[PRE REVIEW]: IPART: A Python Package for Image-Processing based Atmospheric River Tracking

[whedon]

Submitting author: @Xunius (Guangzhi XU)
Repository: https://github.com/ihesp/IPART
Version: v1.0
Editor: @kbarnhart
Reviewers: @sadielbartholomew, @rabernat
Managing EiC: Kristen Thyng

⚠️ JOSS reduced service mode ⚠️

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 @Xunius. Currently, there isn't an JOSS editor assigned to your paper.

@Xunius 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]

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

⚠️ JOSS reduced service mode ⚠️

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

[kthyng]

Hi @Xunius! I have updated the repo address to https://github.com/ihesp/AR_tracker — let me know if this is incorrect.

[kthyng]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.17 s (229.6 files/s, 63563.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16           1491           1837           3341
reStructuredText                14            520            174           1164
TeX                              1             48              0            587
Jupyter Notebook                 5              0           1260            339
Markdown                         2             62              0            194
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            40           2133           3279           5660
-------------------------------------------------------------------------------


Statistical information for the repository '2197' was gathered on 2020/05/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
guangzhi                        14          6835            166          100.00

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
guangzhi                   6669           97.6          0.0                8.68

[kthyng]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2197 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/2197/joss/paper.md): found a tab character that violate intendation while scanning a plain scalar at line 9 column 11 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:125:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/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-45a043c4bfc2/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 `

'

[kthyng]

@openjournals/dev Is there a reference for finding what characters are not allowed in the papers? It looks like that is the problem. Is & ok?

[kthyng]

@Xunius I am conflicted on this paper so I will find another editor.

[kthyng]

@kbarnhart I know I just asked you about another submission, but we plan not to assign over 3 total at the moment. Are you able to edit this submission too? I am a good fit but I am conflicted.

[kbarnhart]

@kthyng I can handle this too.

[kbarnhart]

@whedon assign @kbarnhart as editor

[whedon]

OK, the editor is @kbarnhart

[danielskatz]

@openjournals/dev Is there a reference for finding what characters are not allowed in the papers? It looks like that is the problem. Is & ok?

This is not an issue with the paper body, but with the header.
Specifically, on line 10 of https://github.com/ihesp/AR_tracker/blob/master/joss/paper.md

	orcid: 0000-0001-5877-5608

should be

    orcid: 0000-0001-5877-5608

(basically, a tab needs to be replaced with 4 spaces)

[Xunius]

Thanks. Just made a quick fix: ihesp/IPART@6e617d8

[kbarnhart]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[Xunius]

@kbarnhart I noticed that generated PDF is using this format of citation [@authoryear] with no reference list in the end. In the PDF I compiled myself (using the preview tool or a Linux commandline utility, I can't remember which exactly) the citations look correct. Is it something again related to formatting errors?

[kbarnhart]

@Xunius it looks like your references have been placed in literal quotes: `@Gimeno2014`. This page provides some additional guidance regarding citation formatting.

[Xunius]

@kbarnhart Thanks. I think I must have accidentally reverted to a previous commit or something, I remembered myself fixing these citation issues before. Anyway, I just pushed a new commit fixing this, and tried the online preview service again. Now it compiles correctly.

[Xunius]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[Xunius]

Looking good now.

[kbarnhart]

@Xunius

Thank you for submitting this contribution to JOSS. As part of the review process, one of the JOSS editors (me) does an initial screening to ensure the submission is in scope and identify if there are any issues that should be addressed before the review process starts. I am very excited to see this contribution reviewed at JOSS, but based on examining the contents of the submission and discussing with the JOSS editorial board, there are a number of things that I think should be addressed before the submission proceeds to review. I've outlined these issues below in a checklist.

As always, please do not hesitate to ask questions or raise concerns. You may contact me here on this issue thread or at [email protected]

The typical procedure at JOSS at this point is to label the submission as "paused" while you address these issues. When you are done, you would notify me and I will resume the submission.

• Installation instructions: The contribution is a set of scripts without formal packaging. Formal packaging is not required, but some instructions for how a user might use this package outside of the source directory is merited. In addition, I might consider making a conda-environment specification.
• Example Usage: The set of notebooks you have created provide nice examples but they appear to rely on data from a Google Drive. I would recommend either providing the example data as part of the package or pointing to an existing reanalysis archive.
• API documentation: While it looks like everything that is exposed in a function signature is documented, examining the code itself reveals that there are quite a few local and global variables that are hard coded into the scripts. These include paths to files and the contents of PARAM_DICT. I would recommend that these parameters exposed as user specified without the need to edit the source code (e.g., as function keyword arguments).
• Tests: It appears that tests exist but there are no instructions for running them.
• Atmospheric river algorithm context: Could you place your algorithm more clearly in the context of the ARTMIP effort (Rutz et al., 2019; Shields et al., 2018) and the algorithms considered by that group.

References
Rutz, J. J., Shields, C. A., Lora, J. M., Payne, A. E., Guan, B., Ullrich, P., et al. ( 2019). The atmospheric river tracking method intercomparison project (ARTMIP): quantifying uncertainties in atmospheric river climatology. Journal of Geophysical Research: Atmospheres, 2019; 124: 13777– 13802. https://doi.org/10.1029/2019JD030936

Shields, C. A., Rutz, J. J., Leung, L.-Y., Ralph, F. M., Wehner, M., Kawzenuk, B., Lora, J. M., McClenny, E., Osborne, T., Payne, A. E., Ullrich, P., Gershunov, A., Goldenson, N., Guan, B., Qian, Y., Ramos, A. M., Sarangi, C., Sellars, S., Gorodetskaya, I., Kashinath, K., Kurlin, V., Mahoney, K., Muszynski, G., Pierce, R., Subramanian, A. C., Tome, R., Waliser, D., Walton, D., Wick, G., Wilson, A., Lavers, D., Prabhat, Collow, A., Krishnan, H., Magnusdottir, G., and Nguyen, P.: Atmospheric River Tracking Method Intercomparison Project (ARTMIP): project goals and experimental design, Geosci. Model Dev., 11, 2455–2474, https://doi.org/10.5194/gmd-11-2455-2018, 2018.

[kbarnhart]

@Xunius I wanted to follow up and see if you had any questions about my comments.

[whedon]

👉 Check article proof 📄 👈

[Xunius]

@kbarnhart PDF good.

[kbarnhart]

👋 @ajdawson @doutriaux1 @jwblin @muszyna25 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

This submission is "IPART: A Python Package for Image-Processing based Atmospheric River Tracking" by Guangzhi Xu, Xiaohui Ma and Ping Chang

This is a pre-review issue which is used to find reviewers. Once 2-3 reviewers have been found I'll start the review on a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks. If you are not able to review and have someone to recommend, please mention them here (when mentioning, please place a space after the @ of a github handle, for example, you would refer to me as "@ kbarnhart").

If you are interested in reviewing, I would recommend looking over the journal's conflict of interest policy before the review process starts.

If you have any questions about the JOSS review process, please do not hesitate to reach out to me on this issue or at [email protected]

[muszyna25]

Hi Katy,

Thank you for your invitation to review the submission for JOSS. However, I am not able to review it, I can recommend somebody that may be interested: @burlen @taobrienlbl

Thanks,
Grzegorz

[taobrienlbl]

Unfortunately I am unable to review as well, due to a conflict of interest with one of the authors.

[kbarnhart]

@muszyna25 thanks for the response and for recommending other reviewers. @taobrienlbl thanks also for your response.

[kbarnhart]

👋 @ajdawson @doutriaux1 @jwblin @burlen 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

This submission is "IPART: A Python Package for Image-Processing based Atmospheric River Tracking" by Guangzhi Xu, Xiaohui Ma and Ping Chang

This is a pre-review issue which is used to find reviewers. Once 2-3 reviewers have been found I'll start the review on a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks. If you are not able to review and have someone to recommend, please mention them here (when mentioning, please place a space after the @ of a github handle, for example, you would refer to me as "@ kbarnhart").

If you are interested in reviewing, I would recommend looking over the journal's conflict of interest policy before the review process starts.

If you have any questions about the JOSS review process, please do not hesitate to reach out to me on this issue or at [email protected]

[kbarnhart]

👋 @andreas-h @rabernat @sadielbartholomew 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

This submission is "IPART: A Python Package for Image-Processing based Atmospheric River Tracking" by Guangzhi Xu, Xiaohui Ma and Ping Chang

This is a pre-review issue which is used to find reviewers. Once 2-3 reviewers have been found I'll start the review on a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks. If you are not able to review and have someone to recommend, please mention them here (when mentioning, please place a space after the @ of a github handle, for example, you would refer to me as "@ kbarnhart").

If you are interested in reviewing, I would recommend looking over the journal's conflict of interest policy before the review process starts.

If you have any questions about the JOSS review process, please do not hesitate to reach out to me on this issue or at [email protected]

[sadielbartholomew]

Hi Katy, thank you for offering a review. Yes, I am happy & able to review this submission & do so at least within 6 weeks. I have read the COI Policy & do not have any COI for this submission.

One question to confirm, though, as I have not reviewed for JOSS before: I assume it does not preclude me from being a reviewer overall if I am due to soon be a co-author on a submission to JOSS (completely unrelated to this submission)? It's okay for reviewers also to submit to JOSS generally? Thanks.

[kbarnhart]

@sadielbartholomew thank you for being willing to review this submission! I can confirm that soon-to-be submitting to JOSS does not preclude you from being a reviewer.

I'll add you to the submission as a reviewer. I hope to start the official review thread in the next few days.

Thanks again for participating in the JOSS review process.

[kbarnhart]

@whedon add @sadielbartholomew as reviewer

[whedon]

OK, @sadielbartholomew is now a reviewer

[kbarnhart]

👋 @andreas-h and @rabernat a quick ping to consider reviewing this submission to JOSS.

[rabernat]

Yes, I will provide a review within 6 weeks.

[kbarnhart]

Thanks for being willing to review @rabernat !

[kbarnhart]

@whedon add @rabernat as reviewer

[whedon]

OK, @rabernat is now a reviewer

[kbarnhart]

@whedon start review

[whedon]

OK, I've started the review over in #2407.