[PRE REVIEW]: Atomic Simulation Interface (ASI): application programming interface for electronic structure codes

[editorialbot]

Submitting author: @PavelStishenko (Pavel Stishenko)
Repository: https://gitlab.com/pvst/asi
Branch with paper.md (empty if default branch): master
Version: v1.0
Editor: @rkurchin
Reviewers: @xwang862, @junghans, @srmnitc
Managing EiC: Kevin M. Moerman

Status

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HTML: <a href="https://joss.theoj.org/papers/a46f8b3148ab3fe19c0e51f620ba5815"><img src="https://joss.theoj.org/papers/a46f8b3148ab3fe19c0e51f620ba5815/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a46f8b3148ab3fe19c0e51f620ba5815/status.svg)](https://joss.theoj.org/papers/a46f8b3148ab3fe19c0e51f620ba5815)

Author instructions

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@PavelStishenko 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]

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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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[editorialbot]

Checking the BibTeX entries failed with the following error:

No paper file path

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1133.5 files/s, 80760.9 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
C++                                      8            229             35           1357
Python                                  15            249            305           1056
Bourne Shell                            27            129             10            271
C/C++ Header                             4            116            190            185
YAML                                     1             11              0            151
CMake                                    3             76            169             95
reStructuredText                         5             72             74             74
make                                     3             27              7             64
Windows Module Definition                3             20              0             62
Markdown                                 2             55              0             50
DOS Batch                                1              8              1             26
TOML                                     1              2              0             25
---------------------------------------------------------------------------------------
SUM:                                    73            994            791           3416
---------------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

⚠️ An error happened when generating the pdf. Paper file not found.

[editorialbot]

⚠️ An error happened when generating the pdf. Paper file not found.

[editorialbot]

Hello @PavelStishenko, 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

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@editorialbot generate pdf

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@editorialbot generate preprint

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[PavelStishenko]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

Notes for this submission

The presented software consists of two parts that are hosted in separate repositories. The first part includes the ASI API specification, documentation, and Python wrapper asi4py, and is hosted with the submitted paper (https://github.com/PavelStishenko/asi/ and https://gitlab.com/pvst/asi). The second part includes the ASI API implementaion in DFTB+ code and is hosted as a branch in DFTB+ project (https://github.com/PavelStishenko/dftbplus/tree/api-H-import).

[Kevin-Mattheus-Moerman]

@PavelStishenko thanks for this submission. I am the AEiC for this track and here to help with the first steps and to check if this work is in scope for JOSS.

Can you clarify if the following two links are equivalent/the same or if they contain different functionality:

1. https://github.com/PavelStishenko/asi/
2. https://gitlab.com/pvst/asi

If they are the same, does the main development take place on the first or second link? I am assuming the first since that one is provided as the repository for the paper too.

[Kevin-Mattheus-Moerman]

@editorialbot set joss-paper as branch

[editorialbot]

Done! branch is now joss-paper

[Kevin-Mattheus-Moerman]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (994.6 files/s, 75547.9 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
C++                                      8            229             35           1357
Python                                  15            249            305           1049
TeX                                      1             42              1            350
Bourne Shell                            27            129             10            271
C/C++ Header                             4            116            190            185
Markdown                                 3             98              0            170
YAML                                     2             12              4            169
CMake                                    3             76            169             95
reStructuredText                         5             72             74             74
make                                     3             27              7             64
Windows Module Definition                3             20              0             62
DOS Batch                                1              8              1             26
TOML                                     1              2              0             25
---------------------------------------------------------------------------------------
SUM:                                    76           1080            796           3897
---------------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2186

[Kevin-Mattheus-Moerman]

@PavelStishenko looks like I missed that you added the paper to the master branch. I just switched to the joss-paper branch but perhaps there was no need. Let me know which you prefer.

[Kevin-Mattheus-Moerman]

I ran cloc on the provided additional link: https://github.com/PavelStishenko/dftbplus/tree/api-H-import, which produced:

--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Fortran 90                      356          43401          31009         133790
Fortran 77                       12            369           4844          15196
TeX                              27           1618            221           9700
Python                           76           2335           2886           6909
SVG                               1              3              3           5754
D                                 3             29              0           3747
CMake                            84            901            654           2511
reStructuredText                 13            770             56           1276
Bourne Again Shell                5            233            292           1147
C                                 7            216            239            773
Bourne Shell                     43             91            141            484
YAML                              4             54             25            272
make                              2             47              7            194
C/C++ Header                      3             92            394            141
Markdown                          4             12              0             93
Perl                              1             10              1             65
INI                               2             17              0             39
--------------------------------------------------------------------------------
SUM:                            643          50198          40772         182091
--------------------------------------------------------------------------------

[Kevin-Mattheus-Moerman]

@editorialbot invite @lucydot as editor

@lucydot this looks like your cup of tea, is that right? 🍵

[editorialbot]

Invitation to edit this submission sent!

[lucydot]

@Kevin-Mattheus-Moerman absolutely my cup of tea, I'm happy to edit.

RE: potential Conflict of Interest - I am co-I on a bid submission (unrelated to this project) with two of the authors. The bid submission includes many different researchers from across the UK (I'd say around 30) and relates to community infrastructure - I don't work closely on a day-to-day basis with any of the authors. Personally I don't judge it to be a COI but will disclose here and happy to pass on if it could be perceived as so.

[Kevin-Mattheus-Moerman]

@lucydot thanks for getting back to me so quickly, and for sharing that information. I'm afraid that does sound like it could be perceived as a COI so I'll work to find an alternative editor. Thanks again.

[PavelStishenko]

@editorialbot set master as branch

[editorialbot]

Done! branch is now master

[PavelStishenko]

@PavelStishenko thanks for this submission. I am the AEiC for this track and here to help with the first steps and to check if this work is in scope for JOSS.

Can you clarify if the following two links are equivalent/the same or if they contain different functionality:

1. https://github.com/PavelStishenko/asi/

2. https://gitlab.com/pvst/asi

If they are the same, does the main development take place on the first or second link? I am assuming the first since that one is provided as the repository for the paper too.

@Kevin-Mattheus-Moerman , no, the main development take place on GitLab repo (second link). I have created the GitHub mirror specifically for JOSS submission.

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot invite @jgostick as editor

[editorialbot]

Invitation to edit this submission sent!

[jgostick]

Hi @Kevin-Mattheus-Moerman, I'm sorry but I am not qualified to edit molecular dynamics packages, as I learned this past summer when I was unable to effectively adjudicate a review that went awry.

[rkurchin]

👋 @Kevin-Mattheus-Moerman I could edit this if needed.

[Kevin-Mattheus-Moerman]

@editorialbot assign @rkurchin as editor

[editorialbot]

Assigned! @rkurchin is now the editor

[rkurchin]

👋 @xwang862, @jeffhammond, and @keipertk, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[xwang862]

@rkurchin thanks for inviting. Sure, I'd love to review it.

[rkurchin]

@editorialbot add @xwang862 as reviewer

[editorialbot]

@xwang862 added to the reviewers list!

[rkurchin]

👋 @rangsimanketkaew, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[rkurchin]

👋 @yES, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[rkurchin]

👋 @vijaymocherla, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[vijaymocherla]

Hi @rkurchin,
I am sorry but I may not be able to take this now.

[rkurchin]

👋 @junghans, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[rkurchin]

👋 @srmnitc, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[junghans]

👋 @junghans, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I can do it.

[srmnitc]

👋 @srmnitc, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I can help review this submission

[rkurchin]

@editorialbot add @junghans as reviewer

[editorialbot]

@junghans added to the reviewers list!

[rkurchin]

@editorialbot add @srmnitc as reviewer

[editorialbot]

@srmnitc added to the reviewers list!

[rkurchin]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5186.