[REVIEW]: yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML

[whedon]

Submitting author: @jvanhoefer (Jakob Vanhoefer)
Repository: https://github.com/yaml2sbml-dev/yaml2sbml
Version: v0.2.3
Editor: @kellyrowland
Reviewer: @SirSharpest, @marouenbg
Archive: 10.5281/zenodo.4787416

⚠️ JOSS reduced service mode ⚠️

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 badge code:

HTML: <a href="https://joss.theoj.org/papers/e3bb5ce390699b881fbc1ec64b2ae580"><img src="https://joss.theoj.org/papers/e3bb5ce390699b881fbc1ec64b2ae580/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e3bb5ce390699b881fbc1ec64b2ae580/status.svg)](https://joss.theoj.org/papers/e3bb5ce390699b881fbc1ec64b2ae580)

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

@SirSharpest & @marouenbg, 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 @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 ✨

Review checklist for @SirSharpest

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jvanhoefer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 and who the target audience is?
• 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?

Review checklist for @marouenbg

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jvanhoefer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 and who the target audience is?
• 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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

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:

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

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.20 s (328.1 files/s, 36074.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            588            808           1297
YAML                            20            424             10           1167
SVG                              3              0              0            467
reStructuredText                11            191            106            262
Markdown                         4             51              0            209
Jupyter Notebook                 6              0           1240            182
XML                              1              0              0            179
INI                              1              9              0             76
DOS Batch                        1              8              1             26
Bourne Shell                     2             11              8             25
make                             1              5              7              9
-------------------------------------------------------------------------------
SUM:                            67           1287           2180           3899
-------------------------------------------------------------------------------


Statistical information for the repository '328896896852a3799bcc93e9' was
gathered on 2021/04/23.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Dilan Pathirana                  2           113              4            1.92
Jakob Vanhoefer                 97          3592           1389           81.79
Yannik Schälte                   5            64             90            2.53
dilpath                          3            10             16            0.43
martamatos                       9           698             77           12.73
yannikschaelte                   1            27             10            0.61

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
Dilan Pathirana             104           92.0          1.9               14.42
Jakob Vanhoefer            2196           61.1          4.0               11.52
Yannik Schälte               51           79.7          1.3               39.22
dilpath                       2           20.0          1.7              100.00
martamatos                  331           47.4          1.2               18.73
yannikschaelte                9           33.3         11.5                0.00

[whedon]

PDF failed to compile for issue #3215 with the following error:

 Can't find any papers to compile :-(

[kellyrowland]

@whedon generate pdf from branch JOSS_review

[whedon]

Attempting PDF compilation from custom branch JOSS_review. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[AoifeHughes]

@kellyrowland could you have whedon assign me, I'm not able to tick the checkboxes.

[kellyrowland]

Thanks for the ping, sorry about that!

@whedon add @SirSharpest as reviewer

[kellyrowland]

@SirSharpest I've assigned you to this manually.

[arfon]

@whedon re-invite @SirSharpest as reviewer

[whedon]

The reviewer already has a pending invite.

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

[arfon]

@SirSharpest - I think you need to accept the repository invite to be able to update the checkboxes.

[marouenbg]

Hi @kellyrowland, I should be able to do the review in 2 weeks, I have a grant deadline right now. Would that be ok with you?

[AoifeHughes]

@kellyrowland I've completed my review + checklist, this software package is an excellent example of open source software. I have given the authors some minor suggestions regarding potential issues which users on certain OS's may encounter. I am very happy to recommend acceptance.

[whedon]

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

[kellyrowland]

Hi @marouenbg - that's fine by me, thanks for the heads up. Apologies for the ping from Whedon, I'm a new editor and haven't quite figured my way around all of the moving pieces in these review issues.

[kellyrowland]

@whedon remind @marouenbg in two weeks

[whedon]

Reminder set for @marouenbg in two weeks

[marouenbg]

Hi @kellyrowland , I finished the review of yaml2sbml and the authors addressed all of my comments. I think it is a high quality contribution (docs, CI, notebook tutorial) and I wanted to congratulate the authors for such an amazing work and attention to detail.

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3215 with the following error:

 Can't find any papers to compile :-(

[kellyrowland]

@whedon generate pdf from branch JOSS_review

[whedon]

Attempting PDF compilation from custom branch JOSS_review. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kellyrowland]

@whedon accept from branch JOSS_review

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1093/bioinformatics/btv405 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btn051 is OK
- 10.1101/030312 is OK
- 10.1093/bioinformatics/btw056 is OK
- 10.1093/bioinformatics/btp401 is OK
- 10.1016/0378-4371(92)90283-V is OK
- 10.1063/1.2145882 is OK
- 10.1016/j.copbio.2008.06.011 is OK
- 10.1098/rspa.1927.0118 is OK

MISSING DOIs

- 10.1101/085001 may be a valid DOI for title: Dynamic Modeling, Parameter Estimation, and Uncertainty Analysis in R
- 10.1093/nar/gkj092 may be a valid DOI for title: BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
- 10.1049/ip-syb:20060010 may be a valid DOI for title: ScrumPy: metabolic modelling with Python
- 10.1073/pnas.6.7.410 may be a valid DOI for title: Analytical note on certain rhythmic relations in organic systems
- 10.1007/978-0-387-21830-4_2 may be a valid DOI for title: Deterministic nonperiodic flow

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2340

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2340, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch JOSS_review 

[jvanhoefer]

I just noticed, that the reference to the PEtab paper was broken and fixed that. Unfortunately the preview server is (currently) not working for me, which seems to be unrelated to that change.

The rest looks good and I am happy to see the paper accepted :)

[arfon]

@whedon accept from branch JOSS_review

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1093/bioinformatics/btv405 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btn051 is OK
- 10.1101/030312 is OK
- 10.1093/bioinformatics/btw056 is OK
- 10.1093/bioinformatics/btp401 is OK
- 10.1016/0378-4371(92)90283-V is OK
- 10.1063/1.2145882 is OK
- 10.1016/j.copbio.2008.06.011 is OK
- 10.1098/rspa.1927.0118 is OK

MISSING DOIs

- 10.1101/085001 may be a valid DOI for title: Dynamic Modeling, Parameter Estimation, and Uncertainty Analysis in R
- 10.1093/nar/gkj092 may be a valid DOI for title: BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
- 10.1049/ip-syb:20060010 may be a valid DOI for title: ScrumPy: metabolic modelling with Python
- 10.1073/pnas.6.7.410 may be a valid DOI for title: Analytical note on certain rhythmic relations in organic systems
- 10.1007/978-0-387-21830-4_2 may be a valid DOI for title: Deterministic nonperiodic flow

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2341

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2341, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch JOSS_review 

[arfon]

@jvanhoefer – can I just check that you've reviewed the suggested DOIs from Whedon above? If any of them are correct, please add them to your BibTeX file with e.g., doi = 10.1101/085001 for the first entry.

[jvanhoefer]

Thank you, I just added DOIs to all citations that I could find a DOI to (including all in the list).

[arfon]

@whedon accept from branch JOSS_review

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1093/bioinformatics/btab227 is OK
- 10.1093/bioinformatics/btv405 is OK
- 10.18637/jss.v088.i10 is OK
- 10.1093/nar/gkj092 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btn051 is OK
- 10.1101/030312 is OK
- 10.1093/bioinformatics/btw056 is OK
- 10.1093/bioinformatics/btp401 is OK
- 10.1049/ip-syb:20060010 is OK
- 10.1016/0378-4371(92)90283-V is OK
- 10.1063/1.2145882 is OK
- 10.1016/j.copbio.2008.06.011 is OK
- 10.1073/pnas.6.7.410 is OK
- 10.1113/jphysiol.1952.sp004764 is OK
- 10.1098/rspa.1927.0118 is OK
- 10.1038/120363a0 is OK
- 10.1175/1520-0469(1963)020<0130:DNF>2.0.CO;2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2344

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2344, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch JOSS_review 

[jvanhoefer]

Looks good to me! 👍

[arfon]

@whedon accept deposit=true from branch JOSS_review

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03215 joss-papers#2345
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03215
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@SirSharpest, @marouenbg – many thanks for your reviews here and to @kellyrowland for editing their first JOSS submission 🥳. JOSS relies upon the volunteer efforts of people like you and we simply wouldn't be able to do this without you ✨

@jvanhoefer – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03215/status.svg)](https://doi.org/10.21105/joss.03215)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03215">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03215/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03215/status.svg
   :target: https://doi.org/10.21105/joss.03215

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss