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[REVIEW]: pyam: a Python Package for the Analysis and Visualization of Assessment Models #1095

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whedon opened this Issue Nov 22, 2018 · 37 comments

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whedon commented Nov 22, 2018

Submitting author: @gidden (Matthew Gidden)
Repository: https://github.com/IAMconsortium/pyam
Version: v0.1.2
Editor: @lheagy
Reviewer: @jtmiclat, @Chilipp
Archive: 10.5281/zenodo.1491662

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/356bc013105642ec4e94a3b951836cfe"><img src="http://joss.theoj.org/papers/356bc013105642ec4e94a3b951836cfe/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/356bc013105642ec4e94a3b951836cfe/status.svg)](http://joss.theoj.org/papers/356bc013105642ec4e94a3b951836cfe)

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) 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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @lheagy know.

Please try and complete your review in the next two weeks

Review checklist for @jtmiclat

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.1.2)?
  • Authorship: Has the submitting author (@gidden) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • 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

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @Chilipp

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.1.2)?
  • Authorship: Has the submitting author (@gidden) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • 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

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Nov 22, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jtmiclat, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands
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whedon commented Nov 22, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 22, 2018

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lheagy commented Nov 22, 2018

@jtmiclat, @Chilipp, many thanks for being willing to review!!

In the main thread above, there is a checklist for each of you to help guide your review. It would be greatly appreciated if you could submit your review in the next two weeks. Please let me know if you have any questions or if I can provide any clarification.

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gidden commented Nov 26, 2018

@whedon generate pdf

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whedon commented Nov 26, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 26, 2018

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gidden commented Nov 26, 2018

Hi @lheagy, per your suggestion, I have updated the title to more accurately reflect the scientific domains in which pyam is or is envisioned being used. Looking forward to the reviews of @jtmiclat and @Chilipp.

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danielhuppmann commented Nov 29, 2018

@whedon generate pdf

Reintroduce a reference to the NCC manuscript to describe the process for analysing scenarios in the IPCC SR15 context using pyam and the aim of increasing transparency and reproducibility of the assessment, see IAMconsortium/pyam#146

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whedon commented Nov 29, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 29, 2018

PDF failed to compile for issue #1095 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 16 0 16 0 0 158 0 --:--:-- --:--:-- --:--:-- 160
Error reading bibliography ./paper.bib (line 98, column 1):
unexpected end of input
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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danielhuppmann commented Nov 29, 2018

@whedon generate pdf

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whedon commented Nov 29, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 29, 2018

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Chilipp commented Dec 5, 2018

Dear @gidden and @danielhuppmann . I reviewed your software today and I very much appreciate your work. I find this as a very useful and nicely documented piece of software and I very much appreciated the review. There are only minor revisions that I can present

  • Installation instructions

    Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

    The list of dependencies is missing in the install instructions. From your setup.py I get, that pyam is built on

    • numpy
    • pandas >=0.21.0
    • matplotlib
    • seaborn

    They should at least be listed in the requirements, together with the necessary citations as specified on the webpages (e.g. for matplotlib it requires a link to https://matplotlib.org/ and a citation such as

    Hunter, J. D., Matplotlib: A 2D Graphics Environment, Computing in Science Engineering, 2007, 9, 90-95
    (see https://matplotlib.org/citing.html)

  • Automated tests

    Are there automated tests or manual steps described so that the function of the software can be verified?

    I highly recommend to include coverage tests into your software, e.g. by installing pytest-cov (pip install pytest-cov) on you CI services and then using some free services, such as [codecov.io (https://codecov.io/) or coveralls.io. When I run your tests with coverage tests, I get

    pytest -v --mpl tests --cov=pyam
    Name                  Stmts   Miss  Cover
    -----------------------------------------
    pyam/__init__.py         18      0   100%
    pyam/_version.py        277    152    45%
    pyam/core.py            538     64    88%
    pyam/iiasa.py            92      3    97%
    pyam/logger.py            8      0   100%
    pyam/plotting.py        378    194    49%
    pyam/run_control.py      62     19    69%
    pyam/statistics.py      151     23    85%
    pyam/timeseries.py       53      2    96%
    pyam/utils.py           152     23    85%
    -----------------------------------------
    TOTAL                  1729    480    72%
    

    Overall, your package seems to be very well covered, but there are clearly some modules underrepresented in your tests (pyam/plotting.py and pyam/_version.py). However, JOSS does not formally require a report on your test coverage, so this is just a recommendation from my side.

  • 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

    These are missing (see https://help.github.com/articles/setting-guidelines-for-repository-contributors/ for guidance)

Additionally there are some minor things that I added as issues and PRs to your project

Once all these items are checked off, I recommend to publish your paper.

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jtmiclat commented Dec 6, 2018

I just reviewed your software and I am pretty amazed by the quality. pyam is very well made library. My only comment is I can't seem to find documentation on how to contribute to it and would have to leave this unchecked.

  • 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

@danielhuppmann danielhuppmann referenced this issue Dec 17, 2018

Merged

add contributor guidelines #156

3 of 3 tasks complete
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lheagy commented Dec 18, 2018

👋 hi @gidden, please keep us posted on your progress and post here when you are done with your revisions.

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gidden commented Dec 18, 2018

Hi @lheagy! Thanks for the prod. We are working on the suggested updates (I have been wrestling with circleci and coveralls for some time now + AGU, etc.). Hoping to have a final submission ready by tomorrow.

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gidden commented Dec 19, 2018

Hello all. First of all, thank you very much to @Chilipp and @jtmiclat for their very useful reviews. We have striven to implement all suggestions both of you made.

Notably these include:

  • adding contributor/community guidance (pr, site)
  • adding coveralls support (pr, site)
  • adding explicit required dependencies outside of setup.py/pip/conda (pr, site)

From our view, we believe the article is now ready for publication. Please let us know if we should do anything further.

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Chilipp commented Dec 19, 2018

I am okay with accepting his software for publication @lheagy. Thank you very much @gidden and @danielhuppmann for your work on this! 🎉 🎉

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lheagy commented Dec 19, 2018

Thanks @Chilipp! Just a quick question, there are a couple items still not checked on your checklist -were those just missed?

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Chilipp commented Dec 19, 2018

were those just missed?

Yes, my apologies

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lheagy commented Dec 19, 2018

Many thanks @Chilipp and @jtmiclat for taking the time to review! 🎉

Congratulations @gidden on your submission! To finalize the acceptance, please archive your software on zenodo or similar and post the doi here.

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danielhuppmann commented Dec 27, 2018

thanks @lheagy, @Chilipp and @jtmiclat for the useful feedback and positive reviews.

@gidden is on an extended Christmas break and I'd rather wait for his return with making a new release and generating the doi. We'll get back to you mid-January at the latest.

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danielhuppmann commented Jan 7, 2019

@lheagy, the stable doi for the project on zenodo is
10.5281/zenodo.1470400, the doi for the latest release is 10.5281/zenodo.1491662.

There are a few minor updates since release 0.1.2 (also thanks to issues raised and comments by @Chilipp), but nothing critical, so we'll probably hold off on the next release until we get a few more features implemented.

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lheagy commented Jan 7, 2019

@whedon set 10.5281/zenodo.1491662 as archive

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whedon commented Jan 7, 2019

OK. 10.5281/zenodo.1491662 is the archive.

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lheagy commented Jan 7, 2019

Many thanks @Chilipp and @jtmiclat for your review! and congratulations @danielhuppmann on your submission 🎉

@arfon: this is ready to be published 🎉

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arfon commented Jan 7, 2019

@whedon accept

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whedon commented Jan 7, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Jan 7, 2019

Check final proof 👉 openjournals/joss-papers#427

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#427, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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arfon commented Jan 7, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Jan 7, 2019

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whedon commented Jan 7, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Jan 7, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#428
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01095
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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arfon commented Jan 7, 2019

@jtmiclat, @Chilipp - many thanks for your reviews here and to @lheagy for editing this submission

@gidden - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Jan 7, 2019

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whedon commented Jan 7, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01095/status.svg)](https://doi.org/10.21105/joss.01095)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01095">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01095/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01095/status.svg
   :target: https://doi.org/10.21105/joss.01095

This is how it will look in your documentation:

DOI

We need your help!

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:

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gidden commented Jan 7, 2019

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