[PRE REVIEW]: Hankel Transformation for Noisy Data - The Multiple Scattering Problem

whedon commented 5 years ago

Submitting author: @hfriel69 (Henrich Frielinghaus) Repository: https://jugit.fz-juelich.de/sans/muscatt Version: v1.0.0 Editor: @katyhuff Reviewer: Pending

Author instructions

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

@h.frielinghaus if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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:

@whedon commands

whedon commented 5 years ago

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

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

@whedon commands

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

PDF failed to compile for issue #1375 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1375/paper.md): found unexpected document indicator while scanning a quoted scalar at line 2 column 8 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:68:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

whedon commented 5 years ago

Failed to discover a valid open source license.

labarba commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

PDF failed to compile for issue #1375 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1375/paper.md): found unexpected document indicator while scanning a quoted scalar at line 2 column 8 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:68:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

labarba commented 5 years ago

@arfon : I have no clue why this paper is not compiling. Help!

labarba commented 5 years ago

@katyhuff 👋 — the submitting author suggested you as handling editor. Looks like there's some physics in here! I'll assign you now, but let me know if you're disinclined for any reason.

labarba commented 5 years ago

@whedon assign @katyhuff as editor

whedon commented 5 years ago

OK, the editor is @katyhuff

arfon commented 5 years ago

There's an unmatched quotation on the title line of the paper. Line #2 of paper.md needs to be modified to be this:

title: 'Hankel Transformation for Noisy Data - The Multiple Scattering Problem'

I would @-mention the author but they appear to have used an invalid GitHub handle when submitting the paper (I've emailed them directly about this).

hfriel69 commented 5 years ago

Dear Kathryn, does the PDF compile now? It should work now. Or does the make command not work. In any case please send error list - then I know better....

katyhuff commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

PDF failed to compile for issue #1375 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1375/paper.md): found character that cannot start any token while scanning for the next token at line 7 column 11 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:68:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

hfriel69 commented 5 years ago

Dear all, this looks ok for me now. Best, Henrich

Am 29.04.2019 um 15:23 schrieb whedon notifications@github.com<mailto:notifications@github.com>:

PDF failed to compile for issue #1375https://github.com/openjournals/joss-reviews/issues/1375 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1375/paper.md): found character that cannot start any token while scanning for the next token at line 7 column 11 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:68:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/1375#issuecomment-487577617, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AL6I7KVTOK2X4HSQAJMIC7TPS3ZEHANCNFSM4HF2P5ZQ.

Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt

hfriel69 commented 5 years ago

Looks ok for me now

katyhuff commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

katyhuff commented 5 years ago

Thank you @hfriel69 - it is indeed building a pdf now! A few comments, before we start assigning reviewers.

I'm going to edit this issue to incorporate your github username (@hfriel69) rather than your bitbucket one.
The "name" parameter in the paper.md file typically contains the author's actual name, rather than their username. (in your case, "Henrich Frielinghaus" is the appropriate entry.) Would you mind please editing the paper to use your name?
The paper does describe the high-level functionality and purpose of the software, but as written, the purpose and domain of use may not be clear to a diverse, non-specialist audience. A few extra introductory sentences should help. Specifically, please mention what kind of physics this small-angle scattering data comes from ( I assume neutrons, but a reader may wonder if it applies to photons, electrons, all of the above? high energy, low energy?). Ideally, the reader of the paper will then understand which small-angle scattering interactions this can be applied to. This requirement is in the author documentation here.
Also, while I appreciate the mathematical overview describing the method, this paper is somewhat lacking in a key requirement, which is "a clear statement of need that illustrates the purpose of the software". A good way to satisfy this requirement is to answer, in the paper, the following question "Who will use this tool and how are existing tools insufficient for their needs?"

While making these changes, please double check that your paper mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it. I assume that this work was created for a specific task at JCNS. Perhaps this could be mentioned?

hfriel69 commented 5 years ago

My suggestions for Referees: Stefano Cozzini, https://dssc.units.it/people/stefano-cozzini, cozzini@iom.cnr.it Joachim Wuttke, Sci Computing Group at MLZ, Garching, j.wuttke@fz-juelich.de Piotr Zolnierczuk, Instrument responsible ORNL, USA, p.zolnierczuk@fz-juelich.de Andrew Jackson, ESS Lund, Sweden, andrew.jackson@esss.se

katyhuff commented 5 years ago

@hfriel69 Thank you for these suggestions. As soon as you are able to make the preliminary changes I suggested above, I will assign reviewers.

hfriel69 commented 5 years ago

Intro added for non specialists

hfriel69 commented 5 years ago

Dear Kathy, I added an intro for non-specialists. Best, Henrich

Am 29.04.2019 um 17:04 schrieb Katy Huff notifications@github.com<mailto:notifications@github.com>:

@hfriel69https://github.com/hfriel69 Thank you for these suggestions. As soon as you are able to make the preliminary changes I suggested abovehttps://github.com/openjournals/joss-reviews/issues/1375#issuecomment-487605023, I will assign reviewers.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/1375#issuecomment-487616558, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AL6I7KXB53FFPD4KNVU47RLPS4E7DANCNFSM4HF2P5ZQ.

Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt

katyhuff commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

katyhuff commented 5 years ago

@hfriel69 : I think you may have misunderstood my comment about the name field.

The "name" parameter in the paper.md file typically contains the author's actual name, rather than their username. (in your case, "Henrich Frielinghaus" is the appropriate entry.) Would you mind please editing the paper to use your name?

hfriel69 commented 5 years ago

Name is correct now. Other smaller changes added. Sorry: I'm completely new to the github world, and especially the convention of md files is a little confusing.

hfriel69 commented 5 years ago

@katyhuff: Is there everything fine with the manuscript and the program? I assume you are searching for referees...

hfriel69 commented 5 years ago

two more referee could be: Jan Skov Pedersen, Uni Aarhus, jsp@chem.au.dk Torsten Bögershausen, ESS - DMSC Copenhagen, Torsten.Bogershausen@esss.se

katyhuff commented 5 years ago

Thanks for these suggestions. Indeed, I'm identifying referees from our pool and am investigating your suggestions. I'll be able to give this some more attention this weekend.

hfriel69 commented 5 years ago

Dear Katy, do I need to bring more reviewers? Do you need anything else? Best, Henrich

katyhuff commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

katyhuff commented 5 years ago

@hfriel69 Thank you for your patience. Before finalizing reviewer assignments, I typically conduct a cursory check that the basic review criteria have a chance of passing the process. In the case of your MuScatt repository, I notice a number of key review criteria that are missing. I cannot move forward with assigning reviewers without such elements, and I recommend that you withdraw your submission in order to take some time to incorporate those elements so that a future resubmission will be successful. Finally, I noticed there is a file, fftsg.c which appears to have been copied verbatim from elswhere (perhaps http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html). Their license requests attribution, which is missing in your repository.

For reference, the review criteria can be found in the JOSS author guidelines.

The missing elements include:

Installation instructions

I predict make all will likely work if the user has all dependencies installed. However, there is no list of dependencies and there seem to be two makefiles present in your repository with no distinction between them in the readme.

From the review criteria page:

Installation Instructions There should be a clearly-stated list of dependencies. Ideally these should be handled with an automated package management solution.

Good: A package management file such as a Gemfile or package.json or equivalent OK: A list of dependencies to install Bad (not acceptable): Reliance on other software not listed by the authors

Contributor instructions

I do not see any contributor guidelines in MuScatt.

Community guidelines There should be clear guidelines for third-parties wishing to:

Contribute to the software Report issues or problems with the software Seek support

Tests

I see no tests in the MuScatt repository. Though I see a handful of scattered .dat files, I cannot immediately tell their purpose, and I assume they are supportive rather than validating.

Tests Authors are strongly encouraged to include an automated test suite covering the core functionality of their software.

Good: An automated test suite hooked up to an external service such as Travis-CI or similar OK: Documented manual steps that can be followed to objectively check the expected functionality of the software (e.g. a sample input file to assert behaviour) Bad (not acceptable): No way for you the reviewer to objectively assess whether the software works

API Documentation

Though I see that MuScatt.c has a few scattered comments, there is no API to speak of. Instead, all logic is embedded in a single procedural block of code (in the main() function.). The exception is the fftsg.c file, which, as mentioned above, seems to have been copied from elsewhere without attribution.

API documentation Reviewers should check that the software API is documented to a suitable level.

Good: All functions/methods are documented including example inputs and outputs OK: Core API functionality is documented Bad (not acceptable): API is undocumented

labarba commented 5 years ago

@hfriel69 — We haven't heard back from you after @katyhuff's pre-review assessment. I'm going to add the "paused" tag here for now, but please respond with your intentions.

arfon commented 4 years ago

It's been more than four months since we last heard from the submitting author. I'm therefore going to assume they are no longer interested in pursuing this publication and withdraw the submission on their behalf.

@hfriel69 - we'd welcome a re-submission in the future if you're able to address @katyhuff's feedback here.

openjournals / joss-reviews