pombast.toml

[common]
default-java-version = 8
repositories = ["scijava.public=https://maven.scijava.org/content/groups/public"]
settings = "pombast/settings.xml"

[status]
output = "target/pombast/index.html"
rules = "rules.xml"
header = "pombast/header-status.html"
footer = "pombast/footer-status.html"
nexus-base = "https://maven.scijava.org"
cuttable = [
  "de.nanoimaging:*",
  "fr.inra.ijpb:*",
  "io.scif:*",
  "jitk:*",
  "mpicbg:*",
  "net.imagej:*",
  "net.imglib2:*",
  "net.preibisch:*",
  "org.bonej:*",
  "org.embl.mobie:*",
  "org.janelia*:*",
  "org.morphonets:*",
  "org.scijava:*",
  "sc.fiji:*",
]

[team]
output = "target/pombast/team.html"
header = "pombast/header-team.html"
footer = "pombast/footer-team.html"
includes = [
  "de.nanoimaging:*",
  "fr.inra.ijpb:*",
  "io.scif:*",
  "jitk:*",
  "mpicbg:*",
  "net.imagej:*",
  "net.imglib2:*",
  "net.preibisch:*",
  "org.bonej:*",
  "org.embl.mobie:*",
  "org.janelia*:*",
  "org.morphonets:*",
  "org.scijava:*",
  "sc.fiji:*",
]

[badges]
output = "target/pombast/badges.json"
includes = [
  "de.nanoimaging:*",
  "fr.inra.ijpb:*",
  "io.scif:*",
  "jitk:*",
  "mpicbg:*",
  "net.imagej:*",
  "net.imglib2:*",
  "net.preibisch:*",
  "ome:*",
  "org.bonej:*",
  "org.embl.mobie:*",
  "org.janelia*:*",
  "org.morphonets:*",
  "org.openmicroscopy:*",
  "org.scijava:*",
  "sc.fiji:*",
]

[javadoc]
output = "target/pombast/javadoc"
redirect-format = "rewritemap"

# JavaFX javadoc that javadoc.scijava.org serves at /JavaFX{major}/, for each
# JavaFX LTS plus the versions SciJava ships (19 here, 23 in Fiji), whether or
# not this BOM manages them. Each javafx-* javadoc JAR holds all of JavaFX, so
# javafx-base suffices.
extras = [
  "org.openjfx:javafx-base:11.0.2",
  "org.openjfx:javafx-base:17.0.21",
  "org.openjfx:javafx-base:19.0.2.1",
  "org.openjfx:javafx-base:21.0.13",
  "org.openjfx:javafx-base:23.0.2",
  "org.openjfx:javafx-base:25.0.5",
]

# Named unions over parts of the BOM, served at
# /org.scijava/pom-scijava/{version}/{name}/: a -link target and landing page
# per project, and the scope that project's legacy deep links resolve in.
[javadoc.unions]
"bio-formats" = ["ome:*", "org.openmicroscopy:*"]
"io.scif" = ["io.scif:*"]
"net.imagej" = ["net.imagej:*"]
"net.imglib2" = ["net.imglib2:*"]
"org.bonej" = ["org.bonej:*"]
"org.embl.mobie" = ["org.embl.mobie:*"]
"org.openjfx" = ["org.openjfx:*"]
"org.scijava" = ["org.scijava:*"]
"sc.fiji" = ["sc.fiji:*"]

[melt]
# Some managed components require Java 21+, so we melt with that Java
# version. But pom-scijava sets scijava.jvm.version to 11 by default.
# So beyond just using OpenJDK 21 to run Maven, we also need to set the
# scijava.jvm.version property to target the right bytecode version.
# Otherwise, the enforcer complains about any Java libraries targeting >11.
java-version = 21
properties = { "scijava.jvm.version" = "21" }

template = "pombast/melt-template.xml"
excludes = [
  # TEMP: Exclude org.bytedeco:hdf5 until cisd:jhdf5 is gone.
  "org.bytedeco:hdf5",
  # NB: The following artifacts have messy dependency trees.
  # Too many problems to test as part of the melt action.
  # See WARNING block in pom-scijava's pom.xml for details.
  "net.imagej:imagej-server",
  "org.apache.spark:spark-core_2.11",
  # NB: Skip alternate flavors of other managed components.
  "org.jogamp.gluegen:gluegen",     # uberjar flavor of gluegen-rt
  "org.jogamp.jogl:jogl-all-noawt", # slimmed down flavor of jogl-all
  # NB: All the SWT platform JARs have the same classes.
  # The current platform will be brought in transitively.
  "org.eclipse.swt:org.eclipse.swt.cocoa.macosx",
  "org.eclipse.swt:org.eclipse.swt.cocoa.macosx.x86_64",
  "org.eclipse.swt:org.eclipse.swt.gtk.aix.ppc",
  "org.eclipse.swt:org.eclipse.swt.gtk.aix.ppc64",
  "org.eclipse.swt:org.eclipse.swt.gtk.hpux.ia64",
  "org.eclipse.swt:org.eclipse.swt.gtk.linux.ppc",
  "org.eclipse.swt:org.eclipse.swt.gtk.linux.ppc64",
  "org.eclipse.swt:org.eclipse.swt.gtk.linux.s390",
  "org.eclipse.swt:org.eclipse.swt.gtk.linux.s390x",
  "org.eclipse.swt:org.eclipse.swt.gtk.linux.x86",
  "org.eclipse.swt:org.eclipse.swt.gtk.linux.x86_64",
  "org.eclipse.swt:org.eclipse.swt.gtk.solaris.sparc",
  "org.eclipse.swt:org.eclipse.swt.gtk.solaris.x86",
  "org.eclipse.swt:org.eclipse.swt.win32.win32.x86",
  "org.eclipse.swt:org.eclipse.swt.win32.win32.x86_64",
  # NB: All SLF4J bindings have the same classes.
  # We'll rely on logback-classic being present here.
  "org.slf4j:slf4j-jcl",
  "org.slf4j:slf4j-jdk14",
  "org.slf4j:slf4j-nop",
  "org.slf4j:slf4j-simple",
  # NB: Cannot include both commons-logging and jcl-over-slf4j;
  # see: http://www.slf4j.org/codes.html#jclDelegationLoop
  "org.slf4j:jcl-over-slf4j",
]

[smelt]
output = "target/pombast/smelt.json"
includes = [
  "de.nanoimaging:*",
  "fr.inra.ijpb:*",
  "io.scif:*",
  "jitk:*",
  "mpicbg:*",
  "net.imagej:*",
  "net.imglib2:*",
  "net.preibisch:*",
  "org.bonej:*",
  "org.embl.mobie:*",
  "org.janelia*:*",
  "org.morphonets:*",
  "org.scijava:*",
  "sc.fiji:*",
]
excludes = [
  # TEMP: Until scijava-ops-image 2.0.0 is released.
  "org.scijava:scijava-ops-image",
  # NB: Skip closed-source artifacts.
  "org.bonej:bonej-plus",
  # NB: Skip scijava forks of third-party projects.
  # These are very stable, with few/no dependencies, and
  # don't need to be retested as pom-scijava evolves.
  "org.scijava:j3dcore",
  "org.scijava:j3dutils",
  "org.scijava:jep",
  "org.scijava:junit-benchmarks",
  "org.scijava:vecmath",
]
skip-tests = [
  # Error while checking the CLIJ2 installation: null
  "sc.fiji:labkit-pixel-classification",
]

[remove-tests]

# CachedOpEnvironmentTest fails intermittently. Of course, it should be
# somehow fixed in imagej-ops. But for now, let's not let it ruin the smelt.
"net.imagej:imagej-ops" = ["net.imagej.ops.cached.CachedOpEnvironmentTest"]

# In org.janelia.saalfeldlab.n5.metadata.ome.ngff.v04.WriteAxesTests.testXYT:
# java.util.NoSuchElementException: No value present
#"org.janelia.saalfeldlab:n5-ij" = ["org.janelia.saalfeldlab.n5.metadata.ome.ngff.v04.WriteAxesTests"]

# In org.janelia.saalfeldlab.n5.s3.AmazonS3UtilsTest.testUriParsing:
# SdkClient Unable to load region from any of the providers in the chain
# software.amazon.awssdk.regions.providers.DefaultAwsRegionProviderChain@427475a2:
# [software.amazon.awssdk.regions.providers.SystemSettingsRegionProvider@768b79db:
# Unable to load region from system settings. Region must be specified either
# via environment variable (AWS_REGION) or  system property (aws.region).,
# software.amazon.awssdk.regions.providers.AwsProfileRegionProvider@3b59d246:
# No region provided in profile: default,
# software.amazon.awssdk.regions.providers.InstanceProfileRegionProvider@11b0cf30:
# Unable to contact EC2 metadata service.]
"org.janelia.saalfeldlab:n5-aws-s3" = ["org.janelia.saalfeldlab.n5.s3.AmazonS3UtilsTest"]

# Skip n5-universe slow tests.
"org.janelia.saalfeldlab:n5-universe" = [
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.ZarrStorageTests",            # Time elapsed: 1753 s
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2HttpFactoryTest",  # Time elapsed: 947.2 s
  "org.janelia.saalfeldlab.n5.universe.storage.n5.N5StorageTests",                # Time elapsed: 843.5 s
  "org.janelia.saalfeldlab.n5.universe.storage.n5.N5HttpFactoryTest",             # Time elapsed: 832.3 s
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3HttpFactoryTest",  # Time elapsed: 785.5 s

  # And these are all dependent on the above removed classes. :-(
  "org.janelia.saalfeldlab.n5.universe.BackendStorageFormatTests",
  "org.janelia.saalfeldlab.n5.universe.storage.n5.N5AmazonS3FactoryTest",
  "org.janelia.saalfeldlab.n5.universe.storage.n5.N5FileSystemTest",
  "org.janelia.saalfeldlab.n5.universe.storage.n5.N5GoogleCloudFactoryTest",
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2AmazonS3FactoryTest",
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2FileSystemTest",
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr2.Zarr2GoogleCloudFactoryTest",
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3AmazonS3FactoryTest",
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3FileSystemTest",
  "org.janelia.saalfeldlab.n5.universe.storage.zarr.zarr3.Zarr3GoogleCloudFactoryTest",
]

"sc.fiji:labkit-ui" = [
  "sc.fiji.labkit.ui.GarbageCollectionTest",                                      # Too slow (7 s)
  "sc.fiji.labkit.ui.plugin.LabkitProbabilityMapForImagesInDirectoryPluginTest",  # Too slow (65 s)
  "sc.fiji.labkit.ui.plugin.SegmentRGBImageTest",                                 # Too slow (35 s)
  "sc.fiji.labkit.ui.segmentation.SegmentationToolTest",                          # Too slow (34 s)
]

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ci-build = "build-main"

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last-vetted = "20190101000000"

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[components."io.scif:scifio-lifesci"]
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[components."jitk:jitk-tps"]
ci-build = "build-main"

[components."net.imagej:ij"]
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[components."net.imagej:imagej-mesh-io"]
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[components."net.imglib2:imglib2-mesh"]
# NOTE: Workaround for: error: Could not load processor class file due to
# 'org/scijava/ops/indexer/OpImplNoteParser has been compiled by a more recent
# version of the Java Runtime (class file version 55.0), this version of the
# Java Runtime only recognizes class file versions up to 52.0'.
java-version = 11

[components."net.preibisch:multiview-simulation"]
ci-build = "build-main"

[components."ome:formats-api"]
ci-build = "maven"

[components."ome:formats-bsd"]
ci-build = "maven"

[components."ome:formats-gpl"]
ci-build = "maven"

[components."org.bonej:bonej-plugins"]
# TEMP: Until a BoneJ release exists incorporating bonej-org/BoneJ2#414.
properties = { "skipTests" = "true" }

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[components."org.codehaus.groovy:groovy-yaml"]
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[components."org.janelia:H5J_Loader_Plugin"]
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[components."org.janelia.saalfeldlab:n5-google-cloud"]
ci-build = "build-main"

[components."org.janelia.saalfeldlab:n5-hdf5"]
ci-build = "build-main"

[components."org.janelia.saalfeldlab:n5-ij"]
ci-build = "build-main"

[components."org.janelia.saalfeldlab:n5-imglib2"]
ci-build = "build-main"

[components."org.janelia.saalfeldlab:n5-universe"]
ci-build = "build-main"

[components."org.janelia.saalfeldlab:n5-viewer_fiji"]
ci-build = "build-main"

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[components."org.openmicroscopy:metakit"]
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ci-build = "maven"

[components."org.openmicroscopy:ome-codecs"]
ci-build = "maven"

[components."org.openmicroscopy:ome-common"]
ci-build = "maven"

[components."org.openmicroscopy:ome-poi"]
ci-build = "maven"

[components."org.openmicroscopy:ome-xml"]
project-url = "https://github.com/ome/ome-model"
ci-build = "maven"

[components."org.openmicroscopy:omero-blitz"]
ci-build = "gradle"

[components."org.openmicroscopy:omero-common"]
ci-build = "gradle"

[components."org.openmicroscopy:omero-dsl-plugin"]
ci-build = "gradle"

[components."org.openmicroscopy:omero-gateway"]
project-url = "https://github.com/ome/omero-gateway-java"
ci-build = "gradle"

[components."org.openmicroscopy:omero-model"]
ci-build = "gradle"

[components."org.openmicroscopy:omero-renderer"]
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[components."org.openmicroscopy:omero-romio"]
ci-build = "gradle"

[components."org.openmicroscopy:omero-server"]
ci-build = "gradle"

[components."org.openmicroscopy:specification"]
project-url = "https://github.com/ome/ome-model"
ci-build = "maven"

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[components."org.scijava:java3d-core"]
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[components."org.scijava:java3d-utils"]
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[components."org.scijava:jep"]
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[components."org.scijava:junit-benchmarks"]
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last-vetted = "20230309000000"

[components."sc.fiji:Siox_Segmentation"]
last-vetted = "20230309000000"

[components."sc.fiji:Skeletonize3D_"]
last-vetted = "20230309000000"

[components."sc.fiji:SplineDeformationGenerator_"]
last-vetted = "20230309000000"

[components."sc.fiji:Stack_Manipulation"]
last-vetted = "20230309000000"

[components."sc.fiji:Statistical_Region_Merging"]
last-vetted = "20230309000000"

[components."sc.fiji:Sync_Win"]
last-vetted = "20230309000000"

[components."sc.fiji:Thread_Killer"]
last-vetted = "20230309000000"

[components."sc.fiji:Time_Lapse"]
last-vetted = "20230309000000"

[components."sc.fiji:Time_Stamper"]
last-vetted = "20230309000000"

[components."sc.fiji:ToAST_"]
last-vetted = "20230309000000"

[components."sc.fiji:TopoJ_"]
last-vetted = "20230309000000"

[components."sc.fiji:VIB-lib"]
last-vetted = "20230309000000"

[components."sc.fiji:Vaa3d_Reader"]
last-vetted = "20230309000000"

[components."sc.fiji:Vaa3d_Writer"]
last-vetted = "20230309000000"

[components."sc.fiji:Video_Editing"]
last-vetted = "20230309000000"

[components."sc.fiji:bUnwarpJ_"]
last-vetted = "20230309000000"

[components."sc.fiji:bigvolumeviewer"]
# NOTE: Using the release flag disallows access to sun.misc.Unsafe.
properties = { "maven.compiler.release" = "" }

[components."sc.fiji:bij"]
last-vetted = "20230309000000"

[components."sc.fiji:fiji-lib"]
last-vetted = "20230309000000"

[components."sc.fiji:level_sets"]
last-vetted = "20230309000000"

[components."sc.fiji:pal-optimization"]
last-vetted = "20230309000000"

[components."sc.fiji:panorama_"]
last-vetted = "20230309000000"

[components."sc.fiji:registration_3d"]
last-vetted = "20230309000000"

[components."sc.fiji:trakem2-transform"]
last-vetted = "20230309000000"

[components."sc.fiji:weave_jy2java"]
last-vetted = "20230309000000"