[REVIEW]: CWInPy: a Python package for inference with continuous gravitational-wave signals from pulsars #4568

editorialbot · 2022-07-15T08:17:32Z

Submitting author: @mattpitkin (Matthew Pitkin)
Repository: https://github.com/cwinpy/cwinpy
Branch with paper.md (empty if default branch): paper
Version: v0.9.0
Editor: @dfm
Reviewers: @GregoryAshton, @ColmTalbot
Archive: 10.5281/zenodo.7121400

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/758efd099304e45c86e8f430b61ed221"><img src="https://joss.theoj.org/papers/758efd099304e45c86e8f430b61ed221/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/758efd099304e45c86e8f430b61ed221/status.svg)](https://joss.theoj.org/papers/758efd099304e45c86e8f430b61ed221)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ColmTalbot & @GregoryAshton, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dfm know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @GregoryAshton

📝 Checklist for @ColmTalbot

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

editorialbot · 2022-07-15T08:17:34Z

Hello humans, 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:

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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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editorialbot · 2022-07-15T08:17:42Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.40 s (290.1 files/s, 113659.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          65           5517           7951          22759
reStructuredText                18           1287           2069           1792
INI                             17            306            155           1158
SVG                              2              0              3            793
TeX                              1             30              0            471
Jupyter Notebook                 1              0            289            374
YAML                             6             20             46            285
Markdown                         3             69              0            266
make                             2             10             11             63
Cython                           1             20             16             60
TOML                             1              1              0             11
-------------------------------------------------------------------------------
SUM:                           117           7260          10540          28032
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-07-15T08:17:43Z

Wordcount for paper.md is 1708

editorialbot · 2022-07-15T08:17:45Z

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

OK DOIs

- 10.1086/428488 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.00538 is OK
- 10.21105/joss.00024 is OK
- 10.1016/j.softx.2021.100657 is OK
- 10.48550/arXiv.1705.08978 is OK
- 10.1103/PhysRevD.98.063001 is OK
- 10.3847/1538-4365/ab06fc is OK
- 10.7935/GT1W-FZ16 is OK
- 10.1016/j.softx.2020.100634 is OK
- 10.1093/mnras/staa278 is OK
- 10.1103/PhysRevD.72.102002 is OK
- 10.3847/1538-4357/ab20cb is OK
- 10.1051/0004-6361/200912222 is OK
- 10.1080/01621459.1982.10477856 is OK
- 10.3847/1538-4357/abe62f is OK
- 10.1111/j.1365-2966.2006.10302.x is OK
- 10.1088/1742-6596/610/1/012021 is OK
- 10.1016/j.softx.2021.100658 is OK
- 10.1103/PhysRevD.95.062002 is OK
- 10.1146/annurev-astro-082214-122339 is OK
- 10.1002/cpe.938 is OK
- 10.1038/s43586-022-00121-x is OK
- 10.3847/1538-4357/aa677f is OK
- 10.3847/2041-8213/abb655 is OK
- 10.1103/PhysRevD.102.123027 is OK
- 10.1017/pasa.2015.35 is OK
- 10.48550/arXiv.2111.13106 is OK

MISSING DOIs

- None

INVALID DOIs

- None

dfm · 2022-07-15T08:18:36Z

@ColmTalbot, @GregoryAshton — This is the review thread for the paper. All of our communications will happen here from now on. Thanks again for agreeing to participate!

Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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 openjournals/joss-reviews#4568 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 the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

editorialbot · 2022-07-15T08:19:39Z

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

mattpitkin · 2022-07-15T08:29:36Z

@GregoryAshton @ColmTalbot thanks very much for agreeing to perform the review. When looking at the documentation it's worth looking at the latest version rather than the stable version. The internal LVK review (you should be able to see that material if you want to) of the code should be concluding soon, and I expect to release a v1.0.0 version at that point. If you have any issues feel free to submit them here.

mattpitkin · 2022-07-15T08:45:45Z

@editorialbot generate pdf

editorialbot · 2022-07-15T08:47:16Z

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

GregoryAshton · 2022-07-22T15:37:02Z

@editorialbot generate my checklist

editorialbot · 2022-07-22T15:37:03Z

@GregoryAshton I can't do that because you are not a reviewer

GregoryAshton · 2022-07-22T15:37:38Z

@dfm it looks like I am not tagged as a reviewer?

dfm · 2022-07-22T15:41:16Z

@editorialbot add @GregoryAshton as reviewer

Whoa - strange!! Let's try again and see if it works now?

editorialbot · 2022-07-22T15:41:17Z

@GregoryAshton added to the reviewers list!

GregoryAshton · 2022-07-22T15:42:32Z

Review checklist for @GregoryAshton

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 https://github.com/cwinpy/cwinpy?
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 (@mattpitkin) 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?

GregoryAshton · 2022-07-25T10:57:11Z

@mattpitkin regarding the paper, there is a typo in the summary: a missing "to" between "user" and "search" in paragraph 2.

I also wondered if there is an appropriate link to documentation on what an "ephemeris" file should be? While this is a well-understood concept in radio pulsar astronomy, users of this package may be unfamiliar and unable to create an ephemeris. Moreover, the definition of an ephemeris may yet change (there are standard formats I think). Would you consider adding to the documentation the fields that cwinpy expects (e.g. key/value information) and perhaps linking that from the paper?

mattpitkin · 2022-07-26T10:30:44Z

@GregoryAshton Thanks for spotting the typo. I'll get that fixed.

I think the appropriate reference for the ephemeris file format is the Tempo2 manual. I'll add a link to that. I can also add to the documentation explicit information about the required parameters that must be in a par file for CWInPy.

…iews#4568 (comment)

…/joss-reviews#4568 (comment)

…iews#4568 (comment)

mattpitkin · 2022-07-26T13:11:42Z

@editorialbot generate pdf

mattpitkin · 2022-07-26T13:12:26Z

@GregoryAshton I've added a section to the documentation about the parameter file specification https://cwinpy.readthedocs.io/en/latest/pipelines.html#source-parameter-specification. I've also linked to this in the paper and added a reference to the Tempo2 manual.

mattpitkin · 2022-09-28T22:01:37Z

Increment the version number of the software and report that version number back here.

I've updated the version to v0.9.0 and released this on PyPI.

mattpitkin · 2022-09-28T22:22:27Z

Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

The Zenodo DOI is 10.5281/zenodo.7121400

dfm · 2022-09-29T17:40:00Z

@editorialbot set v0.9.0 as version

editorialbot · 2022-09-29T17:40:01Z

Done! version is now v0.9.0

dfm · 2022-09-29T17:41:58Z

@editorialbot set 10.5281/zenodo.7121400 as archive

editorialbot · 2022-09-29T17:42:00Z

Done! Archive is now 10.5281/zenodo.7121400

dfm · 2022-09-29T17:42:28Z

@editorialbot check references

dfm · 2022-09-29T17:42:55Z

@editorialbot generate pdf

editorialbot · 2022-09-29T17:44:11Z

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

OK DOIs

- 10.1086/428488 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.00538 is OK
- 10.21105/joss.00024 is OK
- 10.1016/j.softx.2021.100657 is OK
- 10.48550/arXiv.1705.08978 is OK
- 10.1103/PhysRevD.98.063001 is OK
- 10.3847/1538-4365/ab06fc is OK
- 10.7935/GT1W-FZ16 is OK
- 10.1016/j.softx.2020.100634 is OK
- 10.1093/mnras/staa278 is OK
- 10.1103/PhysRevD.72.102002 is OK
- 10.3847/1538-4357/ab20cb is OK
- 10.1051/0004-6361/200912222 is OK
- 10.1080/01621459.1982.10477856 is OK
- 10.3847/1538-4357/abe62f is OK
- 10.1111/j.1365-2966.2006.10302.x is OK
- 10.1088/1742-6596/610/1/012021 is OK
- 10.1016/j.softx.2021.100658 is OK
- 10.1103/PhysRevD.95.062002 is OK
- 10.1146/annurev-astro-082214-122339 is OK
- 10.1002/cpe.938 is OK
- 10.1038/s43586-022-00121-x is OK
- 10.3847/1538-4357/aa677f is OK
- 10.3847/2041-8213/abb655 is OK
- 10.1103/PhysRevD.102.123027 is OK
- 10.1017/pasa.2015.35 is OK
- 10.48550/arXiv.2111.13106 is OK
- 10.1016/j.softx.2021.100765 is OK
- 10.1088/1742-6596/78/1/012057 is OK
- 10.48550/arXiv.2206.06447 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-09-29T17:44:26Z

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

dfm · 2022-09-29T17:47:38Z

@openjournals/dev — There's an issue with this compiled PDF where the reviewers are listed twice. I think this happened because their usernames were initially saved as all lowercase and I had to re-add them to get the usernames saved properly. I updated the first comment in this thread to remove the duplicate usernames, but the generated PDF still has the lowercase usernames listed. Should we just accept and fix this post? Or is there something else we can do to fix this in advance? Thanks!

Scratch that - it was an issue with my browser caching the old PDF. Looks good now!

dfm · 2022-09-29T17:49:21Z

@editorialbot recommend-accept

editorialbot · 2022-09-29T17:49:23Z

Attempting dry run of processing paper acceptance...

dfm · 2022-09-29T17:50:07Z

@mattpitkin — I've now handed this off to the managing editors who may have some final edits before publication. Thanks for your submission and your responses to the reviewers!!

@GregoryAshton, @ColmTalbot — Thanks again for your reviews!!

editorialbot · 2022-09-29T17:50:58Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3566, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2022-09-29T17:50:59Z

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

OK DOIs

- 10.1086/428488 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.00538 is OK
- 10.21105/joss.00024 is OK
- 10.1016/j.softx.2021.100657 is OK
- 10.48550/arXiv.1705.08978 is OK
- 10.1103/PhysRevD.98.063001 is OK
- 10.3847/1538-4365/ab06fc is OK
- 10.7935/GT1W-FZ16 is OK
- 10.1016/j.softx.2020.100634 is OK
- 10.1093/mnras/staa278 is OK
- 10.1103/PhysRevD.72.102002 is OK
- 10.3847/1538-4357/ab20cb is OK
- 10.1051/0004-6361/200912222 is OK
- 10.1080/01621459.1982.10477856 is OK
- 10.3847/1538-4357/abe62f is OK
- 10.1111/j.1365-2966.2006.10302.x is OK
- 10.1088/1742-6596/610/1/012021 is OK
- 10.1016/j.softx.2021.100658 is OK
- 10.1103/PhysRevD.95.062002 is OK
- 10.1146/annurev-astro-082214-122339 is OK
- 10.1002/cpe.938 is OK
- 10.1038/s43586-022-00121-x is OK
- 10.3847/1538-4357/aa677f is OK
- 10.3847/2041-8213/abb655 is OK
- 10.1103/PhysRevD.102.123027 is OK
- 10.1017/pasa.2015.35 is OK
- 10.48550/arXiv.2111.13106 is OK
- 10.1016/j.softx.2021.100765 is OK
- 10.1088/1742-6596/78/1/012057 is OK
- 10.48550/arXiv.2206.06447 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon · 2022-09-29T21:24:40Z

@editorialbot accept

editorialbot · 2022-09-29T21:24:41Z

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

editorialbot · 2022-09-29T21:26:29Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-09-29T21:26:29Z

🚨🚨🚨 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.04568 joss-papers#3571
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04568
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-09-29T21:29:07Z

@GregoryAshton, @ColmTalbot – many thanks for your reviews here and to @dfm for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@mattpitkin – your paper is now accepted and published in JOSS ⚡🚀💥

editorialbot · 2022-09-29T21:29:08Z

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

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editorialbot added Cython Jupyter Notebook Python review labels Jul 15, 2022

editorialbot assigned dfm Jul 15, 2022

editorialbot mentioned this issue Jul 15, 2022

[PRE REVIEW]: CWInPy: a Python package for inference with continuous gravitational-wave signals from pulsars #4476

Closed

editorialbot assigned GregoryAshton Jul 22, 2022

mattpitkin added a commit to cwinpy/cwinpy that referenced this issue Jul 26, 2022

Fix typo in summary - refs openjournals/joss-reviews#4568 (comment)

07d3fc0

mattpitkin added a commit to cwinpy/cwinpy that referenced this issue Jul 26, 2022

Add info on parameter file specification - refs openjournals/joss-rev…

55b05f8

…iews#4568 (comment)

mattpitkin added a commit to cwinpy/cwinpy that referenced this issue Jul 26, 2022

Add info to paper on parameter file specification - refs openjournals…

3e81820

…/joss-reviews#4568 (comment)

mattpitkin added a commit to cwinpy/cwinpy that referenced this issue Jul 26, 2022

Add info on parameter file specification - refs openjournals/joss-rev…

008bf76

…iews#4568 (comment)

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 29, 2022

editorialbot added accepted published Papers published in JOSS labels Sep 29, 2022

arfon closed this as completed Sep 29, 2022

editorialbot mentioned this issue Dec 26, 2023

[PRE REVIEW]: KerrGeoPy: A Python Package for Computing Timelike Geodesics in Kerr Spacetime #6172

Closed

editorialbot mentioned this issue Aug 27, 2024

[PRE REVIEW]: GWPopulation: Hardware agnostic population inference for compact binaries and beyond #7147

Open

This was referenced Nov 18, 2024

[PRE REVIEW]: CompactObject: An open-source Python package for full-scope neutron star equation of state inference #7487

Open

[PRE REVIEW]: QhX: A Python package for periodicity detection in red noise #7516

Open

[REVIEW]: CWInPy: a Python package for inference with continuous gravitational-wave signals from pulsars #4568

[REVIEW]: CWInPy: a Python package for inference with continuous gravitational-wave signals from pulsars #4568

Comments

editorialbot commented Jul 15, 2022 • edited by dfm Loading

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GregoryAshton commented Jul 22, 2022 • edited Loading

Review checklist for @GregoryAshton

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

GregoryAshton commented Jul 25, 2022

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editorialbot commented Jul 15, 2022 •

edited by dfm

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edited

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edited

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