[PRE REVIEW]: FourierTools.jl - Working with Fourier Space #79

whedon · 2021-09-16T03:11:38Z

Submitting author: @roflmaostc (Felix Wechsler)
Repository: https://github.com/bionanoimaging/FourierTools.jl
Version:
Editor: @vchuravy
Reviewer: Pending
Managing EiC: Valentin Churavy

Author instructions

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

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

@roflmaostc 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 · 2021-09-16T03:11:43Z

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 · 2021-09-16T03:11:53Z

Failed to discover a Statement of need section in paper

whedon · 2021-09-16T03:11:53Z

Wordcount for paper.tex is 4433

whedon · 2021-09-16T03:11:54Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/jrproc.1949.232969 is OK
- 10.1017/s0370164600017806 is OK
- 10.5334/jors.151 is OK

MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1109/jproc.2004.840301 may be a valid DOI for title: The Design and Implementation of FFTW3
- 10.1016/b978-0-08-050753-8.50046-2 may be a valid DOI for title: A Fast Algorithm for General Raster Rotation

INVALID DOIs

- None

whedon · 2021-09-16T03:11:55Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (409.4 files/s, 53625.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              8            303            209           2731
Julia                           40            758            433           2715
TOML                             5            214              1            996
Markdown                         9             64              0            240
YAML                             4              3              0            107
Bourne Shell                     1              1              0              2
-------------------------------------------------------------------------------
SUM:                            67           1343            643           6791
-------------------------------------------------------------------------------


Statistical information for the repository '4569946e1d31dc7bde557700' was
gathered on 2021/09/16.
No commited files with the specified extensions were found.

whedon · 2021-09-16T03:11:58Z

PDF failed to compile for issue #79 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

carstenbauer · 2021-09-23T14:30:33Z

@whedon assign @vchuravy as editor

whedon · 2021-09-23T14:30:37Z

OK, the editor is @vchuravy

vchuravy · 2021-10-07T14:04:11Z

@roflmaostc the paper doesn't compile could you look at that?

Also any proposals for potential reviewers?

roflmaostc · 2021-10-07T14:08:36Z

I believe that's the same issue as in #75. It seems like pgfplots causes some trouble.

Since pgfplots is a rather large package (in contrast to siunitx) I cannot add a single .sty file to solve it.

In my view, it looks like that @whedon is not using a full LaTeX installation which would be better here.

vchuravy · 2021-10-07T14:27:48Z

The failure on https://whedon.theoj.org/ is:

Your paper failed to compile with the following errors:

Looks like we failed to compile the PDF with the following error: Error producing PDF. ! LaTeX Error: Can be used only in preamble. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.313 \documentclass

@arfon @matbesancon Could we add a full Latex installation?

roflmaostc · 2021-10-20T15:39:35Z

I wanted to ask again if there is any chance to fix the LaTeX installation on the whedon backend?

vchuravy · 2021-12-02T15:18:05Z

@whedon generate pdf

whedon · 2021-12-02T15:18:16Z

PDF failed to compile for issue #79 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

roflmaostc · 2021-12-02T15:19:47Z

Did you change the pdflatex packages of whedon?

vchuravy · 2021-12-02T15:26:32Z

Ah right, I thought we didn't but we haven't

Depend on openjournals/heroku-buildpack-tex#2

arfon · 2021-12-05T21:40:32Z

@whedon generate pdf

whedon · 2021-12-05T21:40:45Z

PDF failed to compile for issue #79 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"'
------------
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"'
------------
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"'
------------
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 · 2021-12-05T21:46:43Z

@roflmaostc – the paper is failing to compile with:

! Package PGF Math Error: Could not parse input '2 * 3.1414' as a floating poin
t number, sorry. The unreadable part was near '* 3.1414'..

See the PGF Math package documentation for explanation.
Type  H <return>  for immediate help.

roflmaostc · 2021-12-05T22:50:02Z

Hm strange, locally it compiles fine.

roflmaostc · 2021-12-05T22:50:09Z

@whedon generate pdf

whedon · 2021-12-05T22:50:20Z

PDF failed to compile for issue #79 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"'
------------
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"'
------------
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"'
------------
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

roflmaostc · 2021-12-13T16:51:22Z

What's the error this time? I can't see detailed log?

roflmaostc · 2022-01-19T13:14:26Z

Is there any progress? Anything I can help with?

vchuravy · 2022-01-27T15:45:55Z

You can try https://whedon.theoj.org/

vchuravy · 2022-01-27T15:47:01Z

It gives the following:

Looks like we failed to compile the PDF with the following error: Error producing PDF. ! LaTeX Error: Can be used only in preamble. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.313 \documentclass

roflmaostc · 2022-01-27T15:50:18Z

Error does not really help. Locally it compiles fine.

I'm not sure if it's the same l. 313, but that one looks ok

        \begin{equation}
            u(\mathbf x+ \Delta \mathbf x) = \mathcal{F}^{-1}\big[\mathcal{F}[u(\mathbf x)](\mathbf k) \cdot \exp(i \mathbf k \Delta \mathbf x) \big]
            \label{eq:shifting}
        \end{equation}
        where $\Delta x$ can be an arbitrary shift not restricted to integer values.

roflmaostc · 2022-02-22T17:16:46Z

Any updates?
I can only emphasize that it perfectly compiles on any machine so the issue is definitely with the Whedon Bot :/

roflmaostc · 2022-03-18T16:28:57Z

ping :)

roflmaostc · 2022-04-29T11:10:31Z

@whedon generate pdf

whedon · 2022-04-29T11:10:42Z

PDF failed to compile for issue #79 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"'
------------
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"'
------------
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"'
------------
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

vchuravy · 2022-05-05T14:15:10Z

Your paper failed to compile with the following errors:

Looks like we failed to compile the PDF with the following error: Error producing PDF. ! LaTeX Error: Can be used only in preamble. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.313 \documentclass

matbesancon · 2022-05-05T14:20:04Z

@roflmaostc it seems the compiling toolchain wasn't supporting arithmetic in TikZ
https://github.com/bionanoimaging/FourierTools.jl/blob/main/paper/paper.tex#L130

                    \addplot[sharp plot, domain=-1:9, color=red, samples=100] {1 * cos(deg(x) - 78.46};

^ this is missing a parenthesis

roflmaostc · 2022-05-05T14:25:57Z

@whedon generate pdf

whedon · 2022-05-05T14:26:07Z

PDF failed to compile for issue #79 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"'
------------
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"'
------------
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"'
------------
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

roflmaostc · 2022-05-05T14:26:57Z

Thanks for catching it!

For some reason, now it fails locally as well. I try to update first my LaTeX

roflmaostc · 2022-05-05T15:00:31Z

Hm, didn't fix it. Not sure what's going on but suddenly

! LaTeX Error: Command \subcaption already defined.
               Or name \end... illegal, see p.192 of the manual.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.254 ...viation\subcaption\caption\caption@gobble

Not sure what broke it

roflmaostc · 2022-05-05T15:37:38Z

On my Ubuntu machine it still compiles but Arch Linux is broken.
Probably subcaption was updated which breaks it.
But since it's still compiling here still it should be also ok here

roflmaostc · 2022-05-09T09:03:53Z

Also tried to remove all lines where I calculate in tikz, still fails

roflmaostc · 2022-05-09T09:03:58Z

@whedon generate pdf

whedon · 2022-05-09T09:04:09Z

PDF failed to compile for issue #79 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"'
------------
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"'
------------
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"'
------------
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

roflmaostc · 2023-01-27T13:33:46Z

Hi,

Any progress regarding this? Also tagging @devmotion since he struggled with the bot too.

luraess · 2023-09-07T20:30:45Z

Dear author @roflmaostc, we are in the process of resuming the stalled JuliaCon reviews. If you are still interested in getting your work published, please start addressing the author-action-required items within the coming 3 weeks. If no action is taken within the coming 3 weeks, we will close the submission. Thank you for your understanding. The new editorial team

lucaferranti · 2024-04-25T17:29:47Z

@editorialbot reject

editorialbot · 2024-04-25T17:29:49Z

Paper rejected.

whedon added the pre-review label Sep 16, 2021

whedon added Julia TeX labels Sep 16, 2021

whedon assigned vchuravy Sep 23, 2021

vchuravy added the author action required label Oct 7, 2021

devmotion mentioned this issue Nov 18, 2022

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

Closed

luraess closed this as completed Oct 8, 2023

editorialbot added the rejected label Apr 25, 2024

[PRE REVIEW]: FourierTools.jl - Working with Fourier Space #79

[PRE REVIEW]: FourierTools.jl - Working with Fourier Space #79

Comments

whedon commented Sep 16, 2021 • edited Loading

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arfon commented Dec 5, 2021

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