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##### Activity
Curtis Rueden
@ctrueden
Today I worked a bit on the PyImageJ paper.
Curtis Rueden
@ctrueden
Today I have some internal bureaucracy to work on. If I have time, I'll work more on PyImageJ and/or the log4j-free component stack releases. Tomorrow I will be off, so if you don't hear from me again before Monday: happy new year to all! :star2:
Nicolas Chiaruttini
@NicoKiaru
And happy new year to all as well! Cheers
Jan Eglinger
@imagejan
:+1: for the gradle documentation @NicoKiaru, and a happy start of the new year to all!
Curtis Rueden
@ctrueden
Happy new year. 🥳 Today I will work on fixing all the failing daily CI builds.
Curtis Rueden
@ctrueden
Today I'll continue fixing daily builds, starting with javadoc generation. I've already disabled the javadoc aggregator builds, but I'm still working on the new system that will unpack existing -javadoc JARs into the javadoc.scijava.org web space, and then stitch together the content into one index per version of pom-scijava. After that, I still have to fix fiji-builds, and redesign ij1-builds, but those are unlikely to happen today.
Jan Eglinger
@imagejan
Hi all, and happy new year! Is there a standup meeting today?
18 replies
Curtis Rueden
@ctrueden
Today I'm continuing work on my new javadoc monstrosity. Links explaining WTH I'm doing are forthcoming.
Curtis Rueden
@ctrueden
And here are the promised forthcoming details: https://github.com/scijava/javadoc-wrangler#readme. Implementation is pretty far along but not finished yet. If anyone sees any glaring problems with this idea, let me know.
Related issue: scijava/pom-scijava#130
Curtis Rueden
@ctrueden
Today (and Fridays in general) I will focus on community support: responding on forum, GitHub issues, etc. I'll also create the poll for the weekly meeting schedule and advertise it here and via email.
Curtis Rueden
@ctrueden
I lied, and worked on the javadoc-wrangler some more. I finally pushed a first ostensibly working version. I am running it now on all versions of pom-scijava 12.0.0 and later. If I don't find major problems, I'll work on integrating the output into javadoc.scijava.org next week. I will do a community support day on Monday. I will still send out the poll shortly.
Curtis Rueden
@ctrueden
@/all If you are in this room, I assume you care at least somewhat about the day-to-day runnings of Fiji. Therefore, you might be interested in joining a weekly 30-minute standup meeting where we each present what Fiji-related things we have been doing lately and/or will be doing soon. If so, please fill out the poll with your availability. Ignore the specific dates—it's just for time slots. I chose Jan 24 - 28 because that's the week I'm thinking we will start these.
Curtis Rueden
@ctrueden
OK, I advertised it on forum.image.sc rather than using email. Now we see whether we get any spam entries. 😆
Curtis Rueden
@ctrueden
@imagejan @axtimwalde You expressed interest in the weekly Fiji dev standup meeting. Would you care to vote in the poll?
Deborah Schmidt
@frauzufall
Happy new year everyone! I'm still quite affected by limited available daycare, like last year - I put all side projects on ice, including SciJava related work. I'm really sorry for being so bad at communicating as well, I'm just tired, but we are fine in general and I do hope to see and speak to you all soon again!
Jean-Yves Tinevez
@tinevez
We are :100: with you (and sometimes in the same situation.)
Deborah Schmidt
@frauzufall
thank you @tinevez!
Curtis Rueden
@ctrueden
Same here, @frauzufall! Last year was frustratingly unproductive for me—just could not work the normal number of hours due to family obligations. I have the dubious "benefit" of living in the USA where the pressure to get things back to "normal" is high, so my kids are now back in school full time, and I am back in the office full time. We'll see whether the schools are able to keep functioning—unfortunately, cases are spiking across the US and in my state and county, and the biggest school district in town went back to full virtual, so hard to say what will happen next. Anyway, I sympathize, and wish you the best navigating it, and look forward to hacking with you again someday. ^_^
Curtis Rueden
@ctrueden
Status update for today and yesterday: I spent these days doing community support. A few forum post replies and PRs merged. I need to return to javadoc.scijava.org and status.scijava.org work tomorrow; I had meant to work on them today, but got sidetracked into community issues (which is not a bad thing).
Curtis Rueden
@ctrueden
This morning I worked on some community issues. This afternoon I worked on the new status.scijava.org and javadoc.scijava.org.
Curtis Rueden
@ctrueden
Late last week I continued work on status.scijava.org. Today I have some meetings, and will try to finish status.scijava.org and javadoc.scijava.org. Each of them is perhaps 80% complete now—initial working systems, but need refinement and debugging. I also really need to get the ij1-builds fixed (imagej/imagej1#142); will probably work on that next.
Nicolas Chiaruttini
@NicoKiaru

Hi, I'm trying to make a new release for some repos, and it seems javadoc building takes forever. Any idea what could cause this ?
I'm running mvn javadoc:javadocand this is getting stuck at:

[INFO] --- build-helper-maven-plugin:3.2.0:regex-property (sanitize-version) @ bigdataviewer-playground-display ---
[INFO]
[INFO] --- build-helper-maven-plugin:3.2.0:regex-property (guess-package) @ bigdataviewer-playground-display ---
[INFO]
[INFO] --- buildnumber-maven-plugin:1.4:create (default) @ bigdataviewer-playground-display ---
[INFO] Executing: cmd.exe /X /C "git rev-parse --verify HEAD"
[INFO] Working directory: C:\Users\nicol\Dropbox\BIOP\bigdataviewer-playground-display
[INFO] Storing buildNumber: 51e799c29d6278d48a01310b5f8b88929b706985 at timestamp: 1642536683830
[INFO] Storing buildScmBranch: master
[INFO]
[INFO] --- scijava-maven-plugin:2.1.0:set-rootdir (set-rootdir) @ bigdataviewer-playground-display ---
[INFO] Setting rootdir: C:\Users\nicol\Dropbox\BIOP\bigdataviewer-playground-display
[INFO]
[INFO] --- jacoco-maven-plugin:0.8.7:prepare-agent (jacoco-initialize) @ bigdataviewer-playground-display ---
[INFO] argLine set to -javaagent:C:\\Users\\nicol\\.m2\\repository\\org\\jacoco\\org.jacoco.agent\\0.8.7\\org.jacoco.agent-0.8.7-runtime.jar=destfile=C:\\Users\\nicol\\Dropbox\\BIOP\\bigdataviewer-playground-display\\target\\jacoco.exec
[INFO]
[INFO]
[INFO]
[INFO] No previous run data found, generating javadoc.

And it's been 10 minutes (tested on two repos)

Nicolas Chiaruttini
@NicoKiaru
I'm running mvn javadoc:javadoc -X to get more info
Curtis Rueden
@ctrueden
Maybe one of the links is timing out.
10 minutes is not unheard of—javadoc generation can be very slow. I am in the process of updating javadoc.scijava.org so that there is always only one link per build, which should greatly improve javadoc build times.
Nicolas Chiaruttini
@NicoKiaru

[DEBUG] Could not follow https://javadoc.scijava.org/JHotDraw/. Reason: Read timed out

But there's a line executing after that:


[DEBUG] cmd.exe /X /C ""C:\Program Files\Java\jdk1.8.0_212\jre\..\bin\javadoc.exe" -J-Xmx1024m @options @packages @argfile"

Ok, I'll wait

Curtis Rueden
@ctrueden
Probably waiting won't fix it... I think 10 minutes is on the long side, and I'm guessing one of the link proxies is broken.
I'm testing them each now.
Nicolas Chiaruttini
@NicoKiaru
Micro-Manager-Studio looks fine, but JHotDraw does not respond
Curtis Rueden
@ctrueden
Heh, yeah, I was just about to paste that. Same here.
Once I complete the reworking of javadoc.scijava.org, we won't be proxying any external javadoc anymore. But for now, this is a quick fix.
Nicolas Chiaruttini
@NicoKiaru
:-) ! Thanks a lot!
Curtis Rueden
@ctrueden
Just to be sure, I tested all the other links, and all the rest are currently working.
Curtis Rueden
@ctrueden
Argh, it seems like the JHotDraw server just doesn't like other servers proxying their content.
It times out with the old and new URLs both.
Curtis Rueden
@ctrueden
I am generating the JHotDraw 7.6 javadocs by hand, and will serve them directly from javadoc.scijava.org.
Fixed!
@NicoKiaru Give it another go.
Nicolas Chiaruttini
@NicoKiaru
Works!
Curtis Rueden
@ctrueden
Woo! :clap:
Nicolas Chiaruttini
@NicoKiaru
I've started it just before you asked
telepathic gitter
Great! I'll start filling maven.scijava again
Curtis Rueden
@ctrueden
Very good.
Curtis Rueden
@ctrueden
Today I am pausing my work on status & javadoc to address the ImageJ builds not being published to Maven Central. As usual, the squeaky wheel gets the grease. imagej/imagej1#142
Curtis Rueden
@ctrueden
I have updated the issue with details on the problems with the current deployment infrastructure, and questions for Wayne on how to proceed. https://github.com/imagej/imagej1/issues/142#issuecomment-1016721652
For those who use the original ImageJ (i.e. version 1.x) for anything, I would appreciate you chiming in with any opinions you have about how you would prefer these resources to be deployed. Wayne does not want to change his current deployment workflow, but it is error-prone and does not lend itself ideally to reproducibility, so it would be helpful to hear from others in the community with technical expertise on this and who care about it.