[PRE REVIEW]: DeconvOptim.jl - Signal Deconvolution with Julia

[whedon]

Submitting author: @roflmaostc (Felix Wechsler) Repository: https://github.com/roflmaostc/DeconvOptim.jl Version: Editor: @vchuravy Reviewers: @sloede, @matbesancon Managing EiC: Arfon Smith

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

@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).

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[whedon]

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

@whedon generate pdf

[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Wordcount for paper.tex is 5007

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.14 s (614.9 files/s, 125864.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             10            320            178           3069
TOML                             6            559              2           2621
Julia                           28            592            313           1987
SVG                              2              0              0            740
Markdown                        20            198              0            526
Jupyter Notebook                15              0           6031            504
YAML                             4              1              0            108
Ruby                             1              8              4             45
Bourne Shell                     1              1              0              2
-------------------------------------------------------------------------------
SUM:                            87           1679           6528           9602
-------------------------------------------------------------------------------

Statistical information for the repository 'a2de92fc8ca0489178f25e71' was
gathered on 2021/08/24.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
roflmaostc                       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
roflmaostc                   57          100.0          0.0                7.02

[whedon]

PDF failed to compile for issue #75 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: '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

[whedon]

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

OK DOIs

- 10.1364/JOSA.62.000055 is OK
- 10.1086/111605 is OK
- 10.21105/joss.00615 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1364/JOSAA.15.001077 is OK
- 10.1145/1401132.1401152 is OK
- 10.1017/9781108552660 is OK
- 10.5281/zenodo.5047410 is OK
- 10.1109/TPDS.2018.2872064 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/iccv.2017.491 may be a valid DOI for title: Learning to Push the Limits of Efficient FFT-Based Image Deconvolution
- 10.1109/jproc.2004.840301 may be a valid DOI for title: The Design and Implementation of FFTW3
- 10.1007/bf01589116 may be a valid DOI for title: On the Limited Memory BFGS Method for Large Scale Optimization
- 10.2307/2334515 may be a valid DOI for title: Nonparametric Roughness Penalties for Probability Densities
- 10.1016/j.ymeth.2016.12.015 may be a valid DOI for title: DeconvolutionLab2: An Open-Source Software for Deconvolution Microscopy
- 10.1038/s41598-018-29768-x may be a valid DOI for title: A convex 3D deconvolution algorithm for low photon count fluorescence imaging
- 10.1016/j.advengsoft.2019.02.002 may be a valid DOI for title: Rapid software prototyping for heterogeneous and distributed platforms

INVALID DOIs

- https://doi.org/10.1016/j.micron.2006.07.009 is INVALID because of 'https://doi.org/' prefix

[roflmaostc]

Thanks for activating the review!

It looks like that PDF building has failed because of the missing pgfplots.sty. Usually, that's included with the normal LaTeX distributions, so I'm not quite sure what's installed on the backend and why that's missing.

[roflmaostc]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #75 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: '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]

For potential reviewers, matbesancon might be a suitable candidate since his favored topics include Mathematical optimization which we also do here.

[vchuravy]

@whedon assign @vchuravy as editor

[whedon]

OK, the editor is @vchuravy

[vchuravy]

@matbesancon would you be interested in reviewing this?

[matbesancon]

yes I'll be able to review it

[roflmaostc]

Anything I can help with to fix the LaTeX errors? However, similar errors are also in the other review.

[roflmaostc]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #75 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

[matbesancon]

@roflmaostc it seems it's not included. The easiest solution for now would be to add the sty file in your project paper folder directly

[roflmaostc]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #75 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

[roflmaostc]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #75 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

[roflmaostc]

I tried to use the same siunitx files as #76 is using but without success...

Error might be due to pgfplots but can't we update or change the LaTeX backend of @whedon? That would be simpler than adding manually all dependencies.

[ranjanan]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #75 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

[vchuravy]

Dependent on https://github.com/openjournals/heroku-buildpack-tex/pull/2

[roflmaostc]

Thanks a lot for pushing this forward!

[arfon]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #75 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: 'here.sty' from line
  '! LaTeX Error: File `here.sty' not found.'
Latexmk: Missing input file: 'here.sty' from line
  '! LaTeX Error: File `here.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

[arfon]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[roflmaostc]

What are the next steps to do?

[roflmaostc]

Any updates?

[roflmaostc]

Ping :)

[roflmaostc]

@matbesancon I was wondering if you're still interested to review this article? Thanks!

[vchuravy]

@whedon

[whedon]

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

@whedon commands

[vchuravy]

@whedon assign @matbesancon as reviewer

[whedon]

OK, @matbesancon is now a reviewer

[vchuravy]

@roflmaostc do you have suggestions for a potential second reviewer?

[roflmaostc]

Is the list still up-to-date? The only other person I can see is @sloede :smile:

[roflmaostc]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[vchuravy]

@whedon assign @sloede as reviewer

[whedon]

OK, @sloede is now a reviewer

[vchuravy]

@whedon commands

[whedon]

Here are some things you can ask me to do:

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[vchuravy]

@whedon add @matbesancon as reviewer

[whedon]

OK, @matbesancon is now a reviewer

[vchuravy]

@whedon start review