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[PRE REVIEW]: PyFstat: a Python package for continuous gravitational-wave data analysis #2994

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @dbkeitel (David Keitel) Repository: https://github.com/PyFstat/PyFstat/ Version: v1.11.1 Editor: @danielskatz Reviewers: @khanx169, @RobertRosca Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

@dbkeitel if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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 3 years ago

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.27 s (265.2 files/s, 73563.4 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           41           2066           4227          12221
Markdown                          2             93              0            498
YAML                              6             25             23            159
CUDA                              2             38             66            142
reStructuredText                 14             52             67            104
JSON                              1              0              0             40
DOS Batch                         1              8              1             26
Bourne Shell                      2              6             14             20
Bourne Again Shell                1              6              4             18
Dockerfile                        1              4              7             14
make                              1              5              7             13
--------------------------------------------------------------------------------
SUM:                             72           2303           4416          13255
--------------------------------------------------------------------------------

Statistical information for the repository 'a8658face0a8c6503406fcd4' was
gathered on 2021/01/28.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
David Keitel                   348         15016           6978           36.50
Gregory Ashton                 285         13432           8478           36.36
Reinhard Prix                   10          4217           2311           10.83
Rodrigo Tenorio                 15          1279            546            3.03
Rodrigo-Tenorio                142          2406           1779            6.95
gregory.ashton                 111          3086            723            6.32

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
David Keitel              10614           70.7          6.0                9.31
Gregory Ashton             2832           21.1         40.5                4.38
Reinhard Prix              2359           55.9         18.9                0.42
Rodrigo Tenorio             215           16.8          5.8                0.47
Rodrigo-Tenorio            2494          103.7          3.4                6.98
whedon commented 3 years ago

PDF failed to compile for issue #2994 with the following error:

Can't find any papers to compile :-(

danielskatz commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

PDF failed to compile for issue #2994 with the following error:

/app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in initialize': No such file or directory @ rb_sysopen - af475834051feb14868d9a04/joss-paper/paper.yml (Errno::ENOENT) from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:inopen' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in load_file' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:125:inload_yaml' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:innew' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:66:inprepare' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `

'

danielskatz commented 3 years ago

@whedon check references from branch joss

whedon commented 3 years ago 
Attempting to check references... from custom branch joss
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.7935/GT1W-FZ16 is OK
- 10.1103/PhysRevD.58.063001 is OK
- 10.1007/978-3-540-76965-1_24 is OK
- 10.1016/j.parco.2011.09.001 is OK
- 10.1103/PhysRevD.89.064023 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1093/mnras/stv2422 is OK
- 10.1142/S021773231730035X is OK
- 10.1103/PhysRevD.97.103020 is OK
- 10.1103/PhysRevD.98.063011 is OK
- 10.1088/1361-6382/aade34 is OK
- 10.3390/universe5110217 is OK
- 10.1103/PhysRevLett.124.191102 is OK
- 10.1093/mnras/staa3624 is OK
- 10.1016/j.softx.2020.100634 is OK

MISSING DOIs

- None

INVALID DOIs

- None
danielskatz commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

PDF failed to compile for issue #2994 with the following error:

/app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in initialize': No such file or directory @ rb_sysopen - d08b089bfd93fdba0f8da8b4/joss-paper/paper.yml (Errno::ENOENT) from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:inopen' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in load_file' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:125:inload_yaml' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:innew' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:66:inprepare' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `

'

danielskatz commented 3 years ago

👋 @openjournals/dev - can you help with this compilation error? I don't see anything in the error message that I can use to diagnose the problem

arfon commented 3 years ago

I think the presence of a paper.tex file is confusing Whedon: https://github.com/PyFstat/PyFstat/blob/joss/joss-paper/paper.tex

I would suggest removing this and trying again.

danielskatz commented 3 years ago

👋 @dbkeitel - can you remove paper.tex from the repo, and then try the compilation, by putting @whedon generate pdf from branch joss in a new comment here? I'm going to mark this as paused for the minute

dbkeitel commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

dbkeitel commented 3 years ago

Thanks @danielskatz @arfon that has fixed it! And thanks for getting thing started, too.

danielskatz commented 3 years ago

@whedon assign me as editor

whedon commented 3 years ago

OK, the editor is @danielskatz

danielskatz commented 3 years ago

@dbkeitel - do you have any suggestions for potential reviewers? Please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

danielskatz commented 3 years ago

👋 @khanx169, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html (You were suggested by @eliu23)

danielskatz commented 3 years ago

👋 @svigeland - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

dbkeitel commented 3 years ago

If those first wo people you asked aren't available, cmbiwer would be a great choice (GW analyst with experience developing similar packages, but no direct contact with this project).

Some more likely-looking people (with python & astro listed as language/field) going up from the bottom of the table would be e.g.: RobertRosca arjunsavel sibirrer JBorrow cavestruz .

danielskatz commented 3 years ago

👋 @cmbiwer - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

khanx169 commented 3 years ago

👋 @khanx169, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html (You were suggested by @eliu23)

@danielskatz yes I'd be happy to review.

danielskatz commented 3 years ago

@khanx169 - thanks. I'll assign you now, but we won't actually start the review until we get at least one more reviewer as well

danielskatz commented 3 years ago

@whedon assign @khanx169 as reviewer

whedon commented 3 years ago

OK, @khanx169 is now a reviewer

svigeland commented 3 years ago

👋 @svigeland - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Apologies, but I'm unable to review now.

danielskatz commented 3 years ago

👋 @RobertRosca - would you be willing to review this submission for JOSS?

RobertRosca commented 3 years ago

Hey, sure I'd be happy to review! I can read through the guidelines and get started Monday.

danielskatz commented 3 years ago

Thanks - I'll assign you and we'll start the review in a new issue

danielskatz commented 3 years ago

@whedon add @RobertRosca as reviewer

whedon commented 3 years ago

OK, @RobertRosca is now a reviewer

danielskatz commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3000.