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

whedon commented 2 years ago

Submitting author: !--author-handle-->@roflmaostc<!--end-author-handle-- (Felix Wechsler) Repository: https://github.com/roflmaostc/DeconvOptim.jl Branch with paper.md (empty if default branch): Version: v0.7.1 Editor: Reviewers: @sloede, @matbesancon Archive:

Status

Status badge code:

HTML: <a href="https://proceedings.juliacon.org/papers/fbb7d7d0388a8a9f2f97cecc632cf29a"><img src="https://proceedings.juliacon.org/papers/fbb7d7d0388a8a9f2f97cecc632cf29a/status.svg"></a>
Markdown: [![status](https://proceedings.juliacon.org/papers/fbb7d7d0388a8a9f2f97cecc632cf29a/status.svg)](https://proceedings.juliacon.org/papers/fbb7d7d0388a8a9f2f97cecc632cf29a)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@sloede & @matbesancon, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @vchuravy know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @sloede

Conflict of interest

[x] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Authorship: Has the submitting author (@roflmaostc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Paper format

[x] Authors: Does the paper.tex file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
[x] Page limit: Is the page limit for full papers respected by the submitted document?

Content

[x] Context: is the scientific context motivating the work correctly presented?
[x] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[x] Results: are the results presented and compared to approaches with similar goals?

Review checklist for @matbesancon

Conflict of interest
[x] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Authorship: Has the submitting author (@roflmaostc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Paper format

[x] Authors: Does the paper.tex file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
[x] Page limit: Is the page limit for full papers respected by the submitted document?

Content

[x] Context: is the scientific context motivating the work correctly presented?
[x] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[x] Results: are the results presented and compared to approaches with similar goals?

roflmaostc commented 1 year ago

Hi! Just pinging again :smile:

roflmaostc commented 1 year ago

Another Ping :)

roflmaostc commented 1 year ago

Hi @matbesancon, anything to do from our side?

roflmaostc commented 1 year ago

Hi, it would be really cool to get some kind of feedback!

Best, Felix CC: @RainerHeintzmann

matbesancon commented 1 year ago

@roflmaostc very sorry for the delay, this slipped off my list for a while. You should get a review soon from me

matbesancon commented 1 year ago

thank you for all revisions, all good on my side

matbesancon commented 1 year ago

@vchuravy all good here I believe

roflmaostc commented 1 year ago

Thanks @matbesancon !

Anything to do from our side @vchuravy ?

roflmaostc commented 1 year ago

@vchuravy any help needed?

roflmaostc commented 1 year ago

@vchuravy ping :)

roflmaostc commented 1 year ago

:)

matbesancon commented 1 year ago

@whedon recommend-accept

whedon commented 1 year ago

No archive DOI set. Exiting...

matbesancon commented 1 year ago

@whedon set v0.7.1 as version

whedon commented 1 year ago

OK. v0.7.1 is the version.

matbesancon commented 1 year ago

@roflmaostc you will need to create a zenodo archive of the repository, once this is done can you post the DOI here?

roflmaostc commented 1 year ago

Thanks!

10.5281/zenodo.8058675

https://doi.org/10.5281/zenodo.8058675

roflmaostc commented 11 months ago

@matbesancon Is that ok?

matbesancon commented 10 months ago

@whedon set 10.5281/zenodo.8058675 as archive

whedon commented 10 months ago

OK. 10.5281/zenodo.8058675 is the archive.

matbesancon commented 10 months ago

@whedon recommend-accept

whedon commented 10 months ago

Attempting dry run of processing paper acceptance...

whedon commented 10 months ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1364/JOSA.62.000055 is OK
- 10.1086/111605 is OK
- 10.1109/ICCV.2017.491 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.21105/joss.00615 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.48550/arXiv.1810.07951 is OK
- 10.1007/BF01589116 is OK
- 10.1364/JOSAA.15.001077 is OK
- 10.2307/2334515 is OK
- 10.1016/j.ymeth.2016.12.015 is OK
- 10.1038/s41598-018-29768-x is OK
- 10.1145/1401132.1401152 is OK
- 10.1016/j.micron.2006.07.009 is OK
- 10.1017/9781108552660 is OK
- 10.5281/zenodo.5047410 is OK
- 10.1016/j.advengsoft.2019.02.002 is OK
- 10.48550/arXiv.1608.04295 is OK
- 10.5334/jors.151 is OK
- 10.1109/TPDS.2018.2872064 is OK

MISSING DOIs

- None

INVALID DOIs

- 2946.001.0001 is INVALID

whedon commented 10 months ago

PDF failed to compile for issue #99 with the following error:

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 Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235]
[236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247]
[248] [249] [250] [251] [252] [253] [254] [255])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf
 Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139]
[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151]
[152] [153] [154] [155] [156] [157])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf
 Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170]
[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182]
[183] [184] [185] [186] [187] [188])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf
 Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125]
[95] [127] [32]) (/app/.texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf
 Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58]
[59] [61] [96] [189] [17] [45] [16] [21] [22])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf
 Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf
 Ok [24] [34] [35] [36] [37] [64] [191] [159])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf
 Ok [25] [26] [28] [27] [29] [30] [31])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf
 Ok [38] [63] [190])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf
 Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78]
[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf
 Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108]
[109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120]
[121] [122]) (/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf
 Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57])
(/app/.texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf
 Ok) ) ) )
Font metrics written on ectt1000.tfm.
Output written on ectt1000.600gf (256 characters, 43832 bytes).
Transcript written on ectt1000.log.
mktexpk: /app/.texlive/var/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1000.600pk: successfully generated.
Latexmk: Non-existent bbl file 'paper.bbl'
 No file paper.bbl.
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'paper.pdf'
Latexmk: List of undefined refs and citations:
  Citation `BenchmarkTools.jl-2016' on page 4 undefined on input line 323
  Citation `CUDA' on page 1 undefined on input line 94
  Citation `FFTW05' on page 1 undefined on input line 87
  Citation `Good:71' on page 3 undefined on input line 269
  Citation `Kruse_2017_ICCV' on page 1 undefined on input line 58
  Citation `LBFGS' on page 2 undefined on input line 172
  Citation `Richardson:72' on page 1 undefined on input line 54
  Citation `Verveer:98' on page 3 undefined on input line 269
  Citation `Zygote.jl-2018' on page 2 undefined on input line 171
  Citation `besard2018juliagpu' on page 2 undefined on input line 169
  Citation `bezanson2017julia' on page 1 undefined on input line 60
  Citation `deconvlab2' on page 6 undefined on input line 538
  Citation `deconvlab2' on page 6 undefined on input line 546
  Citation `ikoma2018convex' on page 6 undefined on input line 546
  Citation `jax2018github' on page 5 undefined on input line 528
  Citation `lucy:74' on page 1 undefined on input line 54
  Citation `michael_abbott_2021_5047410' on page 3 undefined on input line 286
  Citation `mogensen2018optim' on page 2 undefined on input line 172
  Citation `rel_energy_regain' on page 4 undefined on input line 419
  Citation `wiener2013extrapolation' on page 1 undefined on input line 55
  Reference `eq:fftconv' on page 1 undefined on input line 88
  Reference `eq:gradpoisson' on page 3 undefined on input line 263
  Reference `eq:poisson_loss' on page 3 undefined on input line 263
  Reference `fig:1D_dataset' on page 4 undefined on input line 328
  Reference `fig:1D_datasetb' on page 4 undefined on input line 348
  Reference `fig:1D_datasetb' on page 4 undefined on input line 357
  Reference `fig:fabioa' on page 4 undefined on input line 363
  Reference `fig:fabiob' on page 4 undefined on input line 409
  Reference `fig:fabioc' on page 4 undefined on input line 413
  Reference `fig:fabioc' on page 4 undefined on input line 459
  Reference `fig:fabiod' on page 4 undefined on input line 416
  Reference `fig:ncc' on page 4 undefined on input line 451
  Reference `fig:pipeline' on page 2 undefined on input line 150
  Reference `fig:rel_energy_regain' on page 4 undefined on input line 419
  Reference `fig:result_3d' on page 5 undefined on input line 465
  Reference `fig:withoutpad' on page 2 undefined on input line 99
  Reference `fig:withpad' on page 2 undefined on input line 104
  Reference `fig:wrap_around' on page 3 undefined on input line 199
  Reference `img:results' on page 6 undefined on input line 578
  Reference `sec:wrap' on page 2 undefined on input line 142
  Reference `tab:deconv' on page 6 undefined on input line 538
  Reference `tab:deconvprop' on page 6 undefined on input line 539
  Reference `tab:deconvprop' on page 6 undefined on input line 562
  Reference `tab:reg' on page 5 undefined on input line 489
Latexmk: Found bibliography file(s) [ref.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 27 reference(s)
  Latex failed to resolve 22 citation(s)
Rule 'bibtex paper': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
   Non-existent destination files:
      'paper.bbl'
------------
Run number 1 of rule 'bibtex paper'
------------
------------
Running 'bibtex  "paper"'
------------
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
      'paper.bbl'
      'paper.out'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: Found input bbl file 'paper.bbl'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'paper.pdf'
Latexmk: List of undefined refs and citations:
  Citation `BenchmarkTools.jl-2016' on page 4 undefined on input line 323
  Citation `CUDA' on page 1 undefined on input line 94
  Citation `FFTW05' on page 1 undefined on input line 87
  Citation `Good:71' on page 3 undefined on input line 269
  Citation `Kruse_2017_ICCV' on page 1 undefined on input line 58
  Citation `LBFGS' on page 2 undefined on input line 172
  Citation `Richardson:72' on page 1 undefined on input line 54
  Citation `Verveer:98' on page 3 undefined on input line 269
  Citation `Zygote.jl-2018' on page 2 undefined on input line 171
  Citation `besard2018juliagpu' on page 2 undefined on input line 169
  Citation `bezanson2017julia' on page 1 undefined on input line 60
  Citation `deconvlab2' on page 6 undefined on input line 538
  Citation `deconvlab2' on page 6 undefined on input line 546
  Citation `ikoma2018convex' on page 6 undefined on input line 546
  Citation `jax2018github' on page 5 undefined on input line 528
  Citation `lucy:74' on page 1 undefined on input line 54
  Citation `michael_abbott_2021_5047410' on page 3 undefined on input line 286
  Citation `mogensen2018optim' on page 2 undefined on input line 172
  Citation `rel_energy_regain' on page 4 undefined on input line 419
  Citation `wiener2013extrapolation' on page 1 undefined on input line 55
Latexmk: Found bibliography file(s) [ref.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 22 citation(s)
Rule 'bibtex paper': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'bibtex paper'
------------
------------
Running 'bibtex  "paper"'
------------
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: Found input bbl file 'paper.bbl'
Latexmk: Log file says output to 'paper.pdf'
Latexmk: Found bibliography file(s) [ref.bib]
/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:82:in `doi_citation': undefined method `encode' for nil:NilClass (NoMethodError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:64:in `make_citation'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:50:in `block in generate_citations'
    from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:149:in `each'
    from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:149:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:43:in `generate_citations'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/compilers.rb:202:in `crossref_from_latex'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/compilers.rb:19:in `generate_crossref'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:100:in `compile'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:88:in `compile'
    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>'

matbesancon commented 10 months ago

@whedon generate pdf

whedon commented 10 months ago

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

matbesancon commented 10 months ago

@whedon recommend-accept

whedon commented 10 months ago

Attempting dry run of processing paper acceptance...

whedon commented 10 months ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1364/JOSA.62.000055 is OK
- 10.1086/111605 is OK
- 10.1109/ICCV.2017.491 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.21105/joss.00615 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.48550/arXiv.1810.07951 is OK
- 10.1007/BF01589116 is OK
- 10.1364/JOSAA.15.001077 is OK
- 10.2307/2334515 is OK
- 10.1016/j.ymeth.2016.12.015 is OK
- 10.1038/s41598-018-29768-x is OK
- 10.1145/1401132.1401152 is OK
- 10.1016/j.micron.2006.07.009 is OK
- 10.1017/9781108552660 is OK
- 10.5281/zenodo.5047410 is OK
- 10.1016/j.advengsoft.2019.02.002 is OK
- 10.48550/arXiv.1608.04295 is OK
- 10.5334/jors.151 is OK
- 10.1109/TPDS.2018.2872064 is OK

MISSING DOIs

- None

INVALID DOIs

- 2946.001.0001 is INVALID

whedon commented 10 months ago

PDF failed to compile for issue #99 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: Non-existent bbl file 'paper.bbl'
 No file paper.bbl.
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'paper.pdf'
Latexmk: List of undefined refs and citations:
  Citation `BenchmarkTools.jl-2016' on page 4 undefined on input line 323
  Citation `CUDA' on page 1 undefined on input line 94
  Citation `FFTW05' on page 1 undefined on input line 87
  Citation `Good:71' on page 3 undefined on input line 269
  Citation `Kruse_2017_ICCV' on page 1 undefined on input line 58
  Citation `LBFGS' on page 2 undefined on input line 172
  Citation `Richardson:72' on page 1 undefined on input line 54
  Citation `Verveer:98' on page 3 undefined on input line 269
  Citation `Zygote.jl-2018' on page 2 undefined on input line 171
  Citation `besard2018juliagpu' on page 2 undefined on input line 169
  Citation `bezanson2017julia' on page 1 undefined on input line 60
  Citation `deconvlab2' on page 6 undefined on input line 538
  Citation `deconvlab2' on page 6 undefined on input line 546
  Citation `ikoma2018convex' on page 6 undefined on input line 546
  Citation `jax2018github' on page 5 undefined on input line 528
  Citation `lucy:74' on page 1 undefined on input line 54
  Citation `michael_abbott_2021_5047410' on page 3 undefined on input line 286
  Citation `mogensen2018optim' on page 2 undefined on input line 172
  Citation `rel_energy_regain' on page 4 undefined on input line 419
  Citation `wiener2013extrapolation' on page 1 undefined on input line 55
  Reference `eq:fftconv' on page 1 undefined on input line 88
  Reference `eq:gradpoisson' on page 3 undefined on input line 263
  Reference `eq:poisson_loss' on page 3 undefined on input line 263
  Reference `fig:1D_dataset' on page 4 undefined on input line 328
  Reference `fig:1D_datasetb' on page 4 undefined on input line 348
  Reference `fig:1D_datasetb' on page 4 undefined on input line 357
  Reference `fig:fabioa' on page 4 undefined on input line 363
  Reference `fig:fabiob' on page 4 undefined on input line 409
  Reference `fig:fabioc' on page 4 undefined on input line 413
  Reference `fig:fabioc' on page 4 undefined on input line 459
  Reference `fig:fabiod' on page 4 undefined on input line 416
  Reference `fig:ncc' on page 4 undefined on input line 451
  Reference `fig:pipeline' on page 2 undefined on input line 150
  Reference `fig:rel_energy_regain' on page 4 undefined on input line 419
  Reference `fig:result_3d' on page 5 undefined on input line 465
  Reference `fig:withoutpad' on page 2 undefined on input line 99
  Reference `fig:withpad' on page 2 undefined on input line 104
  Reference `fig:wrap_around' on page 3 undefined on input line 199
  Reference `img:results' on page 6 undefined on input line 578
  Reference `sec:wrap' on page 2 undefined on input line 142
  Reference `tab:deconv' on page 6 undefined on input line 538
  Reference `tab:deconvprop' on page 6 undefined on input line 539
  Reference `tab:deconvprop' on page 6 undefined on input line 562
  Reference `tab:reg' on page 5 undefined on input line 489
Latexmk: Found bibliography file(s) [ref.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 27 reference(s)
  Latex failed to resolve 22 citation(s)
Rule 'bibtex paper': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
   Non-existent destination files:
      'paper.bbl'
------------
Run number 1 of rule 'bibtex paper'
------------
------------
Running 'bibtex  "paper"'
------------
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
      'paper.bbl'
      'paper.out'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: Found input bbl file 'paper.bbl'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'paper.pdf'
Latexmk: List of undefined refs and citations:
  Citation `BenchmarkTools.jl-2016' on page 4 undefined on input line 323
  Citation `CUDA' on page 1 undefined on input line 94
  Citation `FFTW05' on page 1 undefined on input line 87
  Citation `Good:71' on page 3 undefined on input line 269
  Citation `Kruse_2017_ICCV' on page 1 undefined on input line 58
  Citation `LBFGS' on page 2 undefined on input line 172
  Citation `Richardson:72' on page 1 undefined on input line 54
  Citation `Verveer:98' on page 3 undefined on input line 269
  Citation `Zygote.jl-2018' on page 2 undefined on input line 171
  Citation `besard2018juliagpu' on page 2 undefined on input line 169
  Citation `bezanson2017julia' on page 1 undefined on input line 60
  Citation `deconvlab2' on page 6 undefined on input line 538
  Citation `deconvlab2' on page 6 undefined on input line 546
  Citation `ikoma2018convex' on page 6 undefined on input line 546
  Citation `jax2018github' on page 5 undefined on input line 528
  Citation `lucy:74' on page 1 undefined on input line 54
  Citation `michael_abbott_2021_5047410' on page 3 undefined on input line 286
  Citation `mogensen2018optim' on page 2 undefined on input line 172
  Citation `rel_energy_regain' on page 4 undefined on input line 419
  Citation `wiener2013extrapolation' on page 1 undefined on input line 55
Latexmk: Found bibliography file(s) [ref.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 22 citation(s)
Rule 'bibtex paper': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'bibtex paper'
------------
------------
Running 'bibtex  "paper"'
------------
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: Found input bbl file 'paper.bbl'
Latexmk: Log file says output to 'paper.pdf'
Latexmk: Found bibliography file(s) [ref.bib]
/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:82:in `doi_citation': undefined method `encode' for nil:NilClass (NoMethodError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:64:in `make_citation'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:50:in `block in generate_citations'
    from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:149:in `each'
    from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:149:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:43:in `generate_citations'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/compilers.rb:202:in `crossref_from_latex'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/compilers.rb:19:in `generate_crossref'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:100:in `compile'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:88:in `compile'
    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>'

matbesancon commented 10 months ago

@roflmaostc I believe the part to blame for the cryptic message above is the fact that one DOI seems invalid

roflmaostc commented 10 months ago

@whedon recommend-accept

whedon commented 10 months ago

I'm sorry @roflmaostc, I'm afraid I can't do that. That's something only editors are allowed to do.

matbesancon commented 10 months ago

@whedon recommend-accept

whedon commented 10 months ago

Attempting dry run of processing paper acceptance...

whedon commented 10 months ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1364/JOSA.62.000055 is OK
- 10.1086/111605 is OK
- 10.7551/mitpress/2946.003.0001 is OK
- 10.1109/ICCV.2017.491 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.21105/joss.00615 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.48550/arXiv.1810.07951 is OK
- 10.1007/BF01589116 is OK
- 10.1364/JOSAA.15.001077 is OK
- 10.2307/2334515 is OK
- 10.1016/j.ymeth.2016.12.015 is OK
- 10.1038/s41598-018-29768-x is OK
- 10.1145/1401132.1401152 is OK
- 10.1016/j.micron.2006.07.009 is OK
- 10.1017/9781108552660 is OK
- 10.5281/zenodo.5047410 is OK
- 10.1016/j.advengsoft.2019.02.002 is OK
- 10.48550/arXiv.1608.04295 is OK
- 10.5334/jors.151 is OK
- 10.1109/TPDS.2018.2872064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 10 months ago

:wave: @JuliaCon/jcon-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/JuliaCon/proceedings-papers/pull/71

If the paper PDF and Crossref deposit XML look good in https://github.com/JuliaCon/proceedings-papers/pull/71, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

matbesancon commented 10 months ago

@roflmaostc the paper is here: https://github.com/JuliaCon/proceedings-papers/blob/jcon.00099/jcon.00099/10.21105.jcon.00099.pdf

one thing maybe, could we have the code block on a single page instead of cut in two?

roflmaostc commented 10 months ago

@whedon generate pdf

whedon commented 10 months ago

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

roflmaostc commented 10 months ago

@matbesancon fixed

matbesancon commented 10 months ago

@whedon recommend-accept

whedon commented 10 months ago

Attempting dry run of processing paper acceptance...

whedon commented 10 months ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1364/JOSA.62.000055 is OK
- 10.1086/111605 is OK
- 10.7551/mitpress/2946.003.0001 is OK
- 10.1109/ICCV.2017.491 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.21105/joss.00615 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.48550/arXiv.1810.07951 is OK
- 10.1007/BF01589116 is OK
- 10.1364/JOSAA.15.001077 is OK
- 10.2307/2334515 is OK
- 10.1016/j.ymeth.2016.12.015 is OK
- 10.1038/s41598-018-29768-x is OK
- 10.1145/1401132.1401152 is OK
- 10.1016/j.micron.2006.07.009 is OK
- 10.1017/9781108552660 is OK
- 10.5281/zenodo.5047410 is OK
- 10.1016/j.advengsoft.2019.02.002 is OK
- 10.48550/arXiv.1608.04295 is OK
- 10.5334/jors.151 is OK
- 10.1109/TPDS.2018.2872064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 10 months ago

:wave: @JuliaCon/jcon-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/JuliaCon/proceedings-papers/pull/72

If the paper PDF and Crossref deposit XML look good in https://github.com/JuliaCon/proceedings-papers/pull/72, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

matbesancon commented 10 months ago

@whedon accept deposit=true

whedon commented 10 months ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 10 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JCON! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/JuliaCon/proceedings-papers/pull/73
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jcon.00099
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

matbesancon commented 10 months ago

perfect, thanks everyone for the submission and reviews :)

whedon commented 10 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://proceedings.juliacon.org/papers/10.21105/jcon.00099/status.svg)](https://doi.org/10.21105/jcon.00099)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00099">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00099/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00099/status.svg
   :target: https://doi.org/10.21105/jcon.00099

This is how it will look in your documentation:

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