Repository navigation
Martini #164
Description
Submitting Author: Kyle Oman (@kyleaoman)
All current maintainers: (@kyleaoman)
Package Name: martini
One-Line Description of Package: MARTINI is a modular package for the creation of synthetic resolved HI line observations (data cubes) of smoothed-particle hydrodynamics simulations of galaxies.
Repository Link: https://github.com/kyleaoman/martini
Version submitted: 2.0.11 (note JOSS paper is in branch joss-paper, and that branch is somewhat behind main & 2.0.11)
EiC: @isabelizimm
Editor: @hamogu
Reviewer 1: @taldcroft
Reviewer 2: @MicheleDelliVeneri
Archive: https://zenodo.org/doi/10.5281/zenodo.11193206
JOSS DOI: https://doi.org/10.21105/joss.06860
Version accepted: 2.0.15
Date accepted (month/day/year): 06/03/2024
Code of Conduct & Commitment to Maintain Package
- I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package after should it be accepted.
- I have read and will commit to package maintenance after the review as per the pyOpenSci Policies Guidelines.
Description
MARTINI is a modular package for the creation of synthetic resolved HI line observations (data cubes) of smoothed-particle hydrodynamics simulations of galaxies. The various aspects of the mock-observing process are divided logically into sub-modules handling the data cube, source, beam, noise, spectral model and SPH kernel. MARTINI is object-oriented: each sub-module provides a class (or classes) which can be configured as desired. For most sub-modules, base classes are provided to allow for straightforward customization. Instances of each sub-module class are given as parameters to the Martini class; a mock observation is then constructed by calling a handful of functions to execute the desired steps in the mock-observing process.
Scope
-
Please indicate which category or categories.
Check out our package scope page to learn more about our
scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):- Data retrieval
- Data extraction
- Data processing/munging
- Data deposition
- Data validation and testing
- Data visualization1
- Workflow automation
- Citation management and bibliometrics
- Scientific software wrappers
- Database interoperability
Domain Specific
- Geospatial
- Education
Community Partnerships
If your package is associated with an
existing community please check below:
- Astropy: Link coming soon to standards
- Pangeo: My package adheres to the Pangeo standards listed in the pyOpenSci peer review guidebook
-
For all submissions, explain how the 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):
- Who is the target audience and what are scientific applications of this package?
The target audience is research astronomers interested in galaxies (broadly, "extragalactic astronomers") from both the theoretical and observational communities. The package provides a way to transform data products from the theory community (smoothed-particle hydrodynamics based simulations of galaxy formation and evolution) into data products closely resembling the atomic hydrogen signal observed with a radio telescope at 21-cm wavelengths. This enables much more faithful comparisons between theoretical predictions and measurements.
- Are there other Python packages that accomplish the same thing? If so, how does yours differ?
I am not aware of any other actively maintained packages with similar purpose.
- If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or
@tagthe editor you contacted:
N/A (I had previously submitted to astropy under their affiliated package scheme and have been redirected here)
Technical checks
For details about the pyOpenSci packaging requirements, see our packaging guide. Confirm each of the following by checking the box. This package:
- does not violate the Terms of Service of any service it interacts with.
- uses an OSI approved license.
- contains a README with instructions for installing the development version.
- includes documentation with examples for all functions.
- contains a tutorial with examples of its essential functions and uses.
- has a test suite.
- has continuous integration setup, such as GitHub Actions CircleCI, and/or others.
Publication Options
- Do you wish to automatically submit to the Journal of Open Source Software? If so:
JOSS Checks
- The package has an obvious research application according to JOSS's definition in their submission requirements. Be aware that completing the pyOpenSci review process does not guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS.
- The package is not a "minor utility" as defined by JOSS's submission requirements: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria.
- The package contains a
paper.mdmatching JOSS's requirements with a high-level description in the package root or ininst/. - The package is deposited in a long-term repository with the DOI: https://zenodo.org/doi/10.5281/zenodo.11193206
Since I'm coming in through the new astropy route, I had not prepared for JOSS requirements, but was thinking of submitting to JOSS soon anyway. I've now pushed a paper.md in the joss-paper branch. My package is indexed in the ASCL which in turn is indexed in ADS, but neither of these seems to provide an actual DOI so I will need to look into other repositories (probably Zenodo). As far as I understand submission to JOSS happens after the pyOpenSci review so there is a little bit of time to get this done - I expect to have these two items ticked off by the time the pyOpenSci review process is completed.
Note: JOSS accepts our review as theirs. You will NOT need to go through another full review. JOSS will only review your paper.md file. Be sure to link to this pyOpenSci issue when a JOSS issue is opened for your package. Also be sure to tell the JOSS editor that this is a pyOpenSci reviewed package once you reach this step.
Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?
This option will allow reviewers to open smaller issues that can then be linked to PR's rather than submitting a more dense text based review. It will also allow you to demonstrate addressing the issue via PR links.
- Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.
Confirm each of the following by checking the box.
- I have read the author guide.
- I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed.
Please fill out our survey
- Last but not least please fill out our pre-review survey. This helps us track
submission and improve our peer review process. We will also ask our reviewers
and editors to fill this out.
P.S. Have feedback/comments about our review process? Leave a comment here
Editor and Review Templates
The editor template can be found here.
The review template can be found here.
Footnotes
-
Please fill out a pre-submission inquiry before submitting a data visualization package. ↩
Metadata
Metadata
Assignees
Type
Projects
- Status
Activity
[-]Martini - Mock array telescope interferometry of the neutral ISM[/-][+]Martini[/+]isabelizimm commentedon Mar 8, 2024
Hello there! Just letting you know we have seen this issue and will be following up with pre-review checks shortly!
isabelizimm commentedon Mar 23, 2024
Thank you so much for this submission! It's so exciting to see these
astropysubmissions roll in ☄️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.
import package.README.mdfile with clear explanation of what the package does, instructions on how to install it, and a link to development instructions.CONTRIBUTING.mdfile that details how to install and contribute to the package.CODE_OF_CONDUCT.mdfile.NOTE: We prefer that you have development instructions in your documentation too.
YAMLheader of the issue (located at the top of the issue template).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
In your README can you add a quick installation piece? It doesn't have to be too fancy, something like the # Installation section on the
rdatapackage would be perfect. In the meantime, I'll sort out finding an editor for this review 🙌Also, are you able to to add a "version submitted"? I'm assuming it is the latest, but we'll want to know what version the review started at. It's okay if there are releases during the review/the accepted version is different, that is expected as you make edits!
isabelizimm commentedon Mar 23, 2024
Also, we have an editor lined up; @hamogu will be the editor lined up for this review 🙌
kyleaoman commentedon Mar 23, 2024
@isabelizimm I added the version submitted. Not sure what you're requesting for the installation information in README - there's a paragraph there already so if something else/different is needed I'm not sure what it is. Or do you not mean the package README?
isabelizimm commentedon Mar 29, 2024
Ah, I was specifically looking for the way to pip install martini, a section similar to "Installation" on this package. I do see this command in your installation paragraph, but it's quite easy to miss, so it would be ideal to pull it out into its own line, rather than be part of a larger paragraph.
This change is non-blocking to your review, just a note to make it easier to skim through details 😄
25 remaining items
hamogu commentedon Jun 3, 2024
🎉 has been approved by pyOpenSci! Thank you for submitting and many thanks to 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 of . The badge should be
- 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:[](https://github.com/pyOpenSci/software-review/issues/issue-number).🎉 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:
6/pyOS-approved6 🚀🚀🚀.6/pyOS-approvedlabel). Once accepted add the label9/joss-approvedto the issue. Skip this check if the package is not submitted to JOSS.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.
hamogu commentedon Jun 3, 2024
@kyleaoman Just to confirm: I see you did a very recent release on May15th. Is that the version that includes the responses to @taldcroft comments? Or do you plan to make a new release now that it's accepted? I just want to make sure I'm linking to the correct release number.
kyleaoman commentedon Jun 3, 2024
@hamogu release 2.0.12 contains the latest commit so yes, that's up to date. There's also a Zenodo DOI for it. I'll do the JOSS submission and other little to-do items asap, probably tomorrow. Thanks!
hamogu commentedon Jun 4, 2024
Congratulations! I switched to accepted - just remember to fill out the post-review survey and add a badge pointing to this issue, if you want to.
Also, we want to invite you 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
movingpandas
and here is a markdown example that you could use as a guide when creating your post.
If you are too busy for this no worries. But if you have time - we'd love to spread the word about your package!
Last, a huge thanks to @taldcroft and @MicheleDelliVeneri for their review - without reviewers like you PyOpenSci would not be possible.
Also, we want to invite all of you (authors and reviewers) you to join the PyOpenSci slack - it's a very active community (more than astropy!) with lots if technical discussion and people happy to help with packaging and related Python questions. Let me know if you are interested, and we'll send you an invite yo any email address you choose!
kyleaoman commentedon Jun 4, 2024
I've completed the post-review survey, added the badge, and just now submitted to JOSS - will come back once that process has run its course :)