[PRE REVIEW]: GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size #811

whedon · 2018-07-07T21:35:55Z

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.

Editor instructions

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The text was updated successfully, but these errors were encountered:

whedon · 2018-07-07T21:35:58Z

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 🎉

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

@whedon commands

whedon · 2018-07-07T21:35:58Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-07T21:36:09Z

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:in collect!'
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:in find_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:in run'
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:in dispatch'
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 <top (required)>'
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

'

arfon · 2018-07-07T21:36:16Z

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

arfon · 2018-07-07T21:37:01Z

@whedon generate pdf

whedon · 2018-07-07T21:37:04Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-07T21:37:16Z

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:in parse_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:in load'
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:in open'
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:in initialize'
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:in set_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:in run'
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:in dispatch'
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 <top (required)>'
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

'

arfon · 2018-07-07T21:38:57Z

👋 @marcoalopez - this PR should fix the paper compilation issue: marcoalopez/GrainSizeTools#1

marcoalopez · 2018-07-10T15:29:02Z

@whedon generate pdf

whedon · 2018-07-10T15:29:04Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-10T15:29:15Z

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:in parse_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:in load'
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:in open'
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:in initialize'
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:in set_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:in run'
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:in dispatch'
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 <top (required)>'
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

'

arfon · 2018-07-10T15:38:28Z

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

THIS
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"

marcoalopez · 2018-07-10T15:45:01Z

@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.

lheagy · 2018-07-10T15:56:38Z

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

lheagy · 2018-07-10T15:56:51Z

@whedon generate pdf

whedon · 2018-07-10T15:57:02Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-10T15:57:14Z

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:in parse_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:in load'
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:in open'
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:in initialize'
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:in set_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:in run'
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:in dispatch'
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 <top (required)>'
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

'

arfon · 2018-07-10T15:58:38Z

Looks like you need to change:

affiliations:
  - name: Present address - Géosciences Montpellier, Université de Montpellier & CNRS, CC 60, Place E.
7 Bataillon, 34095 Montpellier cedex 5, France
    index: 1
  - name: Departamento de Geología, Universidad de Oviedo, c/Jesús Arias de Velasco s/n, 33005, Oviedo, Spain
    index: 2

to:

affiliations:
  - name: Present address - Géosciences Montpellier, Université de Montpellier & CNRS, CC 60, Place E. 7 Bataillon, 34095 Montpellier cedex 5, France
    index: 1
  - name: Departamento de Geología, Universidad de Oviedo, c/Jesús Arias de Velasco s/n, 33005, Oviedo, Spain
    index: 2

marcoalopez · 2018-07-10T16:13:24Z

@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.

arfon · 2018-07-10T16:15:23Z

@whedon generate pdf

whedon · 2018-07-10T16:15:27Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-10T16:15:38Z

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

arfon · 2018-07-10T16:16:49Z

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

marcoalopez · 2018-07-10T16:23:38Z

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

arfon · 2018-07-10T16:28:24Z

@whedon generate pdf

whedon · 2018-07-10T16:28:27Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-10T16:28:37Z

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

arfon · 2018-07-10T16:32:29Z

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

marcoalopez · 2018-07-10T19:27:59Z

@whedon generate pdf

whedon · 2018-07-10T19:28:02Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-10T19:28:35Z

--> Check article proof 📄 <--

marcoalopez · 2018-07-10T19:42:44Z

@whedon generate pdf

whedon · 2018-07-10T19:42:46Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-07-10T19:43:10Z

--> Check article proof 📄 <--

marcoalopez · 2018-07-10T19:46:38Z

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

lheagy · 2018-07-10T20:43:22Z

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!

marcoalopez · 2018-07-11T07:51:46Z

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

lheagy · 2018-07-16T15:37:43Z

@marcoalopez: do you have any recommendations for reviewers?

marcoalopez · 2018-07-17T13:57:26Z

@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.

lheagy · 2018-07-19T16:44:39Z

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

khaors · 2018-07-19T19:27:17Z

@lheagy Sure, I can help with the review.

lheagy · 2018-07-19T19:32:43Z

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

lheagy · 2018-07-27T16:36:22Z

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

jsta · 2018-07-30T16:31:03Z

@lheagy Yes, I can help with this review.

lheagy · 2018-07-30T17:04:00Z

Excellent, thanks @jsta!

lheagy · 2018-07-30T17:04:10Z

@whedon add @jsta as reviewer

whedon · 2018-07-30T17:04:14Z

OK, @jsta is now a reviewer

lheagy · 2018-07-30T17:04:23Z

@whedon start review

whedon · 2018-07-30T17:04:27Z

OK, I've started the review over in #863. Feel free to close this issue now!

whedon assigned lheagy Jul 7, 2018

whedon added the pre-review label Jul 7, 2018

whedon added HTML Python TeX labels Jul 7, 2018

lheagy mentioned this issue Jul 11, 2018

organization and packaging marcoalopez/GrainSizeTools#2

Closed

3 tasks

whedon unassigned lheagy Jul 30, 2018

whedon assigned jsta and lheagy Jul 30, 2018

lheagy closed this as completed Jul 30, 2018

[PRE REVIEW]: GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size #811

[PRE REVIEW]: GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size #811

Comments

whedon commented Jul 7, 2018 • edited

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arfon commented Jul 10, 2018 • edited

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lheagy commented Jul 10, 2018 • edited

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whedon commented Jul 7, 2018 •

edited

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edited