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[REVIEW]: libecpint: A C++ library for the efficient evaluation of integrals over effective core potentials #3039

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @robashaw (Robert A. Shaw) Repository: https://github.com/robashaw/libecpint Version: v1.0.4 Editor: @poulson Reviewer: @felipeZ, @lorenzo-rovigatti Archive: 10.5281/zenodo.4694353

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Markdown: [![status](https://joss.theoj.org/papers/fe715624763307a55c899bff685da1a8/status.svg)](https://joss.theoj.org/papers/fe715624763307a55c899bff685da1a8)

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

@felipeZ & @lorenzo-rovigatti, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @poulson 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 ✨

Review checklist for @felipeZ

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @lorenzo-rovigatti

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @felipeZ, @lorenzo-rovigatti it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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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whedon commented 3 years ago

PDF failed to compile for issue #3039 with the following error:

Can't find any papers to compile :-(

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.56 s (1272.6 files/s, 129098.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                             72              0              0          31587
C++                             37           1106           1000           7140
reStructuredText               541           8438          13726           4342
XSD                              3            111             10           1175
C/C++ Header                    15            274           1091            934
Python                           4            111             98            410
CMake                           32             68             26            385
YAML                             3              8              8            102
Bourne Shell                     2              8              0             44
Markdown                         1             21              0             38
DOS Batch                        1              8              1             27
XSLT                             1              0              5             10
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           713          10157          15971          46204
-------------------------------------------------------------------------------

Statistical information for the repository '9b85b328717684284cc20214' was
gathered on 2021/02/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jens                             1             8             19            0.04
Peter Bygrave                    1            23             10            0.05
Robert Shaw                     38         38052          25918           97.02
Thomas Dresselhaus               2           283            250            0.81
pk                               1             2              0            0.00
robashaw                         2            75              3            0.12
thomas-dresselhaus               2           720            572            1.96

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
Jens                          8          100.0          0.0                0.00
Peter Bygrave                 9           39.1          1.3                0.00
Robert Shaw               11620           30.5          1.5               19.06
Thomas Dresselhaus          212           74.9          1.5                5.66
thomas-dresselhaus          322           44.7          2.0                1.55
robashaw commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

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

felipeZ commented 3 years ago

Dear Robert (@robashaw), I think that you library is a much needed contribution for the development of open source software on computational chemistry. I also think that the API is straightforward and the documentation is pretty clear. If you agree, I will open some issues in the libecpint repository that I will link back here to discuss several topics about the software that are still not clear to me.

robashaw commented 3 years ago

Of course @felipeZ, thanks for taking the time to review.

lorenzo-rovigatti commented 3 years ago

Hi Robert (@robashaw), thanks a lot for your contribution. The libecpint library looks neat! I'll also be opening a few issues in the libecpint repo in the next days to discuss some of the aspects that may need improvement.

whedon commented 3 years ago

:wave: @felipeZ, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @lorenzo-rovigatti, please update us on how your review is going (this is an automated reminder).

felipeZ commented 3 years ago

@robashaw and I have been discussing some issues in the libecpint repository. Robert has addressed the issues that I have raised and solved the questions that I had.

whedon commented 3 years ago

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

@whedon commands
robashaw commented 3 years ago

@poulson @felipeZ @lorenzo-rovigatti If there are no further changes, I will merge robashaw/libecpint/pull/38. Thank you for your time and helpful suggestions :)

felipeZ commented 3 years ago

@robashaw I think you have answered, cleared or solved all the issues that I have opened on libecpint

lorenzo-rovigatti commented 3 years ago

Likewise, you answer all my questions/solved all the issues I did raise. Great job!

danielskatz commented 3 years ago

👋 @poulson - it looks like this is done, or very close? What's the next step?

kyleniemeyer commented 3 years ago

@whedon generate pdf

Hi @robashaw, I am the AEIC on duty this week. It looks like this submission has reached the final stages, so I'm going to help it past the finish line.

kyleniemeyer commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

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

whedon commented 3 years ago

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

kyleniemeyer commented 3 years ago

@robashaw Your article looks good; can you now archive your software repository (e.g., on Zenodo) and provide the DOI here? That is the last thing we need to accept this.

robashaw commented 3 years ago

@kyleniemeyer Thanks, I've archived it on Zenodo, the DOI is 10.5281/zenodo.4694353

kyleniemeyer commented 3 years ago

@whedon set 10.5281/zenodo.4694353 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4694353 is the archive.

kyleniemeyer commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2231

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2231, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/S1380-7323(02)80040-1 is OK
- 10.1063/1.448800 is OK
- 10.1063/1.448799 is OK
- 10.1021/cr2001383 is OK
- 10.1016/0021-9991(81)90053-X is OK
- 10.1002/jcc.20410 is OK
- 10.1021/acs.jpca.7b12679 is OK
- 10.1063/1.4986887 is OK
- 10.1063/1.4922844 is OK
- 10.1063/5.0006002 is OK
- 10.5281/zenodo.4059510 is OK

MISSING DOIs

- None

INVALID DOIs

- None
kyleniemeyer commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2232
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03039
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

kyleniemeyer commented 3 years ago

Congrats @robashaw on your article's publication in JOSS!

Many thanks to @felipeZ and @lorenzo-rovigatti for reviewing this, and @poulson for editing.

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03039/status.svg)](https://doi.org/10.21105/joss.03039)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03039">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03039/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03039/status.svg
   :target: https://doi.org/10.21105/joss.03039

This is how it will look in your documentation:

DOI

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