Joss-reviews: [REVIEW]: ytree: A Python package for analyzing merger trees

[whedon]

Submitting author: @brittonsmith (Britton Smith)
Repository: https://github.com/ytree-project/ytree
Version: 2.3
Editor: @xuanxu
Reviewer: @mgckind, @aureliocarnero
Archive: 10.5281/zenodo.3580978

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5a26201bd9bf75e762f1f7b8d9ff198e"><img src="https://joss.theoj.org/papers/5a26201bd9bf75e762f1f7b8d9ff198e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5a26201bd9bf75e762f1f7b8d9ff198e/status.svg)](https://joss.theoj.org/papers/5a26201bd9bf75e762f1f7b8d9ff198e)

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

@mgckind & @aureliocarnero, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @xuanxu know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @mgckind

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@brittonsmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

Review checklist for @aureliocarnero

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@brittonsmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mgckind, @aureliocarnero it looks like you're currently assigned to review this paper :tada:.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[xuanxu]

@brittonsmith, @mgckind, @aureliocarnero: this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. 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#1881 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@xuanxu) if you have any questions/concerns.

[aureliocarnero]

Hello @brittonsmith.
Your code does not contain a plain-text LICENSE file with the contents of an OSI approved software license.
Please add one to the repository in order to continue with the review.
Cheers

[brittonsmith]

@aureliocarnero, sure thing, done!

[aureliocarnero]

Thank you @brittonsmith - Could you please clarify me which license from this list, https://opensource.org/licenses/alphabetical correspond to yours.? Cheers

[aureliocarnero]

@xuanxu I cannot open the draft:
https://github.com/openjournals/joss-papers/blob/joss.01881/joss.01881/10.21105.joss.01881.pdf

[aureliocarnero]

@brittonsmith I'm having troubles installing your code with pip.
It tells me the following:
Stored in directory: /home/carnero/.cache/pip/wheels/63/9d/8e/37c3f6506ed3f152733a699e92d8e0c9f5e5f01dea262f80ad
Successfully built mpmath
Installing collected packages: mpmath, sympy, yt, ytree
Found existing installation: sympy 0.7.6.1
ERROR: Cannot uninstall 'sympy'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

Any idea how can I solve this?

[brittonsmith]

@aureliocarnero, the license is the BSD-3-Clause.

For the installation issues, I'm not entirely sure. In the first instance, it looks like sympy was installed in a manner that cannot be upgraded by pip. In the second case, it looks like there is a conflicting version of yt that also cannot be updated. My recommendation would be to try creating a fresh conda environment from which to try installing from pip or source. I've just tried this now myself and it's working for me. Barring that, you might need to reinstall anaconda/miniconda. Please let me know if none of those suggestions work.

[aureliocarnero]

Hello @brittonsmith Im trying to download the data from here: https://ytree.readthedocs.io/en/latest/Data.html trying both the manual download and the one using the girder-cl app and it failed in both cases.
Could you please check that the data is correct? Maybe it is just me, but it would be good to know.
Cheers

Solved! I managed to download the data. No need to do anything

[aureliocarnero]

Also, in terms of documentation, I think more information should be given in the landing page of the github. In my opinion, you do not explain well what are the application of the trees. May I suggest you explain the context is used, in terms of cosmological simulations. If it can be used for other applications than that, please explain as well

[aureliocarnero]

You should also explain better what this mean, please:

• loading merger-tree data from the Amiga Halo Finder, Consistent-Trees, Rockstar, LHaloTree, and treefarm formats
• on-demand loading of trees and fields
• symbolic units, derived fields, and alias fields
• saving trees to a universal format

Plus you have a typo, correct the following error: see the full ytree documenation.

Cheers
Aurelio

[aureliocarnero]

In term of the paper, it would be good to give it a last review on the text to improve readability.

[aureliocarnero]

So @brittonsmith please read comments above.
Some changes in the documentation front needs to be done before I give green light for the publication.
Still I need to mark:
1) A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Please improve the landing page introduction stating clearly what the program is for.
2) Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
Please give a last reading to the paper, improving it a bit

[brittonsmith]

@aureliocarnero, sorry I was absolutely swamped last week and also wasn't sure if I should wait for a second review. Thank you for your comments. I'm happy to clarify the text on the landing page as per all of your suggestions there. I will take care of everything this week.

As to your second comment above, I'm not sure I understand what you would like to see improved about the paper itself. Could you please clarify this?

[xuanxu]

@mgckind: How is your review going?

[mgckind]

@mgckind: How is your review going?

Hi @xuanxu , I got it installed and started looking at the documentation (and getting some data bbut that went too slow which I'll revisit ) and reading @aureliocarnero comments. I've been traveling more than I planned to. I'll get this done as soon as I can, thanks!

[brittonsmith]

@aureliocarnero, I've issued a pull request to address your comments on the landing page. I chose to remove the bullet point list of features and to replace it with a short code demo as that seemed more illustrative.

Can you provide some more specific comments on how you'd like to see the paper improved?

[aureliocarnero]

I answered through github I think. The README is much better, thanks. I
will send you comments about the paper shortly.

El mar., 3 dic. 2019 a las 18:17, Britton Smith ([e-mail])
escribió:

@aureliocarnero https://github.com/aureliocarnero, I've issued a pull
request https://github.com/ytree-project/ytree/pull/34 to address your
comments on the landing page. I chose to remove the bullet point list of
features and to replace it with a short code demo as that seemed more
illustrative.

Can you provide some more specific comments on how you'd like to see the
paper improved?

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[aureliocarnero]

@brittonsmith about improving the readability of the paper. I think it could be improve, for example, I suggest the following changes:

In the phrase:
1) In the early Universe, matter is very evenly distributed, with only small fluxuations
about the average density.
Change to
In the early Universe, matter is distributed homogeneously, with only small fluctuations
about the average density.

2) Halos grow via accretion of the surrounding material and mergers with other halos.
Change to
Halos grow via accretion of the surrounding material and by merging with other halos.

3) This process of merging to form increasingly massive halos is very naturally conceptualized as an inverted tree, where small branches connect up to continually larger ones, leading eventually to the trunk.
Change to
This process of merging to form increasingly massive halos is naturally conceptualized as an inverted tree, where small branches connect up to continually larger ones, leading eventually to a trunk.

4) One of the main products of a cosmological simulation is a series of catalogs of all halos within
the simulated volume at a number of epochs.
Change to
One of the main products of cosmological simulations is a series of catalogs of halos within
the simulated volume at different epochs.

5) Halos within succesive catalogs can be linked together to create merger trees that describe a halo’s growth history.
Change to
Halos within successive epochs can be linked together to create merger trees that describe a halo’s growth history.

6) About figure 1. It is confusing for, according to the text, first small halos are formed and then more massive halos results. According to the caption, it seems the contrary. According to the explanation in the text, descendents are going upward, not downward. Could you check this please? Also, it would be nice if on the left of the plot, you put an arrow representing time, this would facilitate the explanation

Cheers

[brittonsmith]

@aureliocarnero, thanks for your suggestions on the paper. I've implemented them all, including for Figure 1, in this PR. The wording in the Figure caption was a mistake; I had ancestor and descendents switched. It should make sense now. Anyway, please let me know if that looks ok.

[brittonsmith]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[aureliocarnero]

After checking all the issues, I consider this publication is ready for submission and publication to JOSS

[mgckind]

I've started with the review. I should be done by today/tomorrow.

[mgckind]

@brittonsmith , @xuanxu. I'm sorry again for being late but here I am.
Great package and nice documentation, I went through every point, I checked aurelio's comments and installed and used ytree. Everything looks good to me.
I've created 2 issues in the original repo in regards to the paper and some functionalities. These are minor suggestions, other than that and after @aureliocarnero comments being addressed the paper looks good. Congrats!

[brittonsmith]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[brittonsmith]

@mgckind, I've just issued a new pull request to address your functionality comments. Please let me know if that looks ok.

[mgckind]

I went through the PR and it looks awesome, thanks for the extra effort of adding those. Congrats on such a nice module!. @xuanxu , @brittonsmith This is ready to go.

[brittonsmith]

@mgckind, thanks so much and thank you for reviewing the latest PRs so quickly!

[xuanxu]

Thanks @aureliocarnero and @mgckind for your review!

[xuanxu]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[xuanxu]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1088/0067-0049/192/1/9 is OK
• 10.5281/zenodo.1174374 is OK
• 10.1109/MCSE.2011.37 is OK
• 10.21105/joss.00809 is OK
• 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N is OK
• 10.1088/0004-637X/763/1/18 is OK
• 10.3847/1538-4357/aabe8f is OK
• 10.3847/1538-4357/ab378f is OK
• 10.1093/mnras/sty2103 is OK
• 10.1093/mnras/stz2507 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[xuanxu]

OK @brittonsmith, everything looks good, here are the next steps:

• Please release a new tagged version from the current master so it includes all the changes made during the review process
• Then archive that latest release in Zenodo
• Check the Zenodo deposit has the correct metadata: title and author name should match the paper; you may also add your ORCID.

Once you do that please report here the version number and archive DOI

[brittonsmith]

Hi @xuanxu, I've just done the release.

Version: 2.3
DOI: 10.5281/zenodo.3580978

The metadata for the Zenodo entry looks good to me. Our ORCIDs are there, too. I think we're ready to go.

Thanks for all your help!

[xuanxu]

@whedon set 2.3 as version

[whedon]

OK. 2.3 is the version.

[xuanxu]

@whedon set 10.5281/zenodo.3580978 as archive

[whedon]

OK. 10.5281/zenodo.3580978 is the archive.

[xuanxu]

Thanks @brittonsmith!
Everything is ready :tada:
@openjournals/joss-eics sending it your way for final acceptance! :rocket:

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1088/0067-0049/192/1/9 is OK
• 10.5281/zenodo.1174374 is OK
• 10.1109/MCSE.2011.37 is OK
• 10.21105/joss.00809 is OK
• 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N is OK
• 10.1088/0004-637X/763/1/18 is OK
• 10.3847/1538-4357/aabe8f is OK
• 10.3847/1538-4357/ab378f is OK
• 10.1093/mnras/sty2103 is OK
• 10.1093/mnras/stz2507 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1178

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1178, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1179
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01881
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[arfon]

@mgckind, @aureliocarnero - many thanks for your reviews here and to @xuanxu for editing this submission ✨

@brittonsmith - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01881/status.svg)](https://doi.org/10.21105/joss.01881)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01881">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01881/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01881/status.svg
   :target: https://doi.org/10.21105/joss.01881

This is how it will look in your documentation:

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[brittonsmith]

Thanks everyone for all their work! This was a great experience.