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[PRE REVIEW]: ASGarD: Adaptive Sparse Grid Discretization #3953

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@quantumsteve<!--end-author-handle-- (Steven Hahn) Repository: https://github.com/project-asgard/asgard Branch with paper.md (empty if default branch): Version: v0.4.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @joglekara, @drobnyjt, @cticenhour Managing EiC: Kevin M. Moerman

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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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Markdown: [![status](https://joss.theoj.org/papers/dbc8b3d352b73a460d8cc57f1de1debf/status.svg)](https://joss.theoj.org/papers/dbc8b3d352b73a460d8cc57f1de1debf)

Author instructions

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

@quantumsteve 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).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

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whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

: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.

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf
whedon commented 2 years ago

PDF failed to compile for issue #3953 with the following error: 

 Can't find any papers to compile :-(
whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.74 s (156.4 files/s, 78157.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                    42           4443           2605          24659
C++                             54           3234           1517          18830
CMake                            7            179            275           1034
Markdown                         6             66              0            189
MATLAB                           2             41             21            177
YAML                             3              7             11            174
Bourne Shell                     1              2              0              7
-------------------------------------------------------------------------------
SUM:                           115           7972           4429          45070
-------------------------------------------------------------------------------

Statistical information for the repository '7c9f1dea305737e4e344c902' was
gathered on 2021/11/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Benjamin T. McDaniel           469         45166          23951           32.44
Cole Kendrick                   26          1765            842            1.22
David Green                     69          8865           4531            6.29
Graham Lopez                   108         31364          14058           21.32
Harry Hughes                    16          3421           2410            2.74
Hugo Brunie                      5           884            781            0.78
Mark Cianciosa                   3            98            117            0.10
McDaniel, Benjamin T             5          2236             33            1.07
Steven Hahn                     22          1710            263            0.93
T McDaniel                       3           218            312            0.25
Tim Younkin                      7           215            155            0.17
Timothy Younkin                  7          1127            735            0.87
Tyler                            2            76             62            0.06
Tyler McDaniel                 392         20000          22180           19.80
adam-mcdaniel                   11          1449             59            0.71
elwasif                         26          1301            171            0.69
none                            19         14265           8220           10.55

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
Benjamin T. McDaniel       5458           12.1         31.6               10.17
Cole Kendrick               957           54.2          7.1                7.21
David Green                2618           29.5         27.2               19.60
Graham Lopez              14180           45.2         11.4               10.47
Harry Hughes                514           15.0         24.2                4.09
Hugo Brunie                 842           95.2          8.5                0.59
Mark Cianciosa               98          100.0          1.2               22.45
McDaniel, Benjamin T       1400           62.6         34.3                4.36
Steven Hahn                1523           89.1          1.0                2.82
Tim Younkin                  90           41.9         27.3               51.11
Timothy Younkin              49            4.3         27.9                0.00
Tyler McDaniel            16188           80.9         18.8                6.02
adam-mcdaniel                29            2.0         27.5                3.45
elwasif                     366           28.1         24.8                9.02
none                      10976           76.9         18.6                2.73
Kevin-Mattheus-Moerman commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 2 years ago

PDF failed to compile for issue #3953 with the following error: 

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:155:in `block in check_orcids': Problem with ORCID (0000-0000-0000-0000) for Hao Lau (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:90:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'
Kevin-Mattheus-Moerman commented 2 years ago

@quantumsteve please remove the invalid (all zero) orcid id's from the paper. Instead leave out the orcid specification for these if they do not have an orcid id, see also below and: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

authors:
  - name: Adrian M. Price-Whelan^[co-first author] # note this makes a footnote saying 'co-first author'
    orcid: 0000-0003-0872-7098
    affiliation: "1, 2" # (Multiple affiliations must be quoted)
  - name: Author Without ORCID^[co-first author] # note this makes a footnote saying 'co-first author'
    affiliation: 2

After fixing the paper you can update the pdf draft here by calling @whedon generate pdf from branch paper

Kevin-Mattheus-Moerman commented 2 years ago

@whedon invite @jarvist as editor

whedon commented 2 years ago

@jarvist has been invited to edit this submission.

quantumsteve commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon 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:

jarvist commented 2 years ago

@whedon assign @jarvist as editor

OK, happy to edit this.

whedon commented 2 years ago

OK, the editor is @jarvist

jarvist commented 2 years ago

@quantumsteve - do you have any reviewer suggestions?

quantumsteve commented 2 years ago

We suggest Nick Murphy (namurphy), Sterling Smith (smithsp), Archis Joglekar (joglekara), Rogerio Jorge (rogeriojorge) or Carsten Fortmann-Grote (CFGrote).

joglekara commented 2 years ago

@jarvist, happy to take it on

jarvist commented 2 years ago

@whedon add @joglekara as reviewer

Wonderful! Welcome aboard.

whedon commented 2 years ago

OK, @joglekara is now a reviewer

jarvist commented 2 years ago

Still looking for reviewers! Apologies for the delay.

quantumsteve commented 2 years ago

May we suggest two more reviewers? Casey Icenhour (cticenhour), John Drobny (drobnyjt)

quantumsteve commented 2 years ago

@jarvist Any updates on finding a second reviewer? How do you recommend proceeding?

joglekara commented 2 years ago

@quantumsteve sorry for the wait here...

@jarvist @Kevin-Mattheus-Moerman , is there anything I can do to help get the review process started? Perhaps, we can just proceed with 1 reviewer?

arfon commented 2 years ago

Just a heads up that I've pinged @jarvist over email to give us an update.

arfon commented 2 years ago

@editorialbot assign me as reviewer

editorialbot commented 2 years ago

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

@editorialbot commands

arfon commented 2 years ago

@editorialbot assign me as editor

editorialbot commented 2 years ago

Assigned! @arfon is now the editor

arfon commented 2 years ago

@quantumsteve @joglekara – apologies for the delay here. I'll take this submission on to help @jarvist out here.

arfon commented 2 years ago

:wave: @cticenhour & @drobnyjt - would either of 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/reviewer_guidelines.html

The submission under consideration is ASGarD: Adaptive Sparse Grid Discretization

drobnyjt commented 2 years ago

Hi @arfon - I'm attending the Exascale Computing Project's annual meeting, so would not be able to start in earnest until next week. If that's okay, I'd be happy to.

cticenhour commented 2 years ago

Hi @arfon! I also would be available, but I do need to disclose that the first author on this work (David L Green) is a member of my PhD committee (not my dissertation advisor, however). We have not collaborated on this particular work. If this is a CoI, please let me know.

arfon commented 2 years ago

@editorialbot add @drobnyjt as reviewer

editorialbot commented 2 years ago

@drobnyjt added to the reviewers list!

arfon commented 2 years ago

@editorialbot add @cticenhour as reviewer

Hi @arfon! I also would be available, but I do need to disclose that the first author on this work (David L Green) is a member of my PhD committee (not my dissertation advisor, however). We have not collaborated on this particular work. If this is a CoI, please let me know.

Thank you for flagging this @cticenhour. I'm happy to waive this possible conflict.

editorialbot commented 2 years ago

@cticenhour added to the reviewers list!

arfon 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/4378.

arfon commented 2 years ago

@joglekara, @drobnyjt, @cticenhour – see you over in #4378 where the actual review will take place!