editorialbot commented 7 months ago

Submitting author: !--author-handle-->@mohitpundir@rkurchin<!--end-editor-- Reviewers: @yaomz16, @sudarshanv01 Archive: 10.5281/zenodo.11213255

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/70f75ac2c37f013f8edaa35774759183"><img src="https://joss.theoj.org/papers/70f75ac2c37f013f8edaa35774759183/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/70f75ac2c37f013f8edaa35774759183/status.svg)](https://joss.theoj.org/papers/70f75ac2c37f013f8edaa35774759183)

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

@yaomz16 & @sudarshanv01, 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 @rkurchin 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 @yaomz16

📝 Checklist for @sudarshanv01

editorialbot commented 7 months 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 7 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (983.0 files/s, 258491.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              1              1           4248
Python                          19            456            525           1489
Jupyter Notebook                10              0           2798            568
Markdown                         2             32              0            116
TeX                              1              9              0             61
TOML                             1             12              1             33
DOS Batch                        1              8              1             26
reStructuredText                 3             21             26             15
YAML                             1             25             16             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            40            568           3375           6575
-------------------------------------------------------------------------------

Commit count by author:

    70  Mohit Pundir
    49  Furcas  Fabio
     9  Anja Korber
     4  Mohit pundir
     3  Fabio

editorialbot commented 7 months ago

Paper file info:

📄 Wordcount for paper.md is 1462

✅ The paper includes a Statement of need section

editorialbot commented 7 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 7 months ago

:warning: An error happened when generating the pdf.

rkurchin commented 7 months ago

@openjournals/bcm-eics, any insight on this compilation error? From the stacktrace, seems like it might just be an errant tab character that the parser doesn't like or something?

yaomz16 commented 7 months ago

Review checklist for @yaomz16

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://gitlab.com/cmbm-ethz/pourbaix-diagrams?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mohitpundir) 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?

yaomz16 commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

:warning: An error happened when generating the pdf.

rkurchin commented 7 months ago

Pinging @openjournals/bcm-eics again about the pdf generation error

rkurchin commented 7 months ago

@yaomz16, thanks for getting your review started! @sudarshanv01, let me know if you have any questions about the process.

sudarshanv01 commented 7 months ago

Hi @rkurchin, thanks - will let you know!

sudarshanv01 commented 7 months ago

Review checklist for @sudarshanv01

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://gitlab.com/cmbm-ethz/pourbaix-diagrams?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mohitpundir) 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?

yaomz16 commented 7 months ago

@rkurchin I looked through paper.md without compiling a pdf. I'll read through the pdf version of the paper after the compiling issue is fixed just to make sure I got everything right, but right now I think everything on the checklist is good. Any additional things I shall do as a reviewer?

rkurchin commented 7 months ago

@yaomz16 nope, if you think it looks good and is ready for acceptance, you're all set. Thanks for your help!

sudarshanv01 commented 7 months ago

@rkurchin I have completed the first round of review and left a few issues on the gitlab repo (these are minor) - I will tick the remaining bullet points on the checklist once the discussions on the gitlab issues are complete.

yaomz16 commented 7 months ago

@rkurchin I raised one issue in their gitlab repo (also a minor one). Overall this package is good. Once they address the issue I raised, the paper will be ready for acceptance.

rkurchin commented 6 months ago

Hi @mohitpundir, checking in regarding responses to the remaining couple of issues filed by reviewers!

mohitpundir commented 6 months ago

Hi @rkurchin, Thanks for checking. Yes, we are working on the remaining issues. I was waiting for my co-workers to return from conferences. We should be done with these issues in the next few days.

mohitpundir commented 6 months ago

Hi @rkurchin, Thanks for the wait. We have addressed all the issues related to the review and introduced the changes in the merge request branch corresponding to them.

rkurchin commented 6 months ago

Great – let us know once those are merged and we can ping the reviewers to take another look.

mohitpundir commented 6 months ago

Hi @rkurchin All the branches have been merged and the repo is ready for another look.

rkurchin commented 5 months ago

@sudarshanv01 and @yaomz16, please take a look and see what you think!

yaomz16 commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

yaomz16 commented 5 months ago

I have updated the checklist. No more questions from me and I think the paper is good to go now

sudarshanv01 commented 5 months ago

Looks great to me!

rkurchin commented 5 months ago

@mohitpundir can you take a look at what's going on with the pdf render? Looks like there might just be an errant tab or newline in the author metadata that's causing it troubles, perhaps if you just retype that section of the markdown it will fix it?

mohitpundir commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

mohitpundir commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

:warning: An error happened when generating the pdf.

mohitpundir commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

mohitpundir commented 5 months ago

@rkurchin Thanks for pointing out the exact issue. I have corrected it now.

rkurchin commented 5 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
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.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
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 pull request)
[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

rkurchin commented 5 months ago

@editorialbot check references

editorialbot commented 5 months ago

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Atlas d’Équilibres Électrochimiques: Eau Oxygénée
- 10.1063/1.4812323 may be a valid DOI for title: Commentary: The Materials Project: A materials gen...
- 10.1016/0098-3004(92)90029-q may be a valid DOI for title: SUPCRT92: A software package for calculating the s...
- 10.3133/wri994259 may be a valid DOI for title: User’s guide to PHREEQC (Version 2): A computer pr...
- 10.3133/tm6a43 may be a valid DOI for title: Description of input and examples for PHREEQC vers...
- No DOI given, and none found for title: Introduction to Corrosion science
- No DOI given, and none found for title: Corrosion Science and Engineering
- 10.1103/physrevb.85.235438 may be a valid DOI for title: Prediction of solid-aqueous equilibria: Scheme to ...
- 10.1021/acs.chemmater.7b03980.s001 may be a valid DOI for title: Electrochemical stability of metastable materials
- No DOI given, and none found for title: The atomic simulation environment — a Python libra...

INVALID DOIs

- None

rkurchin commented 5 months ago

@mohitpundir make sure to address the missing DOI's shown above

rkurchin commented 5 months ago

Also, you can go ahead and start working on the other bullet points in the list above (version tags, archiving, etc.) and send me the relevant information. I'll send editorial comments shortly...

rkurchin commented 5 months ago

Editorial suggestions:

line 8: suggest changing to "PourPy is an open-source Python package for generating thermodynamic stability diagrams [...]"
13: missing an Oxford comma after "metals"
14: change to "PourPy is a tool enabling users [...]"
16: phrasing feels awkward, suggest something like "custom reactive systems containing multiple solid, aqueous, and gaseous species [...]"
17: suggest replacing "displayed" with "considered"
19: remove "to" before "calculate" to fix parallelism
30: remove comma and "namely"
32: suggest to remove "essentially"
37: probably replace "iron oxides" with just "oxides" since you give steel as an example but are making a more general statement
42: replace "given" with "provided"
46: suggest replacing "and" in parenthetical with "and/or"
55: remove comma after "Another"
57: fix typo "carthesian" --> "Cartesian"
60: looks like you might have the $\Delta G_f^0$ typeset as {\Delta G^0}_f or something, the subscript is sticking out weirdly
60-61: perhaps "reaction constituents" should just be "reactants" here?
87: missing a comma before "and protons"
93: same comment as above about "reactants"
102: remove "a" between "define" and "regions"

References:

fix DOI's as noted above
134: inconsistent capitalization in title

mohitpundir commented 5 months ago

@editorialbot check references

editorialbot commented 5 months ago

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

OK DOIs

- 10.1063/1.4812323 is OK
- 10.1016/0098-3004(92)90029-Q is OK
- 10.3133/wri994259 is OK
- 10.3133/tm6a43 is OK
- 10.1007/978-1-4419-0455-3 is OK
- 10.1007/978-3-319-97625-9 is OK
- 10.1103/physrevb.85.235438 is OK
- 10.1021/acs.chemmater.7b03980 is OK
- 10.1021/acs.chemmater.7b03980.s001 is OK

MISSING DOIs

- No DOI given, and none found for title: Atlas d’Équilibres Électrochimiques: Eau Oxygénée

INVALID DOIs

- None

mohitpundir commented 5 months ago

@rkurchin I have modified the paper.md and paper.bib to incorporate the suggestions. However, for one of reference there seems to be no DOI. Could I proceed without this DOI?

mohitpundir commented 5 months ago

@rkurchin The version number is 1.1.1 and the DOI on Zenodo is 10.5281/zenodo.11213255.

rkurchin commented 5 months ago

@editorialbot set 1.1.1 as version

editorialbot commented 5 months ago

Done! version is now 1.1.1

rkurchin commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

rkurchin commented 5 months ago

@editorialbot set 10.5281/zenodo.11213255 as archive

openjournals / joss-reviews

[REVIEW]: PourPy - A python package to generate potential-pH diagrams #6536

Status

Reviewer instructions & questions

Checklists

Review checklist for @yaomz16

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sudarshanv01

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