search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

[REVIEW]: Analysis of Prehistoric Iconography with the R package iconr #3191

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @zoometh (Huet Thomas) Repository: https://github.com/zoometh/iconr Version: v0.1.1 Editor: @hugoledoux Reviewer: @fbiljecki, @benmarwick Archive: 10.5281/zenodo.4767529

: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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e68e041e66a613918f76bf43db3f8b02"><img src="https://joss.theoj.org/papers/e68e041e66a613918f76bf43db3f8b02/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e68e041e66a613918f76bf43db3f8b02/status.svg)](https://joss.theoj.org/papers/e68e041e66a613918f76bf43db3f8b02)

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

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

  1. Make sure you're logged in to your GitHub account
  2. 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 @hugoledoux 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 @fbiljecki

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @benmarwick

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fbiljecki, @benmarwick it looks like you're currently assigned to review this paper :tada:.

: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.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

OK DOIs

- 10.11588/propylaeumdok.00000512 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.79 s (99.2 files/s, 20571.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            27           1332            286           8832
Rmd                              9            605            994            833
R                               15             58            262            796
CSS                              4            153             53            641
Markdown                         5            176              0            324
JavaScript                       5             64             34            274
XML                              5              0              0            182
TeX                              3             13              0            118
YAML                             4             19              9            111
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            78           2420           1639          12122
-------------------------------------------------------------------------------

Statistical information for the repository '39b3ce48a6f3950b5b869b0f' was
gathered on 2021/04/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Shennan                          4           436              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
Shennan                     436          100.0          0.0                9.63
whedon commented 3 years ago

Failed to discover a valid open source license.

whedon commented 3 years ago

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

whedon commented 3 years ago

:wave: @benmarwick, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @fbiljecki, please update us on how your review is going (this is an automated reminder).

fbiljecki commented 3 years ago

Kudos to the authors for developing this software and releasing it openly. Some comments:

hugoledoux commented 3 years ago

@zoometh the first review (from a GIS perspective) is in and it is a good idea to fix what is missing and update the submission now, you do not need to wait for the other reviewer (archeology perspective).

The part about citing and comparing in the paper to other similar software would be especially important to add.

zoometh commented 3 years ago

@hugoledoux, @fbiljecki: sorry for the delay, I will make the required changes in the very coming days

zoometh commented 3 years ago

@hugoledoux:

The part about citing and comparing in the paper to other similar software would be especially important to add.

We have made the required changes. The R package iconr is the first software that gives a parsimonious manner to model 'graphical units' and 'graphical compositions'. And, as a consequence, that permits to conduct cross-cultural and over the long-term comparisons with a minimal loss of information. Since not such a tool exists before, we insist on the theoretical background and the historiography of Archaeology.

@fbiljecki:

There is no LICENSE file, and the license is not explicit in the readme/documentation

We have added the GPL-3 license (https://github.com/zoometh/iconr/blob/master/LICENSE)

I cannot replicate the example in the paper before Fig 2 including the function plot_dec_grph() (I get object 'imgs' not found)

We have added the missing code lines before the plot_dec_grph() call:

nds.df <- read_nds(site, decor, dataDir)
eds.df <- read_eds(site, decor, dataDir)
imgs <- read.table(paste0(dataDir, "/imgs.tsv"),
                   sep="\t", stringsAsFactors = FALSE)
plot_dec_grph(nds.df, eds.df, imgs,
              site, decor, dataDir)

Please let me know if additional changes are needed

hugoledoux commented 3 years ago

@fbiljecki can you confirm that the changes made now allow you to run the example? If yes then please tick the checkbox above

fbiljecki commented 3 years ago

I confirm that I can now replicate the example code. Expecting that the same code will be included in the updated version of the paper, I do not have further comments.

hugoledoux commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

benmarwick commented 3 years ago

Congratulations to the authors on such as interesting and comprehensive package! Really wonderful to see this, and I am keen to employ it in my research. I could not edit the checklist above, so I paste it below here.

Conflict of interest

  • [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@zoometh) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality of the software can be verified?
  • [ No ] 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

    I have opened an issue for this here: https://github.com/zoometh/iconr/issues/73

Software paper

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
hugoledoux commented 3 years ago

@whedon re-invite @benmarwick as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@benmarwick please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

hugoledoux commented 3 years ago

thanks @benmarwick

I guess you didn't accept the invite a while ago and it wasn't valid anymore. I re-invited you, but also clicked the checkboxes on your behalf above.

Really wonderful to see this, and I am keen to employ it in my research.

Very nice to read this, this is the whole point of JOSS!

hugoledoux commented 3 years ago

@zoometh the review was very smooth so far, I suggest you look at the issue opened by @benmarwick and make the appropriate change, and then we can move forward with the acceptance of the paper.

zoometh commented 3 years ago

@hugoledoux As far as I understand, the only issue was about missing docs for contributors. I've added these docs and closed the issue. Is there's something I've forgotten?

hugoledoux commented 3 years ago

@whedon generate pdf

hugoledoux commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.11588/propylaeumdok.00000512 is OK

MISSING DOIs

- 10.2307/412043 may be a valid DOI for title: Cours de linguistique générale

INVALID DOIs

- None
whedon commented 3 years ago

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

hugoledoux commented 3 years ago

oh my bad, I had not noticed you already answered, sorry.

I have fixed a few things in the paper/bib and made 2 PR: https://github.com/zoometh/iconr/pull/74 https://github.com/zoometh/iconr/pull/75

and I have 3 things I am not sure about:

  1. the DOI checker complains about one book but not the others. I am not sure if all old books have DOIs, but we like DOIs at JOSS so could you check if all the books you cite have one? If you you add it?
  2. l.40: speaks of "Harris diagram", and a a layman I have no idea what those are. A reference perhaps?
  3. l.50: (birel: touches): here I have no clue what "birel" means. Perhaps it's me? Could you explain here and eventually in the text?
zoometh commented 3 years ago

I have fixed a few things in the paper/bib and made 2 PR: zoometh/iconr#74 zoometh/iconr#75

I've merged your corrections on paper.bib

  1. the DOI checker complains about one book but not the others. I am not sure if all old books have DOIs, but we like DOIs at JOSS so could you check if all the books you cite have one? If you you add it?

I found 1 supplementary DOI (for Hodder's book). I've added it

  1. l.40: speaks of "Harris diagram", and a a layman I have no idea what those are. A reference perhaps?

Done. I've added a short description of what is a Harris diagram, and a reference

  1. l.50: (birel: touches): here I have no clue what "birel" means. Perhaps it's me? Could you explain here and eventually in the text?

Done. I've changed "birel: touches" to a more explicit "binary topological relationship: touches"

zoometh commented 3 years ago

I've committed these changes and added also minor changes to avoid closing and opening parenthesis touching each other, e.g.: "..)(..".

I've run the Whedon preview: it seems fine

hugoledoux commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

hugoledoux commented 3 years ago

OK, both reviewers recommend acceptance so we're moving towards this.

At this point could you:

I can then move forward with accepting the submission.

zoometh commented 3 years ago

Make a tagged release of your software, and list the version tag of the archived version here

Done -> Warrior stelae

Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)... Please list the DOI of the archived version here.

Done. The DOI of the archive is 10.5281/zenodo.4767529

hugoledoux commented 3 years ago

Thanks @fbiljecki and @benmarwick for your reviews, it seems the quality of @zoometh submission was already very high and thus everything went very smoothly and quick 👍

Paper is now accepted, it will go to the editors who might have some further small comments.

hugoledoux commented 3 years ago

@whedon set 10.5281/zenodo.4767529 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4767529 is the archive.

hugoledoux commented 3 years ago

@whedon set v0.1.1 as version

whedon commented 3 years ago

OK. v0.1.1 is the version.

hugoledoux commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.11588/propylaeumdok.00000512 is OK
- 10.1017/CBO9780511558252 is OK

MISSING DOIs

- 10.2307/412043 may be a valid DOI for title: Cours de linguistique générale

INVALID DOIs

- None
whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2312

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2312, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
zoometh commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

I'm sorry @zoometh, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

zoometh commented 3 years ago

I guess the publishing process is about to be achieved, I would like to thank you: @fbiljecki, @benmarwick, and @hugoledoux for your editorial work

zoometh commented 3 years ago

I'm sorry @zoometh, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

Sorry @whed. I thought it was my turn to accept...

kyleniemeyer commented 3 years ago

@zoometh I'm the AEIC on duty this week, so I'll be doing some final checks on your submission before doing the official accept/publish steps.

kyleniemeyer commented 3 years ago

All looks good to me, moving to accept.

kyleniemeyer commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦