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[REVIEW]: CapacityExpansion: A capacity expansion modeling framework in Julia #2034

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @YoungFaithful (Lucas Elias Kuepper) Repository: https://github.com/YoungFaithful/CapacityExpansion.jl Version: v0.2.0 Editor: @katyhuff Reviewer: @sjpfenninger, @ali-ramadhan Archive: 10.5281/zenodo.4003566

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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) 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.)

Reviewer instructions & questions

@sjpfenninger & @ali-ramadhan, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @katyhuff know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @sjpfenninger

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ali-ramadhan

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sjpfenninger, @ali-ramadhan it looks like you're currently assigned to review this paper :tada:.

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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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whedon commented 4 years ago

PDF failed to compile for issue #2034 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2034 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

YoungFaithful commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

PDF failed to compile for issue #2034 with the following error:

sh: 1: cd: can't cd to tmp/2034 /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2034 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

YoungFaithful commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #2034 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2034 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

YoungFaithful commented 4 years ago

@arfon - Do you have a clue how to generate the pdf? In comparison to the pre-review, the Repository now contains /tree/paper and neither @whedon generate pdf nor @whedon generate pdf from branch paper worked

arfon commented 4 years ago

@YoungFaithful - this is because the URL for the repository needs to be something Whedon can clone (e.g. https://github.com/YoungFaithful/CapacityExpansion.jl/).

I've now fixed this.

arfon commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

sjpfenninger commented 4 years ago

I'm aware of the delay I'm injecting here. I'll get my review done next week!

sjpfenninger commented 4 years ago

All right, I'm through with my review. Generally looks good, but I do have a couple of bigger points below. Happy to clarify anything if unclear!

Minor comments

Statement of need in documentation and software paper / state of field

I think these need some work.

You describe the software as "Input-data-scaling, multi-sector capacity expansion modeling framework." Can you clarify what "input-data-scaling" means? Also, as far as I see, what you call "capacity expansion modeling" is functionally equivalent to the term "energy system modeling", correct?

It would be useful here to give more information on how, if at all, the functionality of your tool differs from existing software packages in this area (especially since you already list a selection of them, and since there are so many pre-existing packages which all essentially do the same thing). Is there any reason for a prospective user to go for your software rather than an older, more established, better tested tool?

You should also list PyPSA amongst the existing packages.

You might also want to refer to EnergyModels.jl, which as far as I'm aware of is not yet officially published, but I think under active development -- and based on the first public commit, is older than CapacityExpansion.jl:

https://github.com/PyPSA/EnergyModels.jl

Tests

There seem to be no automated tests. A test dir exists but not referred to anywhere. It looks like a single test model. Can you clarify what testing is done?

YoungFaithful commented 4 years ago

@sjpfenninger Thanks for your review. I'll handle your single comments throughout the next week.

YoungFaithful commented 4 years ago

All right, I'm through with my review. Generally looks good, but I do have a couple of bigger points below. Happy to clarify anything if unclear!

Minor comments

* One of the paper authors seems to have made no contributions to the code.

Our professor didn't contribute to the code via github, but during our weekly meetings.

* Installation: is using environments generally a thing in the Julia world? Would it make sense to update instructions accordingly? (https://docs.julialang.org/en/v1/stdlib/Pkg/index.html)

I fear that I don't fully understand your question about environments in the Julia context: Each package defines its dependencies in Project.toml (https://github.com/YoungFaithful/CapacityExpansion.jl/blob/master/Project.toml). The Pkg-Manager uses the dependencies of the different packages and tries to satisfy all of them. The user only uses using Pkg Pkg.add("CapacityExpansion")``, which is the same to] add CapacityExpansion`

* Documentation was hard to find. Link more prominently in the README, ideally with a separate section that contains the link(s) to where built docs live? It took me a while to spot that the way to get to docs is through the badge at the top of the README. Also set the repository link to point to the docs.

Great point. Wasn't even aware of repository links :+1: 

* I cannot see contribution or community guidelines anywhere.

Good catch that the README doesn't include a link to them.

* There are quite a few spelling and grammar errors throughout the documentation, making it harder than necessary to parse. Not necessarily for now, but at some point, a round of proofreading might be an hour or two well spent.

I'll have a second look at this

* In the paper: "The scale of the modeled energy system can range from quarters to entire global regions" - I believe you mean "districts", not "quarters".

True :)

Statement of need in documentation and software paper / state of field

I think these need some work.

You describe the software as "Input-data-scaling, multi-sector capacity expansion modeling framework." Can you clarify what "input-data-scaling" means? Also, as far as I see, what you call "capacity expansion modeling" is functionally equivalent to the term "energy system modeling", correct?

I wanted to express that the scale of the energy system is dependent on the input data. Which formulation would you suggest? I think that the terms capacity expansion modeling and energy system modeling are equivalent.

It would be useful here to give more information on how, if at all, the functionality of your tool differs from existing software packages in this area (especially since you already list a selection of them, and since there are so many pre-existing packages which all essentially do the same thing). Is there any reason for a prospective user to go for your software rather than an older, more established, better tested tool?

I added a section at the end of the comparison to other packages.

You should also list PyPSA amongst the existing packages.

You might also want to refer to EnergyModels.jl, which as far as I'm aware of is not yet officially published, but I think under active development -- and based on the first public commit, is older than CapacityExpansion.jl:

Oh great. Didn't know this one.

https://github.com/PyPSA/EnergyModels.jl

Tests

There seem to be no automated tests. A test dir exists but not referred to anywhere. It looks like a single test model. Can you clarify what testing is done? Testing validates the results of multiple cases (different optimization settings) for five energy system models against the expected values. The TX model is validated against the capacity expansion planning model of James Merrick.

sjpfenninger commented 4 years ago

@YoungFaithful thanks for the clarifications and updates!

Just four more comments:

katyhuff commented 4 years ago

Thank you for moving forward with this review @sjpfenninger .

@ali-ramadhan: Do you intend to complete your review? Thank you.

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

YoungFaithful commented 4 years ago

@sjpfenninger thanks for your additional comments :)

Just four more comments:

* "input-data-scaling": perhaps you mean "scale-independent"? "Input-data-scaling" implies that some part of your code actively scales input data.

That's a good way to phrase it. Thank you.

* Testing: You do of course have a CI job set up, so that was my bad! Still, I would add your explanation of the tests to the docs and/or the README to briefly flag what testing is done, tell users (=potential contributors) how to run the tests, or even better, provide something like a Makefile that does that.

I included a description of the testing in the README and added a new "testing" page in the documentation that includes a detailed step by step description on how to run the testing.

* Environments: My question is whether it would make sense to update the installation documentation to explicitly include creating a separate environment (i.e. something like `pkg> activate capacityexpansion` as a first installation step). See https://julialang.github.io/Pkg.jl/v1/environments/. As far as I understand the Julia package manager doesn't sequester all of the package's dependencies into an environment by default -- but I may be wrong about that.

I have a different understanding of the Pkg-Manager in that regard. I think that something like pkg> activate capacityexpansion is used in order to update the dependencies of the package, which should only be done by developers. julia only allows one environment to my best knowledge. All package dependencies have to be fulfilled in that environment and one cannot build something like containers for certain packages.

* Thanks for adding the paragraph on what the added value of CapacityExpansion.jl is. I accept that it is the first published Julia package to do the things it does, but it is not the only such tool to permit policy constraints. See [YoungFaithful/CapacityExpansion.jl@151a9a9#r37583878](https://github.com/YoungFaithful/CapacityExpansion.jl/commit/151a9a986c7ccdac0602a9a307c8f46f95520026#r37583878).

I agree that it is not the only package that allows to constrain policy constraints. To my best knowledge it is the only open source package that allows you to limit any kind of life cycle assessment category (also multiple at once) that you include in the input data. Maybe I am wrong about that. I excluded the sentence from the paper.

YoungFaithful commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

arfon commented 4 years ago

:wave: @ali-ramadhan, just a friendly check-in to see how things are going with this review?

arfon commented 4 years ago

👋 @ali-ramadhan - today we reopened JOSS for new submissions and are checking in on our existing reviews. Do you think you might be able to wrap up your review in the next 2-3 weeks?

YoungFaithful commented 4 years ago

Hi @ali-ramadhan, is there any additional information that you need from my side for the review?

ali-ramadhan commented 4 years ago

Hi @YoungFaithful, please accept my apologies for my extremely late review. I completely fell off the grid in the past few months. My review is below.

I think CapacityExpansion.jl is a well made and well documented Julia package. Everything worked out of the box and I was able to play around with it a bit. More detailed comments follow but I couldn't find any major faults. I opened a few issues and PRs on the repository but they're all minor. I'm happy to check off all the items on the review checklist but can't seem to do so right now.

Functionality

Installation: Does installation proceed as outlined in the documentation?

Yes. I was able to install CapacityExpansion 0.2.0 with no problems on Linux with Julia 1.4.2.

I only have one tiny suggestions:

The installation instructions use the older method of adding packages. It might be more future proof to suggest installing your package using the package mode available since Julia 1.0, e.g. ] add CapacityExpansion which is also more concise. However, as you've pointed out earlier in this review they are identical and most Julia users are familiar with both methods.

Functionality: Have the functional claims of the software been confirmed?

I believe so. I am not an expert in energy systems modeling but I was able to follow and play around with the example in the documentation quickstart which showed how to optimize the German renewable solar+wind energy grid subject to some constraints. The test suite seems to test these high-level functions pretty comprehensively.

Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

No performance claims have been made.

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

Yes. The problems solved by the software package are stated in the README and the software paper. The target audience is not explicitly stated, however the software package can be used to "address a diverse set of research questions" which to me implicitly states that the target audience is researchers. At the end of the software paper it states that it's been used as an educational tool as well, which is nice to see. So students are a potential target audience too.

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

Yes. However I might actually suggest removing the explicit list of dependencies from the README.

A list of dependencies in the README might give beginners to Julia the impression that they must install these dependencies themselves as virtually every Julia package does not list dependencies in the README. They are always handled automatically.

Perhaps a more useful way of listing dependencies is to point out that they are listed in the Project.toml file, which is automatically updated every time the dependencies change while the README must be edited manually.

I opened an issue about this: https://github.com/YoungFaithful/CapacityExpansion.jl/issues/55

Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

Yes. I was able to run the example in the README. I was able to follow and run the example in the Quickstart. It is well documented to help users understand what the package is doing.

I even got back a result with the exact same objective so it seems very reproducible!

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

Yes. The API is documented across a few different pages, one page per functionality which helps split things up. Examples, variable explanations, and plots are included which help a lot. Looks great!

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

Automated tests are available and run through Travis CI Linux builds which is great. I was also able to run the tests on my laptop and they passed.

I have two small suggestions regarding the automated tests:

  1. Rename the test/cpl.jl file to test/runtests.jl to follow Julia conventions. This way you can test the package automatically through the REPL. I opened a PR suggesting this change: https://github.com/YoungFaithful/CapacityExpansion.jl/pull/58

  2. Currently tests only run on Julia 1.0 which is fine as Julia 1.0.5 is the long-term support version. However, a lot of people are running more recent Julia versions so it might be worth running Julia 1.4 or dev test builds to ensure the tests pass for those users.

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. Other packages are extensively discussed which I found super useful.

Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?

It's great. I only found a few tiny typos which I opened a PR to fix: https://github.com/YoungFaithful/CapacityExpansion.jl/pull/60

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. The citations were all appropriate and there is a good amount of them for completenes and pedagogical insight. I only found a tiny typo in one of the BiBTeX references and opened a PR to fix it: https://github.com/YoungFaithful/CapacityExpansion.jl/pull/61

YoungFaithful commented 4 years ago

Hi @ali-ramadhan, thanks for your detailed review, the pull requests you prepared and issues you posted. I included your feedback and recommendations in a new update. Are you able to check off the items after whedon assigned you?

YoungFaithful commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

ali-ramadhan commented 4 years ago

Thanks @YoungFaithful for addressing the issues I opened. I closed them as they've been resolved.

Still can't check the boxes in the review checklist. I'm logged into the correct account and tried clicking on the invitation link but got this message:

Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.

so maybe the invitation expired or something? I had no issues ticking the boxes on a previous review but maybe a new invitation is needed for each review?

YoungFaithful commented 4 years ago

@ali-ramadhan, thanks for your response and closing the issues. I have no idea about the issues with the boxes. @katyhuff, do you have an idea what we could do to activate the boxes?

YoungFaithful commented 4 years ago

@sjpfenninger, I hope you're doing fine. I saw that there are some unchecked boxes remaining from your review. Did the last commits already solve the open aspects or is there anything else that we should improve?

katyhuff commented 4 years ago

Sorry for the delay in responding. @ali-ramadhan I'm not sure what's happened with your permissions, but I believe that it may be due to non-responsiveness earlier. I have checked all the boxes that you have affirmed as completed in your review. So, all are now checked except the confirmations of Conflict of interest and reading the JOSS code of conduct. Can you confirm @ali-ramadhan in a comment here the following statements :

1) I have read the JOSS conflict of interest (COI) 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 2) I confirm that I read and will adhere to the JOSS code of conduct.

katyhuff commented 4 years ago

@YoungFaithful I will look over this paper one more time over the next few days and make my own comments if I find anything still needs attention after your two thorough reviews. Thank you for your patience.

ali-ramadhan commented 4 years ago

Thank you @katyhuff.

I have read the JOSS conflict of interest (COI) 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.

I confirm that I read and will adhere to the JOSS code of conduct.

katyhuff commented 4 years ago

Thank you. I will do my final checks in the next couple of days and hopefully we can move this one forward. Thank you for your patience.

sjpfenninger commented 4 years ago

@YoungFaithful @katyhuff I've ticked all boxes now, apologies for the oversight. Nothing more from my side!

YoungFaithful commented 4 years ago

@katyhuff, thanks for looking over the paper one more time. Looking forward to your feedback. @sjpfenninger and @ali-ramadhan thank you both for your helpful feedback and improvements!

katyhuff commented 4 years ago

I'm sorry this is taking so long. It's on my list for this evening.

katyhuff commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

katyhuff commented 4 years ago

@whedon check references

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1016/j.apenergy.2018.01.023 is OK
- 10.21105/joss.01573 is OK
- 10.1137/15M1020575 is OK
- 10.1137/141000671 is OK
- 10.3390/en12061153 is OK
- 10.21105/joss.00825 is OK
- 10.1016/j.rser.2018.08.043 is OK
- 10.1016/j.apenergy.2019.02.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None
katyhuff commented 4 years ago

Thank you @sjpfenninger, @ali-ramadhan for your reviews -- we couldn't do this without you. Thank you @YoungFaithful for your patience, a strong submission, and for engaging actively in the review process! I have looked over the paper, double-checked all the DOI links, and have conducted a high-level review of the code itself. Everything looks ship-shape to me. At this point, please

Until then, now is your moment for final touchups!

katyhuff commented 4 years ago

@YoungFaithful Please let me know when you've completed the tasks in my previous comment.

labarba commented 4 years ago

👋 hi everybody!

It looks like this submission was ready to progress to acceptance, but some final items are required of the authors. @YoungFaithful : can you update us on your status? The editor listed the final steps for you—they are not onerous!

YoungFaithful commented 4 years ago

Dear @katyhuff and @labarba, sorry for the delay on my end. I now found the time to go through the paper and docs and to find any grammar and spelling mistakes left. I connected the repository with Zenodo and the DOI is DOI: 10.5281/zenodo.4003566 Thanks for your support!

arfon commented 4 years ago

@whedon set 10.5281/zenodo.4003566 as archive