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[PRE REVIEW]: Delta-Rice: A HDF5 Compression Plugin optimized for Digitized Detector Data #6521

Closed editorialbot closed 6 months ago

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@david-mathews-1994<!--end-author-handle-- (David Mathews) Repository: https://github.com/david-mathews-1994/deltarice Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @macrocosme, @DanNixon, @dineshchitlangia Managing EiC: Daniel S. Katz

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/deb15ad629d7261988ec28b0e79d849a"><img src="https://joss.theoj.org/papers/deb15ad629d7261988ec28b0e79d849a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/deb15ad629d7261988ec28b0e79d849a/status.svg)](https://joss.theoj.org/papers/deb15ad629d7261988ec28b0e79d849a)

Author instructions

Thanks for submitting your paper to JOSS @david-mathews-1994. Currently, there isn't a JOSS editor assigned to your paper.

@david-mathews-1994 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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

@editorialbot commands
editorialbot commented 6 months ago

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

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (686.3 files/s, 257311.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                                6            293            645           4989
Markdown                         3            173              0            643
Python                           3            105             82            540
TeX                              1             26              0            205
YAML                             2              3              6             41
Cython                           1             24             13             34
C/C++ Header                     2             12              2             20
diff                             1              1              7              5
DOS Batch                        1              0              0              3
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            21            637            755           6482
-------------------------------------------------------------------------------

Commit count by author:

    83  david-mathews-1994
    48  David Mathews
     4  dgma224
editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 6756

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 6 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 6 months ago

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

editorialbot commented 6 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/JRPROC.1952.273898 is OK
- 10.1109/TIT.1966.1053907 is OK
- 10.1109/TCOM.1971.1090789 is OK
- 10.1007/s10751-018-1538-7 is OK
- 10.1051/epjconf/201921904002 is OK
- 10.1088/1748-0221/14/11/P11017 is OK
- 10.1088/1748-0221/17/09/P09020 is OK
- 10.5281/zenodo.7568214 is OK
- 10.1088/1748-0221/14/11/P11017 is OK

MISSING DOIs

- No DOI given, and none found for title: Measurement of the Fierz Interference Term for Cal...
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: GNU Gzip
- No DOI given, and none found for title: 7-Zip
- No DOI given, and none found for title: DeltaRice
- No DOI given, and none found for title: Delta-Rice
- 10.1109/99.660313 may be a valid DOI for title: OpenMP: an industry standard API for shared-memory...

INVALID DOIs

- https://doi.org/10.1016/j.nima.2020.163961 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.ascom.2015.07.002 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.13023/etd.2022.446 is INVALID because of 'https://doi.org/' prefix
danielskatz commented 6 months ago

👋 @david-mathews-1994 - thanks for your submission.

Your paper needs a lot of work before we can proceed. Please see the example paper. JOSS papers are expected to be short, pointing at documentation and other documents in the software repo, totaling 250-1000 words, while yours is almost 7000 words. You also need a section titled Statement of need.

Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF. You can also use @editorialbot check repository to check the length of the paper. editorialbot commands need to be the first entry in a new comment.

I'm going to pause this submission until you let me know that you've made changes and I should review this again.

david-mathews-1994 commented 6 months ago

Apologies for the different paper format than expected. JOSS appears to expect extremely different things from most traditional journals, and this paper was originally intended for a different destination so its format is more aligned with those requirements. I'll work on tweaking it to be more in line with the expectation of this journal.

danielskatz commented 6 months ago

The other choice is that JOSS may not be the right journal for what you want to accomplish with your paper and software. Please see https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages for other suggestions for how you might receive credit for your software, and https://www.software.ac.uk/top-tip/which-journals-should-i-publish-my-software for other journals that publish software papers.

david-mathews-1994 commented 6 months ago

I appreciate the links to other candidate journals. I'll start with some rough edits to the existing document to reduce the word count and length and see how that goes. If it seems possible to keep it short and still properly represent the material, then I'd prefer to continue using JOSS, but if not I may explore other options.

Thank you! I'd like to keep this open while I continue my editing if possible.

david-mathews-1994 commented 6 months ago

@editorialbot check repository

editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (692.3 files/s, 256177.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                                6            293            645           4989
Markdown                         4            232              0            851
Python                           3            105             82            540
TeX                              1             26              0            205
YAML                             2              3              6             41
Cython                           1             24             13             34
C/C++ Header                     2             12              2             20
diff                             1              1              7              5
DOS Batch                        1              0              0              3
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            22            696            755           6690
-------------------------------------------------------------------------------

Commit count by author:

    87  david-mathews-1994
    48  David Mathews
     4  dgma224
editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 5291

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

david-mathews-1994 commented 6 months ago

@editorialbot check repository

editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (706.2 files/s, 261074.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                                6            293            645           4989
Markdown                         4            228              0            847
Python                           3            105             82            540
TeX                              1             26              0            205
YAML                             2              3              6             41
Cython                           1             24             13             34
C/C++ Header                     2             12              2             20
diff                             1              1              7              5
DOS Batch                        1              0              0              3
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            22            692            755           6686
-------------------------------------------------------------------------------

Commit count by author:

    89  david-mathews-1994
    48  David Mathews
     4  dgma224
editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 3843

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

david-mathews-1994 commented 6 months ago

@editorialbot check repository

editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (681.6 files/s, 251790.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                                6            293            645           4989
Markdown                         4            221              0            840
Python                           3            105             82            540
TeX                              1             27              0            212
YAML                             2              3              6             41
Cython                           1             24             13             34
C/C++ Header                     2             12              2             20
diff                             1              1              7              5
DOS Batch                        1              0              0              3
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            22            686            755           6686
-------------------------------------------------------------------------------

Commit count by author:

    91  david-mathews-1994
    48  David Mathews
     4  dgma224
editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 3049

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

david-mathews-1994 commented 6 months ago

@danielskatz It appears the word count from the robot is also including tables, author information, as well as acknowledgements, but not references. Just the author list and funding acknowledgements is 565 words. Are these words that are taken into account when trying to keep the papers between 250 and 1000 words? For example, if I only count the words of actual paper content (section labels, each paragraph, image captions), ignoring tables, figures, author information, references, and acknowledgements, I'm seeing around 1800 words. I just want to be sure I'm understanding the recommendation when I'm doing my editing.

danielskatz commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

danielskatz commented 6 months ago

@david-mathews-1994 - I think you may be right about how the word count is done. However, having said that, your paper still seems quite long to me. I think if you could get your current self-measurement of 1800 words to 1000, this would likely be good. I think much of the performance section could be a performance.md file in the repo, with a small bit kept in the paper and then a link to that file, for example.

david-mathews-1994 commented 6 months ago

@danielskatz It's definitely a little bit too long still, I can work on that. I like the suggestion about the performance information. I'll see about moving that and some of the figures to a different document to keep it neater. I'm used to writing documents like this in Latex and not markdown files so the formatting of the various figures and tables is a bit rough at the moment. I appreciate the advice and I'll keep working on this.

david-mathews-1994 commented 6 months ago

@editorialbot check repository

editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (548.7 files/s, 336569.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                                7            484           1126          12087
Markdown                         7            242              0            871
Python                           3            105             82            540
TeX                              1             27              0            212
YAML                             2              3              6             41
Cython                           1             24             13             34
C/C++ Header                     2             12              2             20
diff                             1              1              7              5
DOS Batch                        1              0              0              3
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            26            898           1236          13815
-------------------------------------------------------------------------------

Commit count by author:

   109  david-mathews-1994
    49  David Mathews
     4  dgma224
editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 1821

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

david-mathews-1994 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

david-mathews-1994 commented 6 months ago

@danielskatz I'm getting a word count of just below 1000 words when only counting the actual content (ignoring stuff like tables and author information). I went through and moved a lot of the specifics to new markdown files in the docs/ folder within the repo so that information is still available to the end user if they're interested.

danielskatz commented 6 months ago

thanks - this content looks good to me now. I'll also check the references to make sure we've got all the DOIs...

danielskatz commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/JRPROC.1952.273898 is OK
- 10.1109/TIT.1966.1053907 is OK
- 10.1109/TCOM.1971.1090789 is OK
- 10.1007/s10751-018-1538-7 is OK
- 10.1051/epjconf/201921904002 is OK
- 10.1088/1748-0221/14/11/P11017 is OK
- 10.1088/1748-0221/17/09/P09020 is OK
- 10.5281/zenodo.7568214 is OK
- 10.1088/1748-0221/14/11/P11017 is OK

MISSING DOIs

- No DOI given, and none found for title: Measurement of the Fierz Interference Term for Cal...
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: GNU Gzip
- No DOI given, and none found for title: 7-Zip
- No DOI given, and none found for title: DeltaRice
- No DOI given, and none found for title: Delta-Rice
- 10.1109/99.660313 may be a valid DOI for title: OpenMP: an industry standard API for shared-memory...
- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- https://doi.org/10.1016/j.nima.2020.163961 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.ascom.2015.07.002 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.13023/etd.2022.446 is INVALID because of 'https://doi.org/' prefix
danielskatz commented 6 months ago

@david-mathews-1994 - please check to see if the one specific missing DOI above is correct (as it appears to be), and if so, please add it to your bib file, the regenerate your pdf again.

danielskatz commented 6 months ago

👋 @emdupre - do you think you would be able to edit this submission?

danielskatz commented 6 months ago

@editorialbot invite @emdupre as editor

editorialbot commented 6 months ago

Invitation to edit this submission sent!

david-mathews-1994 commented 6 months ago

@danielskatz It looks like Cupy doesn't actually have a DOI link, or at least their official guide doesn't provide one: https://github.com/cupy/cupy/blob/main/CITATION.bib. Otherwise there were a few old references that the paper doesn't actually use anymore (just leftovers from a previous version) so I removed all of those

david-mathews-1994 commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago

Checking the BibTeX entries failed with the following error: 

Failed to parse BibTeX on value "}" (RBRACE) [#<BibTeX::Bibliography data=[6]>, "@", #<BibTeX::Entry >, {:title=>["HDF5-Version 1.12.0"], :author=>["The HDF Group, None and Koziol, Quincey and USDOE Office of Science"], :abstractnote=>["The HDF5 library and file format implement the HDF5 data model for storing and managing data. This implementation supports an unlimited variety of datatypes and is designed for flexible and efficient I/O and for high volume and complex data. It is highly portable and extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format and other implementations."], :url=>["https://www.osti.gov/biblio/1631295"], :doi=>["10.11578/dc.20180330.1"], :year=>["2020"], :month=>["2"]}, ",", "note", "="]
david-mathews-1994 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

david-mathews-1994 commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.nima.2020.163961 is OK
- 10.1109/JRPROC.1952.273898 is OK
- 10.1109/TIT.1966.1053907 is OK
- 10.1109/TCOM.1971.1090789 is OK
- 10.1007/s10751-018-1538-7 is OK
- 10.1016/j.ascom.2015.07.002 is OK
- 10.11578/dc.20180330.1 is OK
- 10.13023/etd.2022.446 is OK
- 10.1051/epjconf/201921904002 is OK
- 10.1088/1748-0221/14/11/P11017 is OK
- 10.1088/1748-0221/17/09/P09020 is OK
- 10.5281/zenodo.7568214 is OK
- 10.1109/99.660313 is OK
- 10.1088/1748-0221/14/11/P11017 is OK

MISSING DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- None
emdupre commented 6 months ago

Thanks for the invitation, @danielskatz ! This is a bit outside of my expertise, but I think I should still be able to edit it. I'll go ahead and assign myself.

emdupre commented 6 months ago

@editorialbot assign @emdupre as editor