[PRE REVIEW]: Shapelets: A Python package implementing shapelet functions and their applications

[editorialbot]

Submitting author: !--author-handle-->@nasserma<!--end-author-handle-- (Nasser Mohieddin Abukhdeir) Repository: https://github.com/uw-comphys/shapelets Branch with paper.md (empty if default branch): publications Version: v0.1 Editor: !--editor-->@AoifeHughes<!--end-editor-- Reviewers: @tbmiller-astro, @Anshuman5 Managing EiC: Kyle Niemeyer

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Author instructions

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

@nasserma if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (715.0 files/s, 73343.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         3            136              0            230
Python                           6            138            350            173
TeX                              1             16              0            166
YAML                             1              1              0             18
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            12            291            350            590
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2373

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- 10.1111/j.1365-2966.2005.09453.x may be a valid DOI for title: Polar shapelets
- 10.1088/1361-6528/aaf353 may be a valid DOI for title: A generalized shapelet-based method for analysis of nanostructured surface imaging
- 10.1103/physreve.91.033307 may be a valid DOI for title: Theory and application of shapelets to the analysis of surface self-assembly imaging
- 10.1093/mnras/stz787 may be a valid DOI for title: Exponential shapelets: basis functions for data analysis of isolated features
- 10.1088/2053-1591/3/8/082001 may be a valid DOI for title: Computational characterization of ordered nanostructured surfaces
- 10.1364/opex.12.005760 may be a valid DOI for title: Optical coherence tomography of skin for measurement of epidermal thickness by shapelet-based image analysis
- 10.1007/s10827-008-0107-5 may be a valid DOI for title: Contextual modulation of V1 receptive fields depends on their spatial symmetry
- 10.1152/jn.00498.2005 may be a valid DOI for title: Responses of V1 neurons to two-dimensional hermite functions
- 10.1088/0004-637x/813/2/102 may be a valid DOI for title: Gravitational lens modeling with basis sets
- 10.1093/mnras/stu2611 may be a valid DOI for title: Generative pulsar timing analysis
- 10.1007/978-1-4612-2812-7_1 may be a valid DOI for title: Bond-Orientational Order

INVALID DOIs

- None

[kyleniemeyer]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[kyleniemeyer]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (797.7 files/s, 120257.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15            485           1094            940
reStructuredText                 4            255             82            343
Markdown                         3            136              0            230
TeX                              1             16              0            166
YAML                             1              1              0             18
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            25            893           1176           1700
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2373

[kyleniemeyer]

@editorialbot set publications as branch

[editorialbot]

Done! branch is now publications

[kyleniemeyer]

@editorialbot invite @jgostick as editor

Hi @jgostick, could you edit this submission related to image analysis? Although it has applications in astronomy, it also seems relevant to materials science as well.

[editorialbot]

Invitation to edit this submission sent!

[jgostick]

The author of this package is my colleague and collaborator. It'll pretty awkward in the lunch room when I have to reject his submission!

[kyleniemeyer]

@jgostick ah, yes that's a clear conflict! I'll find someone else.

[nasserma]

The author of this package is my colleague and collaborator. It'll pretty awkward in the lunch room when I have to reject his submission!

Just for the record, lunch room conversations with @jgostick have always been awkward.

[nasserma]

Happy (Canadian) Thanksgiving! I just wanted to check-in on the status of assigning an editor and also point out a somewhat special situation regarding the development of the shapelets package.

The core package was developed internally and included as supplemental information for the research publication that introduced one of the application methods (self_assembly). This code was developed by R. Suderman (@rsuderman) and later modified by T. Akdeniz as part of another research publication; both are co-authors of this submission.

Myself, @mptino, and @abaacus have rewritten, enhanced, and added to the core package in order to improve its usability for researchers interested in the use of shapelet functions for their own purposes, but also included several past applications (astronomy and self_assembly). Thus the three of us have made all of the commits to the relatively new public repo, the past contributions of Rob and Thomas are in various internal repos and are not reflected in the public repo. However, all of the authors have made significant contributions to both the development of methods and the code itself.

[kyleniemeyer]

@nasserma understood, thanks for the explanation.

[kyleniemeyer]

@editorialbot invite @AoifeHughes as editor

Hi @AoifeHughes, could you edit this submission? It may fall outside your primary areas of expertise but involves image analysis. Thanks!

[editorialbot]

Invitation to edit this submission sent!

[AoifeHughes]

Hi @kyleniemeyer, sure I can edit

[AoifeHughes]

@editorialbot generate pdf

[kyleniemeyer]

@editorialbot assign @AoifeHughes as editor

[editorialbot]

Assigned! @AoifeHughes is now the editor

[AoifeHughes]

hmm, why didn't that work before?

[AoifeHughes]

@editorialbot generate pdf

[xuanxu]

The pdf compilation is failing because the metadata of the paper.md file includes incorrect values for some authors' orcid. Updating those XXXX-XXXX-XXXX-XXXX values or removing them should fix it.

[danielskatz]

@xuanxu - we used to get error messages in this case - can we get them back? (It will save you time too 🙂)

[nasserma]

I'll correct the paper.md file and add the missing DOIs to the references later today, sorry for the inconvenience.

[xuanxu]

@xuanxu - we used to get error messages in this case - can we get them back? (It will save you time too 🙂)

Yes, I'll take a look into it. I'm not sure why the messages are not automatically posted by editorialbot

[nasserma]

@AoifeHughes The invalid ORCIDs and missing DOIs have been corrected.

@xuanxu Also, note that the workflow we added to the repo per the JOSS instructions has always resulted in a PDF being created, so we were not aware that the invalid ORCIDs were a problem until now.

[AoifeHughes]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[AoifeHughes]

Hi @nasserma , I'm just putting out some requests to reviewers and haven't gotten responses yet, please feel free to make some suggestions of potential reviewers from your own knowledge or by using https://reviewers.joss.theoj.org/ to help us proceed faster

[nasserma]

Hello @AoifeHughes , thanks for putting out requests to reviewers, here are a few from different areas (astrophysics, materials science, computational science) that have relevant background from the list of registered reviewers:

@tbmiller-astro , @rmorgan10 ; @vsangelidakis , @Anshuman5 ; @ziatdinovmax , @ml-evs

[vsangelidakis]

Hello, Unfortunately I cannot review this work due to limited available time. Good luck with your submission!

[mptino]

Hi @AoifeHughes - any luck with finding reviewers?

[AoifeHughes]

@editorialbot add @tbmiller-astro as reviewer

[editorialbot]

@tbmiller-astro added to the reviewers list!

[AoifeHughes]

@mptino Im trying, I sent out a dozen requests last week and we have one so far, if you have any other suggestions that would be helpful, otherwise I'll go through some more later myself.

[nasserma]

@tbmiller-astro , @rmorgan10 ; @vsangelidakis , @Anshuman5 ; @ziatdinovmax , @ml-evs

@AoifeHughes Thanks for your efforts. I just want to confirm that these suggested reviewers were all contacted before I look for more. Also, should we be limiting ourselves to the JOSS reviewers list for suggested reviewers, or also look outside of this list?

[AoifeHughes]

Yes, and those qualified to review but not on our list are acceptable

[Anshuman5]

Hello, I would be able to review this work. Let me know the deadline for submitting the review.

[AoifeHughes]

@editorialbot add @Anshuman5 as reviewer

[editorialbot]

@Anshuman5 added to the reviewers list!

[AoifeHughes]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6058.