[REVIEW]: Taguette: open-source qualitative data analysis

whedon commented 3 years ago

Submitting author: @remram44 (Rémi Rampin) Repository: https://gitlab.com/remram44/taguette Version: 1.1.1 Editor: @Nikoleta-v3 Reviewers: @cmaimone, @vaneseltine Archive: 10.5281/zenodo.5574555

: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

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Markdown: [![status](https://joss.theoj.org/papers/41a812345a7342402c65c51dc7381774/status.svg)](https://joss.theoj.org/papers/41a812345a7342402c65c51dc7381774)

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

@alexhanna & @cmaimone, 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 @Nikoleta-v3 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 @vaneseltine

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

[x] I confirm that I read and will adhere to the JOSS 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 (@remram44) 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?
[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

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?

Review checklist for @cmaimone

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

[x] I confirm that I read and will adhere to the JOSS 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 (@remram44) 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?
[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

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?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @alexhanna , @cmaimone 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:

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Nikoleta-v3 commented 3 years ago

👋🏼 @remram44 @alexhanna @cmaimone this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements 🆙 As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3522 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@Nikoleta-v3 ) if you have any questions/concerns 😄

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.14 s (670.0 files/s, 168142.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          29           1074            735           6477
SVG                              5              0             32           4550
PO File                         12           1110           1457           3105
JavaScript                       5            179            144           1511
HTML                            20             92             17            952
Markdown                         5            141              0            383
CSS                              3             69             29            283
YAML                             1              9              0            121
TOML                             1             12              1             61
INI                              1             18              0             56
reStructuredText                 1             34              0             52
Bourne Shell                     5             10              1             51
Dockerfile                       1             10              4             23
Mako                             1              7              0             17
diff                             1              0              4              6
-------------------------------------------------------------------------------
SUM:                            91           2765           2424          17648
-------------------------------------------------------------------------------

Statistical information for the repository '8fbd5a1f22d0d6b1356ac09d' was
gathered on 2021/07/22.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Guillaume Deflaux                2             3              4            0.03
Kosovskih Svyatoslav             1            21              0            0.10
Mikaël Francoeur                 1             2              2            0.02
Remi Rampin                    668         15642           5579           99.59
Vicky Steeves                    4            34              6            0.19
vagrant                          2            12              3            0.07

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
Guillaume Deflaux             3          100.0          4.5                0.00
Kosovskih Svyatoslav          6           28.6         21.7                0.00
Mikaël Francoeur              2          100.0         18.8                0.00
Remi Rampin               10099           64.6         17.7                6.47
Vicky Steeves                 2            5.9         32.3                0.00
vagrant                       8           66.7         33.0                0.00

whedon commented 3 years ago

PDF failed to compile for issue #3522 with the following error:

 Can't find any papers to compile :-(

remram44 commented 3 years ago

@whedon generate pdf from branch 2021-joss-paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch 2021-joss-paper. Reticulating splines etc...

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

whedon commented 3 years ago

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

cmaimone commented 3 years ago

I'm not assigned to this issue currently (not sure why), so I can't edit the checklist

danielskatz commented 3 years ago

@whedon re-invite @cmaimone as reviewer

whedon commented 3 years ago

The reviewer already has a pending invite.

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

cmaimone commented 3 years ago

@whedon re-invite @cmaimone as reviewer

whedon commented 3 years ago

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

cmaimone commented 3 years ago

I need a new invite - the linked one expired or was revoked (I got both errors)

danielskatz commented 3 years ago

@whedon re-invite @cmaimone as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

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

danielskatz commented 3 years ago

👋 @arfon - I suspect a there's bug in whedon/etc here, as this has happened to me too many times, where I try to re-invite someone, whedon says they have a pending invitation, they try it and it doesn't work, and then the whedon command used again does give them a new invitation they can accept

Nikoleta-v3 commented 3 years ago

Thank you @danielskatz for taking care of the invites 🙏🏻

cmaimone commented 3 years ago

@remram44 - do you have documentation of the code anywhere? I see and appreciate the user guides and documentation. I'm looking for documentation other developers/contributors might use.

@Nikoleta-v3 - any guidance on whether documentation of the code is expected for GUI applications? Taguette has good user guides, but it may not have much in the way of documentation of the code -- such documentation would only be used by contributors to the software, not users of it.

remram44 commented 3 years ago

Thanks @cmaimone, we have contributing instructions in CONTRIBUTING.md and an overview of the code in ARCHITECTURE.md. We also have instructions to set up the repository for development in the README.

Otherwise we have docstrings in the code, but we don't render them to HTML.

cmaimone commented 3 years ago

@Nikoleta-v3 - thoughts on https://gitlab.com/remram44/taguette/-/issues/235?

cmaimone commented 3 years ago

@remram44 the database schema in ARCHITECTURE.md is particularly helpful for those who export their data. I'd consider referencing it in the user guide when you tell people they could export the database and work with it directly. I wouldn't have necessarily found that file on my own.

remram44 commented 3 years ago

@whedon generate pdf from branch 2021-joss-paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch 2021-joss-paper. Reticulating splines etc...

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:

Nikoleta-v3 commented 3 years ago

Hey :wave: @cmaimone. Apologies for taking some time to reply.

I agree that there should be documentation regarding contributing to the project.

The project does have a CONTRIBUTING.md file which alongside ARCHITECTURE.md they give enough information for more experienced developers to contribute. However, a “Running Tests” section is missing from the CONTRIBUTING.md @remram44.

I do feel like less experienced developers would struggle to contribute code to the project. This is not a requirement for publication but as a suggestion one could include more examples of “What you can contribute” and “How to” in the CONTRIBUTING.md.

Now regarding https://gitlab.com/remram44/taguette/-/issues/235.

There is no standard. Authors often cite direct dependencies, and I would also argue that it is better to cite too much as opposed to too little. I like the rule “I would tend to cite at least any dependencies that provide citation guidance”.

remram44 commented 3 years ago

Good point, I added instructions for running the tests: https://gitlab.com/remram44/taguette/-/blob/master/CONTRIBUTING.md#running-tests

cmaimone commented 3 years ago

Done with my review - recommend publishing

Nikoleta-v3 commented 3 years ago

Thank you very much for your review and your time @cmaimone 😄 👍🏻

Nikoleta-v3 commented 3 years ago

👋🏻 @alexhanna This is just a little nudge 📳 Any updates on your review?

Nikoleta-v3 commented 3 years ago

👋🏻 @alexhanna 📳 Any updates on your review?

Nikoleta-v3 commented 2 years ago

Hey @remram44 just to update you. I have spoken with the second reviewer 😃 They will be submitting their review soon.

Nikoleta-v3 commented 2 years ago

@whedon remove @alexhanna as reviewer

whedon commented 2 years ago

OK, @alexhanna is no longer a reviewer

Nikoleta-v3 commented 2 years ago

Hey @remram44 just to update you 👋🏻 I have emailed a few people asking them to review this submission. Apologies for the delay! We'll get this moving as soon as possible.

Nikoleta-v3 commented 2 years ago

@whedon add @vaneseltine as reviewer

whedon commented 2 years ago

OK, @vaneseltine is now a reviewer

Nikoleta-v3 commented 2 years ago

👋🏼 @vaneseltine this is the review thread for the paper. Thank you again for agreeing to review this submission! 😃

You have a checklists at the top of this thread with the JOSS requirements 🔝 As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #3522 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@Nikoleta-v3 ) if you have any questions/concerns 👍🏻 😄

vaneseltine commented 2 years ago

As I've been added in later, there's no checklist with my own name on it -- should I use the first (empty) list or a new one?

Nikoleta-v3 commented 2 years ago

@vaneseltine my bad -- sorry! 🙏🏻 Please use the first one, it should have your name now.

vaneseltine commented 2 years ago

I have completed my review of this software and its documentation. This is a nicely developed and stable project that has produced, and continues to improve, a useful open source tool for qualitative social science research. The paper is well-written and, in sum, Taguette will be a great addition to JOSS. I recommend publication.

Nikoleta-v3 commented 2 years ago

Thank you very much @vaneseltine for your review and for your time! 🙏🏻 @remram44 I will aim to have a final look over the submission by the latest tomorrow and then we should be good to go 🎉

Nikoleta-v3 commented 2 years ago

@whedon generate pdf from branch 2021-joss-paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch 2021-joss-paper. Reticulating splines etc...

whedon commented 2 years ago

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

Nikoleta-v3 commented 2 years ago

Thank you very much for your patience @remram44! Everything looks good 👍🏻

There are just two minor typos in the paper. Line 6 helps instead of help and line performs instead of perform

After you tweak the paper could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

I can then move forward with accepting the submission

Nikoleta-v3 commented 2 years ago

@whedon check references

Nikoleta-v3 commented 2 years ago

@whedon check references from branch 2021-joss-paper

whedon commented 2 years ago

Attempting to check references... from custom branch 2021-joss-paper

openjournals / joss-reviews