swiftgalaxy

[kyleaoman]

Submitting Author: @kyleaoman
All current maintainers: @kyleaoman
Package Name: swiftgalaxy
One-Line Description of Package: Load in particles of a simulated galaxy, rotate coordinates, easy spherical/cylindrical coordinates, access integrated properties, and more.
Repository Link: https://github.com/SWIFTSIM/swiftgalaxy
Version submitted: 2.1.1
EiC: @coatless
Editor: @crhea93
Reviewer 1: @blakeaw
Reviewer 2: @steventgk
Archive: TBD
JOSS DOI: TBD
Version accepted: TBD
Date accepted (month/day/year): TBD

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Description

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SWIFTGalaxy is a module that extends SWIFTSimIO tailored to analyses of particles belonging to individual simulated galaxies. It inherits from and extends the functionality of the SWIFTDataset. It understands the content of halo catalogues (supported: Velociraptor, Caesar, SOAP) and therefore which particles belong to a galaxy or other group of particles, and its integrated properties. The particles occupy a coordinate frame that is enforced to be consistent, such that particles loaded on-the-fly will match e.g. rotations and translations of particles already in memory. Intuitive masking of particle datasets is also enabled. Finally, some utilities to make working in cylindrical and spherical coordinate systems more convenient are also provided.

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  • Who is the target audience and what are scientific applications of this package? The package is for scientists analysing SWIFT simulations of galaxies. It facilitates extracting a subset of a simulation containing many galaxies that corresponds to a single galaxy and manipulating the data.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ? pynbody has some points in common, but swiftgalaxy is specifically designed for SWIFT simulations by (i) using swiftsimio as a backend and (ii) having features that leverage the particular data layout and metadata annotations of SWIFT outputs.

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[coatless]

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Editor comments

Given the astronomy nature of this package, would you like to also pursue Astropy as well?

Please address the following:

Package Dependency

Please emphasize the requirement for NumPy >= 2.0

https://github.com/SWIFTSIM/swiftgalaxy/blob/c79cd0f190f052f021313000c56c432f3d4740a5/pyproject.toml#L20

README

Please add installation instructions:

https://www.pyopensci.org/python-package-guide/documentation/repository-files/readme-file-best-practices.html#installation-instructions

Please show a brief example of the package in action:

https://www.pyopensci.org/python-package-guide/documentation/repository-files/readme-file-best-practices.html#brief-demonstration-of-how-to-use-the-package

Please add a community section:

https://www.pyopensci.org/python-package-guide/documentation/repository-files/readme-file-best-practices.html#a-community-section-with-links-to-contributing-guide-code-of-conduct

Please add a section that links to the gallery/alternative tutorials.

https://www.pyopensci.org/python-package-guide/documentation/repository-files/readme-file-best-practices.html#descriptive-links-to-package-documentation-short-tutorials

Please update the repository information to add the readthedocs webpage.

https://swiftgalaxy.readthedocs.io/en/latest/

Should be here:

https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/classifying-your-repository-with-topics#adding-topics-to-your-repository

(Sorry, there's only a "topics" help page for showing this... But, it's in the same location!)

Package website

Please try to organize the landing page with:

https://www.pyopensci.org/python-package-guide/documentation/write-user-documentation/get-started.html#four-elements-of-a-good-open-source-documentation-landing-page

Example: https://www.fatiando.org/verde/latest/

Please consider placing tutorials under a clear website section, c.f.

https://www.pyopensci.org/python-package-guide/documentation/write-user-documentation/create-package-tutorials.html#sphinx-gallery

Example: https://www.fatiando.org/verde/latest/gallery/index.html#

Or, see the "User Guide" portion on the left hand side bar.

Please make available a way to obtain example data, e.g. snap.hdf5. This could be through a function or a simple bash script that could be run by a user to download and setup the data in an expected format.

https://swiftgalaxy.readthedocs.io/en/latest/getting_started/index.html#quick-start

Action

Please take the necessary steps to address the README file and website requirements. We cannot send the package onto a later stage until these issues are addressed as our reviewers and your future users will need to be able to more easily navigate the documentation.

[hamogu]

This package seems to be astronomy-focussed and the source code does have astropy as a dependency. So, I wonder if it makes sense to treat this as an astropy/astronomy related package; to me it looks like that would make sense, but the authors have not set the tick-box for "astropy community".

@kyleaoman: Just checking if that's intentional or should we add it?

[kyleaoman]

@hamogu As far as I understand the astropy community packages look for use of astropy features where this is relevant, which is not really the case for this package. For example, astropy.units enables attaching physical units to arrays, so I think that it would be expected that a community package uses this. However, swiftgalaxy uses the unyt package from the yt project for physical units, so doesn't really fit into the astropy ecosystem in this sense. There are options to convert to astropy Quantity arrays if a user wants to pass output to an astropy-affiliated package (this is part of where the dependency comes in), but the connection feels weak so I left the box un-ticked. It's a similar story for other aspects such as coordinate arrays.

[hamogu]

Great, thanks for the fast reply; I agree. I just wanted to check to make sure we don't overlook it!

[coatless]

@kyleaoman thank you for the clarifications!

[kyleaoman]

Just so I can keep track:

• Please emphasize the requirement for NumPy >= 2.0
• Please add installation instructions
• Please show a brief example of the package in action
• Please add a community section
• Please add a section that links to the gallery/alternative tutorials
• Please update the repository information to add the readthedocs webpage
• Please try to organize the landing page following best practice
• Please consider placing tutorials under a clear website section, c.f.
• Or, see the "User Guide" portion on the left hand side bar.
• Please make available a way to obtain example data, e.g. snap.hdf5. This could be through a function or a simple bash script that could be run by a user to download and setup the data in an expected format.

[kyleaoman]

@coatless I think that I've addressed all of your requested changes now! I edited the submitted version to 2.1.1, just made a release including the updates.