)
Already up-to-date.

Conflicting PRs (not included):
  - 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#714 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/714/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 15, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
954d84a 
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.

Generated by BIOFORMATS-push#1664 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1664/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 15, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
3fe1151 
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#1664 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1664/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 16, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
e67ae3e 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 16, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
ed8bc77 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

Generated by BIOFORMATS-push#715 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/715/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 16, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
22e54d4 
Repository: ome/bio-formats-build
Already up-to-date.

Merged PRs:
  - PR 469 jburel 'install sphinx'
  - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up-to-date.

Merged PRs:
  - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0'
  - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions'

Repository: ome/bio-formats-documentation
Already up-to-date.

Merged PRs:
  - PR 355 dgault 'Adding checkerframework.org to link check ignore'

Repository: ome/bio-formats-examples
Already up-to-date.

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

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

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.

Repository: ome/ome-common-java
Excluded PRs:
  - 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.

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' (stage: draft)
Already up-to-date.

Conflicting PRs (not included):
  - 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#715 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/715/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 16, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
60b9f13 
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.

Generated by BIOFORMATS-push#1665 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1665/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 16, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
57bf1a5 
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/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 17, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
22d99c6 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 17, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
ad76c50 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

Generated by BIOFORMATS-push#716 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/716/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 17, 2023
@snoopycrimecop
merge master -Dorg -Ssuccess-only
75ccad1 
Repository: ome/bio-formats-build
Already up-to-date.

Merged PRs:
  - PR 469 jburel 'install sphinx'
  - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up-to-date.

Merged PRs:
  - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0'
  - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions'

Repository: ome/bio-formats-documentation
Already up-to-date.

Merged PRs:
  - PR 355 dgault 'Adding checkerframework.org to link check ignore'

Repository: ome/bio-formats-examples
Already up-to-date.

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

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude)
  - 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 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' (stage: draft)
  - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - 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 4061 CGDogan 'Don't fail on non-4:4:4 JPEG'
  - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes'
  - PR 4112 melissalinkert 'Imaris HDF: populate channel names'
  - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'

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.

Repository: ome/ome-common-java
Excluded PRs:
  - 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.

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' (stage: draft)
Already up-to-date.

Conflicting PRs (not included):
  - 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#716 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/716/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Dec 17, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
c267f8c 
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.

Generated by BIOFORMATS-push#1666 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1666/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Dec 17, 2023
@snoopycrimecop
merge master -Dnone -Ihotfix -Ssuccess-only
ddf68b2 
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#1666 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1666/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue May 31, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
693dea2 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue May 31, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
08437a8 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#22 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/22/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue May 31, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
7633d10 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#22 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/22/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue May 31, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
5962d3a 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue May 31, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
694f0b7 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#86 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/86/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue May 31, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
78f0280 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#86 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/86/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 1, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
f336f25 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 1, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
89d59c0 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#23 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/23/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 1, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
4eeb402 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#23 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/23/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 1, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
d867ac6 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 1, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
4c87ef9 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#87 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/87/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 1, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
e017004 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#87 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/87/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 2, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
c73dfd0 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 2, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
920e2f0 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#24 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/24/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 2, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
66a6384 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#24 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/24/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 2, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
2a26223 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 2, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
524563b 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#88 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/88/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 2, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
5a175a6 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#88 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/88/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 3, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
6a2f81f 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 3, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
3135bb6 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#25 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/25/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 3, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
ada6c6a 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'
  - PR 39 dependabot[bot] 'Bump io.airlift:aircompressor from 0.21 to 0.27'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#25 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/25/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 3, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
646fd14 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 3, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
e1a9279 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#89 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/89/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 3, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
5277c9f 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'
  - PR 39 dependabot[bot] 'Bump io.airlift:aircompressor from 0.21 to 0.27'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Merged PRs:
  - PR 191 pwalczysko 'Add Telight to list of ome-tiff cf. mailing list'

Conflicting PRs (not included):
  - 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#89 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/89/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 4, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
4d88a41 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 4, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
272311b 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#26 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/26/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 4, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
54912f9 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'
  - PR 610 dependabot[bot] 'Bump ome-model from `db24e3a` to `be5b189`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'
  - PR 39 dependabot[bot] 'Bump io.airlift:aircompressor from 0.21 to 0.27'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Conflicting PRs (not included):
  - 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#26 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/26/)
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 4, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only: PR 4130 (matlab/bfGetPlane.m: avoi…
21a63a2 
…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))
snoopycrimecop added a commit to snoopycrimecop/bioformats that referenced this issue Jun 4, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
f75917a 
Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes ome#4184'

Generated by BIOFORMATS-push#90 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/90/)
snoopycrimecop added a commit to snoopycrimecop/bio-formats-build that referenced this issue Jun 4, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
697d456 
Repository: ome/bio-formats-build
Already up to date.

Merged PRs:
  - PR 604 dependabot[bot] 'Bump bio-formats-examples from `74d4def` to `9955ace`'
  - PR 608 dependabot[bot] 'Bump bioformats from `682bc7e` to `bf2c462`'
  - PR 609 dependabot[bot] 'Bump bio-formats-documentation from `afd4c11` to `7a2cfff`'
  - PR 610 dependabot[bot] 'Bump ome-model from `db24e3a` to `be5b189`'

Repository: ome/ZarrReader
Excluded PRs:
  - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Already up to date.

Merged PRs:
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Repository: ome/bio-formats-documentation
Already up to date.

Repository: ome/bio-formats-examples
Already up to date.

Merged PRs:
  - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
  - PR 127 jburel 'Matlab Examples'
  - PR 128 sbesson 'Relicense Bio-Formats examples under BSD 2-clause'

Repository: openmicroscopy/bioformats
Excluded PRs:
  - PR 4190 melissalinkert 'Extend precompressed support to read DICOM and write TIFF/OME-TIFF' (stage: draft)
  - PR 4181 melissalinkert 'Add support for reading compressed NDPI tiles' (label: exclude)
  - PR 4180 melissalinkert 'Columbus: update to use micrometers instead of `reference frame` for positions' (label: exclude)
  - PR 4172 sbesson 'testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list' (stage: draft)
  - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
  - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
  - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
  - 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' (stage: draft)
  - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
  - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
  - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
  - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
Already up to date.

Merged PRs:
  - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
  - PR 4188 melissalinkert 'Fix a few string comparisons, fixes #4184'

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

Merged PRs:
  - PR 37 melissalinkert 'JPEG: warn if quality is outside [0.25, 1.0]'
  - PR 39 dependabot[bot] 'Bump io.airlift:aircompressor from 0.21 to 0.27'

Repository: ome/ome-common-java
Excluded PRs:
  - 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' (stage: draft)
Already up to date.

Conflicting PRs (not included):
  - 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#90 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/90/)
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@carandraug @jburel @sbesson