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[REVIEW]: The Climate Equity Reference Calculator #1273

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whedon opened this Issue Feb 23, 2019 · 64 comments

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whedon commented Feb 23, 2019

Submitting author: @krueschan (Christian Holz)
Repository: https://github.com/climateequityreferenceproject/cerc-web
Version: v3.2.2
Editor: @jedbrown
Reviewer: @mtobis
Archive: 10.5281/zenodo.2592644

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/3a39361da648816fccf17af893b2b440"><img src="http://joss.theoj.org/papers/3a39361da648816fccf17af893b2b440/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/3a39361da648816fccf17af893b2b440/status.svg)](http://joss.theoj.org/papers/3a39361da648816fccf17af893b2b440)

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

@mtobis, 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 @jedbrown know.

Please try and complete your review in the next two weeks

Review checklist for @mtobis

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: v3.2.2
  • Authorship: Has the submitting author (@krueschan) 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 Feb 23, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mtobis 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:

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whedon commented Feb 23, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 23, 2019

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jedbrown commented Feb 23, 2019

@mtobis 👋 Welcome and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the project repository). I'll be watching this thread if you have any questions.

I ran the docker image locally via

$ docker pull climateequityreferenceproject/cerc-web
$ docker run -it --rm -p 8080:80 climateequityreferenceproject/cerc-web bash
root@c941332d432f:/var/www/cerc-web/public_html# dumb-init /start.sh

and pointing my browser to localhost:8080, which I think is sufficient to demonstrate that this system (or a derivative thereof) can indeed by hosted by external researchers.

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krueschan commented Feb 24, 2019

@whedon set v3.2.1 as version

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whedon commented Feb 24, 2019

I'm sorry @krueschan, I'm afraid I can't do that. That's something only editors are allowed to do.

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krueschan commented Feb 24, 2019

That's ok @whendon - I'll ask one of the humans to do it. @jedbrown or @mtobis, can you please @whedon set v3.2.1 as version? Thanks.

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krueschan commented Mar 7, 2019

@whedon generate pdf

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whedon commented Mar 7, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 7, 2019

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mtobis commented Mar 10, 2019

I think the "installation" question is ambiguous in the present case. The end user is not expected to be able to run the code on their own machine, but only to interact with the system through a web interface. Thus I am treating "installation" as meaning "ability to attain functionality", rather than "ability to replicate the service". I think the latter may present some difficulties.

(My attempt to do "docker run" per Jed's message did not work. A server was instantiated but it did not respond.)

I think it would have been better to make clear that the code is in php in the html directory. I spent some time trying to figure out where in my docker image it was and how to get it out!

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mtobis commented Mar 10, 2019

Is this the full paper?

https://github.com/openjournals/joss-papers/blob/joss.01273/joss.01273/10.21105.joss.01273.pdf

I see only a summary and a reference section.

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jedbrown commented Mar 10, 2019

Thanks, @mtobis.

This is a typical length for a JOSS "paper"; it is not meant to duplicate project documentation, which should be sufficiently complete to enable research using the software.

I'm okay with the present state of installation; having reproduced it locally, I think someone who wishes to run/extend the software (e.g., with new data or alternate analysis methods) would be able to get it working. I'm sure the technical issue you experienced with the docker container is resolvable in principle and won't ask you to spend further time on it.

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mtobis commented Mar 10, 2019

This work is essentially a web wrapper around https://sourceforge.net/p/gdrs/code/HEAD/tree/gdrsclib/

Let me state categorically that this is very important work and it should be available and documented.

I am not sure whether that sourceforge tree is considered part of the review. I gather it is not.

I believe my job here is to validate the suitability of this submission for JOSS, not its importance to the world, so unfortunately I hit some snags.

  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • I defer to Jed on this, so it's okay.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • There is fairly extensive online documentation, but it can't obviously be accessed until some parameters are chosen. It would be better if the help page were the landing page. To my initial exploration no use case examples are provided. This could definitely be improved with modest effort.
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Yes, if 1) sourceforge link is considered and 2) the theoretical basis for the calculations is considered sufficient (The actual algorithmic basis is straightforward.)
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Assuming this is a review only of the wrapper and not of the underlying calculations, the testing presumably is a rather trivial comparison between a few use cases. This could be automated in principle, but I'd be quite confident in this case with manual tests.

    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

  • As a one-off wrapper around a specific code base, scope for contribution is very limited so this is moot. I did not notice a way to report issues or seek support, but again I rather doubt that such issues would arise regarding the wrapper code.

All but one of these issues are not really consequential for the intended uses of the code. I have checked off everything except "example usage".

I strongly recommend altering the code so that a first time user can see the documentation without plunging into parameter choices, and that the online documentation be extended with use cases and user stories.

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mtobis commented Mar 10, 2019

Oh, sorry markdown mangled my bullets. Apologies. The above bulleted items were intended to come in pairs with two bullet styles: alternating between the requirement and my comment.

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krueschan commented Mar 11, 2019

Thanks very much for the review, @mtobis. Below are responses/further questions:

I am not sure whether that sourceforge tree is considered part of the review. I gather it is not.

Correct, that is the intention.

  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
    • There is fairly extensive online documentation, but it can't obviously be accessed until some parameters are chosen. It would be better if the help page were the landing page. To my initial exploration no use case examples are provided. This could definitely be improved with modest effort.

The current design, where the "equity splash screen" is shown first that shows the most salient parameters and a sub-set of parameters for them was the result of feedback from end-users who felt overwhelmed if presented with the full complement of settings on first loading the calculator. The settings on the splash screen are documented through extensive glossary entries (I hope the links to glossary entries are identifiable as links, e.g. that clicking "Historical Responsibility" brings up a substantial glossary entry explaining the concept as used here?). So even upon first loading the calculator, the user has access to the documentation of the specific parameter choices presented to them at that stage, which feels perhaps sufficient to me - what else would you expect at this stage?

As far as use cases are concerned, we considered the literature that is references in the manuscript (Adow, Ware, & Viita, 2018; CSO Equity Review, 2015, 2016, 2017, 2018; Holz
et al., 2018; Kartha, Holz, & Athanaisou, 2018; Metcalfe, 2015; Richards, Wollenberg, &
van Vuuren, 2018)

  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
    • Assuming this is a review only of the wrapper and not of the underlying calculations, the testing presumably is a rather trivial comparison between a few use cases. This could be automated in principle, but I'd be quite confident in this case with manual tests.

Happy to provide manual test cases but I have no idea how I would go about doing that. Can you point me to an example repository that does that? Or some other relevant documentation?

  • 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
    • As a one-off wrapper around a specific code base, scope for contribution is very limited so this is moot. I did not notice a way to report issues or seek support, but again I rather doubt that such issues would arise regarding the wrapper code.

The repository has a CONTRIBUTING.md file and the calculator itself has a "Please send feedback" link at the bottom of each page.

I strongly recommend altering the code so that a first time user can see the documentation without plunging into parameter choices, and that the online documentation be extended with use cases and user stories.

Thanks for the suggestion and see my comments above. I am thinking of adding a line of text on top of the "equity splash screen" that points the first time user to a general introduction of our approach, i.e. this page: https://climateequityreference.org/about-the-climate-equity-reference-project-effort-sharing-approach/
This could look like this:
splash screen with intro
Do you think that would sufficiently address your concerns?

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mtobis commented Mar 11, 2019

yes that would be an adequate and easy fix

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krueschan commented Mar 11, 2019

@whedon generate pdf

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whedon commented Mar 11, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 11, 2019

PDF failed to compile for issue #1273 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 0 105 0 --:--:-- --:--:-- --:--:-- 105
Error reading bibliography ./paper.bib (line 116, column 2):
unexpected "@"
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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krueschan commented Mar 11, 2019

@whedon generate pdf

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whedon commented Mar 11, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 11, 2019

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krueschan commented Mar 11, 2019

@whedon generate pdf

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whedon commented Mar 11, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 11, 2019

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krueschan commented Mar 11, 2019

yes that would be an adequate and easy fix

Ok. @mtobis - I have done this now.

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whedon commented Mar 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 13, 2019

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krueschan commented Mar 13, 2019

found and fixed another minor issue with the bibliography.

@whedon generate pdf

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krueschan commented Mar 13, 2019

@whedon generate pdf

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whedon commented Mar 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 13, 2019

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jedbrown commented Mar 13, 2019

@whedon set v3.2.2 as version

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whedon commented Mar 13, 2019

OK. v3.2.2 is the version.

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jedbrown commented Mar 13, 2019

@krueschan Can you confirm that Sivan Kartha meets the authorship guidelines with respect to this software? https://joss.readthedocs.io/en/latest/submitting.html#authorship (I ask because there are no commits authored by him.)

After confirmation, please archive the software at Zenodo or similar and report the DOI here.

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krueschan commented Mar 13, 2019

Yes, I confirm that Sivan absolutely meets the authorship guidelines.
The Zenodo archive DOI is 10.5281/zenodo.2592644

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jedbrown commented Mar 13, 2019

@whedon set 10.5281/zenodo.2592644 as archive

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whedon commented Mar 13, 2019

OK. 10.5281/zenodo.2592644 is the archive.

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jedbrown commented Mar 13, 2019

@jedbrown jedbrown added the accepted label Mar 13, 2019

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labarba commented Mar 13, 2019

Small editorial fix in the last paragraph:

“In research by the authors and others, most recently in (Adow … ) among other pieces” >> when you use the citation as part of speech in a sentence, you need to use in-text citation; see: https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.htm#citation_syntax

Also, comma after “e.g.” in parenthetical a bit later.

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krueschan commented Mar 13, 2019

Ok, good points, thanks.
I fixed it, though using a different approach than you suggested, by joining putting parts of the sentence into the parenthesis with the citations. Also, the comma after e.g.

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krueschan commented Mar 13, 2019

@whedon generate pdf

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whedon commented Mar 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 13, 2019

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labarba commented Mar 14, 2019

@whedon accept

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whedon commented Mar 14, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Mar 14, 2019

Check final proof 👉 openjournals/joss-papers#556

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#556, 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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whedon commented Mar 14, 2019


OK DOIs

- 10.1007/s10784-017-9371-z is OK
- 10.1002/wcc.201 is OK
- 10.5281/zenodo.1748847 is OK
- 10.1038/nclimate2826 is OK
- 10.1038/nclimate3186 is OK
- 10.1016/j.envsci.2017.04.020 is OK
- 10.7910/DVN/O3H22Z is OK
- 10.7910/DVN/RIBJXF is OK
- 10.6084/m9.figshare.5917399 is OK
- 10.6084/m9.figshare.5917402 is OK
- 10.6084/m9.figshare.5917408 is OK
- 10.6084/m9.figshare.7637669 is OK
- 10.1080/14693062.2018.1430018 is OK
- 10.5281/zenodo.2590636 is OK

MISSING DOIs

- https://doi.org/10.1007/978-3-531-92258-4_12 may be missing for title: The Greenhouse Development Rights Framework. The Right to Development in a Climate Constrained World, Second Edition
- https://doi.org/10.2139/ssrn.3279932 may be missing for title: The Greenhouse Development Rights and Climate Equity Reference Calculator Engine
- https://doi.org/10.1007/978-3-319-69772-7 may be missing for title: Norway’s Fair Share of Meeting the Paris Agreement
- https://doi.org/10.4324/9781315103358-12 may be missing for title: Climate Inequality in the Commonwealth: A Call for Urgent Action
- https://doi.org/10.4135/9781483351384.n48 may be missing for title: Special Report on the Impacts of Global Warming of 1.5°C Above Pre-Industrial Levels and Related Global Greenhouse Gas Emission Pathways, in the Context of Strengthening the Global Response to the Threat of Climate Change, Sustainable Development, and Efforts to Eradicate Poverty
- https://doi.org/10.1007/978-1-4302-0172-4_1 may be missing for title: SQLite (Version 3)
- https://doi.org/10.4135/9781473975101 may be missing for title: Paris Agreement
- https://doi.org/10.2139/ssrn.3286257 may be missing for title: Synthesis Report on the Aggregate Effect of the Intended Nationally Determined Contributions
- https://doi.org/10.1007/springerreference_29771 may be missing for title: The Emissions Gap Report 2015
- https://doi.org/10.1186/s12939-017-0700-1 may be missing for title: Fast, Fair Climate Action Crucial for Health and Equity

INVALID DOIs

- None
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labarba commented Mar 14, 2019

@whedon accept deposit=true

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whedon commented Mar 14, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Mar 14, 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#557
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01273
  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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labarba commented Mar 14, 2019

Congratulations, @krueschan, your JOSS paper is published!

Big thanks to the editor: @jedbrown, and reviewer: @mtobis 🙏

@labarba labarba closed this Mar 14, 2019

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whedon commented Mar 14, 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.01273/status.svg)](https://doi.org/10.21105/joss.01273)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01273">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01273/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01273/status.svg
   :target: https://doi.org/10.21105/joss.01273

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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krueschan commented Mar 14, 2019

Thanks very much, @jedbrown @mtobis @labarba and of course @whedon for this smooth review experience.

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