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

[whedon]

Submitting author: @devmotion (David Widmann)
Repository: https:/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

The JCON submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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]

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]

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

 Can't find any papers to compile :-(

[devmotion]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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]

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]

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]

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:/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]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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]

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]

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]

@whedon assign @odow as editor

[matbesancon]

@whedon assign @odow as editor

[odow]

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

[devmotion]

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]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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]

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]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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]

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]

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

[whedon]

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

[devmotion]

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]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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

[devmotion]

Finally 🎉

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

[ChrisRackauckas]

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

[odow]

Hoorah. Any suggestions for reviewers?

[ChrisRackauckas]

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

[ranocha]

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

[Datseris]

Yeap I'd be happy to review this!

[odow]

@whedon add @Datseris as reviewer

[whedon]

OK, @Datseris is now a reviewer

[odow]

@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]

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

[odow]

@whedon add @ranocha as reviewer

[whedon]

OK, @ranocha is now a reviewer

[odow]

@whedon start review

[whedon]

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