Address melting-pot incompatibilities to facilitate 32.0.0 final release #199

ctrueden · 2022-05-10T20:54:39Z

This is a catch-all issue to keep track of problems across the SciJava component collection which must be resolved in order to regain harmony across the bill of materials. Please edit this summary with issues as they are discovered.

ImageJ 1.53h breaks line bounds imagej/imagej-legacy#279 (behavior breakage in 1.53h)
Make SNT available in scijava-pom morphonets/SNT#108
Update to pom-scijava 29 API imagej/imagej-omero#107
Error with latest Fiji + imagej-server update site imagej/imagej-server#41
Error when starting the server in Fiji imagej/imagej-server#44
bigdataviewer-core.version needs to be >=10.3.1 in order to be compatible with jhdf5.version=19.04.0 (e6e17ce)
`bigdataviewer-core 10.4.0 breaks compilation trackmate-sc/MaMuT#30
Fix CI build for fiji/H5J_Loader_Plugin, so that it can be released

The text was updated successfully, but these errors were encountered:

imagesc-bot · 2022-07-25T19:36:42Z

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/timeline-for-the-next-fiji-update/69640/3

imagesc-bot · 2022-08-16T23:10:26Z

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/timeline-for-the-next-fiji-update/69640/4

ctrueden · 2022-08-16T23:18:20Z

2022-08-16 status update

Fixed but release needed

org.janelia.saalfeldlab/n5-hdf5 -- jhdf5 version skew (fixed by Use datasetExists for dataset specific attributes saalfeldlab/n5-hdf5#17)
sc.fiji:bigwarp_fiji -- bdv version skew (fixed by Fix compile errors with bigdataviewer-core-10.4.1 saalfeldlab/bigwarp#145)

Compile errors (API breakage)

io.scif/scifio-ome-xml -- scifio version skew (0.39.1 -> 0.43.1) -- no such method io.scif.formats.ICSFormat.Metadata.getPixelSizes() -- Project does not build against scifio 0.43.x scifio/scifio-ome-xml#30
sc.fiji/bigdataviewer-server -- missing dependencies: net.imglib2:imglib2-ui, commons-lang:commons-lang
sc.fiji:MaMuT -- bdv version skew -- display has private access in bdv.viewer.ViewerPanel -- bigdataviewer-core 10.4.0 breaks compilation trackmate-sc/MaMuT#30

Test errors (behavior breakage)

net.imagej/imagej-legacy -- ij version skew -- ImageJ 1.53h breaks line bounds imagej/imagej-legacy#279
org.janelia.saalfeldlab/n5-aws-s3 -- The specified bucket does not exist
org.scijava/scripting-kotlin -- kotlin version skew
sc.fiji/KymographBuilder -- ij or imagej-legacy version skew -- javassist.NotFoundException: ij.plugin.MacAdapter
sc.fiji/labkit-pixel-classification -- CLIJ2 problem: Error while checking the CLIJ2 installation: null
org.janelia.saalfeldlab/n5-viewer_fiji -- java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal
- HACK: add xml-apis dependency (just depending on new pom-scijava 32 doesn't fix it, maybe because some dependency upstream already has xml-apis excluded by its use of an older pom-scijava)

EJML 0.24 -> 0.25

net.imglib2/imglib2-realtransform -- java.lang.NoSuchMethodError: org.ejml.factory.LinearSolverFactory.linear(I)Lorg/ejml/factory/LinearSolver
jitk/jitk-tps -- no such class org.ejml.factory.LinearSolver

`502 Bad Gateway` from `dl.bintray.com`

sc.fiji/FS_Align_TrakEM2
sc.fiji/Reconstruct_Reader
sc.fiji/T2-NIT
sc.fiji/T2-TreelineGraph
sc.fiji/TrakEM2_
sc.fiji/TrakEM2_Archipelago
sc.fiji/blockmatching_
sc.fiji/register_virtual_stack_slices
sc.fiji/z_spacing

tpietzsch · 2022-08-17T10:24:15Z

@ctrueden trackmate-sc/MaMuT#31 fixes trackmate-sc/MaMuT#30

I released MaMuT-7.0.6 with the fix.

ctrueden · 2022-08-18T13:29:36Z

@tpietzsch Do you have time to fix bigdataviewer-server today or tomorrow?

tpietzsch · 2022-08-18T15:17:52Z

@tpietzsch Do you have time to fix bigdataviewer-server today or tomorrow?

Sure!

ctrueden · 2022-08-18T15:31:57Z

@tpietzsch Thanks! This diff should be enough to find the problems:

diff --git a/pom.xml b/pom.xml
index 5643f41..09d9b1c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
        <parent>
                <groupId>org.scijava</groupId>
                <artifactId>pom-scijava</artifactId>
-               <version>28.0.0</version>
+               <version>32.0.0-beta-5</version>
                <relativePath />
        </parent>

@@ -86,12 +86,6 @@

                <commons-cli.version>1.2</commons-cli.version>
                <stringtemplate.version>3.2.1</stringtemplate.version>
-
-               <!-- TODO: Remove these version pins and update the code. -->
-               <bigdataviewer-core.version>9.0.3</bigdataviewer-core.version>
-               <imglib2.version>5.9.0</imglib2.version>
-               <imglib2-cache.version>1.0.0-beta-13</imglib2-cache.version>
-               <spim_data.version>2.2.4</spim_data.version>
        </properties>

        <repositories>

ctrueden · 2022-08-18T21:50:44Z

2022-08-18 status update

SOLVED

scifio-ome-xml -- released 0.17.1
imagej-omero -- released 1.0.0-5.5
imagej-omero-legacy -- released 1.0.0-5.5
sc.fiji:MaMuT -- released 7.0.6
org.janelia.saalfeldlab/n5-aws-s3 -- SKIP TESTS (The specified bucket does not exist)
sc.fiji/labkit-pixel-classification -- SKIP TESTS (Error while checking the CLIJ2 installation: null)
org.janelia.saalfeldlab/n5-blosc -- SKIP TESTS (java.lang.UnsatisfiedLinkError: Unable to load library 'blosc')
org.janelia.saalfeldlab/n5-zarr -- SKIP TESTS (java.lang.UnsatisfiedLinkError: Unable to load library 'blosc')

Fixed but release needed

org.janelia.saalfeldlab/n5-hdf5 -- jhdf5 version skew (fixed by Use datasetExists for dataset specific attributes saalfeldlab/n5-hdf5#17)
sc.fiji:bigwarp_fiji -- bdv version skew (fixed by Fix compile errors with bigdataviewer-core-10.4.1 saalfeldlab/bigwarp#145)

Compile errors (API breakage)

sc.fiji/bigdataviewer-server -- missing dependencies: net.imglib2:imglib2-ui, commons-lang:commons-lang

Test errors (behavior breakage)

net.imagej/imagej-legacy -- ij version skew -- ImageJ 1.53h breaks line bounds imagej/imagej-legacy#279
org.scijava/scripting-kotlin -- kotlin version skew
sc.fiji/KymographBuilder -- ij or imagej-legacy version skew -- javassist.NotFoundException: ij.plugin.MacAdapter (affects macOS ONLY)
org.janelia.saalfeldlab/n5-viewer_fiji -- java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal -- needs to inherit xml-apis as a dependency

EJML 0.24 -> 0.25

net.imglib2/imglib2-realtransform -- java.lang.NoSuchMethodError: org.ejml.factory.LinearSolverFactory.linear(I)Lorg/ejml/factory/LinearSolver
jitk/jitk-tps -- no such class org.ejml.factory.LinearSolver

`502 Bad Gateway` from `dl.bintray.com` (see morphonets/SNT#108)

sc.fiji/FS_Align_TrakEM2
sc.fiji/Reconstruct_Reader
sc.fiji/T2-NIT
sc.fiji/T2-TreelineGraph
sc.fiji/TrakEM2_
sc.fiji/TrakEM2_Archipelago
sc.fiji/blockmatching_
sc.fiji/register_virtual_stack_slices
sc.fiji/z_spacing

tpietzsch · 2022-08-19T14:42:25Z

@ctrueden I fixed bigdataviewer-server and released bigdataviewer-server-3.1.0

ctrueden · 2022-08-23T22:11:25Z

2022-08-23 status update

org.morphonets:SNT:4.1.2 has rejoined the SciJava BOM (dd8ee11)
sc.fiji:H5J_Loader_Plugin has been updated to FFMPEG 4.2.1-1.5.2 (fiji/H5J_Loader_Plugin@ed78e51) – this was necessary because scenery depends on that version of FFMPEG, whereas previously this plugin (and therefore Fiji) depended on the older FFMPEG version 4.1-1.4.4. New release of the plugin is forthcoming, pending a fix for the project's Linux-based CI.
org.scijava:pom-scijava-base:15.0.3 (should have been 15.1.0, oops) released with new platform properties.
org.scijava:pom-scijava:32.0.0-beta-6 released based on the new pom-scijava-base, and with version updates bigdataviewer-server 3.1.0, n5-hdf5 1.4.2, and SNT readded.

Next on my list is to examine TrakEM2 and its dependency on SNT, and decide the best way forward there.

ctrueden · 2022-08-26T03:09:30Z

2022-08-25 status update

Today I fixed TrakEM2 to depend on SNT only optionally, and at version 4.1.2, updating the TrakEM2 code to account for backwards-incompatible changes in SNT (trakem2/TrakEM2@6f979cb). I could not test runtime behavior because I do not know how to create a situation in TrakEM2 where the SNT tracer gets invoked. I think it has something to do with left mouse clicking with the pencil tool, but I was not able to trigger the logic with a few minutes of experimentation. I would appreciate help from others (@tferr @acardona @axtimwalde) in testing this update.

List of new releases today facilitating BOM harmony:

sc.fiji:SPIM_Registration:5.0.23
jitk:jitk-tps:3.0.3
org.scijava:scripting-kotlin:0.2.1
net.imagej:ij:1.53t
sc.fiji:TrakEM2:1.3.7

Here are all the components which still fail the mega-melt, why, and how to fix them:

Component	What's wrong	How to fix
`net.imagej:imagej-legacy`	Still two ROI-bounds-related failing tests, despite the merger of imagej/ImageJ#171 and subsequent release of `net.imagej:ij:1.53t` including that fix.	Needs further investigation.
`org.janelia.saalfeldlab:n5-viewer_fiji`	`java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal`	Needs to inherit `xml-apis:xml-apis` as a dependency; already released `sc.fiji:SPIM_Registration:5.0.23` to facilitate this, but `sc.fiji:n5-viewer_fiji` needs an update to pom-scijava 32.0.0-beta-7 (forthcoming) and subsequent release
`org.morphonets:SNT`	Melted against a too-old version of ffmpeg: 4.1-1.4.4 instead of 4.2.1-1.52	Release new version of `sc.fiji:H5J_Loader_Plugin`, which has already been updated to the newer ffmpeg; but we need to fix `H5J_Loader_Plugin`'s CI build first (`no jniavdevice in java.library.path`)
`sc.fiji:Trainable_Segmentation`	three failing tests	Needs further investigation to determine which component update broke behavior.
`sc.fiji:fiji`	`java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal`	Same problem as `n5-viewer_fiji`; needs an update to pom-scijava 32.0.0-beta-7 and subsequent release
`sc.fiji:labkit-ui`	`java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal`	Same problem as `n5-viewer_fiji`; needs `xml-apis:xml-apis` on its runtime classpath

ctrueden · 2022-08-27T00:26:27Z

The pom-scijava 32.0.0 release is complete! Released in conjunction: net.imagej:imagej:2.6.0 and sc.fiji:fiji:2.6.0. 🍻

Here's how the remaining BOM harmony issues were resolved, plus other new releases that happened today along the way:

Component	Resolution
imagej-legacy	0.39.0 released with fixed unit tests (thanks @hinerm)
n5-viewer	filed saalfeldlab/n5-viewer#26; no release needed in the meantime
SNT	released H5J_Loader_Plugin 1.1.4 updating FFMPEG version; no new SNT release needed
Trainable_Segmentation	ImageJ 1.53t breaks three tests; the problematic patch is imagej/ImageJ@`0f942ad`; no resolution yet, TWS results with ImageJ 1.53t may be impacted
labkit-ui	filed juglab/labkit-ui#94; no release needed in the meantime
scripting-beanshell	0.4.1 released fixing erroneous claim on .java source files
batch-processor	0.4.2 released with SciJava task service integration (thanks @NicoKiaru)
imagej-legacy	0.39.0 released with SciJava task service integration (thanks @NicoKiaru) and various fixes (thanks @hinerm @maarzt @imagejan @gselzer)
scijava-ui-swing	0.15.0 released with SciJava task service integration (thanks @NicoKiaru) and enum fix (thanks @imagejan) plus number widget step size fix

Next, I will create tarballs of Fiji 2.6.0 for user & developer testing, before uploading JARs to the production update site. Please follow this forum thread if you are interested in being part of that.

tferr · 2022-08-30T19:15:02Z

@ctrueden, @axtimwalde , @acardona :
I tested very quickly the latest trakEM2 and SNT master branches and everything seems to work as expected. Here is a snapshot of a trakEM2 polyline traced by SNT:

For reference, this is what I did after compiling both projects:

Import the Seg.tar.bz2 demo project into TrakEM2
In the "Template" pane: Right-click on "brain" and choose "New child -> polyline"
In the "Project objects pane: Right-click on "brain" and choose "add... -> polyline"
Locate a layer with something to trace (you may need to hide existing annotations using H)
Select the Pencil tool. In the Tool options tab, select 'invert image' under "semiautomatic neurite tracer"
Click along the structure
The log window will report SNT path finding (this zealous logging seems quite distracting, but I think it has always been like that!?)

TLDR;: I would consider this fully functional. Awesome work Curtis (like always), on behalf of all the neuroanatomists out there, thank you so much for keeping all this alive!

acardona · 2022-08-31T15:42:51Z

And again, thanks so much for testing this feature and keeping it alive.

ctrueden added this to the next-release milestone May 10, 2022

ctrueden assigned ctrueden and hinerm May 11, 2022

scijava deleted a comment from tischi May 19, 2022

ctrueden modified the milestones: next-release, 32.0.0 Jul 25, 2022

ctrueden closed this as completed Aug 27, 2022

tferr mentioned this issue Aug 30, 2022

GUI scaling (hiDPI displays on Linux) trakem2/TrakEM2#30

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Address melting-pot incompatibilities to facilitate 32.0.0 final release #199

Address melting-pot incompatibilities to facilitate 32.0.0 final release #199

ctrueden commented May 10, 2022 •

edited

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imagesc-bot commented Jul 25, 2022

imagesc-bot commented Aug 16, 2022

ctrueden commented Aug 16, 2022 •

edited

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tpietzsch commented Aug 17, 2022

ctrueden commented Aug 18, 2022

tpietzsch commented Aug 18, 2022

ctrueden commented Aug 18, 2022

ctrueden commented Aug 18, 2022

tpietzsch commented Aug 19, 2022

ctrueden commented Aug 23, 2022

ctrueden commented Aug 26, 2022

ctrueden commented Aug 27, 2022

tferr commented Aug 30, 2022 •

edited

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acardona commented Aug 31, 2022

Address melting-pot incompatibilities to facilitate 32.0.0 final release #199

Address melting-pot incompatibilities to facilitate 32.0.0 final release #199

Comments

ctrueden commented May 10, 2022 • edited Loading

imagesc-bot commented Jul 25, 2022

imagesc-bot commented Aug 16, 2022

ctrueden commented Aug 16, 2022 • edited Loading

2022-08-16 status update

Fixed but release needed

Compile errors (API breakage)

Test errors (behavior breakage)

EJML 0.24 -> 0.25

502 Bad Gateway from dl.bintray.com

tpietzsch commented Aug 17, 2022

ctrueden commented Aug 18, 2022

tpietzsch commented Aug 18, 2022

ctrueden commented Aug 18, 2022

ctrueden commented Aug 18, 2022

2022-08-18 status update

SOLVED

Fixed but release needed

Compile errors (API breakage)

Test errors (behavior breakage)

EJML 0.24 -> 0.25

502 Bad Gateway from dl.bintray.com (see morphonets/SNT#108)

tpietzsch commented Aug 19, 2022

ctrueden commented Aug 23, 2022

2022-08-23 status update

ctrueden commented Aug 26, 2022

2022-08-25 status update

ctrueden commented Aug 27, 2022

tferr commented Aug 30, 2022 • edited Loading

acardona commented Aug 31, 2022

ctrueden commented May 10, 2022 •

edited

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ctrueden commented Aug 16, 2022 •

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`502 Bad Gateway` from `dl.bintray.com`

`502 Bad Gateway` from `dl.bintray.com` (see morphonets/SNT#108)

tferr commented Aug 30, 2022 •

edited

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