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[REVIEW]: epipack: An infectious disease modeling package for Python #3097

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @benmaier (Benjamin F. Maier) Repository: https://github.com/benmaier/epipack Version: v0.1.2 Editor: @fboehm Reviewer: @chrisvoncsefalvay, @esteinig Archive: 10.5281/zenodo.4655616

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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

@chrisvoncsefalvay & @esteinig, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @chrisvoncsefalvay

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @esteinig

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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whedon commented 3 years ago

Failed to discover a Statement of need section in paper

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/BF02464423 is OK
- 10.1021/j100540a008 is OK
- 10.1186/1471-2334-11-37 is OK
- 10.18637/jss.v084.i08 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.21105/joss.01731 is OK
- 10.1016/j.physrep.2020.07.005 is OK
- 10.1016/j.cpc.2019.02.008 is OK
- 10.7717/peerj-cs.103 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.18452/20950 is OK
- 10.1016/j.jtbi.2011.07.015 is OK
- 10.21105/joss.00565 is OK
- 10.1007/978-3-319-50806-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=2.67 s (51.7 files/s, 9249.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          85           3433           3717           8790
reStructuredText                34           1396           1934           1571
Markdown                         6            223              0            663
TeX                              1             18              0            246
make                             2             48              6            238
DOS Batch                        1             34              2            227
Jupyter Notebook                 2              0           2035             83
JSON                             3              0              0             10
Bourne Shell                     2              1              0              5
INI                              1              0              0              5
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                           138           5153           7694          11841
-------------------------------------------------------------------------------

Statistical information for the repository '893be85df9210d56380ab9e0' was
gathered on 2021/03/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ben F. Maier                    12           473             96            2.12
Benjamin Maier                 130         20924           5343           97.88

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
Ben F. Maier              15940         3370.0          5.7                7.67
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:

fboehm commented 3 years ago

Thank you, @esteinig and @chrisvoncsefalvay , for agreeing to review this submission. You can see above your checklists for the review process. Please reach out to me when questions come up.

chrisvoncsefalvay commented 3 years ago

The paper does not contain a 'statement of need' section. However, it is my view that the substance of this requirement (pasted below for reference) is addressed adequately in para.s 1 through 3. With that in mind, I would consider requirement 1 of the Documentation section to be met.

The authors should clearly state what problems the software is designed to solve and who the target audience is.

esteinig commented 3 years ago

The authors should clearly state what problems the software is designed to solve and who the target audience is.

Agreed, it is well addressed in the paragraphs

fboehm commented 3 years ago

@esteinig and @chrisvoncsefalvay - how are your reviews going? It looks like you both haven't yet checked the "installation" and "functionality" boxes. Are there issues that the authors should address?

chrisvoncsefalvay commented 3 years ago

@fboehm I have just completed my review. I've left the installation and functionality boxes last, as I wanted to give a thorough opinion. I have managed to install and test functionalities with success on a Mac OS Big Sur system. I am happy to check off the relevant box based on that, although I would note that the author himself states they have tested it on a Mac OS system – there may be issues on, say, Windows systems that would not have shown up in the course of my testing.

Overall, it has been a pleasure to review what is a well-written, concise yet thorough paper supporting a very useful package that answers a clear need, and does so in a way that bundles often disparate techniques for the analysis of epidemic networks into a single cohesive package.

fboehm commented 3 years ago

@esteinig - how is the review going? Please let us know if there are issues that the authors should address. Thanks again!

esteinig commented 3 years ago

Hi my apologies for the delay, finishing my thesis at the moment. I am very pleased with the package and the code base, it's already gotten some attention within our lab. I had opportunity to test it on Linux systems but can't make an assessment on other OS.

The paper is well written, and concise. My only recommendation would be to introduce some better structure with headlines in the paper, but that's all :)

fboehm commented 3 years ago

Thank you, @esteinig! Can you be more specific about the suggestion for headlines in the paper? Can you recommend specific places in paper.md where headlines might be placed?

Thanks again!

fboehm commented 3 years ago

@whedon generate pdf

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:

benmaier commented 3 years ago

Dear @fboehm, @chrisvoncsefalvay, and @esteinig, thank you so much for this lightning-fast editing and reviewing work. This has probably been the smoothest reviewing experience I've ever had! I greatly appreciated all your positive comments about the work I submitted.

Regarding adding more headlines, I started working on the manuscript again to incorporate your point, @esteinig, but noticed that I do like the flow of the text as it is. I fear adding more subsections would make this already very short paper even more fragmented. When I wrote it, I had these two successful submissions in mind:

  1. https://raw.githubusercontent.com/adrn/gala/f6bb2532afeed3c0b0feea3037bf71a3f42b2a12/paper/paper.md
  2. https://github.com/benmaier/netwulf/blob/master/paper/paper.md

where the only subsection was "Summary", as well. I would therefore prefer to keep the text as it is. Of course, this is an editorial decision, ultimately!

(Also, @esteinig, all the best for your thesis!)

fboehm commented 3 years ago

@benmaier - I think that your solution is reasonable.

fboehm commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/BF02464423 is OK
- 10.1021/j100540a008 is OK
- 10.1186/1471-2334-11-37 is OK
- 10.18637/jss.v084.i08 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.21105/joss.01731 is OK
- 10.1016/j.physrep.2020.07.005 is OK
- 10.1016/j.cpc.2019.02.008 is OK
- 10.7717/peerj-cs.103 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.18452/20950 is OK
- 10.1016/j.jtbi.2011.07.015 is OK
- 10.21105/joss.00565 is OK
- 10.1007/978-3-319-50806-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
fboehm commented 3 years ago

@whedon generate pdf

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:

fboehm commented 3 years ago

@benmaier line 16 needs the word spelled "adaptation". You currently have "adaption".

fboehm commented 3 years ago

line 22, please italicize i.e. and place a comma after the second period. "i.e., "

fboehm commented 3 years ago

line 29, please define (i.e., spell out) the meaning of ODE when you first use it.

fboehm commented 3 years ago

@benmaier - please fix the typos that I mentioned immediately above in three comments.

benmaier commented 3 years ago

@whedon generate pdf

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:

benmaier commented 3 years ago

done!

fboehm commented 3 years ago

Great! We now need you, @benmaier to make a new release and to archive the package on zenodo. Please report in this thread the new release's version number and the archive's doi.

benmaier commented 3 years ago
fboehm commented 3 years ago

@whedon set 0.1.2 as version

whedon commented 3 years ago

OK. 0.1.2 is the version.

fboehm commented 3 years ago

@whedon set 10.5281/zenodo.4655616 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4655616 is the archive.

fboehm commented 3 years ago

@whedon set v0.1.2 as version

whedon commented 3 years ago

OK. v0.1.2 is the version.

fboehm commented 3 years ago

I've now downloaded the pdf and verified that all dois in the references section direct to the correct resources.

fboehm commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/BF02464423 is OK
- 10.1021/j100540a008 is OK
- 10.1186/1471-2334-11-37 is OK
- 10.18637/jss.v084.i08 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.21105/joss.01731 is OK
- 10.1016/j.physrep.2020.07.005 is OK
- 10.1016/j.cpc.2019.02.008 is OK
- 10.7717/peerj-cs.103 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.18452/20950 is OK
- 10.1016/j.jtbi.2011.07.015 is OK
- 10.21105/joss.00565 is OK
- 10.1007/978-3-319-50806-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2175

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2175, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
kthyng commented 3 years ago

@benmaier Things look like they are mostly ready to go! One comment on your paper. For lists of inline parenthetical references, use this sort of format: [@ref1; @ref2] so that they should up together in one set of parentheses. More info: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

benmaier commented 3 years ago

Ah, thank you and many apologies for not staying in syntax! Do you want me to fix this and resubmit?

fboehm commented 3 years ago

@benmaier - please fix the formatting issues and post a comment in this thread once the fixes have been made.

benmaier commented 3 years ago

@whedon generate pdf

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:

benmaier commented 3 years ago

ok, @fboehm, fixed!

fboehm commented 3 years ago

@whedon generate pdf

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:

danielskatz commented 3 years ago

@whedon accept