[PRE REVIEW]: DelayDiffEq: Generating Delay Differential Equation Solvers via Recursive Embedding of Ordinary Differential Equation Solvers #109

whedon · 2022-10-27T14:12:45Z

Submitting author: @devmotion (David Widmann)
Repository: https://github.com/SciML/DelayDiffEq.jl
Version:
Editor: @odow
Reviewers: @Datseris, @ranocha
Managing EiC: Valentin Churavy

Author instructions

Thanks for submitting your paper to JCON @devmotion. Currently, there isn't an JCON editor assigned to your paper.

The author's suggestion for the handling editor is @carstenbauer.

@devmotion if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JCON and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

whedon · 2022-10-27T14:12:49Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon · 2022-10-27T14:20:25Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (1545.2 files/s, 134840.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           48            808            506           3567
YAML                             6             13             10            172
Markdown                         2             14              0             78
TOML                             3              3              0             45
TeX                              1              1              0             19
-------------------------------------------------------------------------------
SUM:                            60            839            516           3881
-------------------------------------------------------------------------------


Statistical information for the repository 'c6202a796859590274507599' was
gathered on 2022/10/27.
No commited files with the specified extensions were found.

whedon · 2022-10-27T14:20:37Z

PDF failed to compile for issue #109 with the following error:

 Can't find any papers to compile :-(

devmotion · 2022-11-01T21:39:23Z

@whedon generate pdf from branch paper

whedon · 2022-11-01T21:39:26Z

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon · 2022-11-01T21:39:32Z

PDF failed to compile for issue #109 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:72:in `block in build_affiliation_string': Problem with affiliations for Chris Rackauckas\texorpdfstring{~\orcidlink{0000-0001-5850-0663}}{}, perhaps the affiliations index need quoting? (RuntimeError)
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `each'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `build_affiliation_string'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:17:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `block in parse_authors'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `each'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `parse_authors'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:93:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

devmotion · 2022-11-01T21:41:13Z

Strange, it worked locally (and with Github CI) by following the instructions of the template. Possibly a different ruby version? I'll try to fix it in the next few days.

devmotion · 2022-11-09T00:33:40Z

I'm not sure how to debug and test this issue locally. I can't reproduce it with the JuliaCon instructions and ruby script. I installed ruby 2.6.0 locally and ruby prep.rb works fine (also tried 2.6.6 successfully). So it seems something specific to whedon but I'm not sure how I can run it locally.

devmotion · 2022-11-18T19:38:55Z

Still haven't managed to reproduce this locally, is there really no simple way to run the build pipeline locally? Debugging with CI seems a bit suboptimal...

However, I found https://github.com/openjournals/whedon/blob/92346a0773a4003bf0ef361b661dc2787f492936/lib/whedon/author.rb#L69-L70 and https://bugs.ruby-lang.org/issues/12451, so maybe that's the underlying issue. I tried to address that, let's see if the paper can be compiled now.

devmotion · 2022-11-18T19:39:25Z

@whedon generate pdf from branch paper

whedon · 2022-11-18T19:39:28Z

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon · 2022-11-18T19:39:40Z

PDF failed to compile for issue #109 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'mathtools.sty' from line
  '! LaTeX Error: File `mathtools.sty' not found.'
Latexmk: Missing input file: 'mathtools.sty' from line
  '! LaTeX Error: File `mathtools.sty' not found.'
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

devmotion · 2022-11-18T19:42:46Z

OK, so the first issue is fixed. So what's the common approach here? Adding the LaTeX sty files to the repo? And is there a list with the LaTeX packages that are available when compiling with whedon?

devmotion · 2022-11-18T20:05:04Z

I found #79 (comment) - should mathtools be added to the list of available LaTeX packages, similar to openjournals/heroku-buildpack-tex#2, or should it be added to the repo? I'm also not really sure what would have to be added to the repo - it seems there is not mathtools.sty in https://www.ctan.org/tex-archive/macros/latex/contrib/mathtools?

carstenbauer · 2022-12-12T17:27:38Z

@whedon assign @odow as editor

matbesancon · 2022-12-12T17:33:27Z

@whedon assign @odow as editor

odow · 2022-12-12T19:44:28Z

The easiest solution is just to remove the dependence on mathtools. Why is it needed?

devmotion · 2022-12-12T21:09:13Z

I always use/load mathtools instead of amsmath since it fixes some bugs in amsmath and provides useful additional functionality (see, e.g., https://ftp.acc.umu.se/mirror/CTAN/macros/latex/contrib/mathtools/mathtools.pdf). Here, it seems it is only required for \coloneqq commands. I replaced them with := which hopefully should fix whedon's compilation issues. I think it would be useful nevertheless to support mathtools, as I said it's the package I load for math support in all my LaTeX files and at least I assumed that it is a quite common package.

devmotion · 2022-12-12T21:09:29Z

@whedon generate pdf from branch paper

whedon · 2022-12-12T21:09:32Z

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon · 2022-12-12T21:09:41Z

PDF failed to compile for issue #109 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'orcidlink.sty' from line
  '! LaTeX Error: File `orcidlink.sty' not found.'
Latexmk: Missing input file: 'orcidlink.sty' from line
  '! LaTeX Error: File `orcidlink.sty' not found.'
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

devmotion · 2022-12-12T21:17:12Z

Well well, these LaTeX issues are a bit annoying - my feeling is that this could be improved a bit 😄 Even more so since the paper compiles just fine with standard TeXlive installations (as it was the case for the initial submission and all updates) and at least to me it is still unclear what exactly is supported and why (not).

I guess the easiest solution to the latest error is to include the orcidlink.sty file.

devmotion · 2022-12-12T21:22:17Z

@whedon generate pdf from branch paper

whedon · 2022-12-12T21:22:21Z

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon · 2022-12-12T21:22:30Z

PDF failed to compile for issue #109 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'csquotes.sty' from line
  '! LaTeX Error: File `csquotes.sty' not found.'
Latexmk: Missing input file: 'csquotes.sty' from line
  '! LaTeX Error: File `csquotes.sty' not found.'
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

odow · 2022-12-12T21:28:37Z

Well well, these LaTeX issues are a bit annoying - my feeling is that this could be improved a bit 😄 Even more so since the paper compiles just fine with standard TeXlive installations (as it was the case for the initial submission and all updates) and at least to me it is still unclear what exactly is supported and why (not).

I guess the easiest solution to the latest error is to include the orcidlink.sty file

Just use the minimal set of packages. Do you really need all the extras?

The bot uses a Docker image with a fixed set of packages. There's essentially zero free time on the editorial team to improve things. @vchuravy was looking at it... and from what I understand, it wasn't an enjoyable experience. If you have time, he can probably point you in the right direction.

whedon · 2023-03-02T15:07:49Z

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon · 2023-03-02T15:08:24Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

devmotion · 2023-03-02T15:11:49Z

It seems the main culprit was the acknowledgement environment provided by juliacon as it was necessary to modify it to fix the whedon errors. Possibly other authors did not use the environment.

devmotion · 2023-03-02T15:28:14Z

@whedon generate pdf from branch paper

whedon · 2023-03-02T15:28:18Z

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon · 2023-03-02T15:28:52Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

devmotion · 2023-03-02T15:35:22Z

Finally 🎉

@odow With some fixes of the juliacon class, the submission was compiled successfully by whedon. I think it is ready for review 🙂

ChrisRackauckas · 2023-03-02T16:03:43Z

🎉 dear god almighty. Thanks @devmotion for driving this.

odow · 2023-03-06T17:02:01Z

Hoorah. Any suggestions for reviewers?

ChrisRackauckas · 2023-03-07T08:44:40Z

@ranocha might be a good reviewer, and maybe @Datseris ?

ranocha · 2023-03-07T12:20:54Z

I can have a look but can't promise having enough time for a thorough review in March

Datseris · 2023-03-07T13:43:44Z

Yeap I'd be happy to review this!

odow · 2023-03-07T19:10:54Z

@whedon add @Datseris as reviewer

whedon · 2023-03-07T19:11:00Z

OK, @Datseris is now a reviewer

odow · 2023-03-07T19:12:41Z

@devmotion if you're happy to wait a while for @ranocha I can assign and start the review? Otherwise we can find someone else.

devmotion · 2023-03-07T20:07:57Z

I think @ranocha would be a good reviewer, so I'm happy to wait a while 🙂

odow · 2023-03-07T20:22:40Z

@whedon add @ranocha as reviewer

whedon · 2023-03-07T20:22:47Z

OK, @ranocha is now a reviewer

odow · 2023-03-07T20:22:56Z

@whedon start review

whedon · 2023-03-07T20:23:02Z

OK, I've started the review over in #125.

whedon added the pre-review label Oct 27, 2022

whedon added Julia TeX labels Oct 27, 2022

odow self-assigned this Dec 12, 2022

devmotion mentioned this issue Mar 2, 2023

Improve LaTeX template JuliaCon/JuliaConSubmission.jl#32

Open

whedon assigned Datseris and odow and unassigned odow Mar 7, 2023

whedon assigned Datseris, odow and ranocha and unassigned odow and Datseris Mar 7, 2023

whedon closed this as completed Mar 7, 2023

[PRE REVIEW]: DelayDiffEq: Generating Delay Differential Equation Solvers via Recursive Embedding of Ordinary Differential Equation Solvers #109

[PRE REVIEW]: DelayDiffEq: Generating Delay Differential Equation Solvers via Recursive Embedding of Ordinary Differential Equation Solvers #109

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