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[PRE REVIEW]: Phylotrack: C++ and Python libraries for in silico phylogenetic tracking #5660

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@emilydolson<!--end-author-handle-- (Emily Dolson) Repository: https://github.com/emilydolson/phylotrackpy Branch with paper.md (empty if default branch): Version: v0.1.13 Editor: !--editor-->@fboehm<!--end-editor-- Reviewers: @RussellGarwood, @CFGrote Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/efbcc9a16833768672ac4b0b641018c6/status.svg)](https://joss.theoj.org/papers/efbcc9a16833768672ac4b0b641018c6)

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editorialbot commented 1 year ago

Hello human, 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 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (681.0 files/s, 84089.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             48              0            501
Markdown                         7            174              0            386
DOS Batch                        1             34              2            227
C++                              1             41             37            197
Python                           4            119            199            197
make                             2             36              7            194
YAML                             3             21             32            118
TOML                             1              2              0             12
Bourne Shell                     1              4              0              5
-------------------------------------------------------------------------------
SUM:                            21            479            277           1837
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1078

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.7551/ecal_a_016 is OK
- 10.1145/3319619.3326825 is OK
- 10.1145/2330784.2330799 is OK
- 10.1145/3205651.3205780 is OK
- 10.13140/rg.2.2.33781.93921 is OK
- 10.1007/978-981-16-8113-4_4 is OK
- 10.1162/isal_a_00550 is OK
- 10.21105/joss.04866 is OK
- 10.1162/106454604773563612 is OK
- 10.5281/zenodo.4141943 is OK
- 10.1080/09528130601116113 is OK
- 10.1145/3520304.3534028 is OK
- 10.1162/artl_a_00273 is OK
- 10.1162/isal_a_00488 is OK
- 10.1162/artl_a_00280 is OK
- 10.1162/isal_a_00213 is OK
- 10.1111/brv.12252 is OK
- 10.1111/pala.12420 is OK
- 10.1080/09528130601116113 is OK
- 10.5281/zenodo.3528124 is OK
- 10.1093/sysbio/syr029 is OK
- 10.3389/fevo.2021.750779 is OK
- 10.1016/0006-3207(92)91201-3 is OK
- 10.1371/journal.pone.0203401 is OK
- 10.1371/journal.pone.0000296 is OK
- 10.1007/s004420050379 is OK
- 10.1146/annurev.ecolsys.33.010802.150448 is OK
- 10.3354/meps216265 is OK
- 10.1086/419657 is OK
- 10.2307/2992186 is OK
- 10.1046/j.1466-822X.2003.00015.x is OK

MISSING DOIs

- 10.1162/artl_a_00313 may be a valid DOI for title: Interpreting the Tape of Life: Ancestry-based Analyses Provide Insights and Intuition about Evolutionary Dynamics
- 10.1093/bioinformatics/btu157 may be a valid DOI for title: tqDist: a library for computing the quartet and triplet distances between binary or general trees
- 10.1093/bioinformatics/btq228 may be a valid DOI for title: DendroPy: a Python library for phylogenetic computing
- 10.1093/bioinformatics/btp163 may be a valid DOI for title: Biopython: freely available Python tools for computational molecular biology and bioinformatics
- 10.1007/978-3-030-19318-8_10 may be a valid DOI for title: Phylogenetic trees: applications, construction, and assessment
- 10.1016/j.tree.2008.07.005 may be a valid DOI for title: Phylogenetic analysis of community assembly and structure over space and time

INVALID DOIs

- None
editorialbot commented 1 year ago

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

mmore500 commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @mmore500, here are the things you can ask me to do:


# List all available commands
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@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

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mmore500 commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.7551/ecal_a_016 is OK
- 10.1145/3319619.3326825 is OK
- 10.1145/2330784.2330799 is OK
- 10.1145/3205651.3205780 is OK
- 10.13140/rg.2.2.33781.93921 is OK
- 10.1007/978-981-16-8113-4_4 is OK
- 10.1162/isal_a_00550 is OK
- 10.21105/joss.04866 is OK
- 10.1162/106454604773563612 is OK
- 10.5281/zenodo.4141943 is OK
- 10.1080/09528130601116113 is OK
- 10.1145/3520304.3534028 is OK
- 10.1162/artl_a_00313 is OK
- 10.1162/artl_a_00273 is OK
- 10.1162/isal_a_00488 is OK
- 10.1162/artl_a_00280 is OK
- 10.1162/isal_a_00213 is OK
- 10.1111/brv.12252 is OK
- 10.1111/pala.12420 is OK
- 10.1080/09528130601116113 is OK
- 10.5281/zenodo.3528124 is OK
- 10.1093/bioinformatics/btu157 is OK
- 10.1093/bioinformatics/btq228 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.1007/978-3-030-19318-8_10 is OK
- 10.1016/j.tree.2008.07.005 is OK
- 10.1093/sysbio/syr029 is OK
- 10.3389/fevo.2021.750779 is OK
- 10.1016/0006-3207(92)91201-3 is OK
- 10.1371/journal.pone.0203401 is OK
- 10.1371/journal.pone.0000296 is OK
- 10.1007/s004420050379 is OK
- 10.1146/annurev.ecolsys.33.010802.150448 is OK
- 10.3354/meps216265 is OK
- 10.1086/419657 is OK
- 10.2307/2992186 is OK
- 10.1046/j.1466-822X.2003.00015.x is OK

MISSING DOIs

- None

INVALID DOIs

- None
emilydolson commented 1 year ago

In terms of reviewers, based on the reviewer list it looks like @/CFGrote, @/mtomasini and @/stulacy could be good choices!

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot query scope

editorialbot commented 1 year ago

Submission flagged for editorial review.

Kevin-Mattheus-Moerman commented 1 year ago

@emilydolson thanks for this submission. I am the AEiC for this track and here to help with initial steps. Note that I've just flagged this work for a scope review by the editorial board. This is because of the apparent relatively small size of this submission in terms of LOC. Furthermore the limited functionality provided, as this work appears to be "essentially a wrapper around Phylotracklib" as your README states. Please let us know if the above line counts misrepresent the magnitude of the project of if some aspects are missing from this analysis.

The editorial board will now review this submission to see if it conforms to our substantial scholarly effort criteria. This review should take around 2 weeks to complete.

emilydolson commented 1 year ago

Hi Kevin,

The scope of the paper includes both phylotracklib (the underlying C++ implementation) and phylotrackpy (the python wrapper). They are split across two repositories because phylotracklib is a module in a larger piece of scientific software (included as a submodule in phylotrackpy). I used the phylotrackpy repo as the main one for this paper because I thought that would be less confusing, but perhaps it wasn't - sorry about that! I opened a pre-submission inquiry about this organization issue (https://github.com/openjournals/joss/issues/1233), but didn't hear back so I figured I'd just go ahead with the submission.

If this organization is a problem, I can look at rearranging things (although it wouldn't be super easy).

Thanks!

arfon commented 1 year ago

They are split across two repositories because phylotracklib is a module in a larger piece of scientific software (included as a submodule in phylotrackpy)

@emilydolson – could you link to that code so we can make a judgment on scope that includes that contribution too?

Also, apologies for the lack of response on a pre-submission enquiry. You did the right thing just submitting anyway :-)

emilydolson commented 1 year ago

Oh yes, sorry, here it is: https://github.com/devosoft/Empirical/blob/master/include/emp/Evolve/Systematics.hpp. The SystematicsAnalysis.hpp file in the same directory is also a smaller part of it.

Kevin-Mattheus-Moerman commented 1 year ago

@emilydolson I have just removed the query-scope label as with the above additional repo link the total magnitude of this work seems like it may be in scope for JOSS. Hence I will now proceed to find a handling editor. Note though that many are currently somewhat oversubscribed or on holiday. So it may take some time before we find one, and I may need to waitlist this submission if none are available at the moment.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @fboehm as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

fboehm commented 1 year ago

@editorialbot assign me as editor

editorialbot commented 1 year ago

Assigned! @fboehm is now the editor

fboehm commented 1 year ago

thank you, @Kevin-Mattheus-Moerman ! I'm eager to edit this submission.

fboehm commented 1 year ago

@emilydolson - I'll be editing your submission. The first step is to find two reviewers. Do you have any recommendations of people who might be qualified to review your submission? Please feel free to share their names and email addresses or github handles (if they have github handles) in this thread. I often find that I need to ask at least five prospective reviewers to get two who can commit to reviewing now, so please feel free to suggest a number of possible reviewers. Thank you!

emilydolson commented 1 year ago

I think @/CFGrote, @/mtomasini and @/stulacy could be good choices from the JOSS reviewer list! Some good choices not from the JOSS reviewer list might be @/RussellGarwood (since I just reviewed a JOSS paper from him that involved some related ideas) or @/Tim-Taylor.

fboehm commented 1 year ago

@CFGrote @mtomasini@stulacy @RussellGarwood @Tim-Taylor - would you like to review this submission for JOSS? Unlike those at many journals, our reviews are checklist-driven and involve discussions with the authors. Thank you for considering this invitation!

RussellGarwood commented 1 year ago

@fboehm I'd be very happy to review this contribution (I note that some of my experience is well aligned with reviewing this, but there are some areas this touches on in which I'm not so confident. Presumably I can just highlight these if required).

tim-taylor commented 1 year ago

@CFGrote @mtomasini@stulacy @RussellGarwood @tim-taylor - would you like to review this submission for JOSS? Unlike those at many journals, our reviews are checklist-driven and involve discussions with the authors. Thank you for considering this invitation!

@fboehm I'm sorry but I don't have time to devote to this at present so I will have to decline. Apologies. Just a comment about the invitation - it would be helpful if you could more clearly state exactly what you are requesting is reviewed (the paper, the code, or both) and provide links to these in the invitation. Best wishes, Tim

CFGrote commented 1 year ago

I'm in. I might additional feedback from a colleague of mine who's more into phylogenetic tracking.

CFGrote commented 1 year ago

@CFGrote @mtomasini@stulacy @RussellGarwood @tim-taylor - would you like to review this submission for JOSS? Unlike those at many journals, our reviews are checklist-driven and involve discussions with the authors. Thank you for considering this invitation!

@fboehm I'm sorry but I don't have time to devote to this at present so I will have to decline. Apologies. Just a comment about the invitation - it would be helpful if you could more clearly state exactly what you are requesting is reviewed (the paper, the code, or both) and provide links to these in the invitation. Best wishes, Tim

@tim-taylor, I had the same initial thoughts, but then realized that following the link to this issue provides all the information you requested.

fboehm commented 1 year ago

@RussellGarwood @CFGrote - Thank you for agreeing to review. @CFGrote - just a note that if you seek input from a colleague, we probably should add that colleague as an official reviewer. I'm happy to invite them serve as an additional reviewer if you can share their github handle. Thanks again!

fboehm commented 1 year ago

@tim-taylor and @CFGrote - thank you for the comments on the text of the invitation. I'll try to ensure that the relevant links are included in the text of the invitation message itself in the future. Thanks again!

fboehm commented 1 year ago

@RussellGarwood - in response to your comment above - yes, please review those elements of the submission that you are comfortable reviewing; for those aspects of the submission that you aren't comfortable reviewing, please leave a comment in the "review thread" to indicate which areas you can't review. Thanks again! PS - I'll create the "review thread" in a moment.

fboehm commented 1 year ago

@editorialbot add @RussellGarwood as reviewer

editorialbot commented 1 year ago

@RussellGarwood added to the reviewers list!

fboehm commented 1 year ago

@editorialbot add @CFGrote as reviewer

editorialbot commented 1 year ago

@CFGrote added to the reviewers list!

fboehm commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5754.