ZodiPy

Question

ZodiPy

Closed this issue 8 months ago · 27 comments

Thanks!

Answer 1 · 2024-02-28T01:01:13.000Z

Editor in Chief checks

Hi there! Thank you for submitting your package for pyOpenSci
review. Below are the basic checks that your package needs to pass
to begin our review. If some of these are missing, we will ask you
to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements
below.

Initial onboarding survey was filled out
We appreciate each maintainer of the package filling out this survey individually. 🙌
Thank you authors in advance for setting aside five to ten minutes to do this. It truly helps our organization. 🙌

Editor comments

Hello there and welcome to the pyOpenSci universe (apologies for the bad pun 😂🌟)! We're happy you're here. I've done a quick overview of the zodipy package, and you are in great shape! There are a few things we will need before we start with your review:

Please add a CODE_OF_CONDUCT.md to the root of your repository. For more information, pyOpenSci's packaging guide has some examples and information on CoC files.
Please add a CONTRIBUTING.md to the root of your repository. For more information, pyOpenSci's packaging guide has some templates and information on CONTRIBUTING files.
I'll also nudge each maintainer (so, @MetinSa @dncnwtts) to fill out our onboarding survey.

Let us know when you've made these updates. I'll also use this message to introduce your editor-- @dhomeier will be helping you all through the review process 🎉 Thanks for taking on this role Derek!

Answer 2 · 2024-02-28T11:37:26.000Z

Hi! 👋

I have now added a CODE_OF_CONDUCT.md and a CONTRIBUTING.md to the repository aswell as having filled out the survey. I also added @hermda02 as a maintainer of the project.

Answer 3 · 2024-03-21T21:38:11.000Z

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

A statement of need clearly stating problems the software is designed to solve and its target audience in README.
Installation instructions: for the development version of the package and any non-standard dependencies in README. (Reviewer note: Cosmoglobe/zodipy#4 and Cosmoglobe/zodipy#10)
Vignette(s) demonstrating major functionality that runs successfully locally.
Function Documentation: for all user-facing functions.
Examples for all user-facing functions.
Community guidelines including contribution guidelines in the README or CONTRIBUTING.
Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements
The package meets the readme requirements below:

Package has a README.md file in the root directory.

The README should include, from top to bottom:

The package name
Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website) (Reviewer note: Cosmoglobe/zodipy#5),
- A repostatus.org badge (Reviewer note: Cosmoglobe/zodipy#6),
- Python versions supported (Reviewer note: Cosmoglobe/zodipy#7),
- Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

Short description of package goals.
Package installation instructions
~~Any additional setup required to use the package (authentication tokens, etc.)~~ (Reviewer note: N/A)
Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
Link to your documentation website.
If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem. (Reviewer note: I do not know enough about zodiacal light community to check off this one.)
Citation information

Usability

Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole.
Package structure should follow general community best-practices. In general please consider whether:

Package documentation is clear and easy to find and use.
The need for the package is clear
All functions have documentation and associated examples for use
The package is easy to install

Functionality

For packages also submitting to JOSS

The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

A short summary describing the high-level functionality of the software
Authors: A list of authors with their affiliations
A statement of need clearly stating problems the software is designed to solve and its target audience.
References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 4

Astropy-specific

Relevance to astronomy/astrophysics:
- Out of scope: Not useful for astronomers, or specific to one project/collaboration. (This is a basis for rejection.)
- Specialized package: Useful to astronomers working in a very specific domain/field, or with a specific telescope instrument and usable not just by a single collaboration but any astronomers within that domain. Packages such as sncosmo fall into this category.
- General package: Package that is useful for astronomers across more than a single field/instrument/telescope. Packages such as astroquery or astroplan fall into this category.
Integration with Astropy ecosystem:
- No integration: Does not use Astropy or other Astropy Affiliated packages anywhere where it should be possible, and/or uses other libraries instead, or unnecessarily duplicates functionality found in Astropy or other Astropy Affiliated packages. (This is a basis for rejection.)
- Partial integration: Makes an effort to use Astropy or other Astropy Affiliated packages in places, but still has other places where this could be done.
- Good integration: Uses Astropy or other Astropy Affiliated packages wherever possible. Where not, there are good reasons not to.
  For specific actionable items, reviewer or editor are free to open issues on the package repository directly and link them

Review Comments

~~I skipped the JOSS section because I don't see a paper.md and so assume this package isn't asking for JOSS listing also.~~

2024-04-16: I updated the JOSS section but left References unchecked because paper.md has empty section for that part.

This package is already in Astropy's pre-APE 22 legacy listing over at https://www.astropy.org/affiliated/legacy.html via astropy/astropy.github.com#495 .

Answer 4 · 2024-03-22T13:20:44.000Z

I'm sorry, I had forgotten about the JOSS section but would very much like a JOSS listing. I will start working on a paper.md.

Answer 5 · 2024-03-22T13:25:48.000Z

@MetinSa , thanks for going through Astropy's old process and then again with this one. Your patience and dedication is greatly appreciated.

Answer 6 · 2024-04-10T15:41:29.000Z

Apologies for the delay. I have now added a paper directory containing the paper.md file for the JOSS listing.

Answer 7 · 2024-04-16T19:13:11.000Z

How long does a typical JOSS submission and review process take in this context?

Answer 8 · 2024-04-16T19:40:03.000Z

FYI -- I have updated the checkboxes for JOSS at #161 for my part of the review.

p.s. I never submitted anything to JOSS before so I cannot answer the questions about JOSS timeline. Hopefully others can. Thanks for your patience!

Answer 9 · 2024-04-17T16:27:55.000Z

hi 👋 i can help here. it's normally quick IF the submittor makes it clear when the package is submitted that:

The package has already been reviewed and accepted by pyOpenSci
Links to this review here to make it easier for the editor to see this is a fast track
The editor for this review reminds the JOSS editor that this is a fast tracked submission (which means that no code needs to be re-reviewed). All they have to do is a) check for scope and b) review your paper.

I've seen this go wrong when there is confusion regarding the fast track part and then things take a bit longer. but otherwise it should be a few weeks if the JOSS editor follows the process and the pyOS editor kind of keeps an eye on things ! i hope that helps.

Answer 10 · 2024-04-17T17:00:10.000Z

Thank you for the updates and apologies for the delays in reviewing; getting reviewers with the topical expertise for Astropy into the system is a prolonged process!

Answer 11 · 2024-04-18T18:37:10.000Z

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

A statement of need clearly stating problems the software is designed to solve and its target audience in README.
Installation instructions: for the development version of the package and any non-standard dependencies in README.
Vignette(s) demonstrating major functionality that runs successfully locally.
Function Documentation: for all user-facing functions.
Examples for all user-facing functions.
Community guidelines including contribution guidelines in the README or CONTRIBUTING.
Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements
The package meets the readme requirements below:

Package has a README.md file in the root directory.

The README should include, from top to bottom:

The package name
Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website),
- A repostatus.org badge,
- Python versions supported,
- Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

Short description of package goals.
Package installation instructions
Any additional setup required to use the package (authentication tokens, etc.)
Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
Link to your documentation website.
If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
Citation information

Usability

Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole.
Package structure should follow general community best-practices. In general please consider whether:

Package documentation is clear and easy to find and use.
The need for the package is clear
All functions have documentation and associated examples for use
The package is easy to install

Functionality

For packages also submitting to JOSS

The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

A short summary describing the high-level functionality of the software
Authors: A list of authors with their affiliations
A statement of need clearly stating problems the software is designed to solve and its target audience.
References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 2 (includes original review as an Astropy affiliated package)

Review Comments

Mostly reproduced from my Astropy affiliated package review.

ZodiPy looks like a very healthy package. Here are some spots where there is room for improvement.

It could have much more integration with Astropy core and Astropy affiliated packages. Aside from Astropy units, the public API does not have much integration with Astropy. Here are some issues:

The get_emission_ang method basically depends on two coordinates that define the ray from the observer to the direction in which they are looking (plus a time and a wavelength). The vertex of the ray can be specified in Cartesian coordinates and the direction of the ray in polar coordinates. Internally, the method instantiates SkyCoord objects in order to do positional astronomy calculations. It would be ideal if the user could specify both coordinates using SkyCoord instances. That would unify 5 arguments (theta, phi, obs, obs_pos, lonlat) into only two.
Conversion between coordinate frames is done using healpy.Rotator but could be done more simply and idiomatically with SkyCoord frame transformations.
There is a synthetic photometry feature to integrate the observed flux over a bandpass. ZodiPy could employ the Astropy affiliated package synphot here.
ZodiPy can evaluate the emission on HEALPix maps, but uses healpy to do this. It could use the Astropy affiliated package astropy-healpix here.
ZodiPy can plot emission components on all-sky maps, but uses healpy to do this. It could use reproject + astropy-healpix here for more flexible plotting.

The approaches to Numpy vectorization and Python multiprocessing parallelism are somewhat fixed function, and may not be performant for all use cases.

Methods do not support Numpy broadcasting for arbitrary input shapes. For example, it appears that obs_time must be scalar. For another, this line in get_obs_and_earth_positions discards the shape of the input arguments:

return obs_position.reshape(3, 1, 1).value, earth_position.reshape(3, 1, 1).value
ZodiPy supports parallelism using Python multiprocessing, but it creates its own process pool and discards it when it is done. It would be nice if it supported the pool being passed by the user so that the cost of spawning child Python interpreters is not borne repeatedly. Also there are situations where it is necessary to use a custom Pool subclass (e.g. billiard, https://pypi.org/project/billiard/).

Deviations from pyOpenSci packaging guidelines:

Needs a conda-forge package.
The value of the license in the project metadata (tool.poetry.license) is not an SPDX license identifier. Please set it to either of the allowed values, GPL-3.0-only or GPL-3.0-or-later.
Consider adding more project URLs (project.urls section in pyproject.toml). For project URL names that PyPI displays prominently with icons, see https://github.com/pypi/warehouse/blob/main/warehouse/templates/packaging/detail.html.

Code style

The project uses ruff for code formatting, but it is only run on the module itself. Ruff would make changes to the Python modules in the tests directory. Please consider running ruff on the entire project, including the tests.

Answer 12 · 2024-04-19T09:19:44.000Z

Thank you for the review @lpsinger!

I have made the following changes after going through the review:

Ruff now runs on the entire repository (Cosmoglobe/zodipy@44b3cc0)
The licence is changed to a SPDX license identifier (Cosmoglobe/zodipy@5eb8df7))
The pyproject.toml file now includes urls to the documentation and repository (Cosmoglobe/zodipy@7ae9119)
A PR is open to add ZodiPy as a conda-forge package (conda-forge/staged-recipes#26097)

Additionally, I have opened several issues (see the mentions above) to address your suggestions for improvement and to better integrate ZodiPy with Astropy. I will start working on these as soon as I find the time.

Answer 13 · 2024-04-19T12:13:47.000Z

Thank you for your careful and helpful reviews @pllim and @lpsinger, and for your quick reply @MetinSa!
I'll second the recommendation to include the tests in code style checks, as in a similar attempt in astropy/astropy#16158 we have discovered a number of tests that were not testing exactly the intended functionality.
That should not block acceptance of your package at this time, though.

@pllim I only found one reference, PyEphem, without a DOI in paper.bib, but it does not seem to have one in the ASCL entry either – do you think it should have one?

Answer 14 · 2024-04-19T12:15:35.000Z

I'm not familiar with what JOSS wants in its References section. If it's ok to leave empty, then I'm fine with that. All in all, I don't think it should block acceptance.

Answer 15 · 2024-04-19T12:30:52.000Z

Thank you for the review @lpsinger!

I have made the following changes after going through the review:

You're very welcome! Sorry it took me so long to post it.

I've checked off all of the remaining items in the review template.

Answer 16 · 2024-04-19T12:44:51.000Z

I'm not familiar with what JOSS wants in its References section. If it's ok to leave empty, then I'm fine with that. All in all, I don't think it should block acceptance.

The references are all there in the paper.bib file – I was assuming JOSS would accept a standard LaTeX setup, but not actually sure how it handles it with a .md main text – never mind, this is exactly as prescribed in the Author guide.

Answer 17 · 2024-04-19T13:08:47.000Z

I'm not familiar with what JOSS wants in its References section. If it's ok to leave empty, then I'm fine with that. All in all, I don't think it should block acceptance.

The reference section look all right in this paper draft compiled with the JOSS gh-action.

Answer 18 · 2024-04-19T13:17:34.000Z

Yes, I've checked that off and the reviewers have already checked their final approval.
Just waiting if there is a short term fix for the conda-forge build, but since that is really a healpy issue, it should not block either.

Answer 19 · 2024-04-19T13:38:52.000Z

Ah, sorry I misunderstood how JOSS formatting works. I will check off the References box now (oh nvm, looks like Derek did it for me, thanks!). Thanks for the clarifications!

Answer 20 · 2024-04-19T13:40:21.000Z

I think we better figure out how to list this on our webpage soon? 😬

cc @eteq @lwasser

Answer 21 · 2024-04-19T20:13:15.000Z

Great, with conda-forge succeeding for Linux and macOS, this should be ready for JOSS submission.

🎉 zodipy has been approved by pyOpenSci! Thank you @MetinSa for submitting ZodiPy and many thanks to @pllim and @lpsinger for reviewing this package! 😸

Author Wrap Up Tasks

There are a few things left to do to wrap up this submission:

Activate Zenodo watching the repo if you haven't already done so.
Tag and create a release to create a Zenodo version and DOI.
Add the badge for pyOpenSci peer-review to the README.md. The badge should be [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/issue-number).
Please fill out the post-review survey. All maintainers and reviewers should fill this out.

It looks like you would like to submit this package to JOSS. Here are the next steps:

Once the JOSS issue is opened for the package, we strongly suggest that you subscribe to issue updates. This will allow you to continue to update the issue labels on this review as it goes through the JOSS process.
Login to the JOSS website and fill out the JOSS submission form using your Zenodo DOI. When you fill out the form, be sure to mention and link to the approved pyOpenSci review. JOSS will tag your package for expedited review if it is already pyOpenSci approved.
Wait for a JOSS editor to approve the presubmission (which includes a scope check).
Once the package is approved by JOSS, you will be given instructions by JOSS about updating the citation information in your README file.
When the JOSS review is complete, add a comment to your review in the pyOpenSci software-review repo here that it has been approved by JOSS. An editor will then add the JOSS-approved label to this issue.

🎉 Congratulations! You are now published with both JOSS and pyOpenSci! 🎉

Editor Final Checks

Please complete the final steps to wrap up this review. Editor, please do the following:

Make sure that the maintainers filled out the post-review survey
Invite the maintainers to submit a blog post highlighting their package. Feel free to use / adapt language found in this comment to help guide the author.
Change the status tag of the issue to 6/pyOS-approved6 🚀🚀🚀.
Invite the package maintainer(s) and both reviewers to slack if they wish to join.
If the author submits to JOSS, please continue to update the labels for JOSS on this issue until the author is accepted (do not remove the 6/pyOS-approved label). Once accepted add the label 9/joss-approved to the issue. Skip this check if the package is not submitted to JOSS.
If the package is JOSS-accepted please add the JOSS doi to the YAML at the top of the issue.

If you have any feedback for us about the review process please feel free to share it here. We are always looking to improve our process and documentation in the peer-review-guide.

Answer 22 · 2024-04-19T21:31:26.000Z

🎉🎉 I have completed the Zenodo and pyOpenSci peer-review steps(Cosmoglobe/zodipy@2c03c58, Cosmoglobe/zodipy@b5d0031) and will fill out the post-review survey tomorrow (pre-review survey is filled out already).
Edit: post-review survey is filled out and I have submitted to JOSS referencing this thread and the Zenodo DOI.

Thank you to everyone here for the reviews and all the help:)

Answer 23 · 2024-04-20T10:39:37.000Z

JOSS paper is approved and published https://joss.theoj.org/papers/10.21105/joss.06648!

Answer 24 · 2024-04-23T13:48:39.000Z

Congratulations again @MetinSa to your successful publication with pyOpenSci and JOSS! I'd like to take the opportunity to invite you and your maintainer team to write a blog post (totally optional) on your package for us to promote your work! If you are interested - here are a few examples of other blog posts:

pandera
rdata
SunPy (external blog)

and here is a markdown example that you could use as a guide when creating your post.

It can even be a tutorial-like post that highlights what your package does and how to use it. Then we can share it with people to get the word out about your package.

If you are too busy for this, no worries. But if you have time - we'd love to spread the word about your package!

Answer 25 · 2024-04-25T06:28:59.000Z

Thank you @dhomeier and a big thanks to everyone else involved in the review. I will try to write up a blog post sometime in the future when I find the time.

Answer 26 · 2024-05-13T17:38:26.000Z

Closing the issue as completed as ZodiPy is now listed on https://www.pyopensci.org/python-packages.html

Feel free to follow up with a blog post whenever convenient; also if you wish to join the pyOpenSci Slack space @dncnwtts or @hermda02, you are welcome to send us an email address to be signed up with.

ZodiPy

Code of Conduct & Commitment to Maintain Package

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Scope

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Community Partnerships

Technical checks

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Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

Please fill out our survey

Editor and Review Templates

Editor in Chief checks

Editor comments

Package Review

Documentation

Usability

Functionality

For packages also submitting to JOSS

Final approval (post-review)

Astropy-specific

Review Comments

Package Review

Documentation

Usability

Functionality

For packages also submitting to JOSS

Final approval (post-review)

Review Comments

Author Wrap Up Tasks

Editor Final Checks

Code of Conduct & Commitment to Maintain Package

Description

Scope

Domain Specific

Community Partnerships

Technical checks

Publication Options

Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

Please fill out our survey

Editor and Review Templates

Footnotes

Editor in Chief checks

Editor comments

Package Review

Documentation

Usability

Functionality

For packages also submitting to JOSS

Final approval (post-review)

Astropy-specific

Review Comments

Package Review

Documentation

Usability

Functionality

For packages also submitting to JOSS

Final approval (post-review)

Review Comments

Author Wrap Up Tasks

Editor Final Checks