Joss-reviews: [PRE REVIEW]: YAD: A Learning-based Inductive Logic Programming Tool
Submitting author: @hamedmx (Hamed Karimi)
Repository: https://github.com/hamedmx/YAD-ILP-Tool
Version: v1.0
Editor: @jasonclark
Reviewers: @dredamonsta1
Author instructions
Thanks for submitting your paper to JOSS @hamedmx. 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.
@hamedmx 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
All 74 comments
Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @jasonclark 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
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #816 with the following error:
/app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:91:in block in check_orcids': Problem with ORCID (0000-0000-0000-0000) for Ali Kamandi (RuntimeError)
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:89:ineach'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:89:in check_orcids'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:70: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:inload'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in
whedon
on 9 Jul 2018
:wave: @jasonclark - the submitting author suggested you as the handling editor.
arfon
on 9 Jul 2018
@hamedmx - please see the error above. Authors don't have to include and ORCID but the one you've given here is invalid.
arfon
on 10 Jul 2018
@whedon commands
hamedmx
on 10 Jul 2018
Here are some things you can ask me to do:
# List Whedon's capabilities
@whedon commands
# List of editor GitHub usernames
@whedon list editors
# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers
馃毀 馃毀 馃毀 Experimental Whedon features 馃毀 馃毀 馃毀
# Compile the paper
@whedon generate pdf
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #816 with the following error:
/app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/orcid_validator.rb:12:in initialize': undefined methodstrip' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:91:in new'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:91:inblock in check_orcids'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:89:in each'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:89:incheck_orcids'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:70:in initialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:innew'
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:inprepare'
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:ininvoke_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:instart'
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:inload'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `
whedon
on 10 Jul 2018
@hamedmx - please remove the blank ORCID field, i.e. change:
authors:
- name: Ali Kamandi
orcid:
affiliation: 1
- name: Hamed Karimi
orcid: 0000-0002-9132-593X
affiliation: 2
to:
authors:
- name: Ali Kamandi
affiliation: 1
- name: Hamed Karimi
orcid: 0000-0002-9132-593X
affiliation: 2
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #816 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 0 227 0 --:--:-- --:--:-- --:--:-- 226
100 12 0 12 0 0 226 0 --:--:-- --:--:-- --:--:-- 226
[WARNING] Could not convert image '/tmp/tex2pdf.88/6e81298938ff130e201773573b4fd1fd6d389e60.shtml': Cannot load file
Jpeg Invalid marker used
PNG Invalid PNG file, signature broken
Bitmap Invalid Bitmap magic identifier
GIF Invalid Gif signature :
HDR Invalid radiance file signature
Tiff Invalid endian tag value
TGA not enough bytes
[WARNING] Could not convert image '/tmp/tex2pdf.88/39a2c668737d80b4ecd6961a94a3fc054fddc997.shtml': Cannot load file
Jpeg Invalid marker used
PNG Invalid PNG file, signature broken
Bitmap Invalid Bitmap magic identifier
GIF Invalid Gif signature :
HDR Invalid radiance file signature
Tiff Invalid endian tag value
TGA not enough bytes
[WARNING] Could not convert image '/tmp/tex2pdf.88/e12243540d71df5c2d6ace4fdf0cecbef9862f81.shtml': Cannot load file
Jpeg Invalid marker used
PNG Invalid PNG file, signature broken
Bitmap Invalid Bitmap magic identifier
GIF Invalid Gif signature :
HDR Invalid radiance file signature
Tiff Invalid endian tag value
TGA not enough bytes
Error producing PDF.
! LaTeX Error: Cannot determine size of graphic in /tmp/tex2pdf.88/6e81298938ff
130e201773573b4fd1fd6d389e60.shtml (no BoundingBox).
See the LaTeX manual or LaTeX Companion for explanation.
Type H
...
l.281 ...8938ff130e201773573b4fd1fd6d389e60.shtml}
Looks like we failed to compile the PDF
whedon
on 10 Jul 2018
Hello @arfon and @jasonclark , first of all thank you for your guidance. well, it seems to have some problems to compile my paper.md file i guess and i could not find them to resolve. please help me in compile process.
hamedmx
on 10 Jul 2018
@hamedmx - Pandoc doesn't like the URLs you've given in your paper.md. Please change lines like this:
to:
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
Thank you so much @arfon . Now, i have some problems; firstly, in writing mathematical statements and their symbols and secondly, in going to a new line, using bullets, and writing captions for the figures. So, is there any links to the related guidelines ?
hamedmx
on 10 Jul 2018
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
Thank you so much @arfon . Now, i have some problems; firstly, in writing mathematical statements and their symbols and secondly, in going to a new line, using bullets, and writing captions for the figures. So, is there any links to the related guidelines ?
We're just using standard Pandoc/Markdown here: https://pandoc.org/README.pdf
Looks like the document is compiling now :-)
arfon
on 10 Jul 2018
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
Attempting PDF compilation. Reticulating splines etc...
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
hamedmx
on 10 Jul 2018
Attempting PDF compilation. Reticulating splines etc...
@arfon @jasonclark I checked the last pdf file generated above and it was completely okay and without any problems. So, how can i enter to the review issue now ?
hamedmx
on 10 Jul 2018
I would like to mention @xirdneh as my suggestion to review this submission.
hamedmx
on 10 Jul 2018
@whedon commands
hamedmx
on 10 Jul 2018
Here are some things you can ask me to do:
# List Whedon's capabilities
@whedon commands
# List of editor GitHub usernames
@whedon list editors
# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers
馃毀 馃毀 馃毀 Experimental Whedon features 馃毀 馃毀 馃毀
# Compile the paper
@whedon generate pdf
@hamedmx - first we need to hear back from @jasonclark as to whether he is willing to edit this submission, then we need to identify reviewers, then we can start the actual review.
arfon
on 10 Jul 2018
Thank you very much @arfon . I look forward to your response.
hamedmx
on 10 Jul 2018
@arfon @hamedmx I am willing to edit this submission.
jasonclark
on 20 Jul 2018
@whedon assign @jasonclark as editor
jasonclark
on 20 Jul 2018
OK, the editor is @jasonclark
whedon
on 20 Jul 2018
@hamedmx Can you create a README file for the repository? All JOSS entries require a general description of the software (what is it?, why would I use it?, etc.) along with basic install instructions. You might even use some of the narrative from your article at https://github.com/hamedmx/YAD-ILP-Tool/blob/master/YAD-JOSS.pdf.
jasonclark
on 20 Jul 2018
@jasonclark Yes, sure. Of course all the desired descriptions about the tool exist in the article, i.e. paper.md file in the repository.
hamedmx
on 21 Jul 2018
@jasonclark The required README file is ready in the repository with adequate descriptions about the tool and its usage and also a new additional sample test file has been uploaded there.
hamedmx
on 21 Jul 2018
@arfon , @jasonclark has declared his willing to edit this submission since about 16 days ago and according to his revision on our repository, we have already prepared the desired README file for the repository. So, when should we identify the reviewers for our submission and start the actual review ?
hamedmx
on 5 Aug 2018
@arfon , @jasonclark has declared his willing to edit this submission since about 16 days ago and according to his revision on our repository, we have already prepared the desired README file for the repository. So, when should we identify the reviewers for our submission and start the actual review ?
Yes, time to identify reviewers. @hamedmx - could you take a look a this list of potential reviewers and suggest a few people you think might be suitable? https://bit.ly/joss-reviewers
arfon
on 5 Aug 2018
Thank you @arfon . Okay, sure. Here are my suggestions for reviewers: @xirdneh , @Fusionet24 , @martinmodrak , and @Dredamonsta1 .
hamedmx
on 5 Aug 2018
I've so far never reviewed for JOSS, so I am not sure if I am expected to react to @hamedmx 's suggestion or if I should wait for @jasonclark . Anyway, I feel the software is on the border of my knowledge (honestly, probably some distance on the wrong side of the border). Also I will be out of office for most of August and early September and so will be able to have a first look no sooner than ~ September 7th. Just thought this might be factors in reviewer selection.
martinmodrak
on 9 Aug 2018
@martinmodrak Thank you very much for your notification. @arfon So, what is the next step to begin the actual review section ? I've already suggested some other reviewers for our submission about 5 days ago.
hamedmx
on 10 Aug 2018
@martinmodrak Thank you very much for your notification. @arfon So, what is the next step to begin the actual review section ? I've already suggested some other reviewers for our submission about 5 days ago.
Hi @hamedmx, we just need a little more time here I think. @martinmodrak isn't able to look at this submission until early September and none of the other suggested reviewers have responded yet so I think we're still in the pre-review phase.
@xirdneh @fusionet24 @dredamonsta1 - would one of you be willing to review this submission for JOSS?
arfon
on 10 Aug 2018
Sorry I鈥檓 late to reply my mailbox was full I can start reviewing later today I am also new and not sure but I want to help out as best as I can
dredamonsta1
on 13 Aug 2018
Thank you so much @dredamonsta1 . @arfon , @dredamonsta1 is willing to review this submission for us.
hamedmx
on 13 Aug 2018
@whedon assign @dredamonsta1 as reviewer
jasonclark
on 13 Aug 2018
OK, the reviewer is @dredamonsta1
whedon
on 13 Aug 2018
@whedon start review magic-word=bananas
jasonclark
on 13 Aug 2018
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/892. Feel free to close this issue now!
whedon
on 13 Aug 2018
Closing out of pre-review and setting review at https://github.com/openjournals/joss-reviews/issues/892
jasonclark
on 13 Aug 2018
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Thank you @arfon . Okay, sure. Here are my suggestions for reviewers: @xirdneh , @Fusionet24 , @martinmodrak , and @Dredamonsta1 .