[PRE REVIEW]: Sciris: Simplifying scientific software in Python

[editorialbot]

Submitting author: !--author-handle-->@cliffckerr<!--end-author-handle-- (Cliff Kerr) Repository: https://github.com/sciris/sciris Branch with paper.md (empty if default branch): joss Version: 2.1.0 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @tacaswell, @aflaxman Managing EiC: Daniel S. Katz

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Markdown: [![status](https://joss.theoj.org/papers/e0a824bc62088eeee05f12a029e71f4e/status.svg)](https://joss.theoj.org/papers/e0a824bc62088eeee05f12a029e71f4e)

Author instructions

Thanks for submitting your paper to JOSS @cliffckerr. Currently, there isn't a JOSS editor assigned to your paper.

@cliffckerr if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

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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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.53 s (138.6 files/s, 44942.4 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           37           3575           4951           9842
TeX                               6            314            274           2141
XML                               1              1              0           1004
reStructuredText                 14            403            208            814
Markdown                          3             51              0            151
YAML                              3              2              5             59
CSS                               1             15              5             56
Bourne Again Shell                4             11              4             31
DOS Batch                         1              8              1             26
HTML                              2              7              0             15
make                              1              5              6             14
INI                               1              0              0              3
--------------------------------------------------------------------------------
SUM:                             74           4392           5454          14156
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2311

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

👋 @cliffckerr - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. Please use the command @editorialbot generate pdf after making changes to the .md file to make a new PDF. editorialbot commands need to be the first entry in a new comment.

The problem here is

Problem with ORCID (Sherrie Kelly) for Sherrie Kelly. ORCID looks malformed

which is occurring because the ORCID line has her name and not her ORCID. Please either change this to her ORCID, or if she does not have one, remove this line.

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1101/2020.05.10.20097469 may be a valid DOI for title: Covasim: an agent-based model of COVID-19 dynamics and interventions
- 10.25080/majora-212e5952-00e may be a valid DOI for title: Python vs. the pandemic: a case study in high-stakes software development
- 10.1596/978-1-4648-1523-2_ch13 may be a valid DOI for title: Optima HIV methodology and approach
- 10.12688/gatesopenres.13031.2 may be a valid DOI for title: The Cascade Analysis Tool: software to analyze and optimize care cascades
- 10.1596/31366 may be a valid DOI for title: Optima Nutrition: an allocative efficiency tool to reduce childhood stunting by better targeting of nutrition-related interventions
- 10.1371/journal.pcbi.1009255 may be a valid DOI for title: Optima TB: A tool to help optimally allocate tuberculosis spending
- 10.1371/journal.pone.0260247 may be a valid DOI for title: Using allocative efficiency analysis to inform health benefits package design for progressing towards Universal Health Coverage: Proof-of-concept studies in countries seeking decision support
- 10.1371/journal.pcbi.1008316 may be a valid DOI for title: Ten simple rules for writing Dockerfiles for reproducible data science
- 10.1093/femspd/ftz006 may be a valid DOI for title: Is epidemiology ready for Big Software?
- 10.1101/306951 may be a valid DOI for title: fMRIPrep: a robust preprocessing pipeline for functional MRI
- 10.1093/bioinformatics/bty407 may be a valid DOI for title: Nextstrain: real-time tracking of pathogen evolution
- 10.21105/joss.03021 may be a valid DOI for title: Seaborn: statistical data visualization
- 10.21105/joss.03262 may be a valid DOI for title: DataLad: distributed system for joint management of code, data, and their relationship
- 10.21105/joss.01891 may be a valid DOI for title: Hypothesis: A new approach to property-based testing
- 10.1038/s41592-018-0137-5 may be a valid DOI for title: Easing the burden of code review
- 10.21105/joss.01026 may be a valid DOI for title: Pingouin: statistics in Python.
- 10.3389/fninf.2017.00069 may be a valid DOI for title: Re-run, repeat, reproduce, reuse, replicate: transforming code into scientific contributions
- 10.1109/mcse.2011.35 may be a valid DOI for title: Mayavi: 3D visualization of scientific data
- 10.21105/joss.01450 may be a valid DOI for title: PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK)
- 10.1038/d41586-020-02462-7 may be a valid DOI for title: Challenge to scientists: does your ten-year-old code still run?

INVALID DOIs

- None

[danielskatz]

In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[cliffckerr]

Thanks @danielskatz -- I see the compile error and will address it shortly. I'm surprised though because the GitHub Action ran fine and produced the paper.zip artifact: https://github.com/sciris/sciris/actions/runs/3772305917

I've also been compiling locally without problem. I guess the build system here differs slightly from the GHA (or perhaps it's been updated since we cloned).

[cliffckerr]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1371/journal.pcbi.1009149 is OK
- 10.25080/majora-212e5952-00e is OK
- 10.1596/978-1-4648-1523-2_ch13 is OK
- 10.12688/gatesopenres.13031.2 is OK
- 10.1186/s12889-018-5294-z is OK
- 10.1371/journal.pcbi.1009255 is OK
- 10.1371/journal.pone.0260247 is OK
- 10.1371/journal.pcbi.1008316 is OK
- 10.1093/femspd/ftz006 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1093/bioinformatics/bty407 is OK
- 10.21105/joss.03021 is OK
- 10.21105/joss.03262 is OK
- 10.21105/joss.01891 is OK
- 10.1038/s41592-018-0137-5 is OK
- 10.21105/joss.01026 is OK
- 10.3389/fninf.2017.00069 is OK
- 10.1109/mcse.2011.35 is OK
- 10.21105/joss.01450 is OK
- 10.1038/d41586-020-02462-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[cliffckerr]

@editorialbot generate pdf

[editorialbot]

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

[cliffckerr]

We suggest the following reviewers (email addresses can be provided if needed):

• Maleknaz Nayebi (maleknaz), University of York
• James Hadfield (jameshadfield), Fred Hutch
• Abie Flaxman (aflaxman), University of Washington
• Joel Nothman (jnothman), Canva

[danielskatz]

👋 @tacaswell - would you be available to review this JOSS submission?

[danielskatz]

👋 @akritiko - would you be available to review this JOSS submission?

[danielskatz]

👋 @maleknaz and @jameshadfield - would one of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[danielskatz]

👋 @tacaswell - would you be available to review this JOSS submission? (re-asking after the holiday break)

[danielskatz]

👋 @akritiko - would you be available to review this JOSS submission? (re-asking after the holiday break)

[danielskatz]

👋 @maleknaz and @jameshadfield - would one of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html (re-asking after the holiday break)

[danielskatz]

👋 @aflaxman and @jnothman - would one of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[tacaswell]

I can review this.

[danielskatz]

Thanks @tacaswell - I'll add you in the system, and once we get another reviewer, I'll start the review

[danielskatz]

@editorialbot add @tacaswell as reviewer

[editorialbot]

@tacaswell added to the reviewers list!

[jnothman]

Sorry for the slow reply @cliffckerr! Glad you've got your review team. Cheers

[danielskatz]

@jnothman - we are looking for one more reviewer - Could this be you?

[danielskatz]

@thfriedrich - Would you be able to review this submission?

[danielskatz]

@zfergus - Would you be able to review this submission?

[aflaxman]

Are you still looking for additional reviewers? I can take this on.

From: Daniel S. Katz @.> Sent: Friday, January 6, 2023 11:05 AM To: openjournals/joss-reviews @.> Cc: Abraham Flaxman @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: Sciris: Simplifying scientific software in Python (Issue #5029)

👋 @aflaxmanhttps://urldefense.com/v3/__https:/github.com/aflaxman__;!!K-Hz7m0Vt54!knzz7eFBU3FRVdkQtMuYyK4LZv51KK0uYayhRhRBiP6gMEfz3EoSJNopn6bcLe37J6XRoplObJgpUdoRjyVw$ and @jnothmanhttps://urldefense.com/v3/__https:/github.com/jnothman__;!!K-Hz7m0Vt54!knzz7eFBU3FRVdkQtMuYyK4LZv51KK0uYayhRhRBiP6gMEfz3EoSJNopn6bcLe37J6XRoplObJgpUdDhJS0g$ - would one of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.htmlhttps://urldefense.com/v3/__https:/joss.readthedocs.io/en/latest/review_criteria.html__;!!K-Hz7m0Vt54!knzz7eFBU3FRVdkQtMuYyK4LZv51KK0uYayhRhRBiP6gMEfz3EoSJNopn6bcLe37J6XRoplObJgpUbjzq8V2$

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/openjournals/joss-reviews/issues/5029*issuecomment-1374017462__;Iw!!K-Hz7m0Vt54!knzz7eFBU3FRVdkQtMuYyK4LZv51KK0uYayhRhRBiP6gMEfz3EoSJNopn6bcLe37J6XRoplObJgpUVbn9-mk$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AAAMQJCX4EC6QZ3ZIMZ5WQ3WRBUGXANCNFSM6AAAAAATISRDVY__;!!K-Hz7m0Vt54!knzz7eFBU3FRVdkQtMuYyK4LZv51KK0uYayhRhRBiP6gMEfz3EoSJNopn6bcLe37J6XRoplObJgpUdIidhsf$. You are receiving this because you were mentioned.Message ID: @.**@.>>

[danielskatz]

👋 @aflaxman - yes! Thanks very much. I'll add you, and we can start the review.

[danielskatz]

@editorialbot add @aflaxman as reviewer

[editorialbot]

@aflaxman added to the reviewers list!

[danielskatz]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5076.