editorialbot commented 1 year ago

Submitting author: !--author-handle-->@cmcp-group@dhhagan<!--end-editor-- Reviewers: @yangmr04, @mbagheri20 Archive: 10.5281/zenodo.7953483

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f65f3b6eb2df4e437da1c4ef277347a4"><img src="https://joss.theoj.org/papers/f65f3b6eb2df4e437da1c4ef277347a4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f65f3b6eb2df4e437da1c4ef277347a4/status.svg)](https://joss.theoj.org/papers/f65f3b6eb2df4e437da1c4ef277347a4)

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

@yangmr04 & @mbagheri20, 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 @dhhagan 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 @yangmr04

📝 Checklist for @mbagheri20

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.32 s (123.5 files/s, 26832.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                       7            317             11           2002
Python                          14            408            635           1898
XML                              1              0              0           1149
HTML                             3            202             53           1025
YAML                             5             11             42            217
Markdown                         5             62              0            206
TeX                              1             17              0            183
Dockerfile                       1              5              6             14
CSS                              2              0             11              2
-------------------------------------------------------------------------------
SUM:                            39           1022            758           6696
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

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

OK DOIs

- 10.1021/acs.jpcc.9b02116 is OK
- 10.1021/acs.jpclett.0c01518 is OK
- 10.1007/s10450-019-00168-5 is OK
- 10.1002/adma.202201502 is OK
- 10.1021/ja01269a023 is OK
- 10.1021/jacs.5b10266 is OK
- 10.1021/ja512973b is OK
- 10.1007/BF02479039 is OK
- 10.1016/j.micromeso.2011.08.020 is OK
- 10.1080/08927022.2015.1010082 is OK
- 10.1039/D1TA08021K is OK
- 10.1021/acs.langmuir.2c01390 is OK
- 10.1515/pac-2014-1117 is OK

MISSING DOIs

- 10.1016/s0167-2991(07)80008-5 may be a valid DOI for title: Is the BET Equation Applicable to Microporous Adsorbents?

INVALID DOIs

- None

editorialbot commented 1 year ago

Wordcount for paper.md is 2609

editorialbot commented 1 year ago

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

yangmr04 commented 1 year ago

Review checklist for @yangmr04

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/hjkgrp/SESAMI_web?
[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 (@cmcp-group) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

mbagheri20 commented 1 year ago

Review checklist for @mbagheri20

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/hjkgrp/SESAMI_web?
[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 (@cmcp-group) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

mbagheri20 commented 1 year ago

SESAMI APP works well locally and online. Website design is simple and user-friendly which makes usage easy. In addition, the corresponding manuscript is well structured, and the theory part has enough details. Following are my suggestions:

Manuscript: In the benchmark part, there are good tables and figures which include results for comparison with other existing approaches. But the comparison is limited to this statement “All software are in generally good agreement”. I suggest extending the comparison part a little more and explaining why the approach does not find a surface area in some cases (denoted with N/A)

Installation:
Since I had all the requirements pre-installed on my computer, First I checked app.py locally (without using conda environment) and it worked well but when I used a fresh Ubuntu system to follow the installation part and used the conda environment.yml file, I was unable to install it.
There are some conflicts in yml file which should be resolved. Simple solution for me was installing without using builds and let conda decide about versions. Also, a minor thing like removing the ”prefix” in the file which is not necessary.

yangmr04 commented 1 year ago

Since I had all the requirements pre-installed on my computer, First I checked app.py locally (without using conda environment) and it worked well but when I used a fresh Ubuntu system to follow the installation part and used the conda environment.yml file, I was unable to install it.

I also encountered similar situation on MacOS where I was unable to activate the environment.yml file with conda, although it was no fault of the authors but more of a flaw with conda. Same as @mbagheri20, the app ran fine after I installed all dependencies.

yangmr04 commented 1 year ago

(Sorry for this long comment!)

SESAMI is an excellent tool for estimating the surface area of materials. The web-based app is elegant and lightweight, very easy to use. I have tested the code using the example provided within the SESAMI repo, as well as using an example isotherm from the AIF repo. Everything worked as expected.

The manuscript is in general well-structured and well-written. It fulfills all JOSS publication criteria. However, I have a minor suggestion on how equations can be better introduced. Here is my proposed change, where the equations are introduced before the variables, and eliminate the use of \ref{}s:

The surface area of a material, $S$, can be calculated as 
\begin{equation}\label{eq:surface_area}
S = q_m N A_m,
\end{equation}
where $q_m$ is the molar amount of adsorbate forming a monolayer per unit mass of material, $N$ is the Avogadro constant, and $A_m$ is the area taken up by a single adsorbate molecule in the monolayer. 

In order to attain $q_m$, the monolayer loading region from the isotherm can be identified using the BET equation,
\begin{equation}\label{eq:BET}
\frac{p/p_0}{q(1-p/p_0)} = \frac{1}{q_m C} + \frac{C-1}{q_m C}\frac{p}{p_0},
\end{equation}
where $p$ is the vapor pressure, $p_0$ is the saturation vapor pressure, $q$ is the adsorbate loading, and $C$ is the BET constant.

Please also address the missing DOI picked up by the editorialbot above: https://github.com/openjournals/joss-reviews/issues/5429#issuecomment-1531488976.

@dhhagan Overall, I recommend publication on JOSS after the authors address

[x] the equations format as suggested above
[x] the missing DOI https://github.com/openjournals/joss-reviews/issues/5429#issuecomment-1531488976
[x] and the issue https://github.com/hjkgrp/SESAMI_web/issues/27

Thank you!

gianmarco-terrones commented 1 year ago

Hi @yangmr04, thank you very much for your feedback! I have implemented your requested changes in the most recent version of SESAMI_web.

gianmarco-terrones commented 1 year ago

Quick question, does JOSS use RGB or CMYK images?

gianmarco-terrones commented 1 year ago

Hi @mbagheri20, thank you very much for your feedback as well! I have addressed your comments on the yml file and detailed the changes I made here. I will address your comments on the manuscript shortly.

yangmr04 commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

yangmr04 commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1021/acs.jpcc.9b02116 is OK
- 10.1021/acs.jpclett.0c01518 is OK
- 10.1007/s10450-019-00168-5 is OK
- 10.1002/adma.202201502 is OK
- 10.1021/ja01269a023 is OK
- 10.1021/jacs.5b10266 is OK
- 10.1021/ja512973b is OK
- 10.1007/BF02479039 is OK
- 10.1016/s0167-2991(07)80008-5 is OK
- 10.1016/j.micromeso.2011.08.020 is OK
- 10.1080/08927022.2015.1010082 is OK
- 10.1039/D1TA08021K is OK
- 10.1021/acs.langmuir.2c01390 is OK
- 10.1515/pac-2014-1117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

yangmr04 commented 1 year ago

@gianmarco-terrones Many thanks for your great effort! Everything looks good to me now!

gianmarco-terrones commented 1 year ago

Hi @mbagheri20, I have adjusted the manuscript to address your comments on software comparison and N/A explanation. @cmcp-group tagging you as well since I added some sentences.

The added sentences: "Differences in performance across software on this benchmark set can be attributed to the differing implementations of linear region identification, or in the case of the SESAMI machine learning model, fundamental differences in how the software calculate surface areas.

When a software for isotherm to surface area calculation does not find a surface area, the reason can vary from no ESW minimum being found or no suitable linear region containing an ESW minimum being found in the case of SESAMI 1 (BET+ESW), to an insufficient number of data points in the chosen BET region in the case of pyGAPS."

mbagheri20 commented 1 year ago

Hi @gianmarco-terrones thank you for addressing my comments about the manuscript and fixing the installation problem.

@dhhagan, The authors have revised their manuscript in accordance with the recommendations given in my first report. I recommend publication in the present form.

mtap-research commented 1 year ago

@gianmarco-terrones Looks good to me! Thanks to @mbagheri20 @yangmr04 for their constructive review comments and time.

gianmarco-terrones commented 1 year ago

Yes, thank you @mbagheri20 @yangmr04 for your thoughtful feedback and for helping this review go smoothly!

yangmr04 commented 1 year ago

@dhhagan Here to confirm my recommendation of publication in the present form. The authors have addressed all my requests made in my previous comment. I have now completed my review, thank you @dhhagan for the invitation!

dhhagan commented 1 year ago

@yangmr04 and @mbagheri20 thank you for your quick and comprehensive reviews!

@cmcp-group Can you go ahead and make a final, tagged release, archive it, and report the version number and archive DOI in this thread?

mtap-research commented 1 year ago

@gianmarco-terrones released a new version incorporating the changes requested by the reviewers. Appreciate your time for handling the submission, @dhhagan

gianmarco-terrones commented 1 year ago

Hi @dhhagan, the version number is 1.1.0. Is the DOI generated through Zenodo? If so, I am awaiting approval from my PI to grant Zenodo access to the repo.

gianmarco-terrones commented 1 year ago

The archive DOI is 10.5281/zenodo.7953483, for version 1.1.0.

dhhagan commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

dhhagan commented 1 year ago

@gianmarco-terrones can you directly link me to the Zenodo repository? For some reason, I can't find it when I search for that DOI.

gianmarco-terrones commented 1 year ago

@dhhagan Yes, it is at https://zenodo.org/record/7953483. On my end, searching https://doi.org/10.5281/zenodo.7953483 also worked.

gianmarco-terrones commented 1 year ago

What is the current status of the review/publication?

dhhagan commented 1 year ago

Hi @gianmarco-terrones can you update the Zenodo repository to match the paper? The following should match:

[ ] Title
[ ] Author List

gianmarco-terrones commented 1 year ago

Hi @dhhagan all set

dhhagan commented 1 year ago

@editorialbot set 10.5281/zenodo.7953483 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7953483

dhhagan commented 1 year ago

@editorialbot set v1.1.0 as version

editorialbot commented 1 year ago

Done! version is now v1.1.0

dhhagan commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1021/acs.jpcc.9b02116 is OK
- 10.1021/acs.jpclett.0c01518 is OK
- 10.1007/s10450-019-00168-5 is OK
- 10.1002/adma.202201502 is OK
- 10.1021/ja01269a023 is OK
- 10.1021/jacs.5b10266 is OK
- 10.1021/ja512973b is OK
- 10.1007/BF02479039 is OK
- 10.1016/s0167-2991(07)80008-5 is OK
- 10.1016/j.micromeso.2011.08.020 is OK
- 10.1080/08927022.2015.1010082 is OK
- 10.1039/D1TA08021K is OK
- 10.1021/acs.langmuir.2c01390 is OK
- 10.1515/pac-2014-1117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4287, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

Kevin-Mattheus-Moerman commented 1 year ago

@cmcp-group @dhhagan I have checked the repository, the archive, the paper, and this review. Most seems in order. @cmcp-group the below points require your attention before we can proceed:

@cmcp-group please work on the following:

[x] Edit the license listed on the archive to match your software license. It currently says: Other (Open).
[ ] Please spell out USA as United States of America in your affiliations.

@dhhagan thanks for editing this submission. Note the following new command to create the post-review checklist which will help catch the above type of things.

@editorialbot create post-review checklist

gianmarco-terrones commented 1 year ago

@dhhagan @Kevin-Mattheus-Moerman Thank you for your efforts!

@Kevin-Mattheus-Moerman We have addressed your comments. We specified that we use an MIT License at https://zenodo.org/record/7953483 and changed the PDF such that USA is spelled out.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Terrones given-names: Gianmarco G. orcid: "https://orcid.org/0000-0001-5360-165X" - family-names: Chen given-names: Yu orcid: "https://orcid.org/0000-0002-6530-0974" - family-names: Datar given-names: Archit orcid: "https://orcid.org/0000-0002-5276-0103" - family-names: Lin given-names: Li-Chiang orcid: "https://orcid.org/0000-0002-2821-9501" - family-names: Kulik given-names: Heather J. orcid: "https://orcid.org/0000-0001-9342-0191" - family-names: Chung given-names: Yongchul G. orcid: "https://orcid.org/0000-0002-7756-0589" contact: - family-names: Chung given-names: Yongchul G. orcid: "https://orcid.org/0000-0002-7756-0589" doi: 10.5281/zenodo.7953483 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Terrones given-names: Gianmarco G. orcid: "https://orcid.org/0000-0001-5360-165X" - family-names: Chen given-names: Yu orcid: "https://orcid.org/0000-0002-6530-0974" - family-names: Datar given-names: Archit orcid: "https://orcid.org/0000-0002-5276-0103" - family-names: Lin given-names: Li-Chiang orcid: "https://orcid.org/0000-0002-2821-9501" - family-names: Kulik given-names: Heather J. orcid: "https://orcid.org/0000-0001-9342-0191" - family-names: Chung given-names: Yongchul G. orcid: "https://orcid.org/0000-0002-7756-0589" date-published: 2023-06-09 doi: 10.21105/joss.05429 issn: 2475-9066 issue: 86 journal: Journal of Open Source Software publisher: name: Open Journals start: 5429 title: "SESAMI APP: An Accessible Interface for Surface Area Calculation of Materials from Adsorption Isotherms" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05429" volume: 8 title: "SESAMI APP: An Accessible Interface for Surface Area Calculation of Materials from Adsorption Isotherms" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

openjournals / joss-reviews

[REVIEW]: SESAMI APP: An Accessible Interface for Surface Area Calculation of Materials from Adsorption Isotherms #5429

Status

Reviewer instructions & questions

Checklists

Review checklist for @yangmr04

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mbagheri20

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance