Commit
4b599686d790b3d7b8b71eef126d04ebd335c3fd
by snoopycrimecopmerge master -Dorg -Ssuccess-only
Repository: ome/bio-formats-build
Already up to date.
Repository: ome/ZarrReader
Excluded PRs:
- PR 113 dominikl 'Zarr v3' (stage: draft)
- PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31d6d95..5f3faa4
Previously merged:
- PR 111 Tom-TBT 'Fixed typo in README env var name to set'
Repository: ome/bio-formats-documentation
Updating db99c10d..4c66e7eb
Previously merged:
- PR 455 melissalinkert 'Add TFCYTO page'
- PR 454 melissalinkert 'Release notes for 8.4.0'
- PR 453 pwalczysko 'Fix links'
- PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications'
- PR 450 melissalinkert 'Update a couple of outdated lines in about page'
- PR 446 sbesson 'Add labelPlanes to the list of flags for fake images'
- PR 445 melissalinkert 'Update ome-common to 6.1.1'
- PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16'
- PR 442 will-moore 'Link to Receipt of Sample Data'
- PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck'
- PR 441 melissalinkert 'Update external readers page based upon feedback'
- PR 439 melissalinkert 'Start describing external reader usage'
- PR 438 will-moore 'Fix netcdf-java links'
- PR 437 pwalczysko 'Nis elements and cibc-datasets'
- PR 436 pwalczysko 'Replace broken link in lemkesoft with working one'
- PR 435 pwalczysko 'Replace nikoninstruments link with redirect'
- PR 434 sbesson 'Add format page for Zeiss XRM format'
- PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release'
- PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0'
- PR 431 pwalczysko 'Fix limited javadoc syntax'
- PR 430 pwalczysko 'Fix sourceforge'
- PR 426 jburel 'Update EMAN2 URL'
- PR 427 jburel 'Checking linkcheck config'
- PR 422 melissalinkert 'Add page for JDCE'
- PR 425 melissalinkert 'Release notes for 8.2.0'
- PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link'
- PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki'
- PR 418 sbesson 'Update MATLAB documentation for colormap return value'
- PR 421 dominikl 'Exclude merckmillipore.com from link check'
Merged PRs:
- PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25'
Repository: ome/bio-formats-examples
Updating 3aa7013..0d488b4
Previously merged:
- PR 136 melissalinkert 'Add precompressed tile writing example'
- PR 137 melissalinkert 'Fix output path for in-memory writing test'
- PR 135 melissalinkert 'Bump logback version to 1.3.16'
- PR 134 sbesson 'POM: cleanup outdated metadata'
Repository: openmicroscopy/bioformats
Excluded PRs:
- PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen)
- PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft)
- PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft)
- PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
- PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
Updating 3f70394503..eb8fd308b0
Previously merged:
- PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl'
- PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2'
- PR 4392 melissalinkert 'A few more ND2 dimension fixes'
- PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`'
- PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins'
- PR 4391 melissalinkert 'Add lens IDs 18113 and 18114'
- PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T'
- PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions'
- PR 4388 melissalinkert 'Update to CodeQL v4'
- PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions'
- PR 4384 melissalinkert 'Update ome-common to 6.1.1'
- PR 4383 melissalinkert 'Bump logback version to 1.3.16'
- PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions'
- PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers'
- PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues'
- PR 4374 melissalinkert 'CellH5: reduce memory usage'
- PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense'
- PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.'
- PR 4360 melissalinkert 'Fix several OIR issues'
- PR 4365 melissalinkert 'Fix array sizes in Octave'
- PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML'
- PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files'
- PR 4361 melissalinkert 'Remove unused detector linking logic'
- PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data'
- PR 4359 sbesson 'Report workflow: delay the first execution by 1 h'
- PR 4355 zacsimile 'Fix DCIMG indexing over multiple files'
- PR 4350 sbesson 'Build report workflow: fix failure when no tests failed'
- PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes'
- PR 4353 melissalinkert 'Fix tag encoding for LEO files'
- PR 4348 sbesson 'FakeReader: link instrument to all images'
- PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator'
- PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes'
- PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore'
- PR 4347 melissalinkert 'Fix Metamorph .nd encoding'
- PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series'
- PR 4307 jburel 'Build report'
- PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3'
- PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing'
- PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match'
- PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER'
- PR 4338 sbesson 'org.openmicroscopy component updates'
- PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java'
- PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection'
- PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF'
- PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues'
- PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels'
- PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation'
- PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support'
- PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image'
- PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed'
- PR 4327 melissalinkert 'Check modulo values in repository tests'
- PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy'
- PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory'
- PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.'
- PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data'
- PR 4311 sbesson 'Review declaration of Maven Scijava as a repository'
- PR 4284 ptahmose 'fix for garbled images with CZIs'
- PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending'
- PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID'
- PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE'
- PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions'
- PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles'
- PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs'
- PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000'
- PR 4303 melissalinkert 'Fix Unidata repository URLs'
Merged PRs:
- PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object'
- PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped'
- PR 4362 ngladitz 'OBF: Support complex data stacks'
- PR 4373 melissalinkert 'CZI: ignore plate information if not activated'
- PR 4379 melissalinkert 'DICOM: fix width of values with DS VR'
- PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3'
- PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane'
- PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes'
Repository: ome/ome-codecs
Updating fab1a01..1f655e6
Previously merged:
- PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags'
- PR 43 melissalinkert 'Update to ome-common 6.1.1'
- PR 42 sbesson 'Update publication build system to use Central Portal'
Repository: ome/ome-common-java
Excluded PRs:
- PR 109 dominikl 'Remove jackson dependency' (stage: draft)
- PR 108 dominikl 'Remove S3 handling' (stage: draft)
Updating 2cb0b7b..fae511d
Previously merged:
- PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services'
- PR 107 sbesson 'Add GitHub release creation to Maven workflow'
- PR 106 melissalinkert 'Bump logback-classic to 1.3.16'
- PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name'
- PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal'
- PR 99 melissalinkert 'Fix type of skipped bytes counter'
- PR 98 sbesson 'Add CodeQL workflow running on push and pull request events'
Repository: ome/ome-jai
Updating e70c2ab..9f1b4ef
Previously merged:
- PR 8 sbesson 'Update publication build system to use Central Portal '
- PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction'
Repository: ome/ome-mdbtools
Updating 9193930..9c3c3e2
Previously merged:
- PR 14 sbesson 'Update publication system to use Central Portal'
Repository: ome/ome-metakit
Updating 1ba6cf1..55abb77
Previously merged:
- PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags'
- PR 30 melissalinkert 'Update ome-common to 6.1.1'
- PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16'
- PR 27 sbesson 'Update publication build system to use Central Portal'
Merged PRs:
- PR 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25'
Repository: ome/ome-model
Updating 3d70a1f9..142fd2ec
Previously merged:
- PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references'
- PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references'
- PR 225 melissalinkert 'Update ome-common to 6.1.1'
- PR 223 melissalinkert 'Bump logback-classic to 1.3.16'
- PR 224 sbesson 'Add release step to GitHub Maven workflow'
- PR 222 sbesson 'Update publication build system to use Central Portal'
- PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo'
Repository: ome/ome-poi
Updating da3a5f3..d727828
Previously merged:
- PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags'
- PR 20 melissalinkert 'Update to ome-common 6.1.1'
- PR 19 sbesson 'Update publication system to use Central Portal'
Repository: ome/ome-stubs
Updating 1559997..6a87342
Previously merged:
- PR 12 sbesson 'Update publication build system to use Central Portal'
Generated by BIOFORMATS-push#43 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/43/)
