[PRE REVIEW]: Fruitbat: A Python Package for Estimating Redshifts of Fast Radio Bursts #1377

whedon · 2019-04-14T14:22:00Z

Submitting author: @abatten (Adam Batten)
Repository: https://github.com/abatten/fruitbat
Version: v1.0.0
Editor: @xuanxu
Reviewers: @zingale

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

whedon · 2019-04-14T14:22:03Z

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:

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whedon · 2019-04-14T14:22:03Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-14T14:22:12Z

PDF failed to compile for issue #1377 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:91:in block in check_orcids': Problem with ORCID (0000-0001-7559-6488) for Adam J. Batten (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:89:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:89:in check_orcids' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:70: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

'

labarba · 2019-04-14T14:30:30Z

@abatten 👋 — could there be a typo in your ORCID?

labarba · 2019-04-14T14:32:44Z

@xuanxu — The submitting author suggested you as handling editor, and it does look like your cup of tea. I'll assign you now, but let me know if you're disinclined for any reason.

labarba · 2019-04-14T14:32:56Z

@whedon assign @xuanxu as editor

whedon · 2019-04-14T14:32:59Z

OK, the editor is @xuanxu

abatten · 2019-04-14T22:33:57Z

The ORCID number seems to be correct. It might have failed because my ORCID account didn't have my middle initial. I've changed it now so hopefully it works.

abatten · 2019-04-14T22:36:49Z

@whedon generate pdf

whedon · 2019-04-14T22:36:52Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-14T22:37:01Z

PDF failed to compile for issue #1377 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:91:in block in check_orcids': Problem with ORCID (0000-0001-7559-6488) for Adam J. Batten (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:89:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:89:in check_orcids' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:70: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

'

abatten · 2019-04-14T22:40:13Z

Hmmm. Actually I did miss a number. Trying again.

abatten · 2019-04-14T22:41:11Z

@whedon generate pdf

whedon · 2019-04-14T22:41:13Z

Attempting PDF compilation. Reticulating splines etc...

xuanxu · 2019-04-15T13:49:59Z

@xuanxu — The submitting author suggested you as handling editor, and it does look like your cup of tea. I'll assign you now, but let me know if you're disinclined for any reason.

👍

arfon · 2019-04-15T17:30:54Z

@whedon generate pdf

whedon · 2019-04-15T17:30:57Z

Attempting PDF compilation. Reticulating splines etc...

arfon · 2019-04-15T17:35:59Z

I'm not sure why Whedon is struggling here. I've compiled the PDF locally: 10.21105.joss.01377.pdf

abatten · 2019-04-16T00:13:18Z

Thanks @arfon. Looks like parts of the document didn't render as I'd expect them to. e.g missing citations, listing dot points and figure captions. I'll fix those up.

abatten · 2019-04-17T00:56:15Z

@whedon generate pdf

whedon · 2019-04-17T00:56:17Z

Attempting PDF compilation. Reticulating splines etc...

arfon · 2019-04-17T01:01:15Z

I'm wondering if Whedon is struggling because of the size of the logo: https://github.com/abatten/fruitbat/blob/master/logo/fruitbat_logo.png

abatten · 2019-04-17T01:02:58Z

It could be. The logo isn't super important to the paper, just thought it would be nice. I'll remove it and see.

arfon · 2019-04-17T01:03:06Z

Anyway, here's an update proof: 10.21105.joss.01377.pdf

arfon · 2019-04-17T01:03:58Z

It could be. The logo isn't super important to the paper, just thought it would be nice. I'll remove it and see.

Or just resize it? If you want to try out the change, you can push a modification to a branch and then ask Whedon to compile the paper from that branch for testing (e.g. @whedon generate pdf from branch testing)

whedon · 2019-04-17T01:19:25Z

Attempting PDF compilation. Reticulating splines etc...

arfon · 2019-04-18T11:41:14Z

It looks like the very long author lists on the Planck papers is blowing up the memory usage on the Heroku PDF worker:

2019-04-18T11:20:05.697913+00:00 heroku[router]: at=info method=POST path="/dispatch" host=whedon.herokuapp.com request_id=c5739468-eeda-43e3-bf27-38b7cab4f6dc fwd="140.82.115.12" dyno=web.1 connect=0ms service=2747ms status=200 bytes=253 protocol=https
2019-04-18T11:20:05.711888+00:00 app[worker.1]: 4 TID-1bkjao PDFWorker JID-21ab8dd21ac0cd55cb66681a INFO: start
2019-04-18T11:20:07.406918+00:00 heroku[router]: at=info method=POST path="/dispatch" host=whedon.herokuapp.com request_id=e499a364-b79b-4670-89e4-cc8f7d9e07e2 fwd="140.82.115.5" dyno=web.1 connect=0ms service=2002ms status=200 bytes=228 protocol=https
2019-04-18T11:20:48.119861+00:00 heroku[worker.1]: Process running mem=737M(142.2%)
2019-04-18T11:20:48.121062+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:21:06.931745+00:00 heroku[worker.1]: Process running mem=728M(142.2%)
2019-04-18T11:21:06.931745+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:21:28.033900+00:00 heroku[worker.1]: Process running mem=728M(142.2%)
2019-04-18T11:21:28.033981+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:21:46.996705+00:00 heroku[worker.1]: Process running mem=853M(166.6%)
2019-04-18T11:21:46.996784+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:22:07.247549+00:00 heroku[worker.1]: Process running mem=861M(168.2%)
2019-04-18T11:22:07.247659+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:22:27.579594+00:00 heroku[worker.1]: Process running mem=1020M(199.3%)
2019-04-18T11:22:27.579731+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:22:47.066625+00:00 heroku[worker.1]: Process running mem=1020M(199.3%)
2019-04-18T11:22:47.066721+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:23:06.512981+00:00 heroku[worker.1]: Process running mem=1021M(199.3%)
2019-04-18T11:23:06.513116+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:23:26.883818+00:00 heroku[worker.1]: Process running mem=1020M(199.3%)
2019-04-18T11:23:26.883865+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:23:46.561362+00:00 heroku[worker.1]: Process running mem=1020M(199.3%)
2019-04-18T11:23:46.561420+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:24:06.626757+00:00 heroku[worker.1]: Process running mem=1020M(199.3%)
2019-04-18T11:24:06.626922+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:24:27.698419+00:00 heroku[worker.1]: Process running mem=1020M(199.3%)
2019-04-18T11:24:27.698526+00:00 heroku[worker.1]: Error R14 (Memory quota exceeded)
2019-04-18T11:24:47.311199+00:00 heroku[worker.1]: Process running mem=1279M(249.9%)

I'm not sure there's much we can do to easily fix this unless you can truncate that author list (they won't all render in the paper anyway)?

abatten · 2019-04-18T14:10:49Z

Well that should be an easy fix!

abatten · 2019-04-18T14:12:03Z

@whedon generate pdf from branch joss

whedon · 2019-04-18T14:12:05Z

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon · 2019-04-18T14:12:30Z

👉 Check article proof 📄 👈

abatten · 2019-04-18T14:27:30Z

@whedon generate pdf from branch joss

whedon · 2019-04-18T14:27:33Z

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

abatten · 2019-04-18T14:42:05Z

@whedon generate pdf from branch joss

whedon · 2019-04-18T14:42:07Z

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon · 2019-04-18T14:42:35Z

👉 Check article proof 📄 👈

arfon · 2019-04-18T14:46:52Z

That's looking better. Feel free to add back in the logo now as I don't think this was the source of the problem.

abatten · 2019-04-18T14:56:12Z

Actually it was also an issue. I tried with the logo and it couldn't generate the PDF for 14 minutes, so I have re-scaled the image to see if that now works.

abatten · 2019-04-18T14:56:24Z

@whedon generate pdf from branch joss

whedon · 2019-04-18T14:56:26Z

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon · 2019-04-18T14:56:57Z

👉 Check article proof 📄 👈

abatten · 2019-04-18T15:22:25Z

Alright! Looking good, I'll merge to paper development branch into master.

abatten · 2019-04-18T15:28:29Z

@whedon generate pdf

whedon · 2019-04-18T15:28:32Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-18T15:29:15Z

👉 Check article proof 📄 👈

xuanxu · 2019-04-22T10:09:06Z

👋 @zingale: Would you be willing to review this paper? I think your expertise in Python and Astrophysics makes you a great fit for this submission.

zingale · 2019-04-22T13:33:52Z

yes, I can review this.

xuanxu · 2019-04-22T13:54:08Z

@zingale Great, thanks! I'll assign you and start the review issue now

xuanxu · 2019-04-22T13:54:33Z

@whedon assign @zingale as reviewer

whedon · 2019-04-22T13:54:37Z

OK, the reviewer is @zingale

xuanxu · 2019-04-22T13:55:06Z

@whedon start review

whedon · 2019-04-22T13:55:11Z

OK, I've started the review over in #1399. Feel free to close this issue now!

xuanxu · 2019-04-22T13:55:45Z

@zingale, please head over to #1399 for the actual review

whedon added the pre-review label Apr 14, 2019

whedon added Python TeX labels Apr 14, 2019

whedon assigned xuanxu Apr 14, 2019

whedon assigned xuanxu and unassigned xuanxu Apr 22, 2019

xuanxu closed this as completed Apr 22, 2019

[PRE REVIEW]: Fruitbat: A Python Package for Estimating Redshifts of Fast Radio Bursts #1377

[PRE REVIEW]: Fruitbat: A Python Package for Estimating Redshifts of Fast Radio Bursts #1377

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