software-submission GALFITools: a library for GALFIT

Submitting Author: (@canorve) All current maintainers: (@canorve) Package Name: GALFITools One-Line Description of Package: A library for efficient data processing customized for the GALFIT package Repository Link: https://github.com/canorve/GALFITools Version submitted: v1.15.0 EiC: @SimonMolinsky, @coatless Editor: @hamogu
Reviewer 1: @Jammy2211 Reviewer 2: @ tepickering
Archive: https://zenodo.org/records/17010007 JOSS DOI: TBD Version accepted: 1.18.0 Date accepted (month/day/year): 10/30/2025

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Description

Include a brief paragraph describing what your package does:

GALFIT, a well-established two-dimensional image fitting algorithm (Peng et al. 2002, AJ, 124, 266), is integral to precise modeling of galaxy surface brightness in astronomical images. To optimize GALFIT's utility, GALFITools provides a suite of Python routines that streamline input and output parsing for enhanced efficiency and usability.

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- [ ] Data retrieval
- [x] Data extraction
- [x] Data processing/munging
- [ ] Data deposition
- [ ] Data validation and testing
- [x] Data visualization[^1]
- [ ] Workflow automation
- [ ] Citation management and bibliometrics
- [ ] Scientific software wrappers
- [ ] Database interoperability

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[ ] Geospatial
[ ] Education

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For all submissions, explain how and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each):

GALFITools enhances functionality with a range of features, including mask creation, PSF generation, initial parameter estimation, galaxy image model visualizaton, multigaussian expansion (MGE) fitting, and calculation of sky background along with other key photometric parameters.

Who is the target audience and what are scientific applications of this package?
This a tool for astronomers to streamline image data processing and enhance interpretation of GALFIT outputs
Are there other Python packages that accomplish the same thing? If so, how does yours differ? No, similar tools act as GALFIT wrappers but focus on different objectives, such as automating GALFIT for large galaxy samples.
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Dec 07 '24 00:12 canorve

Editor in Chief checks

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Editor comments

@canorve I've checked your package and have two issues that should be addressed before we assign the editor and reviewers:

You have provided documentation, but I see only raw rst files. Have you built docs somewhere? Do you have a link to the build docs? Here is the guide that might help you: https://www.pyopensci.org/python-package-guide/documentation/hosting-tools/intro.html
Are your tests automated? Have you considered using GitHub Actions for this? Here's an example of how to set up automated tests: https://www.pyopensci.org/python-package-guide/tests/tests-ci.html

We will go forward with the review when you address those two points!

Dec 09 '24 09:12 SimonMolinsky

@canorve

Here are my comments:

I've checked your package and have two issues that should be addressed before we assign the editor and reviewers:

You have provided documentation, but I see only raw rst files. Have you built docs somewhere? Do you have a link to the build docs? Here is the guide that might help you: https://www.pyopensci.org/python-package-guide/documentation/hosting-tools/intro.html
Are your tests automated? Have you considered using GitHub Actions for this? Here's an example of how to set up automated tests: https://www.pyopensci.org/python-package-guide/tests/tests-ci.html We will go forward with the review when you address those two points!

Dec 15 '24 10:12 SimonMolinsky

Hi @canorve

How are you? Could you tell me how updating documentation and automated tests is going?

Feb 03 '25 16:02 SimonMolinsky

Hello @SimonMolinsky,

The documentation and GitHub Actions are new to me, but I'm working on them. The GitHub Actions workflow is already implemented, though I'm not sure if it's working properly. Currently, I'm following the Read the Docs documentation.

Feb 03 '25 19:02 canorve

Dear @SimonMolinsky, I have completed the documentation, which is hosted at GALFITools Documentation.

Additionally, GitHub Actions for automated tests have been implemented and tested.

I am now ready for feedback on both the documentation and the code

Feb 27 '25 00:02 canorve

Hi @canorve !

Sorry for the delay. I'm not as available as I would like to be! I've checked your docs and found one broken link under here—there is a typo in a link path, with an additional / after .html. Just remove it, and it will work fine.

First of all, install [GALFIT](https://users.obs.carnegiescience.edu/peng/work/galfit/galfit.html) if you haven’t done so. Check instructions [here](https://users.obs.carnegiescience.edu/peng/work/galfit/galfit.html/). Make sure that GALFIT can run in any path in your linux/macOS terminal.

GitHub Actions work, your documentation, especially the API description, is ready, and you have fulfilled all EiC checks. We can move forward with the review!

Mar 11 '25 08:03 SimonMolinsky

Don't worry, I appreciate your time in reviewing it. Thanks for informing me about the broken link; it has now been corrected.

Mar 11 '25 21:03 canorve

hi colleagues! I noticed this has the astropy check on it. I"ve alerted the current astropy editors of that fact so it can be considered for astropy affiliation in the review. Someone from the astropy editorial team will be in touch about the next steps. 🚀

@SimonMolinsky thank you so much for continuing to work on this submission 💓 You are so appreciated here.

Mar 14 '25 17:03 lwasser

@SimonMolinsky I'll handle this submission going forward. Thank you again for everything!

@canorve sorry for the delay in moving this forward. I've gone ahead and assigned @hamogu as the editor for the submission as it meets all of our requirements.

I will note that there are scientific similarities with PyAutoGalaxy that is also now under review; but, fundamentally the software is different in the underlying implementation and front facing uses.

Apr 14 '25 06:04 coatless

Editor response to review:

Hi @SimonMolinsky ! Thanks for submitting your package to PyOpenSci. I'll be your editor - please feel free to reach out to me with any questions you might have. I'll now start to look for reviewers; usually that's the most time-consuming part of the process but I'll keep you updated as that goes along!

Editor comments

:wave: Hi @Jammy2211 and @tepickering! Thank you for volunteering to review for pyOpenSci!

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Reviewers: @Jammy2211 @tepickering Due date: 11-Jun-2025

Apr 15 '25 02:04 hamogu

@canorve : You indicated that you intend to have this package also submitted to JOSS by setting the tick mark in the submission. As you may know, the review we do will automatically be accepted as the review by JOSS; they will only do some editorial stuff, but not look at the package again. That means that the reviewers here also need to look at the paper.md that JOSS will publish. Could you point us to where we find that paper in your repro? (See links to JOSS documentation in the first post in this thread for details).

Apr 19 '25 11:04 hamogu

Thank you for pointing this out. I will review the JOSS documentation and upload the paper.md file to the repository at my earliest convenience. Once uploaded, I will notify you here.

Apr 20 '25 01:04 canorve

Dear @canorve, I'm just putting a "pending-maintainer-response" label on this issue for now to mark that we are waiting for the paper.md to review before we proceed. No rush - I just want to make sure that people who look at this issue don't get confused why the review has not started yet.

May 02 '25 11:05 hamogu

Dear @hamogu, Thank you for the update. I’ve received the message and appreciate the clarification. I’ll upload the paper.md as soon as possible.

May 02 '25 17:05 canorve

Dear @hamogu, just to let you know that I have uploaded the paper.md file; it is located in the paper folder. I'm sorry for the delay.

May 15 '25 00:05 canorve

@canorve Thanks for letting me know. I'm looking for a second reviewer now so that we can get started!

May 15 '25 13:05 hamogu

@tepickering and @Jammy2211 Thank you so much for volunteering to review this package. It should all be set for you to start looking. Review instructions are linked here https://github.com/pyOpenSci/software-submission/issues/220#issuecomment-2803592850 and please reach out to me with any questions! As is customary, I set the review due date for there weeks from now, but if you run into problems or need more time let me know and we'll work it out.

May 21 '25 11:05 hamogu

I began my review, but after downloading the GALFIT debian64 kernel from the GALFIT home page, when I run it I get this error

./galfit: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory

I have tried other kernels, but no luck.

ChatGPT suggests I could down a route of changing my libncurses installation, but I have had issues with my windows subsystem for linux breaking when I start to change random libraries.

The alternative would be to try build GALFIT from source, but this would again require me to touch C libraries that I would rather not risk breaking.

I doubt there is a simple fix, so I see two ways forward:

I complete the review without actually running GALFITools, which is not ideal but is probably something I can get most of the way there.
You find another reviewer who (hopefully) has the hardware to run GALFIT.

If there is a fix which doesn't require me to risk running sudo apt install something I would be happy to try that.

Jun 13 '25 09:06 Jammy2211

@canorve Do you have a suggestion? If not, I would also @Jammy2211 to review as good as you can (documentation and JOSS paper for example don't depend on actually installing it) and I will install it and do a partial review myself to be added to that.

Jun 13 '25 10:06 hamogu

now that the AAS is over i'll finally have some time to devote to this. would it be helpful to set up a docker container with galfit and GALFITools installed? that would work around having to match the various dependencies on one's local machine, at least for review purposes.

Jun 13 '25 19:06 tepickering

I don't think there's an easier fix than running sudo apt install libncurses-dev If it's helpful, GALFIT is only invoked when the makePSF function is used; the rest of GALFITools does not depend on it.

Jun 13 '25 23:06 canorve

I attach my review below, as discussed above the vast majority of functionality did not actually require GALFIT and simply ran off of GALFIT results files, so I was able to go through the majority of code without issue.

Package Review

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Final approval (post-review)

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

Estimated hours spent reviewing:

3

Review Comments

My main critique is that the package assumes the user has a lot of Astronomy experience and knowledge in terms of how its documented and phrased.

For example, the documentation for the MGE reads as follows:

Routines that use the Multi-Gaussian Expansion.

mge2galfit fits multi-gaussian expansion of Cappellari (2002) and formats to GALFIT

positional arguments:
  GalfitFile            GALFIT file to obtain the header options
  Ds9regFile            the DS9 ellipse region file containing the galaxy

options:
  -h, --help            show this help message and exit
  -t, --twist           uses twist option for mge
  -c, --center          uses the center given in DS9 region file,otherwise it will found the x,y peak within DS9
                        ellipse
  -p PSF, --psf PSF     the value of PSF sigma
  -gas, --gauss         uses gauss function for galfit file
  -fser, --freeser      leaves the sersic index as a free parameter to fit
  -fsk, --freesky       leaves the sky as a free parameter to fit
  -ng NUMGAUSS, --numgauss NUMGAUSS
SbProf creates a surface brightness profile from a ellipse ds9 region

positional arguments:
  Image                 image fits file
  Ds9Region             Ds9 ellipse region file

options:
  -h, --help            show this help message and exit
  -q AXRAT, --axrat AXRAT
                        axis ratio
  -pa ANGLE, --angle ANGLE
                        angular position (same as GALFIT)
  -mz MGZPT, --mgzpt MGZPT
                        Magnitud zero point
  -m MASK, --mask MASK  mask fits file
  -s SKY, --sky SKY     sky value. Default = 0
  -p PLATE, --plate PLATE
                        plate scale
  -o OUTPUT, --output OUTPUT
                        output file
  -c, --center          uses the center given in DS9 region file,otherwise it will found the x,y
                        peak within DS9 ellipse
  -rx RANX RANX, --ranx RANX RANX
                        provide a range for x-axis: xmin - xmax
  -ry RANY RANY, --rany RANY RANY
                        provide a range for y-axis: ymin - ymax
  -lx, --logx           turn the X-axis to logarithm
  -px, --pix            turn the top x-axis in pixels
  -g, --grid            display a grid in the plot
  -r RAD, --rad RAD     value for a vertical line to add into the plot
  -r2 RAD2, --rad2 RAD2
                        value for a second vertical line to add into the plot

The documentation above, as far as I can tell, is essentially assuming one has used mgefit before and knows what a Multi Gaussian Expansion is.

For users who are not already familiar with a specific set of Astronomy tools (including things like DS9) I think it is quite difficult for one to get their head around what the correct inputs of GALFITools are in many cases.

Another example is this one:

getKappa2 gets the kappa radius from a set of Sersics using an alternative method to getKappa

positional arguments:
  GalfitFile            Galfit File containing the Sersics or gaussians components

options:
  -h, --help            show this help message and exit
  -d DIS, --dis DIS     Maximum distance among components
  -n NUMCOMP, --numcomp NUMCOMP
                        Number of component where it'll obtain center of all components, default = 1
  -a ANGLE, --angle ANGLE
                        Angle of the major axis of the galaxy. Default= it will take the angle of the
                        last components
  -p, --plot            makes plot of double derivative vs. radius
  -rx RANX RANX, --ranx RANX RANX
                        x-axis range to search for the Break radius: xmin - xmax

I don't know what the kappa radius is, I dont know why there is an alternative method to compute it and I don't know what that method does.

I am assuming this package is aimed at people who use a specific set of tools with known conventions and definitions within Astronomy, and that the package essentially acts as a streamlined interface for performing those calculations.

This may be fine and within the scope of a standalone software package, but for someone who only touched GALFIT a few times 10 years ago and hasn't used tools like DS9, I found it difficult to understand what a lot of the functionality does.

I am not sure what to suggest, on the one hand the documentation could be expanded to make this more accessible to a user who is unfamiliar with many of these tools. On the other hand, the package is targeting those with familiarity so the concise nature of the docs may be fine. Nevertheless, I raise here my experience and will see what others think.

I can’t see the statement of need in the docs, only the JOSS paper has one, maybe move it to here: https://galfitools.readthedocs.io/en/latest/index.html
Please include the supported Python versions (e..g. 3.10 - 3.12 ?) in the installation instructions.
The link to “install GALFIT” on the installation page goes to the FAQ, which has no installation instructions. Link here instead: https://users.obs.carnegiescience.edu/peng/work/galfit/galfit.html
Instructions on needing to install pytest-cov for unit testing.

Jun 17 '25 10:06 Jammy2211

My review was done using an Apple M1 platform running Sequoia 15.5. The galfit binary for "Mavericks" works fine using Apple's Rosetta x86_64 emulation and I was able to run through the galfit examples.

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

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The package includes all the following forms of documentation:

[X] A statement of need clearly stating problems the software is designed to solve and its target audience in README.
[X] Installation instructions: for the development version of the package and any non-standard dependencies in README.
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[X] Function Documentation: for all user-facing functions.
[X] Examples for all user-facing functions.
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[X] Package has a README.md file in the root directory.

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[X] The package name
[X] Badges for:
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- [ ] A repostatus.org badge,
- [ ] Python versions supported,
- [X] 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.)

[X] Short description of package goals.
[X] Package installation instructions
[X] Any additional setup required to use the package (authentication tokens, etc.)
[X] 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.
- [X] Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
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[ ] If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
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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:

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

Functionality

[X] Installation: Installation succeeds as documented.
[X] Functionality: Any functional claims of the software been confirmed.
[X] Performance: Any performance claims of the software been confirmed.
[X] Automated tests:
- [X] All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
- [X] Tests cover essential functions of the package and a reasonable range of inputs and conditions.
[X] Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)
[X] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines. A few notable highlights to look at:
- [X] Package supports modern versions of Python and not End of life versions.
- [X] Code format is standard throughout package and follows PEP 8 guidelines (CI tests for linting pass)

For packages also submitting to JOSS

[X] 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:

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

Final approval (post-review)

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

Estimated hours spent reviewing: 3

Review Comments

I found the statement of need to be sufficient because the package has a very specific target audience: the users of galfit. As such, some prior knowledge of galfit and its capabilities can be assumed. A significant background in astronomy and astronomical image analysis is a prerequisite for effectively using galfit and interpreting its results. The same prerequisite applies to this package.
The link to the datafile used for the example, galfit.01, points to a file within the repository tree. As it's currently linked, it is a multi-step process to download into a usable format. One option would be to use a link to the raw file, e.g. https://raw.githubusercontent.com/canorve/GALFITools/refs/heads/master/docs/galfit.01, which would facilitate right-click->"save as", or include the file within the documentation tree and serve from RTD.
The links to the "Module Reference", "Usage guide", and "API Reference" are kinda buried at the bottom of the documentation index page. It would be nice to feature them more prominently so they're easier to find, e.g. in the "Documentation" section which currently only links recursively back to the main page.
The README includes instructions for installation via pip and the instructions for installing a development version are in the documentation under "Contributing". I think this is fine and allows the developer instructions to be more detailed.
Several requested badges are missing.
I tested locally under python 3.13 and everything passed. I would recommend adding 3.13 to the CI test matrix.

My comments are all relatively minor and overall the package works very well for me. It's something I wish I had access to back when I was working on galaxy surface photometry long before even galfit existed...

Jun 17 '25 23:06 tepickering

Thank you for your helpful comments. I will address them as soon as possible

Jun 19 '25 00:06 canorve

Hello, I have released v1.18.0 and will reply to the reviewers’ comments below.

Sep 04 '25 14:09 canorve

Dear reviewer @Jammy2211 :

My main critique is that the package assumes the user has a lot of Astronomy experience and knowledge in terms of how its documented and phrased ...

We have added a new Concepts section in the documentation, which includes a primer on key concepts, GALFIT example file, inline definitions of terms, and a brief Audience statement on the main page. We also reduced the use of jargon and added cross-links to definitions. For each concept, we now provide the related API functions and CLI commands directly below, making it easier for users without a deep astronomy background to navigate the package.

I can’t see the statement of need in the docs, only the JOSS paper has one, maybe move it to here: https://galfitools.readthedocs.io/en/latest/index.html

I have added a clear Statement of Need to the index page of the documentation, adapted from the JOSS paper, so that new users can immediately understand the motivation for GALFITools.

Please include the supported Python versions (e..g. 3.10 - 3.12 ?) in the installation instructions.

The supported Python versions (3.10–3.13) have been added to the installation instructions.

The link to “install GALFIT” on the installation page goes to the FAQ, which has no installation instructions. Link here instead: https://users.obs.carnegiescience.edu/peng/work/galfit/galfit.html

I have updated the installation page so that the link now points to the installation file added to the project’s GitHub repository. The guide provides step-by-step instructions and replaces the previous FAQ link.

 Instructions on needing to install pytest-cov for unit testing.

I have updated the contributing/testing instructions (CONTRIBUTING.rst) to specify that pytest-cov is required.

Sep 04 '25 14:09 canorve

Dear reviewer @tepickering :

I found the statement of need to be sufficient because the package has a very specific target audience: the users of galfit. As such, some prior knowledge of galfit and its capabilities can be assumed. A significant background in astronomy and astronomical image analysis is a prerequisite for effectively using galfit and interpreting its results. The same prerequisite applies to this package.

Thank you. The statement of need has also been included in the documentation, with slight modifications for clarification.

The link to the datafile used for the example, galfit.01, points to a file within the repository tree. As it's currently linked, it is a multi-step process to download into a usable format. One option would be to use a link to the raw file, e.g. https://raw.githubusercontent.com/canorve/GALFITools/refs/heads/master/docs/galfit.01, which would facilitate right-click->"save as", or include the file within the documentation tree and serve from RTD.

The link to galfit.01 has been updated so that it now points directly to the raw file, allowing immediate download.

The links to the "Module Reference", "Usage guide", and "API Reference" are kinda buried at the bottom of the documentation index page. It would be nice to feature them more prominently so they're easier to find, e.g. in the "Documentation" section which currently only links recursively back to the main page.

I have moved the "Module Reference" and "Usage Guide" to a more prominent location in the documentation index to make them easier to find.

Several requested badges are missing.

I have added the remaining requested badges to the README.

I tested locally under python 3.13 and everything passed. I would recommend adding 3.13 to the CI test matrix.

Python 3.13 has been added to the CI test matrix.

Sep 04 '25 14:09 canorve

@tepickering and @Jammy2211: Thanks for your thorough review and good suggestions and to @canorve for addresses them; It hope the team found it all useful!

@tepickering and @Jammy2211: Can you take a look at the changes to the package and see if they address the points you raised in the review? If so, please update the "Final approval (post-review)" in your review and let me know here (I only get a notification from GH if there is a new comment, not if an old comment is updated); if not we welcome your feedback what else can be improved!

Sep 21 '25 12:09 hamogu

@tepickering and @Jammy2211: Can I ping you again to take a look at the changes to the package and see if they address the points you raised in the review? Your approval (or any further points you might see in the responses) is essentially all that's required for package approval at this point!

Oct 29 '25 16:10 hamogu

sorry! yes, the changes all look good to me. sorry to hang up the approval process...

Oct 29 '25 18:10 tepickering