[PRE REVIEW]: pyCADMium: Chemical Atoms in Diatomic Molecules. A prolate spheroidal Python module for embedding calculations.

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@VHchavez@lucydot<!--end-editor-- Reviewers: @raghurama123, @srmnitc Managing EiC: Arfon Smith

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Author instructions

Thanks for submitting your paper to JOSS @VHchavez. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @jarvist.

@VHchavez if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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editorialbot commented 2 years ago

Hello human, 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:

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

@editorialbot generate pdf

editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.19 s (882.7 files/s, 194954.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      14           2517           2692           9887
Python                          86           1953           2389           5480
HTML                            24           1702              3           4544
SVG                              1              0              0           2671
CSS                              7            276             85           1317
Markdown                        10             91              0            281
TeX                              1             15              4            150
reStructuredText                15            252            192            130
YAML                             6             16             21            120
Bourne Shell                     1              5              8             28
DOS Batch                        1              8              1             27
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           167           6839           5401          24645
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 841

editorialbot commented 2 years ago

:warning: An error happened when generating the pdf.

editorialbot commented 2 years ago

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

OK DOIs

- None

MISSING DOIs

- 10.18257/raccefyn.960 may be a valid DOI for title: Towards a density functional theory of molecular fragments. What is the shape of atoms in molecules?
- 10.1103/physreva.82.024501 may be a valid DOI for title: Partition density-functional theory
- 10.1021/jp504058s may be a valid DOI for title: Density-based partitioning methods for ground-state molecular calculations
- 10.1021/acs.jctc.6b01050 may be a valid DOI for title: Accurate reference data for the nonadditive, noninteracting kinetic energy in covalent bonds
- 10.1063/1.5051455 may be a valid DOI for title: Constructing a non-additive non-interacting kinetic energy functional approximation for covalent bonds from exact conditions
- 10.1126/science.1158722 may be a valid DOI for title: Insights into current limitations of density functional theory
- 10.1103/physrevlett.91.146401 may be a valid DOI for title: Climbing the density functional ladder: Nonempirical meta–generalized gradient approximation designed for molecules and solids
- 10.1016/j.cpc.2012.05.007 may be a valid DOI for title: Libxc: A library of exchange and correlation functionals for density functional theory
- 10.1016/c2009-1-28537-6 may be a valid DOI for title: Mathematical methods for physicists
- 10.1039/c5cp00351b may be a valid DOI for title: Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems
- 10.1063/1.442958 may be a valid DOI for title: Numerical Hartree–Fock–Slater calculations on diatomic molecules

INVALID DOIs

- None

VHchavez commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @VHchavez, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot check references

arfon commented 2 years ago

@editorialbot invite @lucydot as editor

:wave: @lucydot – would you be able to edit this submission for JOSS?

editorialbot commented 2 years ago

Invitation to edit this submission sent!

lucydot commented 2 years ago

@arfon, yes! Looks like an interesting package :atom:

lucydot commented 2 years ago

@editorialbot assign me as editor

editorialbot commented 2 years ago

Assigned! @lucydot is now the editor

VHchavez commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.18257/raccefyn.960 is OK
- 10.1103/physreva.82.024501 is OK
- 10.1021/jp504058s is OK
- 10.1021/acs.jctc.6b01050 is OK
- 10.1063/1.5051455 is OK
- 10.1002/qua.25425 is OK
- 10.1002/wcms.1617 is OK
- 10.1126/science.1158722 is OK
- 10.1103/physrevlett.91.146401 is OK
- 10.1016/j.cpc.2012.05.007 is OK
- 10.1016/c2009-1-28537-6 is OK
- 10.1002/qua.24355 is OK
- 10.1039/C5CP00351B is OK
- 10.1063/1.5003825 is OK
- 10.1063/1.442958 is OK

MISSING DOIs

- Errored finding suggestions for "Modern quantum chemistry: introduction to advanced...", please try later

INVALID DOIs

- None

VHchavez commented 2 years ago

Hello @arfon, hello @Kevin-Mattheus-Moerman and lucydot. Thank you for your editorial work.

The references are now updated. I have been unable to find a DOI for one of the books. What is the appropriate way to proceed?
The affiliation for my entry is failing. I have checked for correctness, but I have been unable to find any problem/typo. Any help is very much appreciated.
I believe @ raghurama123 (from your database) would be quite suited for this work.

Thanks again!

lucydot commented 2 years ago

Hello @VHchavez -

I'll be editing the submission rather than reviewing - I'll put a shout out on twitter / send a couple of emails this Monday (after the UK bank holiday which is starting tomorrow) to see if we can secure some well-matched reviewers.

The references are now updated. I have been unable to find a DOI for one of the books. What is the appropriate way to proceed?

I've had a look and can't find one either. Leave the field empty for now.

The affiliation for my entry is failing. I have checked for correctness, but I have been unable to find any problem/typo. Any help is very much appreciated.

This was due to a couple of typos. You also need quotes for multiple affiliations. I've put in a PR that should fix it here: https://github.com/wasserman-group/pyCADMium/pull/7

I believe @ raghurama123 (from your database) would be quite suited for this work.

Thanks for the suggestion!

lucydot commented 2 years ago

@editorialbot generate pdf

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:

lucydot commented 2 years ago

@VHchavez the article has compiled (link in the message above) - please read through to double-check it reads / is formatted as intended.

lucydot commented 2 years ago

@raghurama123 @srmnitc are you available to review this JOSS submission?

raghurama123 commented 2 years ago

Yes, I can review it.

VHchavez commented 2 years ago

Thanks, @lucydot Lucy, the article is formatted as intended.

Thank you, @raghurama123 for kindly helping us with the paper!

lucydot commented 2 years ago

@editorialbot add @raghurama123 as reviewer

editorialbot commented 2 years ago

@raghurama123 added to the reviewers list!

raghurama123 commented 2 years ago

Review checklist for @raghurama123

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/wasserman-group/pyCADMium?
[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 (@VHchavez) 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, who the target audience is, and its relation to other work?
[ ] 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?

raghurama123 commented 2 years ago

I have started the review. Here are some initial comments on the content of Readme.md and paper.md: pull request. In each document, I have a comment in single quotes beginning with [COMMENT raghurama123]: .... Please address these and remove my comments.

Software review will take some time.

srmnitc commented 2 years ago

@lucydot I can also review it.

lucydot commented 2 years ago

Hi @srmnitc @raghurama123, excellent that you are both able to review ✨

This is the pre-review thread, I will ask editorialbot to create a review thread, and our review discussion will take place over there. @raghurama123 please could you re-create your checklist on the review thread?

lucydot commented 2 years ago

@editorialbot add @srmnitc as reviewer

editorialbot commented 2 years ago

@srmnitc added to the reviewers list!

lucydot commented 2 years ago

@editorialbot start review

editorialbot commented 2 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4459.

raghurama123 commented 2 years ago

Review checklist for @raghurama123

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 https://github.com/wasserman-group/pyCADMium?
[ ] 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 (@VHchavez) 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, who the target audience is, and its relation to other work?
[ ] 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?

raghurama123 commented 2 years ago

Review checklist for @raghurama123

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 https://github.com/wasserman-group/pyCADMium?
[ ] 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 (@VHchavez) 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, who the target audience is, and its relation to other work?
[ ] 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?

openjournals / joss-reviews