[REVIEW]: treex: a Python package for manipulating rooted trees

[whedon]

Submitting author: @RomainAzais (Romain Azais)
Repository: https://gitlab.inria.fr/azais/treex
Version: 1.2.0
Editor: @VivianePons
Reviewers: @VivianePons, @dvberkel
Archive: 10.5281/zenodo.3254416

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

Review checklist for @dvberkel

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: 1.2.0
• Authorship: Has the submitting author (@Azais) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @VivianePons

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: 1.2.0
• Authorship: Has the submitting author (@Azais) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dvalters, it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[VivianePons]

Hi @Azais

I am trying to install the software but I am running into issues. I have a miniconda on my machine but I am quite new with it and I can't find how to upgrade the different lib. I created an environment for treex but when I try the install command, I run into:

Fetching package metadata .............
Solving package specifications: 

PackageNotFoundError: Packages missing in current channels:
            
  - treex -> libedit >=3.1.20181209,<3.2.0a0
  - treex -> openssl >=1.1.1a,<1.1.2a -> libgcc-ng >=7.3.0
  - treex -> sqlite >=3.26.0,<4.0a0
  - treex -> xz >=5.2.4,<6.0a0

We have searched for the packages in the following channels:
            
  - https://conda.anaconda.org/mosaic/linux-64
  - https://conda.anaconda.org/mosaic/noarch
  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.continuum.io/pkgs/free/linux-64
  - https://repo.continuum.io/pkgs/free/noarch
  - https://repo.continuum.io/pkgs/r/linux-64
  - https://repo.continuum.io/pkgs/r/noarch
  - https://repo.continuum.io/pkgs/pro/linux-64
  - https://repo.continuum.io/pkgs/pro/noarch

Maybe I am just missing the right channels. As I said, I usually don't use conda that much. I only had a miniconda install for another project and it might be very minimal. Thanks for your help.

[VivianePons]

Note: when I try installing libedit for example, which seems to be required, with this command

conda install -c conda-forge libedit

it only installs version 3.1.20170329 , which is not good enough

[RomainAzais]

Hello @VivianePons
Could you try to update conda with conda update conda?
If it doesn't work, could you comment with the output of conda info?
Thanks.

[VivianePons]

Thanks, it worked!

[VivianePons]

I have started reviewing. I am not finished but I have some remarks.

First, it would be good to have the link to the documentation and the wiki inside the main README. Actually, I think the install should be described directly in the repo and not depend on the wiki (even though, it's good to also have the wiki)

And now, a more specific question. If I create a tree t and add a subtree s, I notice that the id of s is kept.

In [11]: t = Tree()                                                             

In [12]: s = Tree()                                                             

In [13]: print(t)                                                               
140108254638880


In [14]: print(s)                                                               
140108194820336


In [15]: t.add_subtree(s)                                                       

In [16]: print(t)                                                               
140108254638880
	140108194820336

But, if I add s though the add_subtree_to_id method, then, the new subtree in t is not s!

In [5]: t = Tree()                                                              

In [6]: s = Tree()                                                              

In [7]: print(t)                                                                
140108254475768


In [8]: print(s)                                                                
140108280308736


In [9]: t.add_subtree_to_id(s, t.my_id)                                         

In [10]: print(t)                                                               
140108254475768
	140108254642128

Why is that? Is this a bug of a feature? If it's a feature, it see it nowhere explained on the documentation of the method.

[RomainAzais]

Hello Viviane,
Thank you for this first feedback.

• About add_subtree VS add_subtree_to_id: when constructing a tree, we want the ids to be unique. But, we also thought that it should be a good idea to keep the option of replicating the id. I agree that our code is not clear on that point. We can change this (only one method called add_subtree, with an optional variable for copying or not the id).
• OK for the readme file.

How are we expected to process? We can do a new release today for instance.
Romain

[VivianePons]

Yes, I understand the necessity of the two options. My comment was mostly reflecting on the fact that this is not reflected clearly in the documentation.

You can indeed release a new version.

[RomainAzais]

Hello Viviane,

Sorry for my late reply. We released the new version about one week ago, but we got some issues with virtual machines for continuous integration, especially for MacOSX.

In the new version, the two methods add_subtree and add_subtree_to_id (where only add_subtree_to_id copies the subtree to be added) are still present, but the documentation has been clarified on this point:

• https://azais.gitlabpages.inria.fr/treex/_dvlpt/treex.tree.html#treex.tree.Tree.add_subtree
• https://azais.gitlabpages.inria.fr/treex/_dvlpt/treex.tree.html#treex.tree.Tree.add_subtree_to_id

In addition, the variable node_id is now optional in add_subtree_to_id. If None, the subtree is copied then added to the root of the main tree.

The installation procedure is now described in the ReadMe file. We also added the URL of the doc and the wiki.

All the best

[VivianePons]

Thanks, sorry I was also a bit busy here. I will complete my review next week.

@dvalters did you have time to start?

[VivianePons]

@whedon set 1.1.4 as version

[whedon]

OK. 1.1.4 is the version.

[VivianePons]

I have a question for @arfon : the software license is CeCILL-C whereas the OSI accepted one is CeCILL-2.1. Is there a significant difference there, is this an issue at all?

[VivianePons]

@whedon check doi

[VivianePons]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1137/1.9781611975499.4 is OK
- 10.3389/fpls.2012.00076 is OK

MISSING DOIs

- https://doi.org/10.1109/tcbb.2009.29 may be missing for title: Quantifying the degree of self-nestedness of trees: application to the structural analysis of plants
- https://doi.org/10.30757/alea.v16-21 may be missing for title: Inference for conditioned Galton-Watson trees from their Harris path
- https://doi.org/10.1016/0304-4149(94)90101-5 may be missing for title: Combinatorial stochastic processes

INVALID DOIs

- None

[VivianePons]

@RomainAzais could you please add the missing DOI?

[VivianePons]

@whedon remove @dvalters as reviewer

[whedon]

OK, @dvalters is no longer a reviewer

[VivianePons]

@whedon add @dvberkel as reviewer

[RomainAzais]

Hello @arfon

Hi @RomainAzais, the Archive link will become active when you make an archive of the software as requested by @VivianePons in this comment above.

OK, understood.

I'm afraid we don't support customizing the JOSS papers in this way.

No worries.

Yes, that's fine.

OK. I'll come back with the new version and the Zenodo archive.

[ooo]

👋 Hey @RomainAzais...

Letting you know, @VivianePons is currently OOO until Thursday, October 3rd 2019. ❤️

[VivianePons]

Just to let you know that I'm still here. I set up the ooo because I'm not taking new papers but whenever you have the zenodo, I will finish it up here (and update the version number accordingly)

[RomainAzais]

I updated the paper and the bibtex file according to the comments above.
Here is the link of the Zenodo archive: https://zenodo.org/record/3254416 (the DOI is 10.5281/zenodo.3254416).
Let me know if something goes wrong.

[VivianePons]

@whedon set 10.5281/zenodo.3254416 as archive

[whedon]

OK. 10.5281/zenodo.3254416 is the archive.

[VivianePons]

@whedon set 1.2.0 as version

[whedon]

OK. 1.2.0 is the version.

[VivianePons]

Perfect :) :) Your paper is now officially accepted in JOSS. Thank you very much all of you for your work on this! I leave it to @openjournals/joss-eics

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1109/TCBB.2009.29 is OK
- 10.1137/1.9781611975499.4 is OK
- 10.30757/ALEA.v16-21 is OK
- 10.1007/b11601500 is OK
- 10.3389/fpls.2012.00076 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#792

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#792, 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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01351 joss-papers#793
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01351
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[arfon]

@VivianePons, @dvberkel - many thanks for your reviews here and to @VivianePons for editing the submission too ✨

@RomainAzais - your paper is now accepted into JOSS ⚡🚀💥

[ooo]

👋 Hey @arfon...

Letting you know, @VivianePons is currently OOO until Thursday, October 3rd 2019. ❤️

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

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reStructuredText:
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[RomainAzais]

🎊 🎊 🍸
Thank you very much @arfon, @dvberkel, and @VivianePons for your work!
All the best,
Romain

[ooo]

👋 Hey @RomainAzais...

Letting you know, @VivianePons is currently OOO until Thursday, October 3rd 2019. ❤️