[REVIEW]: patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening

[whedon]

Submitting author: @rickhelmus (Rick Helmus)
Repository: https://github.com/rickhelmus/patRoon
Branch with paper.md (empty if default branch): paper20
Version: v2.0.1
Editor: @KristinaRiemer
Reviewers: @wesleyburr, @hechth
Archive: 10.5281/zenodo.6337883

⚠️ 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/d0c9c8c937bbf8f9e00e12d1a9f95715"><img src="https://joss.theoj.org/papers/d0c9c8c937bbf8f9e00e12d1a9f95715/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d0c9c8c937bbf8f9e00e12d1a9f95715/status.svg)](https://joss.theoj.org/papers/d0c9c8c937bbf8f9e00e12d1a9f95715)

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

@wesleyburr & @hechth, 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 @KristinaRiemer 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 @wesleyburr

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@rickhelmus) 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 @hechth

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@rickhelmus) 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. @wesleyburr, @hechth 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:

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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]

PDF failed to compile for issue #4029 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.59 s (335.1 files/s, 158292.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             94              0              1         105126
HTML                           113           6754            879          49415
R                              179           5969           7970          25644
JavaScript                      30           3241           3334          13870
C++                             29           3394           1066          12257
Rmd                             20           1350           2031           1835
C/C++ Header                    31            664            753           1787
CSS                             17            172            118           1527
Markdown                         3            200              0            878
TeX                              2             30              0            388
YAML                             8             24              8            358
XML                              1              0              0            186
Dockerfile                       2             12              2             38
Julia                            1             12              1             30
PowerShell                       1              0              0              9
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           532          21822          16163         213349
-------------------------------------------------------------------------------


Statistical information for the repository '46f44dd325a5f97d69bd1fa6' was
gathered on 2021/12/31.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
CircleCI updater                16         42712          39448           59.85
Rick                             1             6              8            0.01
Rick Helmus                     54         25859           4974           22.46
rhelmus                         18         24154            103           17.67
rickhelmus                       2             6             11            0.01

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
CircleCI updater          27904           65.3         12.7               37.24
Rick Helmus               20289           78.5         29.2                9.18

[hechth]

@whedon generate pdf from branch paper20

[whedon]

Attempting PDF compilation from custom branch paper20. Reticulating splines etc...

[whedon]

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

[rickhelmus]

@whedon generate pdf from branch paper20

[whedon]

Attempting PDF compilation from custom branch paper20. Reticulating splines etc...

[whedon]

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

[whedon]

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

[whedon]

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

[hechth]

Just as quick update - the review is in progress, @rickhelmus already addressed some of my comments, so things are going great! I think it will take a bit more time since I also have to still test some things with different files (which is currently being delayed due to some internal issues). I don't think this will go beyond the 6 weeks usually required for the review.

In case a decision would have to be made before the formal end of the review, I'd highly recommend accepting the submission as the software and the paper are already of more than sufficient quality. Nevertheless, the points mentioned in the issues would be great to address before the publication.

[KristinaRiemer]

Hi @hechth, thank you for the update on the progress of your review! I agree that you and @rickhelmus should carry through with addressing all of your comments before publication.

@wesleyburr have you had a chance to start your review yet? Please check in with your progress and let me know if anything is blocking you!

[wesleyburr]

@KristinaRiemer - only thing is my inability to schedule my life. I'll get started tomorrow - my sincere apologies to the author for the delay.

[KristinaRiemer]

@wesleyburr it's all good, I think we're all familiar with time management struggles, especially these days! Thanks for checking in.

[rickhelmus]

@wesleyburr No worries! Thanks for the update!

[KristinaRiemer]

Hi @wesleyburr, just checking in again about your review?

And @rickhelmus, how is it going with addressing the issues from @hechth's review? It looks like some things are still in progress?

[hechth]

There is only a single issue which would be good to address before release (rickhelmus/patRoon#40), otherwise things are fine from my side - there are some bugs in the packages which are bundled within patRoon, but this is somewhat unavoidable and not the main responsibility of the author.

[rickhelmus]

Hi @KristinaRiemer & @hechth,

I hope to finalize rickhelmus/patRoon#40 this week. The feedback of @hechth has been very useful, many thanks!

[rickhelmus]

@whedon generate pdf from branch paper20

[whedon]

Attempting PDF compilation from custom branch paper20. Reticulating splines etc...

[KristinaRiemer]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.6337883 is OK
- 10.1016/j.trac.2008.09.010 is OK
- 10.1021/es1030799 is OK
- 10.1186/s13321-020-00477-w is OK
- 10.1126/science.aay3164 is OK
- 10.1073/pnas.1516878112 is OK
- 10.1016/j.trac.2021.116409 is OK
- 10.1002/cpz1.217 is OK
- 10.1186/s13321-021-00489-0 is OK
- 10.1016/j.envint.2021.106885 is OK
- 10.5281/zenodo.5644561 is OK
- 10.1186/s13321-016-0115-9 is OK
- 10.1038/nmeth.3959 is OK
- 10.1038/s41592-019-0344-8 is OK
- 10.1186/s13321-018-0324-5 is OK
- 10.1093/nar/gkv1229 is OK
- 10.1093/bioinformatics/btz207 is OK
- 10.1007/s11306-020-01738-3 is OK
- 10.1021/acs.analchem.9b02422 is OK
- 10.1021/acs.analchem.7b01547 is OK
- 10.1021/es5002105 is OK
- 10.32614/RJ-2021-048 is OK
- 10.1021/ci00057a005 is OK
- 10.1021/acs.analchem.5b02905 is OK
- 10.1007/s13361-017-1797-6 is OK
- 10.1016/j.watres.2021.117209 is OK
- 10.1073/pnas.1203689109 is OK
- 10.1016/1044-0305(94)87009-8 is OK
- 10.1186/gb-2003-4-4-210 is OK
- 10.1016/j.chemosphere.2018.09.140 is OK
- 10.1021/acs.analchem.6b01569 is OK
- 10.1093/bioinformatics/btx159 is OK
- 10.1016/j.jchromb.2017.06.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[KristinaRiemer]

@rickhelmus thank you for taking care of the updated archive and new version. The final step here is for an EiC to look over everything and confirm submission acceptance.

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3035

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3035, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[KristinaRiemer]

@editorialbot set v2.0.1 as archive

Whoops! "archive" was supposed to be "version" here, let me try that again.

[KristinaRiemer]

@editorialbot set 10.5281/zenodo.6337883 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6337883

[KristinaRiemer]

@editorialbot set v2.0.1 as version

[editorialbot]

Done! version is now v2.0.1

[KristinaRiemer]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.6337883 is OK
- 10.1016/j.trac.2008.09.010 is OK
- 10.1021/es1030799 is OK
- 10.1186/s13321-020-00477-w is OK
- 10.1126/science.aay3164 is OK
- 10.1073/pnas.1516878112 is OK
- 10.1016/j.trac.2021.116409 is OK
- 10.1002/cpz1.217 is OK
- 10.1186/s13321-021-00489-0 is OK
- 10.1016/j.envint.2021.106885 is OK
- 10.5281/zenodo.5644561 is OK
- 10.1186/s13321-016-0115-9 is OK
- 10.1038/nmeth.3959 is OK
- 10.1038/s41592-019-0344-8 is OK
- 10.1186/s13321-018-0324-5 is OK
- 10.1093/nar/gkv1229 is OK
- 10.1093/bioinformatics/btz207 is OK
- 10.1007/s11306-020-01738-3 is OK
- 10.1021/acs.analchem.9b02422 is OK
- 10.1021/acs.analchem.7b01547 is OK
- 10.1021/es5002105 is OK
- 10.32614/RJ-2021-048 is OK
- 10.1021/ci00057a005 is OK
- 10.1021/acs.analchem.5b02905 is OK
- 10.1007/s13361-017-1797-6 is OK
- 10.1016/j.watres.2021.117209 is OK
- 10.1073/pnas.1203689109 is OK
- 10.1016/1044-0305(94)87009-8 is OK
- 10.1186/gb-2003-4-4-210 is OK
- 10.1016/j.chemosphere.2018.09.140 is OK
- 10.1021/acs.analchem.6b01569 is OK
- 10.1093/bioinformatics/btx159 is OK
- 10.1016/j.jchromb.2017.06.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3042

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3042, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.04029 joss-papers#3046
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04029
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...

[Kevin-Mattheus-Moerman]

Congratualtions @rickhelmus on getting this work published in JOSS! 🥳

Thanks for editing @KristinaRiemer!

And thank you so much to the reviewers: @wesleyburr and @hechth !!!!

[editorialbot]

🎉🎉🎉 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.04029/status.svg)](https://doi.org/10.21105/joss.04029)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04029">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04029/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04029/status.svg
   :target: https://doi.org/10.21105/joss.04029

This is how it will look in your documentation:

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[rickhelmus]

Super happy to see it online now!! Thanks again @hechth, @wesleyburr, @KristinaRiemer! The submission led to a very nice and useful experience with JOSS.

[KristinaRiemer]

Congratulations @rickhelmus! And thanks again to @hechth and @wesleyburr for your reviews!