taskManeage - Tasks: task #16103, Software update 2022-1


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task #16103: Software update 2022-1

Submitted by:  Mohammad Akhlaghi <makhlaghi>
Submitted on:  Fri 31 Dec 2021 02:48:45 AM UTC
Should Start On:  Fri 31 Dec 2021 12:00:00 AM UTC Should be Finished on:  Fri 31 Dec 2021 12:00:00 AM UTC
Category:  Software Priority:  * 5 - Normal
Status:  Done Privacy:  Public
Percent Complete:  100% Assigned to:  makhlaghi
Open/Closed:  Closed Effort:  0.00
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Fri 21 Jan 2022 12:20:24 AM UTC, comment #14: 

The 'version-update' branch is merged into the Maneage branch as Commit 8463df97c. So I am closing this task.

Thank you very much everyone for all the wonderful work in making this possible :-).

We can now easily import this updated software infra structure in our Maneage'd projects :-). Please continue sending bug reports/fixes as you find them.

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Tue 18 Jan 2022 01:39:10 AM UTC, comment #13: 

As part of the update, from Commit d60915548d, all the comments within the recipes start with a '#', then a 'TAB'.

Until now, we first put eight space characters, then a '#'! This would cause different indentation between the comments and codes of the recipes for editors and viewers (including the 'git diff'!) that use different number of characters to represent the TAB! The problem/solution is described more in the commit message.

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Thu 13 Jan 2022 11:10:49 AM UTC, comment #12: 

I found a similar issue every time I tried the full build! Can you please post it as a bug? I doubt we'll have time to address it before this merge ;-).

I am just trying to find some time to do the final checks, write the final commit message and merge it (but in the last few days, I haven't even found 1 hour for doing this!)

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Thu 13 Jan 2022 09:26:48 AM UTC, comment #11: 

I am trying to run the installation of all software of Maneage from scratch. All basic software runs smoothly without any error. Good joob!

For the high-level software there is something strange with Astropy. It crashes about not finding 'jinja2'. But it is a prerequisite of Astropy! If I remove the target of this package (.local/version-info/python/jinja2-3.0.3) and run the configure step again, it finishes without any problem.

The problem described above with 'jinja2' also happen with the package 'extension-helpers'.

I have been investigating a bit the origin of the problem but I found nothing. If you have any idea let me know. Thanks!

Raul Infante-Sainz <infantesainz>
Project Member
Wed 05 Jan 2022 12:45:36 AM UTC, comment #10: 

Thanks for the hint on forgetting to remove those R packages from 'TARGETS.mk'! They have been removed.

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Tue 04 Jan 2022 08:34:40 PM UTC, comment #9: 

Mohammad, in case you didn't notice - 7bb37e58617 has r-cran-cowplot r-cran-gridExtra enabled. That's probably not intended.

Boud Roukema <boud>
Project Member
Sat 01 Jan 2022 11:29:30 AM UTC, comment #8: 

> I think its best to not merge that part into the main 'maneage' branch.

Yes, I fully agree. That's why I described the hack as obsolete :). It's also, in principle, harmless in case we forget to remove it later on in the particular project that uses it.

Boud Roukema <boud>
Project Member
Sat 01 Jan 2022 04:33:54 AM UTC, comment #7: 

Thanks for the clarification Boud.

Indeed, the fact that we download (La)TeX binaries from TeXLive is not good and annoys me every time I build a Maneage'd project! We have started work on fully building TeX Live from source in task #15267 (as as the development branch texlive-from-src). But work didn't progress in the last two years due to time constraints.

About the Commit 74ff0f2f58, the problem has indeed been fixed in CTAN's latest downloads (I tried full builds many times in the last few days!). So to avoid complicating the rule and making it hard to read, I think its best to not merge that part into the main 'maneage' branch. Hopefully such package-specific hacks can be kept much better when task #15267 is complete ;-).

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Fri 31 Dec 2021 10:37:04 PM UTC, comment #6: 

Sorry for the ambiguity. I meant through, inclusively, to the verify checksums, and producing the pdf. Everything looks OK. :)

Just as an aside on the difficulties in reproducibility for the final LaTeX stages, see this temporary hack [1] that was needed in the 'gevcurvtest' project [2].  It happened that a minor bug in one texlive program blocked full LaTeX compilation, and the CTAN mirrors had a README announcing a fix in version 1.701 of newtx, but were - as of a few days ago - still distributing 1.7. In my check of 5255a48, I see that .build/software/installed/texlive/maneage/texmf-dist/tex/latex/newtx/newtxtext.sty is version 1.701, so my hack is (happily) obsolete (but should do no harm).

I spent a long time trying to trace where we had introduced a LaTeX error, but it was not our fault. It was a coincidence of downloading a LaTeX package at the moment in between the introduction of a fatal (though minor) bug and it being fixed. Sooner or later we should think of seeing if there's a way to handle version-frozen and checksummed texlive packages, rather than the current situation of live updates. Users will not always realise that this sort of bug is "low priority" and "easy to fix" and "not the user's fault"...

[1] https://codeberg.org/boud/gevcurvtest/commit/74ff0f2f5801857a1ecf28bf605b38ec4ae499d7
[2] https://codeberg.org/boud/gevcurvtest

Boud Roukema <boud>
Project Member
Fri 31 Dec 2021 10:05:17 PM UTC, comment #5: 

Thanks Boud. I just don't understand what you mean by "through to the verify checksums".

Did the './project configure' script reach the end without a crash? Was there a checksum verification problem?

Indeed, I'll be looking into task #15772 shortly ;-).

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Fri 31 Dec 2021 09:57:19 PM UTC, comment #4: 

5255a48 works fully through to the verify checksums for me on one Debian system.

It would be nice to include the R system... ;) https://savannah.nongnu.org/task/?15772

Boud Roukema <boud>
Project Member
Fri 31 Dec 2021 09:07:19 PM UTC, comment #3: 

Podlators is (are) OK now. :) Thanks.

Boud Roukema <boud>
Project Member
Fri 31 Dec 2021 08:54:24 PM UTC, comment #2: 

Thanks for reporting this Boud! I just committed it into our software repository in Commit 915ad273.

If you run the script again, it should be downloaded properly ;-).

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Fri 31 Dec 2021 08:43:42 PM UTC, comment #1: 

A completely fresh install on commit 5255a48 failed with 10 failed download attempts for:


Boud Roukema <boud>
Project Member
Fri 31 Dec 2021 02:48:45 AM UTC, original submission:  

Most of software used in Maneage have been updated in the 'version-update' branch of this repository. I have tested it on an Arch GNU/Linux, Ubuntu 20.04, and on Debian-slim (within Docker) and all software (with '--all-highlevel') get installed successfully.

I plan to merge it into the 'maneage' branch in one week (by Friday January 7th, 2022). So it would be great if anyone can try it on their various OSs and report any crashs or failures so we can fix them before the merge.

I'll also be looking into recently submitted bugs/tasks about the various software-building phases and including them if necessary.

All the work in this development branch will be squashed into a single commit to avoid complicating the history of the 'maneage' branch which goes into all Maneage'd projects.

Since the software in Maneage are increasing, updating their versions is very time-consuming (it took more more than two months to do it anytime I had some time). To help simplify the process, we can have Maneage software releases coded with a format of 'YYYY-N', where YYYY is the year, and 'N' is the release in that year. So this one will be 2022-1.

We will then start a new branch and gradually (as new software versions are released), we'll add them until they reach a sufficient level to justify a next release (and testing!).

Also, from the next release, I can only commit to maintaining the "default" Maneage software (due to time constraints)! There are too many complexities and dependencies for other software (in particular, the Python packages!). So if you need them, please keep updating them in the development branch yourself, and we'll test them all together when the next release is necessary.

Mohammad Akhlaghi <makhlaghi>
Project Administrator


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    Date Changed by Updated Field Previous Value => Replaced by
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        Percent Complete90% => 100%

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