Joss-reviews: [PRE REVIEW]: GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size

Created on 7 Jul 2018  路  49Comments  路  Source: openjournals/joss-reviews

Submitting author: @marcoalopez (Marco A. Lopez-Sanchez)
Repository: https://github.com/marcoalopez/GrainSizeTools/
Version: v2.0
Editor: @lheagy
Reviewers: @jsta

Author instructions

Thanks for submitting your paper to JOSS @marcoalopez. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@marcoalopez 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.

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picture whedon

All 49 comments

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @lheagy it looks like you're currently assigned as the editor for this paper :tada:

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

@whedon commands
whedon picture whedon on 7 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 7 Jul 2018

PDF failed to compile for issue #811 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

whedon picture whedon on 7 Jul 2018

:wave: @lheagy - the submitting author suggested you as the handling editor.

arfon picture arfon on 7 Jul 2018
👍1

@whedon generate pdf

arfon picture arfon on 7 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 7 Jul 2018

PDF failed to compile for issue #811 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/811/paper.md): mapping values are not allowed in this context at line 2 column 22 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:inparse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:inload'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:inopen'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:68:ininitialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

whedon picture whedon on 7 Jul 2018

:wave: @marcoalopez - this PR should fix the paper compilation issue: https://github.com/marcoalopez/GrainSizeTools/pull/1

arfon picture arfon on 7 Jul 2018

@whedon generate pdf

marcoalopez picture marcoalopez on 10 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Jul 2018

PDF failed to compile for issue #811 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/811/paper.md): mapping values are not allowed in this context at line 2 column 22 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:inparse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:inload'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:inopen'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:68:ininitialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

whedon picture whedon on 10 Jul 2018

@marcoalopez - I think you need to quote your title, i.e. change:

title: GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size

TO:
title: "GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size"
arfon picture arfon on 10 Jul 2018

@arfon I already fixed the whitespace and the title issues in my repository. I'm not sure how to proceed now or if this is the right thing to do.

marcoalopez picture marcoalopez on 10 Jul 2018

Thanks @marcoalopez we can try rebuilding the pdf to make sure it is now working.

lheagy picture lheagy on 10 Jul 2018

@whedon generate pdf

lheagy picture lheagy on 10 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Jul 2018

PDF failed to compile for issue #811 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/811/paper.md): could not find expected ':' while scanning a simple key at line 18 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:inparse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:inload'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:inopen'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:68:ininitialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

whedon picture whedon on 10 Jul 2018

Looks like you need to change:

affiliations:
  - name: Present address - G茅osciences Montpellier, Universit茅 de Montpellier & CNRS, CC 60, Place E.
7 Bataillon, 34095 Montpellier cedex 5, France
    index: 1
  - name: Departamento de Geolog铆a, Universidad de Oviedo, c/Jes煤s Arias de Velasco s/n, 33005, Oviedo, Spain
    index: 2

to:

affiliations:
  - name: Present address - G茅osciences Montpellier, Universit茅 de Montpellier & CNRS, CC 60, Place E. 7 Bataillon, 34095 Montpellier cedex 5, France
    index: 1
  - name: Departamento de Geolog铆a, Universidad de Oviedo, c/Jes煤s Arias de Velasco s/n, 33005, Oviedo, Spain
    index: 2
arfon picture arfon on 10 Jul 2018

@arfon @lheagy Ok I've already fixed it. It seems that the software I use to edit the markdown document cut that long line. I'm sorry for all the inconvenience I've created. I hope it's fixed! Thank you very much for your help.

marcoalopez picture marcoalopez on 10 Jul 2018

@whedon generate pdf

arfon picture arfon on 10 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Jul 2018

PDF failed to compile for issue #811 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12 0 12 0 0 153 0 --:--:-- --:--:-- --:--:-- 155
Error reading bibliography ./paper.bib (line 43, column 5):
unexpected "u"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

whedon picture whedon on 10 Jul 2018

@marcoalopez - looks like you're missing a comma here: https://github.com/marcoalopez/GrainSizeTools/blob/master/paper.bib#L42

arfon picture arfon on 10 Jul 2018

@arfon fixed the missing comma. Again, thanks for your patience.

marcoalopez picture marcoalopez on 10 Jul 2018

@whedon generate pdf

arfon picture arfon on 10 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Jul 2018

PDF failed to compile for issue #811 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12 0 12 0 0 155 0 --:--:-- --:--:-- --:--:-- 157
Error reading bibliography ./paper.bib (line 46, column 24):
unexpected "a"
expecting space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

whedon picture whedon on 10 Jul 2018

@marcoalopez - looks like Pandoc can't handle bibtex keys with spaces in them (e.g. Lopez-Sanchez and Llana-Funez:2015).

arfon picture arfon on 10 Jul 2018

@whedon generate pdf

marcoalopez picture marcoalopez on 10 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Jul 2018

--> Check article proof :page_facing_up: <--

whedon picture whedon on 10 Jul 2018

@whedon generate pdf

marcoalopez picture marcoalopez on 10 Jul 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 10 Jul 2018

--> Check article proof :page_facing_up: <--

whedon picture whedon on 10 Jul 2018

@arfon @lheagy it seems that everything is ok now.

marcoalopez picture marcoalopez on 10 Jul 2018

Thanks @marcoalopez. I have taken a quick look at GrainSizeTools and want to raise a couple things before we get started on the review. The package layout does not follow standard python packaging practices (see for example: https://packaging.python.org/tutorials/packaging-projects/). 

/grain_size_tools  # repo
   /grain_size_tools  # python module
       __init__.py  # contains import to be brought in when the user runs import grain_size_tools
       tools.py
       piezometers.py
       ...

This would allow more flexible use - for example if a user wants to install your package through pypi and import it into a Jupyter notebook as a part of their workflow.

Is this something you would like to look into before we bring reviewers on board? If not, then I would recommend starting an issue if this is something you plan to do, or if not, then there should be some explanation in the readme about why the code is structured the way it is.

Please let me know how you would like to proceed. Thanks!

lheagy picture lheagy on 10 Jul 2018

Hello @lheagy. I was unaware of standard Python packaging practices. My intention is to follow standard Python practices, so I want to follow these guidelines. So for me is ok if you start an issue indicating this.

All the best, Marco

marcoalopez picture marcoalopez on 11 Jul 2018

@marcoalopez: do you have any recommendations for reviewers?

lheagy picture lheagy on 16 Jul 2018

@lheagy: not really since I don't know anyone who works with grain size distributions or paleopiezometry who programs in Python. I know some people who work on similar topics but they program in Matlab.

marcoalopez picture marcoalopez on 17 Jul 2018

:wave: Hi @AdeBytes, @khaors: would you be willing to review this submission for JOSS?

lheagy picture lheagy on 19 Jul 2018

@lheagy Sure, I can help with the review.

khaors picture khaors on 19 Jul 2018
👍1

Excellent, thanks @khaors!
:wave: @jsta would you be willing to help with this review?

lheagy picture lheagy on 19 Jul 2018

Hi @marcoalopez, @khaors: quick update, I have sent an email to @jsta asking if he is willing to review. I will keep you updated

lheagy picture lheagy on 27 Jul 2018
👍1

@lheagy Yes, I can help with this review.

jsta picture jsta on 30 Jul 2018
👍1

Excellent, thanks @jsta!

lheagy picture lheagy on 30 Jul 2018

@whedon add @jsta as reviewer

lheagy picture lheagy on 30 Jul 2018

OK, @jsta is now a reviewer

whedon picture whedon on 30 Jul 2018

@whedon start review

lheagy picture lheagy on 30 Jul 2018

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/863. Feel free to close this issue now!

whedon picture whedon on 30 Jul 2018
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