Closed whedon closed 3 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @DavidNickle, @rvosa it looks like you're currently assigned to review this paper :tada:.
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Failed to discover a Statement of need
section in paper
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.17 s (180.3 files/s, 29345.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
XML 2 6 16 1084
Python 10 318 703 974
Markdown 6 172 0 736
reStructuredText 5 157 294 353
TeX 1 11 0 112
YAML 3 8 4 49
JSON 1 0 0 23
make 1 4 7 9
Bourne Shell 2 1 0 5
-------------------------------------------------------------------------------
SUM: 31 677 1024 3345
-------------------------------------------------------------------------------
Statistical information for the repository '7e95ab623396fc53f9a2293c' was
gathered on 2021/04/15.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
NicolaDM 1 183 1 2.90
Tiago Tresoldi 90 3986 2173 97.10
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
NicolaDM 122 66.7 1.9 48.36
Tiago Tresoldi 1873 47.0 8.3 23.01
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1126/science.283.5406.1310 is OK
- 10.1093/sysbio/syr029 is OK
- 10.1093/molbev/msw046 is OK
MISSING DOIs
- 10.2307/1909876 may be a valid DOI for title: The elements of stochastic processes with applications to the natural sciences
- 10.1093/bioinformatics/btu181 may be a valid DOI for title: geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
- 10.1093/bioinformatics/bty633 may be a valid DOI for title: ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
- 10.1371/journal.pone.0180908 may be a valid DOI for title: BEASTling: A software tool for linguistic phylogenetics using BEAST 2
INVALID DOIs
- None
Conflict of interest: I confirm that I have read the JOSS conflict of interest 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
Repository: The source code for this software is available at the repository url YES
License: The repository contain a plain-text LICENSE file with the contents of an OSI approved software license. YES
Contribution and authorship: The submitting author made major contributions to the software and the full list of paper authors seem appropriate and complete. YES
Functionality: The software is functional and important adding very important knowledge to the public domain. YES
Installation: The installation procedure follows the documentation clearly. I performed many of the examples in the How To Use section of the manuscript. All worked as advertised
Functionality: I confirmed the functional claims of the software as well as some of my own.
Performance: It is pretty quick!
A statement of need: The authors have a clear audience in they have mind and the paper and the software should be readably available to that audience. It is potentially most useful for developing nulls in the evolution of languages
Installation instructions: I installed through PIP without any issues
Example usage: I went through the How To Use section. Everything worked.
Automated tests: YES — tests are available
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. YES
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? YES
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is? YES
State of the field: Do the authors describe how this software compares to other commonly-used packages? YES Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)? YES 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? YES
@majensen I think this paper should be accepted. It is a nice piece of software that can be useful for those that are interested in the evolutionary of languages. It even allows for recombination (words passing from one language into another — can you use the word pajama or pyjama).
Thanks! I will add the DOIs when reviews are over. I can also add a short "Statement of need" if preferred (once more, after the first round of review is over).
:wave: @rvosa, please update us on how your review is going (this is an automated reminder).
:wave: @DavidNickle, please update us on how your review is going (this is an automated reminder).
My review is complete on 14 days ago. See above
@rvosa - how is your progress on this review? Just let me know timing expectations if you can thanks!
pip3
instead. I blame my messy Python configuration though.ngesh
and I get a b/d tree.requirements.txt
@rvosa - rather than adding a new comment with a new checklist, please just use your checklist in the first comment in this issue.
@tresoldi - @rvosa would like to see some text comparing your package to other available tools, and to highlight how your software meets an existing need. JOSS does requirement this so-called "Statement of Need". Can you work to add this? thanks
Sure, will do!
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@majensen I have finished reworking the draft. The last paragraph of the "Background" was reworked into a "Statement of need", with no real changes in what is said. I also removed some filler words from the rest of the draft to make sure it stays within 3 pages when compiled, but contents are otherwise unchanged.
Thanks @tresoldi - I apologize for being out of the loop for a while. I will make every effort to review the current version this weekend.
No problem, it also took me longer than expected to address the "statement of need" issue. Thanks, @majensen !
Sorry for the continued delay @tresoldi -- finally able to have a look.
What I appreciate about the paper is the idea of "technology transfer" of phylogenetic methods from biology to linguistics. (Although, I think biology imported the basic ideas from comparative linguistics a long long time ago!)
I have to agree with @rvosa, however, that there are many and extensive tools that have been developed for simulating trees in the evolutionary biology world - see https://evolution.genetics.washington.edu/phylip/software.html#Simulation for an old list. Now, the fact that there are about 30 listed there suggests that people need certain things for their applications that aren't quite there in other programs, so I am not inclined to dismiss your submission just because others have programs (in other languages or with more specialized algorithms) that perform similar functions.
However - I would like a little more discussion comparing your application with a few of these common evolutionary biology tools. Can I ask you to review the ones suggested by @rvosa (DendroPy, Mesquite, and Bio::Phylo) and compare your application with these. I'm not too concerned with extending the length of the paper. I would also suggest briefly outlining a real workflow in the linguistic space, one that you have used ngesh for, perhaps. This would be helpful to readers in that discipline and I think it would help argue for the usefulness of your contribution.
Sorry to make more work after such a long delay, but I think you'll have a better paper at the end. Plus, we have @rvosa to convince! Thanks for your consideration -
@tresoldi - checking in on your progress, thanks
@tresoldi - please let me know how things are going - if you prefer, feel free to contact me via email - maj -dot- fortinbras -at- gmail -dot- com.
:wave: @tresoldi - hoping to hear from you soon; thanks!
@majensen sorry I have been so much out of touch. I am able to get back to it now, I have now planned to submit the reviewed draft by tomorrow (Friday) evening.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@majensen finally done it, I have sent you an email with a short explanation as well. Sorry for the delay.
Sorry all, I have been AWOL. I hope to return to this within the week.
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1126/science.283.5406.1310 is OK
- 10.1093/sysbio/syr029 is OK
- 10.1093/molbev/msw046 is OK
MISSING DOIs
- 10.1038/sdata.2018.205 may be a valid DOI for title: Cross-Linguistic Data Formats, advancing data sharing and re-use in comparative linguistics
- 10.2307/2333730 may be a valid DOI for title: The elements of stochastic processes with applications to the natural sciences
- 10.1126/science.1219669 may be a valid DOI for title: Mapping the origins and expansion of the Indo-European language family
- 10.16993/baj.h may be a valid DOI for title: The Digital Revolution in Scholarly Editing
- 10.1093/bioinformatics/btu181 may be a valid DOI for title: geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
- 10.1093/bioinformatics/bty633 may be a valid DOI for title: ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
- 10.1371/journal.pone.0180908 may be a valid DOI for title: BEASTling: A software tool for linguistic phylogenetics using BEAST 2
INVALID DOIs
- None
Hi @tresoldi - it is looking good to me. I would still like to see a few sentences describing a typical analysis in historical linguistics and where ngesh fits in to that analysis.
Can you update your paper.bib with the DOIs found by Whedon as MISSING DOIs above.
Also, can you update the reference to Harmon's book with more precise details as follows:
These details are from Amazon.
At the end of Line 26 in the PDF proof: can you replace "constrains" with "constraints".
thanks!
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/sdata.2018.205 is OK
- 10.2307/2333730 is OK
- 10.1126/science.283.5406.1310 is OK
- 10.1093/sysbio/syr029 is OK
- 10.1093/molbev/msw046 is OK
- 10.1126/science.1219669 is OK
- 10.16993/baj.h is OK
- 10.1093/bioinformatics/btu181 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1371/journal.pcbi.1006650 is OK
MISSING DOIs
- 10.32942/osf.io/e3xnr may be a valid DOI for title: Phylogenetic Comparative Methods: Learning from Trees
INVALID DOIs
- None
Sorry for spamming with whedon, but there is always a tiny detail missing... This should be the last round.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/sdata.2018.205 is OK
- 10.2307/2333730 is OK
- 10.1126/science.283.5406.1310 is OK
- 10.32942/osf.io/e3xnr is OK
- 10.1093/sysbio/syr029 is OK
- 10.1093/molbev/msw046 is OK
- 10.1126/science.1219669 is OK
- 10.16993/baj.h is OK
- 10.1093/bioinformatics/btu181 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1371/journal.pcbi.1006650 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Thank you very much, @majensen ! I have updated accordingly, also with a small addition to the Statement of Need. You can compare the current source with the one you checked here: https://github.com/tresoldi/ngesh/compare/172d382..2561440
Ok @tresoldi, I'm happy with this. We are nearly there- can you please use Zenodo, FigShare or other service to create an open archive of the repository? There is a short tutorial using Zenodo here. JOSS prefers that the name of the archive = the name of the paper, and that the archive author list = paper author list.
The service should give you a DOI for the archive - can you post that here when done? Then I will invoke the ancient spell summoning the Associate Editor in Chief.
@majensen I released a version 1.0 (no changes to any file) on GitHub, published on PyPI, and deposited on Zenodo ( https://zenodo.org/record/5552605 ), linking to GitHub and orcid.
The Zenodo DOI is 10.5281/zenodo.5552605
I can of course release a 1.0.1 if necessary, absolutely no problem.
Submitting author: @tresoldi (Tiago Tresoldi) Repository: https://github.com/tresoldi/ngesh Version: 1.0 Editor: @majensen Reviewer: @DavidNickle, @rvosa Archive: 10.5281/zenodo.5552605
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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.
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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.)
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@DavidNickle & @rvosa, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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✨ 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 @DavidNickle
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @rvosa
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper