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[PRE REVIEW]: Adaptive numerical simulations with Trixi.jl: A case study of Julia for scientific computing #76

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: @ranocha (Hendrik Ranocha) Repository: https://github.com/trixi-framework/paper-2021-juliacon Version: Editor: @carstenbauer Reviewers: @johnfgibson, @simonbyrne Managing EiC: Arfon Smith

Author instructions

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

@ranocha 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 commented 2 years ago

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

:warning: JOSS reduced service mode :warning:

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 commented 2 years ago

Failed to discover a Statement of need section in paper

whedon commented 2 years ago

Wordcount for paper.tex is 6292

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (549.9 files/s, 167528.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TOML                             8            919              4           4118
TeX                              7            387            198           3535
Markdown                         7             55              0            355
Julia                            5            120             91            261
INI                              3             18              0            136
Ruby                             1              8              4             45
YAML                             1              0              0             44
JSON                             1              1              0             38
make                             1              3              0             18
-------------------------------------------------------------------------------
SUM:                            34           1511            297           8550
-------------------------------------------------------------------------------

Statistical information for the repository '8f2a4b794e441c1e5f765ab1' was
gathered on 2021/08/24.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Hendrik Ranocha                  1            57              0          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Hendrik Ranocha              57          100.0          0.0                7.02
whedon commented 2 years ago

PDF failed to compile for issue #76 with the following error: 

 rm: cannot remove '*.aux': No such file or directory
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: 'siunitx.sty' from line
  '! LaTeX Error: File `siunitx.sty' not found.'
Latexmk: Missing input file: 'siunitx.sty' from line
  '! LaTeX Error: File `siunitx.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
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/zenodo.5201484 is OK
- 10.1016/j.jcp.2021.110467 is OK
- 10.1007/s42967-021-00148-z is OK
- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.21105/jcon.00068 is OK
- 10.5281/zenodo.4773575 is OK
- 10.1137/15M1020575 is OK
- 10.1109/HPTCDL.2014.10 is OK
- 10.21105/joss.03053 is OK
- 10.21105/joss.02520 is OK
- 10.21105/joss.02018 is OK
- 10.1016/j.camwa.2020.05.004 is OK
- 10.1016/j.jcp.2020.109844 is OK
- 10.1137/100791634 is OK
- 10.1038/467753a is OK
- 10.1093/biostatistics/kxq028 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1093/mnras/stu114 is OK
- 10.1007/978-0-387-72067-8 is OK
- 10.1007/978-90-481-2261-5 is OK
- 10.1090/S0025-5718-1987-0890255-3 is OK
- 10.1137/S003614290240069X is OK
- 10.1016/j.jcp.2013.06.014 is OK
- 10.1007/s10915-017-0618-1 is OK
- 10.1016/j.jcp.2017.05.025 is OK
- 10.1016/S0021-9991(03)00168-2 is OK
- 10.1137/18M1209234 is OK
- 10.1142/9789814313193_0004 is OK
- 10.18419/opus-3895 is OK
- 10.1016/j.jcp.2018.06.027 is OK
- 10.1007/b79761 is OK
- 10.1016/j.jcp.2004.08.020 is OK
- 10.1007/978-3-030-39647-3_42 is OK
- 10.1016/j.jcp.2016.09.013 is OK
- 10.18419/opus-3788 is OK
- 10.1109/PMBS51919.2020.00008 is OK
- 10.1145/2464996.2465020 is OK
- 10.1145/2807591.2807623 is OK

MISSING DOIs

- None

INVALID DOIs

- None
ranocha commented 2 years ago

Failed to discover a Statement of need section in paper

I couldn't find the requirement for a Statement of need section in paper in the author guidelines for JuliaCon. It's of course required for JOSS papers. If we need to have this section in our JuliaCon paper, we could basically rename the "Introduction" to "Statement of need".

ranocha commented 2 years ago

The software report is not really helpful since we set up a dedicated repository with reproducibility material for this paper. Our Julia package Trixi.jl is available in another repository.

ranocha commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 with the following error: 

 rm: cannot remove '*.aux': No such file or directory
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"'
------------
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
ranocha commented 2 years ago

We propose Carsten Bauer (@carstenbauer) as editor.

Possible reviewers are

carstenbauer commented 2 years ago

Failed to discover a Statement of need section in paper

I couldn't find the requirement for a Statement of need section in paper in the author guidelines for JuliaCon. It's of course required for JOSS papers. If we need to have this section in our JuliaCon paper, we could basically rename the "Introduction" to "Statement of need".

It's not required. Just ignore this.

PS: I took the freedom to change @crstnbr -> @carstenbauer. I recently changed my github handle to something more readable / pronouncable 😄

ranocha commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 with the following error: 

 rm: cannot remove '*.aux': No such file or directory
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"'
------------
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
ranocha commented 2 years ago

I can't reproduce the error of whedon locally. Running

latexmk -c; latexmk -bibtex -pdf paper.tex

works fine on my system. Is there a way I can help debugging this? Can we look at paper.log?

ranocha commented 2 years ago

This is the PDF generated on my system: paper.pdf

ranocha commented 2 years ago

Is the failing PDF build a blocking issue? If so, is there anything I might do to debug it?

vchuravy commented 2 years ago

@whedon assing @carstenbauer as editor

whedon commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands
vchuravy commented 2 years ago

@whedon commands

whedon commented 2 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon recommend-accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

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@whedon reject

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@whedon accept deposit=true
vchuravy commented 2 years ago

@whedon assign @carstenbauer as editor

vchuravy commented 2 years ago

@arfon could it be that @carstenbauer username change messed up something in the DB?

vchuravy commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 with the following error: 

 rm: cannot remove '*.aux': No such file or directory
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"'
------------
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
arfon commented 2 years ago

@whedon list editors

whedon commented 2 years ago

Current editors:

@arfon
@carstenbauer
@matbesancon
@ranjanan
@vchuravy
arfon commented 2 years ago

@whedon assign @carstenbauer as editor

arfon commented 2 years ago

@whedon assign @carstenbauer as editor

sloede commented 2 years ago

I think it was a simple typo: image

Thanks for the assistance everyone! If we only could figure out why *.aux needs to be deleted and how to prevent it...

arfon commented 2 years ago

@whedon assign @carstenbauer as editor

arfon commented 2 years ago

@whedon assign @carstenbauer as editor

whedon commented 2 years ago

OK, the editor is @carstenbauer

arfon commented 2 years ago

@arfon could it be that @carstenbauer username change messed up something in the DB?

Yeah, that can confuse Whedon :-). Fixed now.

arfon commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 with the following error: 

 rm: cannot remove '*.aux': No such file or directory
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"'
------------
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
arfon commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 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"'
------------
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
arfon commented 2 years ago

Well, I fixed the first error with https://github.com/openjournals/whedon/commit/c5c16aedb3d6b4377181e859316ed70f1ac0a0b7, but I'm not sure what this new one is about. @matbesancon - the core code for compiling from TeX hasn't changed for a long time.

I wonder if you could assist here to see if there's something inherently different about this paper? I'm struggling a little to figure out what might be going wrong here...

arfon commented 2 years ago

OK, managed to get an error from the log. Not sure what this means (🤣) but perhaps you all will understand...

LaTeX Warning: You have requested, on input line 16, version
               `2020/01/12' of package expl3,
               but only version
               `2018/02/21 L3 programming layer (loader) '
               is available.

(/app/.texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.sty)

! Package siunitx Error: Support package expl3 too old.

See the siunitx package documentation for explanation.
Type  H <return>  for immediate help.
vchuravy commented 2 years ago

Hm... Maybe the best thing for now would be to add a cat paper.log? In case of failure?

but perhaps you all will understand...

That looks helpful xD. Can we update the latex installation used?

ranocha commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 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"'
------------
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
ranocha commented 2 years ago

I tried to manually revert siunitx.sty to an older version from 2011 - we still get the error above

ranocha commented 2 years ago

An alternative to updating the LaTeX installation might be to use a bigger set of standard packages including siunitx.sty (bundled in standard texlive distributions).

sloede commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 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: 'pgfplots.sty' from line
  '! LaTeX Error: File `pgfplots.sty' not found.'
Latexmk: Missing input file: 'pgfplots.sty' from line
  '! LaTeX Error: File `pgfplots.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
sloede commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #76 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: 'siunitx-abbreviations.cfg' from line
  '! LaTeX Error: File `siunitx-abbreviations.cfg' not found.'
Latexmk: Missing input file: 'siunitx-abbreviations.cfg' from line
  '! LaTeX Error: File `siunitx-abbreviations.cfg' not found.'
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'siunitx-abbreviations.cfg' from line
  '! LaTeX Error: File `siunitx-abbreviations.cfg' not found.'
Latexmk: Missing input file: 'siunitx-abbreviations.cfg' from line
  '! LaTeX Error: File `siunitx-abbreviations.cfg' not found.'
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
===========Latexmk: Missing input file: 'siunitx-abbreviations.cfg' from line
  '! LaTeX Error: File `siunitx-abbreviations.cfg' not found.'
Latexmk: Missing input file: 'siunitx-abbreviations.cfg' from line
  '! LaTeX Error: File `siunitx-abbreviations.cfg' 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
sloede commented 2 years ago

@whedon generate pdf