[PRE REVIEW]: pyCSEP: A Python Package For Earthquake Forecast Developers

whedon commented 3 years ago

Submitting author: @wsavran (William Savran) Repository: https://github.com/SCECcode/pycsep Version: v0.4.1 Editor: @kbarnhart Reviewers: @nvanderelst Managing EiC: Daniel S. Katz

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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.

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Author instructions

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

@wsavran 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:

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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=3.57 s (27.4 files/s, 207820.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
XML                               5              0              0         717119
JSON                              9              0              0           7184
Python                           50           1972           3470           6671
YAML                             10            137             15           3482
reStructuredText                 14            476            395            851
Markdown                          3             67              0            180
Perl                              1             10             12             41
HTML                              2              4             11             22
Bourne Again Shell                1             16             28             19
make                              1              5              6             12
Jupyter Notebook                  1              0            180             10
Bourne Shell                      1              0              0              2
--------------------------------------------------------------------------------
SUM:                             98           2687           4117         735593
--------------------------------------------------------------------------------

Statistical information for the repository 'fb64479a7dddf1b274fedccf' was
gathered on 2021/07/17.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
MH                               2             5              4            0.02
Pablo Iturrieta                  3           482            105            1.26
Philip Maechling                 1           386              0            0.83
Thomas Beutin ("tb")             4           103             18            0.26
William                         12            54             48            0.22
William Savran                 297         25334          16064           88.95
bayonato89                       2           104             27            0.28
khawajasim                      14          1161            131            2.78
pciturri                        20           810            333            2.46
tb                               6           124              6            0.28
wsavran                         28           913            328            2.67

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
MH                            4           80.0          1.0               50.00
Pablo Iturrieta             464           96.3          5.8               11.21
Philip Maechling            155           40.2          0.0               54.84
Thomas Beutin ("tb")         29           28.2         15.1                0.00
William Savran            10192           40.2         17.4               14.89
bayonato89                  102           98.1          0.6                9.80
khawajasim                   35            3.0         16.8               11.43
pciturri                    444           54.8          7.8               19.14
wsavran                     688           75.4          4.1                8.87

whedon commented 3 years ago

PDF failed to compile for issue #3507 with the following error:

 Can't find any papers to compile :-(

danielskatz commented 3 years ago

@whedon generate pdf from branch pycsep_Joss

whedon commented 3 years ago

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

whedon commented 3 years ago

PDF failed to compile for issue #3507 with the following error:

 Can't find any papers to compile :-(

danielskatz commented 3 years ago

@whedon generate pdf from branch pycsep_joss

whedon commented 3 years ago

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

whedon commented 3 years ago

PDF failed to compile for issue #3507 with the following error:

 Error producing PDF.
! Use of \\author doesn't match its definition.
\new@ifnextchar ...served@d = #1\def \reserved@a {
                                                  #2}\def \reserved@b {#3}\f...
l.294 ...n@usc.edu}{\nolinkurl{wsavran@usc.edu}}}}

Looks like we failed to compile the PDF

danielskatz commented 3 years ago

@whedon check references from branch pycsep_joss

whedon commented 3 years ago

Attempting to check references... from custom branch pycsep_joss

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1785/gssrl.78.1.30 is OK
- 10.1002/cpe.1519 is OK
- 10.4401/ag-5350 is OK
- 10.2478/s11600-011-0013-5 is OK
- 10.1785/0120090340 is OK
- 10.1785/0120120186 is OK
- 10.1785/0220180033 is OK
- 10.1785/0220180051 is OK
- 10.1785/0220180031 is OK
- 10.1785/0220180053 is OK
- 10.1093/gji/ggaa554 is OK
- 10.1785/0220170045 is OK
- 10.1785/0220180161 is OK
- 10.1785/0120200026 is OK

MISSING DOIs

- 10.1785/gssrl.78.1.7 may be a valid DOI for title: Overview of the Working Group for the Development of Regional Earthquake Likelihood Models (RELM)

INVALID DOIs

- None

danielskatz commented 3 years ago

👋 @wsavran - your paper doesn't compile- please make the headers match those in the example. Also, you might be able to fix the possibly missing DOI that whedon suggests, but note that this may be incorrect. Please feel free to make changes to your .bib file, then use the command @whedon check references from branch pycsep_joss to check again, and the command @whedon generate pdf from branch pycsep_joss when the references are right and the .md file is updated to make a new PDF. Whedon commands need to be the first entry in a new comment.

wsavran commented 3 years ago

@whedon check references from branch pycsep_joss/paper

whedon commented 3 years ago

Attempting to check references... from custom branch pycsep_joss/paper

wsavran commented 3 years ago

@whedon generate pdf from branch pycsep_joss/paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch pycsep_joss/paper. Reticulating splines etc...

whedon commented 3 years ago

PDF failed to compile for issue #3507 with the following error:

 Can't find any papers to compile :-(

wsavran commented 3 years ago

@whedon generate pdf from branch pycsep_joss

whedon commented 3 years ago

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

whedon commented 3 years ago

PDF failed to compile for issue #3507 with the following error:

 Error producing PDF.
! Use of \\author doesn't match its definition.
\new@ifnextchar ...served@d = #1\def \reserved@a {
                                                  #2}\def \reserved@b {#3}\f...
l.294 ...n@usc.edu}{\nolinkurl{wsavran@usc.edu}}}}

Looks like we failed to compile the PDF

danielskatz commented 3 years ago

You can try to merge https://github.com/SCECcode/pycsep/pull/129 and see if that works - if not, the problem is likely the @ in the email address, which perhaps needs to be protected/quoted in some way. Perhaps @arfon will know the answer

wsavran commented 3 years ago

@whedon generate pdf from branch pycsep_joss

whedon commented 3 years ago

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

whedon commented 3 years ago

PDF failed to compile for issue #3507 with the following error:

 Error producing PDF.
! Use of \\author doesn't match its definition.
\new@ifnextchar ...served@d = #1\def \reserved@a {
                                                  #2}\def \reserved@b {#3}\f...
l.294 ...n@usc.edu}{\nolinkurl{wsavran@usc.edu}}}}

Looks like we failed to compile the PDF

wsavran commented 3 years ago

@whedon generate pdf from branch pycsep_joss

whedon commented 3 years ago

Attempting PDF compilation from custom branch pycsep_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:

danielskatz commented 3 years ago

@kbarnhart - could you edit this submission?

danielskatz commented 3 years ago

@whedon invite @kbarnhart as editor

whedon commented 3 years ago

@kbarnhart has been invited to edit this submission.

kbarnhart commented 3 years ago

@danielskatz I can do this.

@wsavran it will later in this week that I start actively handling this.

kbarnhart commented 3 years ago

@whedon assign @kbarnhart as editor

whedon commented 3 years ago

OK, the editor is @kbarnhart

kbarnhart commented 3 years ago

@wsavran thanks for this submission. I have completed my pre-review screening of this submission and will now start soliciting reviewers. If you have reviewer recommendations, please list them here (either list github handle without the @ symbol, or a name if they do not have a github account).

A few minor points regarding the paper to consider.

Line 27 - should be "earthquake prediction methods"?
Line 53 - should the "the" before "monolithic" be deleted?
Line 64 - Europe should be capitalized.
Line 84 - provide citations for cartopy and matplotlib.
Line 90-91 - provide citations for these packages.
Reference section
- check capitalization (for example, California on line 111, use double curly braces in .bib title entry where necessary).
- disambiguate Ned Field references (use the identical first name in all .bib entries)

Any questions, clarifications, or concerns... feel free to contact me here or at krbarnhart@usgs.gov

wsavran commented 3 years ago

@whedon generate pdf from branch pycsep_joss

whedon commented 3 years ago

Attempting PDF compilation from custom branch pycsep_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:

wsavran commented 3 years ago

@kbarnhart, thanks for the feedback on the manuscript. i've asked whedon to compile a new pdf with some changes.

possible reviewers:

leouieda
jedbrown
lheagy

thanks!

kbarnhart commented 3 years ago

@wsavran thanks for making those changes. I have now started to reach out to reviewers. As I am able to confirm reviewers I will add them here. Once I get a sufficient number (2 or 3), I will start the formal review issue.

wsavran commented 3 years ago

@kbarnhart thanks! i look forward to hearing back from the reviewers!

kbarnhart commented 3 years ago

@wsavran I wanted to give you a quick update. Specifically, I'm still actively looking for reviewers for this submission.

wsavran commented 3 years ago

@kbarnhart thanks for the update!

kbarnhart commented 3 years ago

👋 @calum-chamberlain, @megies, @barsch, @mhearne-usgs would you be interested and able to provide a review of a manuscript at the Journal of Open Source Software (JOSS). The submission I'd like you to review is titled: " pyCSEP: A Python Package For Earthquake Forecast Developers" by William H. Savran, Maximilian J. Werner, Danijel Schorlemmer, and Philip J. Maechling and the submission repository is at: https://github.com/SCECcode/pycsep. Given your extensive experience in earthquake seismology and python development, I would value your review of this submission.

A bit of background about JOSS and its review process. JOSS is a free, open-source, community driven and developer-friendly online journal (no publisher is seeking to raise revenue from the volunteer labor of researchers!). The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html. Editors and reviewers post comments on the Review issue, and authors respond to the comments and improve their submission until acceptance (or withdrawal, if they feel unable to satisfy the review).

JOSS has worked hard to recognize that because of the challenges of the COVID-19 pandemic, all members of the research community may have reduced availability. At present we are asking reviewers to complete their reviews within 6 weeks.

If you are interested and able, please review the JOSS Conflict of Interest policy. Otherwise I’d value any recommendations you may have for other reviewers.

calum-chamberlain commented 3 years ago

Kia Ora @kbarnhart - I am interested, but unfortunately will not be able to provide a timely review for this and so must decline. You might try Chet Hopp (cjhopp on github)?

kbarnhart commented 3 years ago

@calum-chamberlain thanks for the prompt response and the recommendation!

kbarnhart commented 3 years ago

👋 @cjhopp would you be interested and able to provide a review of a manuscript at the Journal of Open Source Software (JOSS). The submission I'd like you to review is titled: " pyCSEP: A Python Package For Earthquake Forecast Developers" by William H. Savran, Maximilian J. Werner, Danijel Schorlemmer, and Philip J. Maechling and the submission repository is at: https://github.com/SCECcode/pycsep. Given your extensive experience in earthquake seismology and python development, I would value your review of this submission.

A bit of background about JOSS and its review process. JOSS is a free, open-source, community driven and developer-friendly online journal (no publisher is seeking to raise revenue from the volunteer labor of researchers!). The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html. Editors and reviewers post comments on the Review issue, and authors respond to the comments and improve their submission until acceptance (or withdrawal, if they feel unable to satisfy the review).

JOSS has worked hard to recognize that because of the challenges of the COVID-19 pandemic, all members of the research community may have reduced availability. At present we are asking reviewers to complete their reviews within 6 weeks.

If you are interested and able, please review the JOSS Conflict of Interest policy. Otherwise I’d value any recommendations you may have for other reviewers.

wsavran commented 3 years ago

@kbarnhart, I've copied the github handles of a few other reviewers that should reviewers of this paper. Cheers!

baagaard-usgs willic3 brendanjmeade MatteoTaroniINGV

cjhopp commented 3 years ago

Hi @kbarnhart , apologies for the delay in responding, and thanks for reaching out! In the future, I'd be happy to review for JOSS, but I have to decline this time around. Many weeks of impending fieldwork.

kbarnhart commented 3 years ago

@cjhopp thanks for considering and letting me know. Best of luck with the fieldwork.

@wsavran thanks for those additional recommendations.

openjournals / joss-reviews

[PRE REVIEW]: pyCSEP: A Python Package For Earthquake Forecast Developers #3507

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