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[PRE REVIEW]: PyFPT: A Python package for first-passage times #4509

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editorialbot opened this issue Jun 26, 2022 · 36 comments
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[PRE REVIEW]: PyFPT: A Python package for first-passage times #4509

editorialbot opened this issue Jun 26, 2022 · 36 comments
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@drvinceknight @CFGrote
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Cython pre-review Python TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Jun 26, 2022 •
edited

Submitting author: @Jacks0nJ (Joseph Jackson)
Repository: https://github.com/Jacks0nJ/PyFPT
Branch with paper.md (empty if default branch):
Version: 1.00
Editor: @drvinceknight
Reviewers: @CFGrote, @geraintpalmer
Managing EiC: Arfon Smith

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21"><img src="https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21/status.svg)](https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21)

Author instructions

Thanks for submitting your paper to JOSS @Jacks0nJ. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @drvinceknight.

@Jacks0nJ 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 @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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

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

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (1047.7 files/s, 93101.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          65            621           1231           1649
Jupyter Notebook                 5              0           2646            456
Markdown                         2            103              0            165
Cython                           1             26             25            147
TeX                              1             11              0            100
YAML                             4              9              6             69
reStructuredText                 4             92             80             52
DOS Batch                        1              8              1             26
TOML                             1              0              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            85            874           3996           2683
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.1140/epjc/s10052-015-3643-y is OK
- 10.1088/1475-7516/2017/10/046 is OK
- 10.1142/9789814327183_0010 is OK
- 10.1088/1361-6471/abc534 is OK
- 10.1140/epjb/s10051-021-00246-0 is OK
- 10.1016/S0375-9474(98)00478-3 is OK

MISSING DOIs

- 10.1088/1475-7516/2022/05/027 may be a valid DOI for title: Implications of stochastic effects for primordial black hole production in ultra-slow-roll inflation

INVALID DOIs

- None

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Wordcount for paper.md is 484

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

@arfon
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arfon commented Jun 26, 2022

@editorialbot invite @drvinceknight as editor

👋 @drvinceknight – not sure if you're taking on new submissions yet, but if you are, perhaps you could take this? 😄

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Invitation to edit this submission sent!

@drvinceknight
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Got it @arfon :)

@drvinceknight
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@editorialbot assign me as editor

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Assigned! @drvinceknight is now the editor

@drvinceknight
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@Jacks0nJ would you be able to take a look at the list of potential reviewers and suggest any potential people? (Just let me know their @handles, no need to ping them).

Also, not sure if you saw but editorialbot suggested:

  • 10.1088/1475-7516/2022/05/027 may be a valid DOI for title: Implications of stochastic effects for primordial black hole production in ultra-slow-roll inflation

@Jacks0nJ
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@editorialbot generate pdf

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

@Jacks0nJ
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@drvinceknight I've updated the Github main to hopefully have the correct DOI. When I click on the link (on the draft version I generate through actions) it takes me to the correct paper, so should be correct.

Hopefully I updated the pdf on here too, using the command I wrote above. Apologies if this is incorrect, I'm new to collaborating with git.

The three reviewers I would recommend are:

  • CFGrote
  • FaroukM
  • OsAmaro

@drvinceknight
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Thanks @Jacks0nJ.

@drvinceknight
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@CFGrote @faroukM @OsAmaro I'm pinging you to ask if you would be able to assist with reviewing this submissions to JOSS (The Journal of Open Source Software).

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: “PyFPT: A Python package for first-passage times”. You can find more information at the top of this Github issue.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

@CFGrote
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CFGrote commented Jul 1, 2022 via email

@drvinceknight
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That's great, thank you @CFGrote

@drvinceknight
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@editorialbot add @CFGrote as reviewer

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@CFGrote added to the reviewers list!

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CFGrote commented Jul 4, 2022

@editorialbot commands

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Hello @CFGrote, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers

@CFGrote
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CFGrote commented Jul 4, 2022 •
edited

Review checklist for @CFGrote

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/Jacks0nJ/PyFPT?
  • 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 (@Jacks0nJ) 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, who the target audience is, and its relation to other work?
  • 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?

@CFGrote
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CFGrote commented Jul 18, 2022

@editorialbot generate pdf

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

This was referenced Jul 18, 2022
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CFGrote commented Jul 18, 2022

This concludes my first round of review. I'm really impressed by the quality of the code and documentation and for following OS Dev best practices in general. I'm looking forward to your response @Jacks0nJ .

@Jacks0nJ
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Cheers @CFGrote! I'll try to work on your feedback over the next two days but I'm on holiday 20/07/22-29/07/22, so just to let you know some fixes might come after then.

If there is anything else I should do @drvinceknight apart from what @CFGrote has already highlighted, do let me know.

@Jacks0nJ
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@editorialbot generate pdf

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

@drvinceknight
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Nothing more for you to do @Jacks0nJ, I'm still looking for a second reviewer.

Thanks for the awesome review work @CFGrote, note that once I have a second reviewer an actual review issue will be opened. I'll go ahead and tick off the checkboxes that will appear there.

@drvinceknight
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@editorialbot add @geraintpalmer as reviewer

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@geraintpalmer added to the reviewers list!

@drvinceknight
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This is the paper I was just talking to you about @geraintpalmer.

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@editorialbot start review

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OK, I've started the review over in #4607.

@drvinceknight
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The review will take place on #4607, I know @geraintpalmer that you're heading on leave but thank you for accepting.

@editorialbot editorialbot added the Track: 7 (CSISM) Computer science, Information Science, and Mathematics label Sep 10, 2022
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