[REVIEW]: CESAR-P: A dynamic urban building energy simulation tool

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@kristina-o@timtroendle<!--end-editor-- Reviewers: @olejandro, @noah80, @jasondegraw Archive: 10.5281/zenodo.7150137

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/fcc09a8a4324668a6559e39f98370473"><img src="https://joss.theoj.org/papers/fcc09a8a4324668a6559e39f98370473/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fcc09a8a4324668a6559e39f98370473/status.svg)](https://joss.theoj.org/papers/fcc09a8a4324668a6559e39f98370473)

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

@olejandro & @noah80 & @jasondegraw, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @timtroendle know.

✨ 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 ✨

Checklists

📝 Checklist for @olejandro

📝 Checklist for @noah80

📝 Checklist for @jasondegraw

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.enbuild.2018.03.020 is OK
- 10.1016/S0378-7788(00)00114-6 is OK
- 10.1016/j.enbuild.2022.111844 is OK
- 10.1016/j.buildenv.2021.108574 is OK
- 10.5281/zenodo.4682880 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

Software report:

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Language                     files          blank        comment           code
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Markdown                         2             14              0            107
TeX                              1              6              0             65
TOML                             1              6              0             62
Dockerfile                       1             18             28             41
DOS Batch                        1              8              1             27
INI                              1             12              0             25
make                             1              4              6             10
CSS                              1              1              1              4
Bourne Shell                     1              0              0              3
-------------------------------------------------------------------------------
SUM:                           327           4291           9854          98144
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 782

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

timtroendle commented 2 years ago

@olejandro, @noah80, @jasondegraw, I will set a reminder for each of you in three weeks from now to see where you stand with your review at that point in time.

timtroendle commented 2 years ago

@editorialbot remind @olejandro in three weeks

editorialbot commented 2 years ago

Reminder set for @olejandro in three weeks

timtroendle commented 2 years ago

@editorialbot remind @noah80 in three weeks

editorialbot commented 2 years ago

Reminder set for @noah80 in three weeks

timtroendle commented 2 years ago

@editorialbot remind @jasondegraw in three weeks

editorialbot commented 2 years ago

Reminder set for @jasondegraw in three weeks

olejandro commented 2 years ago

Review checklist for @olejandro

Conflict of interest

[x] I confirm that 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/hues-platform/cesar-p-core?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@kristina-o) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[x] 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?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] 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)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] 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?

LeonieFierz commented 2 years ago

thank you @timtroendle to organize everything and thank you @jasondegraw, @olejandro and @noah80 for reviewing our submission!

editorialbot commented 2 years ago

:wave: @olejandro, please update us on how your review is going (this is an automated reminder).

editorialbot commented 2 years ago

:wave: @noah80, please update us on how your review is going (this is an automated reminder).

editorialbot commented 2 years ago

:wave: @jasondegraw, please update us on how your review is going (this is an automated reminder).

noah80 commented 2 years ago

Review checklist for @noah80

Conflict of interest

[x] I confirm that 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/hues-platform/cesar-p-core?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kristina-o) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

timtroendle commented 2 years ago

👋 @noah80, @olejandro, @jasondegraw, we are approaching the end of the six-week review period. Can you let us know where you stand with your review and by when you plan to finish?

noah80 commented 2 years ago

@timtroendle I was stuck at this point: "Contribution and authorship: Has the submitting author (@kristina-o) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?"

Kristina has not contributed anything to the source code as far as I can tell. She's not listed in the repository at all. How to proceed?

timtroendle commented 2 years ago

Thanks for the update, @noah80. You can simply leave this box unchecked for now.

We don't require contributions of authors to be code contributions. @kristina-o, can you clarify this point?

jasondegraw commented 2 years ago

Review checklist for @jasondegraw

Conflict of interest

[x] I confirm that 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/hues-platform/cesar-p-core?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kristina-o) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

kristina-o commented 2 years ago

Thank you @noah80 for reviewing our submission and @timtroendle for forwarding the question. My contributions to CESAR-P (and also the predecessor CESAR) include the original idea for the tool, contributing to the development of the approach, and supervision of further developments. The current version of CESAR-P was coded by our software engineer Leonie Fierz, she is listed together with me as the main authors. Hope that clarifies my contributions.

jasondegraw commented 2 years ago

@timtroendle I'm working my way through the checklist, currently working on the "Functionality" and "Documentation" sections. I plan on finishing the review this week.

jasondegraw commented 2 years ago

The software described in the paper is intended for modeling and simulation of sets of buildings (urban areas, campuses, etc.) and is implemented in Python. It is well documented and (at least in the files that I looked at) well written. The paper describes the need and features of the software, but I would not recommend acceptance of the paper without revisions. I do not believe these revisions are major revisions. The paper revisions are:

The paper (and the documentation as well) is missing a clear statement of the intended audience. This is particularly important as urban BEM becomes more and more popular. This is why both of the "statement of need" items on the checklist are unchecked.
The paper does not clearly address the state of the field. There are other options available and this one looks like it does have some unique features, but that isn't clear from the paper.
The paper does not have enough about what the software can do. It would be much better if an example analysis was presented (in abbreviated form, perhaps one of the examples).

Other items from the checklist:

The installation documentation works well and there are examples, but there are some minor typos and the simple example fails initially. On the bright side, the error clearly states that there needs to be a TEMP environment variable defined, and doing that allows the example to run. Maybe I missed a step in the directions, but it would be good to make sure that the example runs without modifications. That example also generates a fair number of (probably harmless) deprecation warnings from pandas. I also looked into the EnergyPlus outputs a little, and I did see a warning about unused objects. Those are also probably harmless, but speaking from experience (with EnergyPlus), some users can be put off by even harmless warnings.
There are tests, but I was unable to run them. There's a lot of documentation, so perhaps I just missed that.
There is developer documentation, but I did not find information on how to contribute or get support. Another thing that I maybe just missed.

One thing not really in the checklist:

I did not find a clear statement on supported platforms. It looks like it is probably any platform that E+ runs on that supports Python, but it would be better if there was a clear statement on where it should be expected to work. I ran it on a fresh instance of Ubuntu 20.04 and it worked well as far as I could tell.

In summary, there are some things I'd like to see fixed, but in general @kristina-o and coworkers are to be congratulated on this work. I'm happy to follow up on any of the above items by filing issues or whatever else would be desired.

LeonieFierz commented 2 years ago

@jasondegraw thank you for the review and the constructive feedback! We will go through it in detail and improve the points you mentioned. Just two points from the technical side:

The tests are run in a CI pipeline on our internal GitLab Server and it should actually be possible to run them with pytest after installing the package for development with poetry.
I will think about how we can improve regarding the missing TEMP environment variable, which actually is a default on Windows.

jasondegraw commented 2 years ago

@LeonieFierz You're most welcome, I'll give the tests another try at some point this week.

LeonieFierz commented 2 years ago

@jasondegraw That would be great if you could try to run the tests. To do so, you first need the "development installation" as described in https://cesar-p-core.readthedocs.io/en/latest/development/development-installation.html. With that set up, you can start the tests e.g. with

poetry run pytest tests

Note that some of the tests need EnergyPlus 9.5.0 installed and configured in the environment variables ENERGYPLUS_EXE and ENERGYPLUS_VER (see https://cesar-p-core.readthedocs.io/en/latest/installation.html#energyplus). Tests depending on E+ Installation: tests\test_eplus_adapter\test_eplus_adapter.py, tests\test_eplus_adapter\test_solar_potential.py, tests\test_integration\test_cesar_integration.py, tests\test_model\test_model_pickling.py

And you mentioned that there were a few typos you had to fix in the cesar-p-usage-examples/simple_example. I just tested it again and it run without any adaption on Windows. Do you remember what was the problem if there was any besides the missing TEMP environment variable?

timtroendle commented 2 years ago

@olejandro, @noah80 : Can you please give us update on how the review is going?

timtroendle commented 2 years ago

@olejandro, @noah80, are you still working on the review or do you want to be removed as reviewers of this submission?

olejandro commented 2 years ago

Working on it @timtroendle. Sorry for the 🐢 speed!

timtroendle commented 2 years ago

Ok. Thanks for letting us know, @olejandro !

noah80 commented 2 years ago

I've installed the tool a couple of weeks back, but I stalled after that. I'm still interested in the review, but I would suggest a number of improvements to the authors:

I've found the installation instructions here rather confusing: https://cesar-p-core.readthedocs.io/en/latest/development/development-installation.html https://cesar-p-core.readthedocs.io/en/latest/installation.html#installation
It's not clearly described when I would need the development version and for which use the I want the normal install
Unclear if it needs to be exactly Python 3.8 or only newer than 3.8
There could be a batch file that checks if the install succeeded and does everything automatically, but instead I have a long list of things I might want to check
After installing the core library it's completely unclear how to get a first example running and how to play with that.

Do these suggestions make sense? If so, I'd suggest implementing them and that would make it easier for the reviewers to actually get an example running to review the results. The software sounds pretty amazing after all.

LeonieFierz commented 2 years ago

@noah80 thank you for starting to review our submission

we will try to state the points you mentioned in more detail.

meanwhile to get you started with playing with the library please have a look on https://github.com/hues-platform/cesar-p-usage-examples where you find different usage examples - please let me know if you have troubles with that (if you are running it on a linux system, please set an environment variable named TEMP pointing to location where temporary files can be created - we fixed that issue already but it is not yet pushed to github)

olejandro commented 2 years ago

Thank you @noah80 for reviewing our submission and @timtroendle for forwarding the question. My contributions to CESAR-P (and also the predecessor CESAR) include the original idea for the tool, contributing to the development of the approach, and supervision of further developments. The current version of CESAR-P was coded by our software engineer Leonie Fierz, she is listed together with me as the main authors. Hope that clarifies my contributions.

@kristina-o, could you please clarify contribution of the remaining 3 authors? I've noticed that contributions of two of them are stated in the readme, as well as contributions of 2 other contributors who are not on the authors list. This makes me wonder whether the list of paper authors is appropriate and complete.

olejandro commented 2 years ago

@timtroendle @kristina-o while going through my checklist I've opened a few issues in the software repository which I believe must be addressed before accepting the paper.

kristina-o commented 2 years ago

Dear @olejandro please find below the contributions of the other 3 remaining authors: • James Allan has developed and integrated the Graph Database data for Archetypical constructions • Sven Eggimann developed a shapefile parser for reading site vertices • Natasa Vulic contributed with development testing and support and performed a validation study at national scale. These three parts are important for the functioning of the tool. Additionally all three of them (as well as Leonie Fierz and myself) supported the open access release of CESAR-P, the preparation of the JOSS paper publication and are actively contributing to the further development and testing of CESAR-P. Ricardo Silva has developed an optional feature for CESAR-P but didn't further contribute to the development of the tool, and the main contributions of Aaron Bojarski are not yet implemented in the current open-source version of CESAR-P. That’s why the latter two are not included in the list of authors. I hope this clarifies our motivation for defining the list of authors.

timtroendle commented 2 years ago

@kristina-o, can you let us know by when you think you can address the points mentioned by the three reviewers?

kristina-o commented 2 years ago

@kristina-o, can you let us know by when you think you can address the points mentioned by the three reviewers?

@timtroendle, sorry for the delay. We are almost done with the updates of the paper. We plan to address all the points of the reviewers by the end of next week

LeonieFierz commented 2 years ago

@timtroendle We just released a version 2.3.0 of cesar-p-core as well as an update for cesar-p-usage-examples on github. These version includes the updates addressing the inputs from the reviewers. We now included the paper on the master branch, so the joss-paper branch is no longer the reference for the publication.

LeonieFierz commented 2 years ago

@jasondegraw thank you again for your inputs. here a few short notes how we addressed your points:

The "Statement of need and Key features" section has been updated to include target audience and the state of the field (The statement of need section has been updated by adding information on potential users and use cases; A short review on available methodologies and available literature has been included in the Statement of need section. One of the particular strength is now more prominently mentioned, which is the requirement of only few key input parameters to facilitate the process of setting up simulations of buildings and districts.)
We added a "Example" section to the paper as a showcase what you can do with cesar-p-core library
Installation & Example: instructions were updated, TEMP variable no longer needed on Linux systems, Example should run without errors, deprecation warnings fixed, E+ warning fixed (minor issue about missing field which is actually not used, only occured with E+ 8.5)
How to run the tests is documented under https://cesar-p-core.readthedocs.io/en/latest/development/development-commands.html; added information about required environment to run all tests successfully
Contribution section was added to README
Supported platforms added to README

LeonieFierz commented 2 years ago

@noah80 thank you again for looking into cesar-p-core. Please note following updates with version 2.3.0:

Installation instructions have been improved, for cesar-p-core and cesar-p-usage-examples. See https://cesar-p-core.readthedocs.io/en/latest/installation.html to get started. It links to cesar-p-usage-examples to get you started after the installation.
As the default installation is straight forward (and with the updated instructions easier to follow) a batch script to check the installation should not be necessary
Updated the README to include only Python 3.8 as supported version, as we only run the CI with Python 3.8. Even though it most probably will run with newer Python Versions, but this is up to the user to check.

LeonieFierz commented 2 years ago

@olejandro thank you for your review! we addressed the points you created issues for with version 2.3.0. I closed the issues and mentioned what we did shortly in the issue comment.

timtroendle commented 2 years ago

@LeonieFierz thanks for keeping us updated!

@olejandro @noah80 @jasondegraw could you have a look at these changes and let us know whether they address your comments? Can you please update your checklists accordingly?

timtroendle commented 2 years ago

@olejandro @noah80 @jasondegraw can you please update us on the status of this review? When would you be able to finish it?

jasondegraw commented 2 years ago

@timtroendle I should be able to go back through and update my checklist within the next couple of days.

noah80 commented 2 years ago

I'll take a look this week.

timtroendle commented 2 years ago

Thanks @noah80 for lettings us know.

@olejandro, what's the timeline on your side?

timtroendle commented 2 years ago

/ooo August 22 until September 12

timtroendle commented 2 years ago

👋 @noah80 and @jasondegraw, can you let us know what the status of your reviews are? We should really finish this up. Can you let us know whether further changes are necessary?

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