editorialbot commented 9 months ago

Submitting author: !--author-handle-->@SarahMaman@kellyrowland<!--end-editor-- Reviewers: @CFGrote, @tkchafin, @mjsull Archive: 10.5281/zenodo.14017260

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78/status.svg)](https://joss.theoj.org/papers/28bdee481573be53fe060f10ba415a78)

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

@CFGrote & @tkchafin, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @CFGrote

📝 Checklist for @tkchafin

📝 Checklist for @mjsull

editorialbot commented 9 months ago

Hello humans, 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:

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

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editorialbot commented 9 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.46 s (184.1 files/s, 40390.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
HTML                             24            599            192           8340
Python                           10            460           1394           3029
Markdown                         31            854              0           2015
Perl                              2            151            150            362
Bourne Shell                      4             69             89            246
JavaScript                        6              0             70            179
TeX                               1             13              3            123
YAML                              2              4             16             40
CSS                               3              0              6              3
Bourne Again Shell                1              3             16              2
--------------------------------------------------------------------------------
SUM:                             84           2153           1936          14339
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 9 months ago

Wordcount for paper.md is 1746

editorialbot commented 9 months ago

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

OK DOIs

- 10.1186/1471-2105-15-293 is OK
- 10.1038/nsmb.2143 is OK
- 10.1038/s41477-020-0688-1 is OK
- 10.1101/gr.177790.114 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1038/nmeth.3317 is OK
- 10.1093/bioinformatics/bts635 is OK
- 10.1093/nar/gks251 is OK
- 10.1038/nmeth.3176 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

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

tkchafin commented 9 months ago

Review checklist for @tkchafin

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 https://forgemia.inra.fr/bios4biol/intronseeker?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@SarahMaman) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] 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

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

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] 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, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] 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?

CFGrote commented 9 months ago

Review checklist for @CFGrote

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 https://forgemia.inra.fr/bios4biol/intronseeker?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@SarahMaman) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

kellyrowland commented 8 months ago

thanks for getting started here @tkchafin @CFGrote - please let me know if you have any questions/concerns or need to set the review down.

tkchafin commented 8 months ago

Hi @kellyrowland I have time blocked out for this in 2 weeks if that is ok

kellyrowland commented 8 months ago

totally fine, thanks!

CFGrote commented 8 months ago

Functionality/Installation

I followed the instructions in Install.md and hit this roadblock (after cloning the repo)

▶ conda install -n base --override-channels -c conda-forge mamba 'python_abi=*=*cp*'
...
-> ok

▶ cd intronseeker

▶ CONDA_SOLVER="libmamba" /bin/bash ./setup.sh

### Begin installing intronSeeker...

### Conda environment installing... 

SpecNotFound: Anaconda Client is required to interact with anaconda.org or an Anaconda API. Please run `conda install anaconda-client -n base`.

FAIL : Conda environment installation FAILED.

CFGrote commented 8 months ago

The code's repo (https://forgemia.inra.fr/bios4biol/intronseeker) is not on a public repo hosting service, so I cannot open issues nor push pull requests. This severely limits options for the community to contribute to or comment on the code. I would strongly suggest to move the repo to a public service such as github.com, bitbucket.org, gitlab.com. @SarahMaman, can you comment?

SarahMaman commented 8 months ago

Hello, Thank you for your feedback. We are going to add a site on github for issues so that people can post their issues without being connected to the forge-mia site, they just need a github account. And, if possible, we'll leave the code on forge-mia .

The code's repo (https://forgemia.inra.fr/bios4biol/intronseeker) is not on a public repo hosting service, so I cannot open issues nor push pull requests. This severely limits options for the community to contribute to or comment on the code. I would strongly suggest to move the repo to a public service such as github.com, bitbucket.org, gitlab.com. @SarahMaman, can you comment?

tkchafin commented 8 months ago

One of the submission requirements for JOSS is "The software must be hosted at a location where users can open issues and propose code changes without manual approval of (or payment for) accounts."

I think the proposed solution to separate the code from the public access point would be confusing, and also still not provide a mechanism for users to propose changes (i.e., via forking and a pull request). Contributing guidelines are something else that will come up during the review -- is there a reason why the code needs to be hosted on the private gitlab?

Kevin-Mattheus-Moerman commented 8 months ago

@SarahMaman indeed our requirements state "The software must be hosted at a location where users can open issues and propose code changes without manual approval of (or payment for) accounts.". Please ensure your software is hosted on a public repository and that forking/posting issues are enabled. If you are unable to comply with this requirement we will unfortunately need to reject this submission.

SarahMaman commented 8 months ago

@SarahMaman indeed our requirements state "The software must be hosted at a location where users can open issues and propose code changes without manual approval of (or payment for) accounts.". Please ensure your software is hosted on a public repository and that forking/posting issues are enabled. If you are unable to comply with this requirement we will unfortunately need to reject this submission.

We understand, we'll export intronSeeker to GitHub.

Kevin-Mattheus-Moerman commented 8 months ago

@SarahMaman thanks. Please let us know what the repository address is and myself or @kellyrowland will update it here then.

SarahMaman commented 8 months ago

Functionality/Installation

I followed the instructions in Install.md and hit this roadblock (after cloning the repo)

▶ conda install -n base --override-channels -c conda-forge mamba 'python_abi=*=*cp*'
...
-> ok

▶ cd intronseeker

▶ CONDA_SOLVER="libmamba" /bin/bash ./setup.sh

### Begin installing intronSeeker...

### Conda environment installing... 

SpecNotFound: Anaconda Client is required to interact with anaconda.org or an Anaconda API. Please run `conda install anaconda-client -n base`.

FAIL : Conda environment installation FAILED.

Hello, I have added this command conda install anaconda-client -n base to the installation documentation. Thanks a lot.

kellyrowland commented 7 months ago

thanks for the updates here @SarahMaman - please let me know when the code has been exported to GitHub and I'll ping the reviewers here to continue the review process.

Bios4Biol commented 7 months ago

Please accept our apologies for our late response, we encountered issues during the import from GitLab to GitHub due to the presence of large files in our history. Here is our GitHub repository: https://github.com/Bios4Biol/intronSeeker Thanks you for your patience.

kellyrowland commented 7 months ago

thank you!

@CFGrote @tkchafin the code repository has been migrated to GitHub, so please take a look at your earliest convenience.

CFGrote commented 7 months ago

I'm busy with teaching this and next week. Hope I'll find time to continue my review after Easter.

kellyrowland commented 7 months ago

thanks, that sounds fine. no worries if other things pick up and you need to set this down, just let me know.

Kevin-Mattheus-Moerman commented 7 months ago

@editorialbot set https://github.com/Bios4Biol/intronSeeker as repository

editorialbot commented 7 months ago

Done! repository is now https://github.com/Bios4Biol/intronSeeker

Kevin-Mattheus-Moerman commented 7 months ago

@SarahMaman thanks for moving the repository. Below is another point that requires your attention:

[x] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).

Bios4Biol commented 7 months ago

@SarahMaman thanks for moving the repository. Below is another point that requires your attention:

* [ ]  Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a `CONTRIBUTING.md` file (see here for some examples: https://contributing.md/example/).

Done ! Thanks for your help.

tkchafin commented 7 months ago

Installation issue doesn't seem to have been addressed, so I've been unable to verify any functional claims. I'm moving this week, and starting a new job soon, so I think I will have to withdraw from this. My apologies for the inconvenience.

kellyrowland commented 6 months ago

no problem at all, thanks for the heads up and good luck with everything!

kellyrowland commented 6 months ago

@CFGrote please let me know if you're able to continue with the review with the recent updates - no problem if you have to set it down.

kellyrowland commented 6 months ago

hi @clreda 👋 would you be interested in and available to help review this JOSS submission?

CFGrote commented 6 months ago

I'll be back in office tomorrow after a spring break and will resume my review.

clreda commented 6 months ago

hi @clreda 👋 would you be interested in and available to help review this JOSS submission?

Thanks for the opportunity to review. Unfortunately, I have a lot of deadlines next month so I won't be able to give a good review quickly. Sorry for the inconvenience

kellyrowland commented 6 months ago

no problem, thanks for the quick response!

kellyrowland commented 6 months ago

hi @stevokeyo 👋 would you be interested in and available to help review this JOSS submission?

kellyrowland commented 6 months ago

hi @jnarayan81 👋 would you be interested in and available to help review this JOSS submission?

jnarayan81 commented 6 months ago

@kellyrowland I appreciate the invitation, but unfortunately, due to my current workload, I must decline at this time. Thank you for considering me.

kellyrowland commented 6 months ago

no problem, thanks for the quick response!

CFGrote commented 6 months ago

I closed https://github.com/Bios4Biol/intronSeeker/issues/3. The authors confirmed there are no automated tests and they sound like they do not intend to add such tests. @kellyrowland , I hence cannot check the "Automated Tests" checkbox in https://github.com/openjournals/joss-reviews/issues/6272#issuecomment-1907504163? Is checking that box a requirement for publication in JOSS?

kellyrowland commented 6 months ago

@CFGrote automation of tests is not a requirement, as long as there are

manual steps described so that the functionality of the software can be verified

as listed in the checkbox item.

kellyrowland commented 5 months ago

hi @alexmascension 👋 would you be interested in and available to help review this JOSS submission?

alexmascension commented 5 months ago

hi @alexmascension 👋 would you be interested in and available to help review this JOSS submission?

Hi! I'd love to but the current workload I'm facing doesn't allow me to perform this review. Nonetheless, I'd like to be considered for future reviews if that's the case.

Best!

kellyrowland commented 5 months ago

hi again @clreda 👋 I've been having some trouble getting another reviewer here... is there any chance that you might have some bandwidth for this? or is there anyone you could suggest who might be interested and available for reviewing?

clreda commented 5 months ago

Hi! I have a huge deadline on June 4th. After that day, I can review the paper and the software, if that is acceptable to you. Sorry for the inconvenience

kellyrowland commented 5 months ago

thanks so much for your responsiveness - I'll keep looking for reviewers in the mean time but may end up reaching out after then.

kellyrowland commented 5 months ago

hi @mjsull @MmasterT 👋 would you be interested in and available to help review this JOSS submission?

mjsull commented 5 months ago

Hi @kellyrowland , happy to review.

kellyrowland commented 5 months ago

thanks very much!

kellyrowland commented 5 months ago

@editorialbot add @mjsull to reviewers

editorialbot commented 5 months ago

@mjsull added to the reviewers list!

openjournals / joss-reviews

[REVIEW]: Finding and removing introns from RNA-Seq de novo assemblies with IntronSeeker #6272

Status

Reviewer instructions & questions

Checklists

Review checklist for @tkchafin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @CFGrote

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Functionality/Installation

Functionality/Installation