Update BoneJ version to 7.0.14 #210
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0.8.2 unit tests will fail with imglib2-algorithm >= 0.12.0
Removes the log4j dependency
It prevents ^C to halt, and it breaks the script's exit code.
Save bandwidth, and make debugging easier: only download the script if it's not available from a sibling scijava-scripts directory.
* Fix whitespace issues * Filter out confusing melting-pot output * Remove unused variable
And maven.imagej.net -> maven.scijava.org while we're at it.
* scijava-grab: 0.1.0 -> 0.1.1 * imagej2: 2.3.0 -> 2.4.0 (preemptive) * ij: 1.53f -> 1.53r * ij1-patcher: 1.2.1 -> 1.2.2 (preemptive) * imagej-opencv: 0.1.1 -> 0.1.2 * fiji: 2.3.1 -> 2.4.0 (preemptive)
This disables therapi for now to avoid problems; see: scijava/pom-scijava-base@62b618d
* parsington: 2.0.1 -> 3.0.0 * scripting-kotlin: 0.1.1 -> 0.2.0 * imagej-common: 0.34.1 -> 0.34.2 * imagej-ops: 0.45.8 -> 0.46.1 * imglib2-algorithm: 0.12.0 -> 0.12.1 * imglib2-roi: 0.12.0 -> 0.12.1 * PIV_analyser: 1.1.2 -> 2.0.0 * Trainable_Segmentation: 3.3.0 -> 3.3.1 * Volume_Viewer: 2.01.2 -> 2.01.3 * bigdataviewer-core: 10.2.1 -> 10.2.2 * bigdataviewer_fiji: 6.2.1 -> 6.2.2 * imglib2-label-multisets: 0.10.0 -> 0.11.0 * BigStitcher: 0.8.2 -> 0.8.3 * multiview-reconstruction: 0.11.0 -> 0.11.5
* imagej2: 2.4.0 -> 2.4.1 * fiji: 2.4.0 -> 2.4.1
It was replaced by org.scijava:script-editor-jython.
3.0.9 and 3.0.10 do not play nicely with scripting-groovy's
import retainer:
java.lang.ClassCastException: java.util.ArrayList cannot be cast to java.util.Map
at org.scijava.plugins.scripting.groovy.ImportRetainer.call(ImportRetainer.java:79)
Further investigation needed.
This updates to match JHDF 19.04. Thanks to @tischi for noticing.
Among other changes, this introduces converter plugins from Java types to ImgLib2 types; see: imagej/imagej-common#82
And exclude serializer (and therefore xml-apis).
Otherwise, dependence on bio-formats-tools can clash with xpp3:
Warning: Rule 3: org.apache.maven.plugins.enforcer.BanDuplicateClasses failed with message:
No Duplicate Classes Allowed!
- For duplicate transitive dependencies, add dependency exclusions.
- For duplications between direct dependencies, resolve or add
ignored classes to this rule's configuration.
Found in:
xml-apis:xml-apis:jar:1.3.04:runtime
xpp3:xpp3:jar:1.1.4c:compile
Duplicate classes:
javax/xml/namespace/QName.class
See: https://gitter.im/fiji/DevOps?at=628e4adbc9382316a6211f18
Necessary for compatibility with the removal of OBF from SCIFIO.
Manage ejml as version 0.25 Co-authored-by: Jan Eglinger <jan.eglinger@gmail.com> Co-authored-by: Curtis Rueden <ctrueden@wisc.edu>
ui-behaviour -> 2.0.6 bigdataviewer-core -> 10.4.1 bigdataviewer-vistools -> 1.0.0-beta-30
This includes a security fix identified by Dependabot: The package com.google.code.gson:gson before 2.8.9 is vulnerable to Deserialization of Untrusted Data via the writeReplace() method in internal classes, which may lead to denial of service attacks.
Some projects have tests that are not well-behaved cross-platform on plain systems. Let's skip those to avoid headaches, with comments describing why each one is excluded from testing.
They were excluded because their tests are problematic. But now we have a mechanism to skip their unit tests, while still testing their compilation step. So let's do that.
Thanks to @hinerm's hard work, ImageJ-OMERO is functional again, and version 1.0.0-5.5 has been released. Let's add it to the melting pot.
This brings it in line with bigdataviewer-core 10.4.2.
This reverts commit 7e81353, but with the latest 4.1.2 version of SNT, which improves its dependency structure, making scenery optional and excluding biojava. And it adds the org.morphonets groupId to the mega-melt.
* Fix Eclipse warning about maven-help-plugin * Improve "mvn -Pexec" and make "mvn exec:java" work * Improve scijava.platform.* and scijava.natives.* properties
This brings it in line with jhdf5 19.04.1 and n5 2.5.1.
Used by scripting-kotlin and sciview
Now consistent with managed EJML
Now consistent with managed kotlin version.
Unfortunately, the pipefail flag is not POSIX-friendly, or at least not supported by dash. So to make this script work on Linux, we need to use a shell that supports it (e.g. bash or zsh).
* scijava-common: 2.88.1 -> 2.89.0 * scripting-beanshell: 0.3.4 -> 0.4.0 * ui-behaviour: 2.0.6 -> 2.0.7 * ij: 1.53r -> 1.53t * Fiji_Plugins: 3.1.1 -> 3.1.2 * TrackMate: 7.6.1 -> 7.7.2 * Trainable_Segmentation: 3.3.1 -> 3.3.2 * bigwarp: 7.0.5 -> 7.0.6 * bigdataviewer-core: 10.4.2 -> 10.4.3 * spim_data: 2.2.6 -> 2.2.7 * imglib2-label-multisets: 0.11.0 -> 0.11.4 * n5-ij: 3.2.0 -> 3.2.2 * ome-common: 6.0.7 -> 6.0.13 * metakit: 5.3.3 -> 5.3.4 * ome-poi: 5.3.4 -> 5.3.7 * ome-xml: 6.3.0 -> 6.3.1 * labkit-ui: 0.3.0 -> 0.3.7 * labkit.pixel-classification: 0.1.13 -> 0.1.14
This un-excludes xml-apis as a dependency, so that org.janelia.saalfeldlab:n5-viewer_fiji and sc.fiji:fiji inherit it and work correctly at runtime; see 6cd6c9f.
This brings it in line with SNT 4.1.2, and makes the SNT dependency optional.
This property was used for the net.imagej:ij version prior to pom-scijava 28.0.0. Older releases (e.g. sc.fiji:KymographBuilder:2.1.1) built on too-old pom-scijava parents cannot update their net.imagej:ij version based on consistently named net.imagej.ij.version nor ij.version property overrides, since those properties had not yet been introduced.
This fixes a NullPointerException when caching imports in some cases.
This introduces new API for working with tasks from the TaskService.
Even with pipefail, it wasn't propagating the error code, so the mega-melt process was continuing erroneously. The good thing is: without the POSIX-unfriendly pipefail flag, we can go back to /bin/sh now.
There are a couple of artifacts in pom-scijava that begin with a digit: * sc.fiji:3D_Blob_Segmentation * sc.fiji:3D_Objects_Counter * sc.fiji:3D_Viewer Prior to d0bf752, these used a "Fiji_" or "ImageJ_" prefix for their version properties. But this was standardized to a leading underscore instead, for consistency. So, for backwards compatibility with older pom-scijava parents, we need to set: A) the version props with Fiji/ImageJ prefix; and B) the version props with underscore prefix. Otherwise, these components might not get their versions pinned properly for builds of older components.
This brings it in line with net.imagej:ij:1.53t. It also includes new functionality and bug-fixes.
This updates it from FFMPEG 4.1-1.4.4 to 4.2.1-1.5.2, which brings it in line with SNT 4.1.2, which transitively+optionally depends on that version of FFMPEG via scenery.
It is used by sc.fiji:labkit-ui, so let's manage it with the other monoversioned jackson components.
This fixes a bug where scripting-beanshell claims ownership over .java files, which clashes with scripting-java.
These are preemptive version bumps.
Signed-off-by: Curtis Rueden <ctrueden@wisc.edu>
I was concerned this update might break some components, but the mega-melt identifies no problems with it, so we're good to go. Closes #163.
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https://github.com/bonej-org/BoneJ2/releases/tag/bonej-7.0.14