[REVIEW]: TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization #4021

whedon · 2021-12-21T15:16:00Z

Submitting author: @ni1o1 (Qing Yu)
Repository: https://github.com/ni1o1/transbigdata
Branch with paper.md (empty if default branch):
Version: v0.3.7
Editor: @martinfleis
Reviewers: @jGaboardi, @anitagraser
Archive: 10.5281/zenodo.6236507

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Review checklist for @jGaboardi

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Documentation

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Software paper

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Review checklist for @anitagraser

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@ni1o1) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

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

whedon · 2021-12-21T15:16:07Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jGaboardi, @anitagraser it looks like you're currently assigned to review this paper 🎉.

⚠️ 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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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

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whedon · 2021-12-21T15:16:27Z

Wordcount for paper.md is 630

whedon · 2021-12-21T15:16:32Z

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

OK DOIs

- 10.1016/j.jclepro.2020.119974 is OK
- 10.1016/j.jclepro.2020.122471 is OK
- 10.1016/j.trc.2020.102672 is OK
- 10.1016/j.apenergy.2020.115038 is OK
- 10.1016/j.jclepro.2020.125567 is OK
- 10.1177/03611981211036684 is OK
- 10.1016/j.ijtst.2021.01.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-12-21T15:16:33Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.37 s (175.7 files/s, 69976.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0           9484
reStructuredText                21           1332           2763           1887
Python                          17            194           1059           1875
Markdown                         3            113              0            484
CSS                              1             91             11            405
Jupyter Notebook                 7              0           5352            405
TeX                              1              8              0            117
JSON                             5              0              0             85
YAML                             4             16             10             64
HTML                             2             16              0             63
DOS Batch                        1              8              1             26
make                             1              4              7              9
SVG                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            65           1782           9203          14907
-------------------------------------------------------------------------------


Statistical information for the repository 'f6e8f14381b53d89e9fddf9a' was
gathered on 2021/12/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
ni1o1                            5            72             48            3.33
yuanjian24                       5            79              3            2.27
余庆                            45          2983            422           94.40

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
ni1o1                        60           83.3          0.3                0.00
yuanjian24                   48           60.8          0.0                0.00
余庆                       3020          101.2          1.1                8.34

whedon · 2021-12-21T15:17:03Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

martinfleis · 2021-12-21T15:18:51Z

👋🏼 @ni1o1 @anitagraser @jGaboardi this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #4021 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks but considering upcoming holidays, feel free to start whenever it works for you. Please let me know if any of you require significantly more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@martinfleis) if you have any questions/concerns.

martinfleis · 2021-12-21T15:19:46Z

Moving here a comment by @anitagraser from the pre-review (#3986 (comment))

I haven't had chance to look at the code yet. Concerning the paper, I think there is one point in the review criteria that is currently not addressed:

A description of how this software compares to other commonly-used packages in this research area.

whedon · 2022-01-04T15:16:18Z

👋 @jGaboardi, please update us on how your review is going (this is an automated reminder).

whedon · 2022-01-04T15:16:18Z

👋 @anitagraser, please update us on how your review is going (this is an automated reminder).

jGaboardi · 2022-01-05T02:00:41Z

👋 @jGaboardi, please update us on how your review is going (this is an automated reminder).

This is still very much on my radar, but several personal issues have cropped in the last week. I am going to try to get back to it within the next 2 weeks or so.

anitagraser · 2022-01-05T11:40:25Z

👋 @anitagraser, please update us on how your review is going (this is an automated reminder).

Same here. Will get back to it soon.

jGaboardi · 2022-01-07T02:27:09Z

@ni1o1 @anitagraser @martinfleis

I have completed my first thorough pass of transbigdata and the manuscript, and have opened several issues and a PR, mostly involving documentation. Once the minor language issues, etc. are fixed in the paper, I would comfortable checking off those boxes. However, a sticking point that will ultimately hold back JOSS acceptance is the apparent lack of any testing being performed (ni1o1/transbigdata#7). This must be addressed.

jGaboardi · 2022-01-07T14:45:43Z

@whedon generate pdf

whedon · 2022-01-07T14:45:58Z

PDF failed to compile for issue #4021 with the following error:

 /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/response/raise_error.rb:16:in `on_complete': GET https://api.github.com/repos/JuliaCon/proceedings-review/issues/4021: 404 - Not Found // See: https://docs.github.com/rest/reference/issues#get-an-issue (Octokit::NotFound)
	from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/response.rb:9:in `block in call'
	from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/response.rb:61:in `on_complete'
	from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/response.rb:8:in `call'
	from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/middleware/follow_redirects.rb:73:in `perform_with_redirection'
	from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/middleware/follow_redirects.rb:61:in `call'
	from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/rack_builder.rb:143:in `build_response'
	from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/connection.rb:387:in `run_request'
	from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/connection.rb:138:in `get'
	from /app/vendor/bundle/ruby/2.6.0/gems/sawyer-0.8.2/lib/sawyer/agent.rb:94:in `call'
	from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/connection.rb:156:in `request'
	from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/connection.rb:19:in `get'
	from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/client/issues.rb:114:in `issue'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/review.rb:21:in `issue_body'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:44:in `prepare'
	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:in `invoke_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:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

jGaboardi · 2022-01-07T14:55:32Z

This is a rather strange failure, no? Seems to be trying for a JuliaCon repo?

https://api.github.com/repos/JuliaCon/proceedings-review/issues/4021

martinfleis · 2022-01-07T14:56:42Z

@whedon generate pdf

martinfleis · 2022-03-02T09:09:05Z

Thank you @ni1o1! I'm going to hand this over now to the associate EiC on rotation for the final steps.

martinfleis · 2022-03-02T09:09:18Z

@editorialbot recommend-accept

editorialbot · 2022-03-02T09:09:19Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-03-02T09:10:08Z

⚠️ Error prepararing acceptance.

martinfleis · 2022-03-02T10:49:20Z

@editorialbot generate pdf

arfon · 2022-03-02T10:49:49Z

Looks like this is failing because of the following warning:

Warning: Missing character: There is no ‒ (U+2012) (U+2012) in font [lmsans10-oblique]:+tlig;!
Failing because there were warnings.

@tarleb - could you take a look at what might be going on here?

martinfleis · 2022-03-02T10:50:43Z

@arfon It should be fixed by ni1o1/transbigdata#31 by @xuanxu

editorialbot · 2022-03-02T10:51:53Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

martinfleis · 2022-03-02T10:52:46Z

@editorialbot recommend-accept

editorialbot · 2022-03-02T10:52:47Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-03-02T10:54:55Z

⚠️ Error prepararing acceptance. The generated XML metadata file is invalid.

xuanxu · 2022-03-02T10:59:49Z

The value here for doi is invalid: https://github.com/ni1o1/transbigdata/blob/main/paper.bib#L165
doi.org/10.1111/2041-210X.13374 should be 10.1111/2041-210X.13374

martinfleis · 2022-03-02T11:00:21Z

@ni1o1 Can you fix that please?

ni1o1 · 2022-03-02T11:02:24Z

@ni1o1 Can you fix that please?

OK, it is fixed. Please try again, thanks.

martinfleis · 2022-03-02T11:04:48Z

@xuanxu I guess that check references should catch this.

@ni1o1 Thanks!

martinfleis · 2022-03-02T11:04:56Z

@editorialbot recommend-accept

editorialbot · 2022-03-02T11:04:57Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-03-02T11:07:20Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3007

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3007, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2022-03-03T18:42:39Z

@editorialbot accept

editorialbot · 2022-03-03T18:42:40Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2022-03-03T18:45:12Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-03-03T18:45:12Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04021 joss-papers#3017
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04021
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2022-03-03T18:48:24Z

Congratulations @ni1o1 on your article's publication in JOSS!

Many thanks to @jGaboardi and @anitagraser for reviewing this, and @martinfleis for editing.

editorialbot · 2022-03-03T18:48:26Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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  <img src="https://joss.theoj.org/papers/10.21105/joss.04021/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04021/status.svg
   :target: https://doi.org/10.21105/joss.04021

This is how it will look in your documentation:

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whedon added Jupyter Notebook Python review TeX labels Dec 21, 2021

whedon assigned martinfleis Dec 21, 2021

whedon mentioned this issue Dec 21, 2021

[PRE REVIEW]: TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization #3986

Closed

whedon assigned anitagraser and jGaboardi Dec 22, 2021

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 2, 2022

editorialbot added accepted published Papers published in JOSS labels Mar 3, 2022

kyleniemeyer closed this as completed Mar 3, 2022

editorialbot mentioned this issue Sep 29, 2023

[PRE REVIEW]: GTFS Segments: A fast and efficient library to generate bus stop spacings #5900

Closed

editorialbot mentioned this issue Oct 9, 2023

[PRE REVIEW]: scida: scalable analysis for scientific big data #5930

Closed

[REVIEW]: TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization #4021

[REVIEW]: TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization #4021

Comments

whedon commented Dec 21, 2021 • edited by editorialbot

Status

Reviewer instructions & questions

Review checklist for @jGaboardi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @anitagraser

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Dec 21, 2021

whedon commented Dec 21, 2021

whedon commented Dec 21, 2021

whedon commented Dec 21, 2021

whedon commented Dec 21, 2021

martinfleis commented Dec 21, 2021

martinfleis commented Dec 21, 2021

whedon commented Jan 4, 2022

whedon commented Jan 4, 2022

jGaboardi commented Jan 5, 2022

anitagraser commented Jan 5, 2022

jGaboardi commented Jan 7, 2022

jGaboardi commented Jan 7, 2022

whedon commented Jan 7, 2022

jGaboardi commented Jan 7, 2022

martinfleis commented Jan 7, 2022

martinfleis commented Mar 2, 2022

martinfleis commented Mar 2, 2022

editorialbot commented Mar 2, 2022

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martinfleis commented Mar 2, 2022

arfon commented Mar 2, 2022

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xuanxu commented Mar 2, 2022

martinfleis commented Mar 2, 2022

ni1o1 commented Mar 2, 2022

martinfleis commented Mar 2, 2022

martinfleis commented Mar 2, 2022

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kyleniemeyer commented Mar 3, 2022

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whedon commented Dec 21, 2021 •

edited by editorialbot