Physcraper: Automated phylogenetic updating

[snacktavish]

Submitting Author: Emily Jane McTavish (@snacktavish)
All current maintainers: Emily Jane McTavish (@snacktavish), Luna L. Sanchez Reyes (@LunaSare)
Package Name: Physcraper
One-Line Description of Package: Automated phylogenetic updating
Repository Link: https://github.com/McTavishLab/physcraper
Version submitted: 0.55
Editor: @NickleDave
Reviewer 1: @bpucker
Reviewer 2: @leomrtns
Archive:
JOSS DOI: N/A
Version accepted: v 1.0
Date accepted (month/day/year): 09/14/2021

---

Description

• Include a brief paragraph describing what your package does:

Physcraper is an open‐source, command-line Python program that automatizes the update of published
phylogenies by enriching underlying gene alignments with public DNA sequence data, and linking taxonomic information across databases.

Scope

• Please indicate which category or categories this package falls under:
  • Data retrieval
  • Data extraction
  • Data munging
  • Data deposition
  • Reproducibility
  • Geospatial
  • Education
  • Data visualization*

* Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see this section of our guidebook.

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences):

This package retrieves data from GenBank (https://www.ncbi.nlm.nih.gov/genbank/), the OpenTreeofLife (www.opentreeoflife.org), and TreeBase (www.treebase.org/), and links these datasets together to incorporate new sequence data into evolutionary estimates. Physcraper also provides a framework for comparison of published phylogenies with their updated versions, by using the conflict API of the Open Tree of Life project.

• Who is the target audience and what are scientific applications of this package?

Physcraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on already available expert phylogenetic knowledge.
Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?

The closest analogue in python is PyPhlawd https://fephyfofum.github.io/PyPHLAWD/.
This approach differs from other tools (PyPhlawd, Supersmart) automatize the assembly of DNA alignments from the GenBank database for phylogenetic reconstruction, in that Physcraper leverages existing homology statements in the form of alignments and existing phylogenetic trees to select appropriate loci and improve inference.
Another key feature of Physcraper is linking of taxonomic identifiers across databases including NCBI, GBIF and OpenTree of Life which provides easy interoperability with those resources, and the ability to easily compare relationships between new inferences and existing taxonomy and previously published studies.

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[snacktavish]

Edited to new release (0.55), with some minor updates.

[snacktavish]

Preprint posted at: https://www.biorxiv.org/content/10.1101/2020.09.15.299156v1

[lwasser]

hi there @snacktavish i'm so sorry we have been out of communication here. are you still interested in a review by pyopensci? i've been a bit overwhelemed by current events which has been a hit at work in productivity. We may have an editor for this however if you are still interested in a review.

[snacktavish]

Yes! We are still interested in a review by pyopensci, but we also understand if that isn't possible given the current situation. Thanks!

[NickleDave]

Hi @snacktavish !
I volunteered myself to be editor.

Currently I work in AI / neuro but my background is bio ... and one of the main reasons I made it into science is a really good prof who taught the first non-boring class I took, on bioinformatics where we worked on genome assembly, phylogenetics, and related things.

So I think I get at a high level what physcraper does and it definitely looks like a good fit for PyOpenSci.

One thing: since we are still relatively new, we don't have a huge pool of reviewers to draw from right now. I can think of some places to start asking, but do you by any chance have two people you could recommend as reviewers?

[lwasser]

thank you @NickleDave i'll list you as an editor here at the top!! and @snacktavish THANK YOU for your patience with us. Also you have the best GH handle ever :)

[NickleDave]

Hey @snacktavish just want to check back -- please let me know if you need me to start looking for reviewers

One thing: since we are still relatively new, we don't have a huge pool of reviewers to draw from right now. I can think of some places to start asking, but do you by any chance have two people you could recommend as reviewers?

and I agree with Leah that you have the best GitHub handle ever

[snacktavish]

Sorry for the delay! I started thinking about it, and then forgot to respond. Folks that I think would be good reviewers, or could potentially suggest others who would be include @blackrim @josephwb @jfwalker (Contributors to https://github.com/FePhyFoFum/PyPHLAWD) @rvosa @DomBennett (Contibutors to SuperSmart https://academic.oup.com/sysbio/article/66/2/152/2418028).

@LunaSare - any other suggestions?

Thanks for the username love! When I first joined GitHub I didn't fully realize how much it would be part of my professional identity and was just like, hey, I like snacks! And now 10ish years later, lots of folks call me @snacktavish and I love it. 🍜 🍕 🍟

[NickleDave]

Thank you @snacktavish that likes snacks!

The folks you tagged all sound like perfect reviewers.
I will give them a couple days to respond.
If we don't hear back and it's okay with you I will try reaching out to them by email. Please let me know if that's not ok.

I think I would also like to try and find a third reviewer from outside those you (very helpfully) suggested as @lwasser has asked me to do on other reviews.

[lwasser]

HI there all!! i think IF you can have one that @snacktavish suggests and one outside reviewer (for a total of 2 reviewers) that would be perfect :) thank you so much Dave !!!

[NickleDave]

Understood, thank you @lwasser

[NickleDave]

@snacktavish @lwasser adding initial editor checks.
Very swamped at work right now but I will reach out to reviewers by Thursday at the latest

Editor checks:

• Fit: The package meets criteria for fit and overlap.
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has an OSI accepted license
• Repository: The repository link resolves correctly

---

Editor comments

• Looks like a perfect fit for pyOpenSci, within scope under categories of data retrieval and munging as maintainer has indicated.
• Package appears well-developed and maintained to me. I see no obvious issues at this time.
• Manuscript on biorxiv
• My impression is review would best address how the package meets its goal of usability by a non-specialist. Input from users and developers that have experience with related tools would be most helpful

---

Reviewers: @bpucker @leomrtns
Due date: March 1, 2021

[NickleDave]

@snacktavish @LunaSare @lwasser just an update that I have started reaching out to potential reviewers

[NickleDave]

update: reached out to a couple more reviewers 🤞

[NickleDave]

update update: very excited that @bpucker has accepted the invitation to review!!! 🎉🎉🎉
who has a ton of experience developing bioinformatics tools in Python
(see https://github.com/bpucker -- thank you @NatJWalker-Hale for connecting us)

Boas, just a reminder that our reviewer guide is here:
https://www.pyopensci.org/contributing-guide/open-source-software-submissions/reviewer-guide.html
and our review template is here:
https://www.pyopensci.org/contributing-guide/appendices/templates.html#review-template
Thank you!!!

[bpucker]

Package Review

• As the reviewer I confirm that there are no conflicts of interest for me to review this work.

Documentation

The package includes all the following forms of documentation:

• A statement of need clearly stating problems the software is designed to solve and its target audience in README
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• Vignette(s) demonstrating major functionality that runs successfully locally
• Function Documentation: for all user-facing functions
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Readme requirements
The package meets the readme requirements below:

• Package has a README.md file in the root directory.

The README should include, from top to bottom:

• The package name
• Badges for continuous integration and test coverage, a repostatus.org badge, and any other badges. 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 badge for pyOpenSci peer-review will be provided upon acceptance.)
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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:

• The documentation is easy to find and understand
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Functionality

• Installation: Installation succeeds as documented.
• Functionality: Any functional claims of the software been confirmed.
• Performance: Any performance claims of the software been confirmed.
• Automated tests: Tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
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• Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines.

Review Comments

1. Installation instructions are not in the README.md, but there are links to all relevant pages. Documentation and examples are also provided on different pages. I think this is fine though.

2. Some parts (relabeling/rerooting) are labeled as "under construction" thus I have not tested those.

3. Anaconda/virtualenv installation instructions should be added and these requirements should be specified in the README.

4. Support for additional alignment tools e.g. MAFFT could be included to allow user to choose their favorite one.

5. There are some details missing in the function documentation:
   self.otu_by_gi
   self._to_be_pruned
   self.tmpfi

6. The BLAST jobs run for a very long time (as promised in the documentation). I know this is tricky, but some kind of progress bar would be great.

7. Would it be possible to use peptide sequences? These could show better conservation over large phylogenetic distances.

8. Everything looks fine, but I got an issue when running physcraper on a different dataset. Here are the details:

Description: Ubuntu 18.04.2 LTS
Release: 18.04
Codename: bionic
Python 3.8.5 (on the system)
Python 3.6.11 (in physcraper_env)

anaconda Command line client (version 1.7.2)

physcraper_run.py -s pg_328 -t tree322 -r -tb -o chenopodia

Traceback (most recent call last):
File "/home/ubuntu/anaconda3/envs/physcraper_env/bin/physcraper_run.py", line 7, in
exec(compile(f.read(), file, 'exec'))
File "XXX/physcraper/bin/physcraper_run.py", line 181, in
dataset = physcraper.opentree_helpers.get_dataset_from_treebase(study_id)
File "XXX/physcraper/physcraper/opentree_helpers.py", line 390, in get_dataset_from_treebase
dna = DataSet.get(url=url, schema="nexml")
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/datamodel/datasetmodel.py", line 188, in get
return cls._get_from(**kwargs)
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/datamodel/basemodel.py", line 160, in _get_from
return cls.get_from_url(src=src, schema=schema, **kwargs)
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/datamodel/basemodel.py", line 279, in get_from_url
**kwargs)
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/datamodel/datasetmodel.py", line 129, in _parse_and_create_from_stream
state_alphabet_factory=charstatemodel.StateAlphabet,
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/dataio/ioservice.py", line 255, in read_dataset
global_annotations_target=dataset)
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/dataio/nexmlreader.py", line 284, in _read
subelement_factory=self._subelement_factory)
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/dataio/xmlprocessing.py", line 150, in init
self.parse_file(file_obj)
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/site-packages/dendropy/dataio/xmlprocessing.py", line 166, in parse_file
for event, elem in ElementTree.iterparse(source, events):
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/xml/etree/ElementTree.py", line 1221, in iterator
yield from pullparser.read_events()
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/xml/etree/ElementTree.py", line 1296, in read_events
raise event
File "/home/ubuntu/anaconda3/envs/physcraper_env/lib/python3.6/xml/etree/ElementTree.py", line 1268, in feed
self._parser.feed(data)
xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

Minor comments:
These automated tree > These automated trees (https://physcraper.readthedocs.io/en/latest/how_to_start.html)
mapped a unified taxonomy > mapped to a unified taxonomy

There are formatting issue on https://physcraper.readthedocs.io/en/latest/physcraper_run.html involving

1. "physcraper_run.py -tf tests/data/tiny_test_example/test.tre -tfs newick -a tests/data/tiny_test_example/test.fas -as fasta –taxon_info tests/data/tiny_test_example/main.json -o owndata"
2. "Take a look at the tree, the alignemnt and the out_info csv file. It will list all taxa by their unique identifiers."

final output ree > final output tree

cofniguration > configuration

updtaed > updated (https://physcraper.readthedocs.io/en/latest/data_exploration.html)

Genbank/genbank > GenBank (https://physcraper.readthedocs.io/en/latest/apidocs.html)

It appears that there should be a link on the overview figure, but the pages does not exist: https://physcraper.readthedocs.io/en/latest/how_to_start.html#

[snacktavish]

Thank you so much for the thorough review!
We will create issues, and address them, and then link them here where they are all completed, unless there is a different procedure you would like us to follow.

[NickleDave]

yes 🙏 thank you very much @bpucker -- looks quite helpful

@snacktavish creating issues and linking here is perfect, as was done in this previous review #20 (comment)

I will keep looking for one more reviewer

[NickleDave]

Hi all, just checking in here.
I am still looking for a second reviewer, but I am hesitant to email people right before a major holiday.
@snacktavish I plan to start contacting people again the week of Jan. 11.
Please let me know if that's okay.
It looks like you might still be working through issues from the first review, so I'm hoping you are not feeling too impatient with the editor (me) yet.

[snacktavish]

Not impatient at all! We are still working on addressing the comments from the first review, and the lab is dealing with some covid related setbacks as well as the holidays. Thanks for all your work on this, and no rush.

[NickleDave]

Ok, thank you for the quick reply.
I will resume looking for reviewers the second week of January.
Hope that in spite of having to deal with anything covid-related you are able to relax a little over the holidays

[NickleDave]

Hi @snacktavish and @LunaSare happy to report that @leomrtns has generously accepted our invitation to review

@leomrtns for your convenience here are the links to our reviewer guide and review template:
https://www.pyopensci.org/contributing-guide/open-source-software-submissions/reviewer-guide.html
https://www.pyopensci.org/contributing-guide/appendices/templates.html#review-template
Thank you again

Given everything else that is going on, I have set a due date for this review of five weeks: March 1, 2021
I will update my initial editor checks comment above

As we discussed I think this should be okay given that the authors are still working through issues from the first review

[lwasser]

yahoo! pinging @NickleDave our fearless editor for this package! it looks from the initial submission like this is not slated to move on to JOSS at this point so we may be able to wrap things up!

[NickleDave]

Thanks @lwasser !!! Yes looks like we can wrap things up.

And a big thank you @leomrtns and @bpucker for your reviews and very valuable input.

And thanks to @LunaSare and @snacktavish for responding so clearly that even a non-expert like me can follow what's going on.

Seems like the pyOpenSci review has been helpful for physcraper's development, I hope you'll agree.

[NickleDave]

🎉 physcraper has been approved by pyOpenSci! Thank you @LunaSare @snacktavish for submitting physcraper and many thanks to @bpucker @leomrtns for reviewing! 😸

(I know I just said thanks in the last comment but it's the language in our template and I like the smiling cat emoji)

There are a few things left to do to wrap up this submission:

• [x ] 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 physcraper. In markdown, the badge would be: [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/26)
• Add physcraper to the pyOpenSci website. @LunaSare or @snacktavish , please open a pull request to update this file: to add your package and name to the list of contributors
• @snacktavish @LunaSare @bpucker @leomrtns if you have time and are open to being listed on our website, please add yourselves to this file via a pr so we can list you on our website as contributors!

All -- 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 our documentation in the contributing-guide. We have also been updating our documentation to improve the process so all feedback is appreciated!

[NickleDave]

Adding as a separate comment so I don't overwhelm anyone trying to read that checklist:

@LunaSare looks like you already did a "pyOpenSci review" release? https://github.com/McTavishLab/physcraper/releases/tag/v0.6.1 -- I think you could do a "post-release" where you just add the badge to the README (sorry if I'm telling you something you already know).

I am pretty sure that a Zenodo DOI is still the mechanism we use to track completed reviews though -- @lwasser please correct me if I'm wrong.

@LunaSare you could just do a post release with the 5 more commits you have now, assuming you're okay with that.
Or if you want to also have the badge show up on the README, e.g. on PyPI, you could first add it, and then do the release on GitHub, which will trigger the creation of a DOI through Zenodo. You'd then publish to PyPI and the post release would show the badge there as well.

(Again sorry if I'm explaining something that's already obvious to you--I had to learn this stuff the hard way 😢 so I'm just trying to save you potential packaging pain (AKA PPP)).

[lwasser]

yay @NickleDave this is all awesome! and @LunaSare @snacktavish thank you for all of your work on this review and reviewers @bpucker @leomrtns thank you for your time in reviewing for us!

@NickleDave yes great catch. one post release even if it is a patch with the badge in the readme is appreciated. then we can use that specific zenodo archive in the records here as the version we "approved".

[LunaSare]

Hi @NickleDave and @lwasser! Thanks for the tips! This is the first time I am dealing with official package releases, so explanations are greatly appreciated. I'll give it a go and cry for help if needed!

[NickleDave]

Ah ok.

I might have made things extra confusing by bringing up PyPI.
Definitely no need from our end to have it on PyPI, as long as you create a DOI, e.g. with Zenodo by doing a GitHub release.

but, as long as I brought it up:
re: publishing to PyPI, I always go back to this tutorial
https://packaging.python.org/tutorials/packaging-projects/
which you will notice has moved away from the setup.py / requirements.txt approach it looks like you're using now
I use poetry that handles a lot of the grunt work.
Nice tutorial on packaging in general here that uses 'poetry': https://py-pkgs.org/
An alternative would be flit: https://github.com/takluyver/flit

But again I didn't mean to imply you need to deal with any of that to get the DOI so we can finish up review.

[lwasser]

@LunaSare are you interested in pushing to pypi? i think it is ideal and we could likely help you through it and take notes on any pain points. i have a setup for our packages where it gets pushed when there is a new release using github actions.
we could potentially help you get there as right now pypi's version of your package is behind what we accepted.

But first we would need to know who originally pushed this to pypi so we can get credentials figured out and such and help from there to ensure there is only ONE version of it on pypi!

[snacktavish]

We created a v1.0.0 release updated the PyPi version!
https://pypi.org/project/Physcraper/

We also did these:

• Activate Zenodo watching the repo if you haven't already done so.
• Tag and create a release to create a Zenodo version and DOI.
  https://zenodo.org/record/5512990#.YUPLLntlBhE
• Add the badge for pyOpenSci peer-review to the README.md of physcraper. In markdown, the badge would be:
• Add physcraper to the pyOpenSci website. @LunaSare or @snacktavish , please open a pull request to update this file: to add your package and name to the list of contributors
• @snacktavish @LunaSare @bpucker @leomrtns if you have time and are open to being listed on our website, please add yourselves to this file via a pr so we can list you on our website as contributors!
  PR is here: Add Physcraper, snacktavish and LunaSare to pyOpenSci website pyopensci.github.io#68

[LunaSare]

Thanks so much @lwasser and @NickleDave for the helpful guidance!
@snacktavish did the previous release of Physcraper to pypi. So we gave it a go and we were able to successfully submit the latest version of Physcraper to pypi today, thanks to @snacktavish's amazing coding skills!

@NickleDave, we ended up releasing v1.0.0 of Physcraper. Thanks for teaching us about post-releases, I think it will save us some headaches in the future! Also, the guide to make code citable was super useful!

[NickleDave]

Excellent, @lwasser and I are very glad we could help.

It's official!!! Just merged in the PRs. Thank you all again!

[lwasser]

hey 👋 @snacktavish @NickleDave @bpucker @leomrtns ! I hope that you are all well. I am reaching out here to all reviewers and maintainers about pyOpenSci now that i am working full time on the project (read more here). We have a survey that we'd like for you to fill out so we can:

🔗 HERE IS THE SURVEY LINK 🔗

1. invite you to our slack channel to participate in our community (if you wish to join - no worries if that is not how you prefer to communicate / participate).
2. Collect information from you about how we can improve our review process and also better serve maintainers.
   The survey should take about 10 minutes to complete depending upon how much you decide to write. This information will help us greatly as we make decisions about how pyOpenSci grows and serves the community. Thank you so much in advance for filling it out.

NOTE: this is different from the form designed for reviewers to sign up to review.
IMPORTANT: If there are other maintainers for this project, please ping them here and ask them to fill out the survey as well. It is important that we ensure packages are supported long term or sunsetted with sufficient communication to users. Thus we will check in with maintainers annually about maintenance.

Thank you in advance for doing this and supporting pyOpenSci.

[lwasser]

hi 👋 @snacktavish and @bpucker ! just a friendly reminder to take 5-10 minutes to fill out our survey . We really appreciate it. Emily, if you can have all of the maintainers of your package fill it out that would be great. We will stay in touch with package authors - checking in 1-2 times a year to ensure the package continues to be maintained and see better understand challenges that you face. It's important for us to be able to stay in touch with the package maintenance crew! We also want to list everyone on our website as maintainers. Thank you in advance for helping us by filling out the survey!! 🙌

🔗 HERE IS THE SURVEY LINK 🔗

[lwasser]

hey there @bpucker thank you so much for filling out our survey! ✨

[lwasser]

hey @snacktavish ! i'm just checking in. we do need to ensure that packages are still being maintained that have been accepted to pyopensci. I see that hte last commit to physcraper was in May of this year which is great! Is this package still being maintained?

And can you kindly also fill out our maintainer survey. we need to be able to keep in touch with our maintainers to ensure packages remain supported in our ecosystem.
Many thanks for doing this or if you have questions, feel free to email me at leah at pyopensci.org

All the best!

[snacktavish]

Hi Leah,
Sorry for the very slow response!! Yes, it is being maintained and I will get to the survey ASAP, and will have @LunaSare full it in too.
Thank you,

[lwasser]

hi @snacktavish !! thank you so so much! no worries on the response. I"m excited to know it's still maintained and appreciate you both filling it out! Are you the only two maintainers of the package? 🙌

[snacktavish]

We are!

[lwasser]

Awesome. Thanks so much for the speedy replies today! Leah Leah A Wasser Executive Director, pyOpenSci @leahawasser @pyOpenSci ***@***.***

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On Oct 19, 2022, at 2:48 PM, Emily Jane McTavish ***@***.***> wrote: We are! — Reply to this email directly, view it on GitHub <https://www.google.com/url?q=https://github.com/pyOpenSci/software-review/issues/26%23issuecomment-1284556323&source=gmail-imap&ust=1666817304000000&usg=AOvVaw1WtYFrKHBFZE8SWJG0hz-1>, or unsubscribe <https://www.google.com/url?q=https://github.com/notifications/unsubscribe-auth/AB2LPKVKUAPUN3JQ54OH62DWEBNBPANCNFSM4O3CRLWQ&source=gmail-imap&ust=1666817304000000&usg=AOvVaw195IQFFhKOuv9D0Le9KQ9W>. You are receiving this because you were mentioned.

[LunaSare]

I submitted my answers to the survey Thank you for following up on this @lwasser ⭐

[NickleDave]

Thank you @LunaSare! And thank you for the rare use of squirrel 😆

[lwasser]

the rare .. OMG how did i not know about this ?? it's going to be my new most favorite emoji!

DITTO to what David wrote! @LunaSare thank you so so much! I will be following up via email this week :)

[lwasser]

hey there @snacktavish @LunaSare i have another followup question. we are trying to grasp who "owns" or runs the maintainer team here vs who has contributed etc

I have another name on my list Martha Kandziora and martha seemed to contribute in 2019 but i don't see any recent commits from them. Is it safe to say that Martha is no longer a maintainer? I am just trying to ensure our data are up to date. Many thanks