[REVIEW]: AixCaliBuHA: Automated calibration of building and HVAC systems

[whedon]

Submitting author: @FWuellhorst (Fabian Wüllhorst)
Repository: https://github.com/RWTH-EBC/AixCaliBuHA
Branch with paper.md (empty if default branch):
Version: v_0.3.0
Editor: @fraukewiese
Reviewers: @samanmostafavi, @shamsiharis
Archive: 10.5281/zenodo.6475439

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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

@@shamsiharis & @samanmostafavi, 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
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✨ 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 ✨

Review checklist for @shamsiharis

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@FWuellhorst) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 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

• 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?

Review checklist for @samanmostafavi

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@FWuellhorst) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 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

• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ralphevins, @samanmostafavi it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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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:

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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]

Wordcount for paper.md is 908

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.14 s (349.6 files/s, 170319.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              5              0            135          17082
Python                          26            579           1552           2648
Markdown                         5             73              0            248
Jupyter Notebook                 1              0            566            153
TeX                              1             11              0            123
reStructuredText                 7             34             66             43
YAML                             2              3              4             42
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                            48            704           2329          20349
-------------------------------------------------------------------------------


Statistical information for the repository '2dce1dc2e9f342b8f938c3eb' was
gathered on 2021/10/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Fabian                           1             5             10            0.05
Fabian Wüllhorst                10          6304           5805           37.37
Leonard Schulte                  1             4              4            0.02
Lovis Kauderer                   6           131             52            0.56
MBaranskiEBC                     3           913              0            2.82
MichaMans                        1            12              6            0.06
Philipp Mehrfeld                 3             9              2            0.03
Sebastian                       22           904            692            4.93
Sebastian Borges                 1            39             38            0.24
Sebastian.Borges                 1            10              1            0.03
fabian.wuellhorst              163          8663           6126           45.65
philipp.mehrfeld                36          1291           1067            7.28
zhiyupan                         1           309              3            0.96

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
FWuellhorst                1227          100.0         19.0               14.75
Lovis Kauderer                4            3.1         10.1                0.00
MichaMans                     1            8.3          0.9                0.00
Philipp Mehrfeld              5           55.6         30.2               40.00
Sebastian.Borges            131         1310.0         11.1               25.19
fabian.wuellhorst          3408           39.3          6.7               16.70
zhiyupan                      3            1.0         28.1               66.67

[whedon]

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.1016/j.rser.2014.05.007 is OK
- 10.26868/25222708.2019.210992 is OK
- 10.3384/ecp21181561 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[fraukewiese]

@ralphevins @samanmostafavi - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #3861 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[fraukewiese]

@ralphevins @samanmostafavi : If there are any questions regarding the review, do not hesitate to ask.

[whedon]

👋 @ralphevins, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @samanmostafavi, please update us on how your review is going (this is an automated reminder).

[shantropy]

Hi @fraukewiese, I'll review your software in the next few days, and open up issues in the repository as I go along. Once finished, I'll summarize back here.

[ralphevins]

@fraukewiese I have a question.
The software in question is an API to Dymola, a (very expensive) commercial product.
As is, it opens up Dymola in the system and returns 'Can't find AixLib library' error.
The free version of Dymola cannot support AixLib because the trial version supports limited state-space equations and full models in the library can't be translated or simulated.
So unfortunately it looks as if we must reject, as it's not possible to review (or use) the library without a Dymola license?

[FWuellhorst]

@fraukewiese @ralphevins :
First of all thanks for taking the time to review our software code.

To explain the issue here: You probably started with the first example, which is just there to help users analyze their system and identify inputs, outputs, and parameters of the model they need to calibrate. We think users should think about what they want to calibrate before they actually do it. This would be possible using our main simulation tool, the FMU_API, as well (https://fmi-standard.org/). I apologize that we made this first example for Dymola users only. We will update it directly.
Regarding our Simulation-APIs, note from the paper:

Currently, the package supports the calibration of Functional Mock-up Units (FMUs) based on the Functional Mock-up Interface (FMI) standard (Modelica Association Project, 2021) as well as Modelica models through the python_interfaceof the Software Dymola (Dassault Systems, 2021).

So, the review of code and software should be possible using the FMU_API. If the presence of the DymolaAPI hinders the publication process, we can remove this API from the source code.

All other examples and most importantly the calibration work with the open FMI standard using the interface to fmpy.
We provide two example models. One can be executed on both Linux and windows (Example B) and one only on windows (Example A). If you have trouble running these examples please let me know. I will also update the examples README.md to clarify the points I just made.

Sorry again for any inconvenience due to the bad example description. We hope you will still consider the software for publication after this clarification and the update of the example documentation.

[fraukewiese]

@FWuellhorst Thank you for the explanation.
@ralphevins I agree that it must be possible to review and use the library/software without a license. Do you think that can be assured after the changes made by FWuellhorst?

[fraukewiese]

@ralphevins @samanmostafavi Could you update us on how the review is going?
Thank you.

[ralphevins]

@fraukewiese I had my post-doc @shamsiharis take a look and he's much better qualified than me to complete the review. Can you reassign to him? He should be able to get it completed pretty quickly as he's already seen the codebase. Thanks!

[fraukewiese]

@whedon add @shamsiharis as reviewer

[editorialbot]

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.1016/j.rser.2014.05.007 is OK
- 10.26868/25222708.2019.210992 is OK
- 10.3384/ecp21181561 is OK
- 10.3384/ecp18154121 is OK
- 10.3384/ECP14096647 is OK
- 10.1016/j.enconman.2021.114888 is OK
- 10.1080/19401493.2013.765506 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1145/1577069.1755843 is INVALID

[FWuellhorst]

@fraukewiese
Sadly, these conference papers don't have a DOI. Regarding "King, D. E. (2009). Dlib-ml: A machine learning toolkit. Journal of Machine Learning Research, 10, 1755–1758", a DOI is available on ReserachGate (10.1145/1577069.1755843), however, this DOI is not valid according to https://dx.doi.org/ and thus also for the editorial bot.

Is this a problem? If not, I would continue with the described steps.

[fraukewiese]

@FWuellhorst
I see. Then it is ok to go on without those doi.

[FWuellhorst]

@fraukewiese : Thanks for the quick answer and the time associated with this review process!
I followed all steps:

• Tagged release: https://github.com/RWTH-EBC/AixCaliBuHA/releases/tag/0.3.0
• Release tag: v_0.3.0
• DOI of zenodo: 10.5281/zenodo.6475439

I hope that everything is correct.

[fraukewiese]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[fraukewiese]

@editorialbot set 10.5281/zenodo.6475439 as archive

[fraukewiese]

@editorialbot set v_0.3.0 as version

[editorialbot]

Done! version is now v_0.3.0

[fraukewiese]

@editorialbot set 10.5281/zenodo.6475439 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6475439

[fraukewiese]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.1016/j.rser.2014.05.007 is OK
- 10.26868/25222708.2019.210992 is OK
- 10.3384/ecp21181561 is OK
- 10.3384/ecp18154121 is OK
- 10.3384/ECP14096647 is OK
- 10.1016/j.enconman.2021.114888 is OK
- 10.1080/19401493.2013.765506 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3161

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3161, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[FWuellhorst]

@fraukewiese: Thank you very much for the recommended acceptance! Is the last comment directed at me or at you?

[arfon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03861 joss-papers#3162
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03861
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@samanmostafavi, @shamsiharis – many thanks for your reviews here and to @fraukewiese for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@FWuellhorst – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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reStructuredText:
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[FWuellhorst]

@samanmostafavi @shamsiharis Thanks again for the really good review and all your time put into this!

@fraukewiese @arfon: Thanks for providing the possibility to publish open-source software for research using JOSS. I really appreciate the concept of the journal and the review process. I've signed up as a reviewer. Maybe I can be of help in future reviews as well.