Closed whedon closed 6 years ago
Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @harmn, it looks like you're currently assigned as the reviewer for this paper :tada:.
:star: Important :star:
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To fix this do the following two things:
For a list of things I can do to help you, just type:
@whedon commands
Attempting PDF compilation. Reticulating splines etc...
@Chilipp and @harmn we are starting review on this issue tracker.
@sdtaylor to expedite the review process do you mind going through above list of check boxes and make sure they can be ticked (you can't tick them). Also check the PDF output carefully. Ping us here when you are done.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
As far as I can tell all requirements above are met. I'm also happy with the rendered PDF.
Excellent. @Chilipp you can start review! Note @harmn is on holiday, but he is there to help out when he is back.
Great, I am looking forward to it! I will do it within the next week.
Hey! I really apologize for the late response, sorry.
I had a closer look at your software and enjoyed it a lot, thanks for your work here! To me it looks like a rather small package (only about ~1000 statements) but the editor knew this, when he accepted your software for review. So there are some minor points that need to be corrected from my point of view:
Does the release version given match the GitHub release (v0.5.0)?
Only a minor thing here: in https://github.com/sdtaylor/pyPhenology/releases there are two versions available: https://github.com/sdtaylor/pyPhenology/releases/tag/v0.5.0 and https://github.com/sdtaylor/pyPhenology/releases/tag/0.5.0. I assume, that v0.5.0 is the official release, so what about tag 0.5.0?
Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
What about the different OS? To me, it looks like it runs on all platforms (Linux, MaxOSX and Windows) but it would be better to have written in the docs. This could be solved by merging https://github.com/sdtaylor/pyPhenology/pull/96
Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
You have a quickstart example in your docs (http://pyphenology.readthedocs.io/en/master/quickstart.html) but this is very short. Just be a bit more verbose in order to be more transparent, as well. For example, add some statistics and/or plots on how the prediction compares against the observations (also in order to show the user, how he can compare the two.)
Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
I like your documentation and your classes are well documented. Only the Model.score method needs a better docstring but I have the impression that this method is not really maintained (and tested) anyway, since your are not using it nor testing it.
Are there automated tests or manual steps described so that the function of the software can be verified?
Your tests are fine and complete, however I strongly recommend to use a coverage service as well since this is super easy for a pure python package and adds more transparency to your open source project. Just use pytest-cov on your CI and codecov or coveralls
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
I could not find them, neither in the repository, nor in the docs. Please add the necessary file (e.g. a CONTRIBUTING file in the main repository)
Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@sdtaylor can you address these points?
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@pjotrp here is my reply for @Chilipp's review
Thanks for reviewing my package and your comments, I appreciate the your thoroughness. Though it is a relatively small package, the process of programming phenology models is a major bottleneck for most researchers, so I hope it will help them out in that regard. As detailed below I've implemented all of your suggestions.
The 0.5.0 tag was created mistakenly. I've deleted it and now there is only v0.5.0
pyPhenology does run on all operating systems. Thank you for PR in helping clarifying this, I've merged it.
I've expanded the quickstart to better describe some of the common usage, such as parameter adjustment and saving models. I also included a link at the end to point users towards the examples which represent a more realistic analysis using this package. You can see the changes here
Thanks for pointing this out. I would like the score method to be more prominent. I've updated the docstring to be more clear and added some tests specifically for this here https://github.com/sdtaylor/pyPhenology/pull/98.
I have setup codecov for the repository and added the badge to the GitHub readme.
I've added a CONTRIBUTER.md file outlining the basics of contributing, as well as a CODE_OF_CONDCUCT.md file.
@Chilipp can you check and tick the relevant boxes? If you are happy we can wrap up. @harmn I assume you are happy about this submission?
@pjotr, only two very minor issues: -the minimal required version for pandas (0.18.0) seems to be incorrect,Series does not have an isna method until 0.21 (used in pyPhenology/models/utils/misc.py on line 53) -the Basler reference in the text has additional parentheses around the year
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
Thank you @harmn for reviewing my package. I tested it with pandas 0.18.0 and you are correct that it doesn't work due to this incomparability. I've changed the pandas requirement to 0.21.0.
For the reference issue, I tried changing the ordering from [@tang2016, @basler2016]
to [@basler2016, @tang2016]
and now there is parenthesis around the year of the Tang reference. I'm not sure whats causing that, @pjotrp do you have any ideas?
@pjotrp and @sdtaylor:
@Chilipp can you check and tick the relevant boxes? If you are happy we can wrap up. @harmn I assume you are happy about this submission?
Done! It's all fine from my point of view. So if The two points by @harmn are fixed, this paper should be accepted.
@arfon we are ready to accept this submission. Note there is a small issue with generating the PDF (two boxes up on this page). Great work everyone!
@sdtaylor the review process is now complete. To finalize your submission and accept your paper in JOSS, we need two things. First, can you confirm that all references in your bibliography have a DOI (if one exists) - I think you have
Second, we need you to deposit a copy of your software repository (including any revisions made during the JOSS review process) with a data-archiving service. To do so:
Thanks @pjotrp, The DOI's all look good to me. The current release is no v0.6.0, and I've deposited at zenodo at https://doi.org/10.5281/zenodo.1345528
@whedon set 10.5281/zenodo.1345528 as archive
OK. 10.5281/zenodo.1345528 is the archive.
@arfon all yours.
@arfon note above comment on parenthesis in the PDF.
Looks like the citations need to be separated by semicolons in the paper.md
: http://pandoc.org/MANUAL.html#citations :
Citations go inside square brackets and are separated by semicolons.
I've made this change locally to the paper.md
.
@harmn, @Chilipp - many thanks for your reviews here and to @pjotrp for editing this submission ✨
@sdtaylor - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00827 :zap: :rocket: :boom:
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Submitting author: @sdtaylor (Shawn Taylor) Repository: https://github.com/sdtaylor/pyPhenology Version: v0.5.0 Editor: @pjotrp Reviewer: @harmn, @Chilipp Archive: 10.5281/zenodo.1345528
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@harmn & @Chilipp, 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 try and complete your review in the next two weeks ✨
Review checklist for @harmn
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @Chilipp
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?