taxpasta: TAXonomic Profile Aggregation and STAndardisation

[Midnighter]

Submitting Author: Moritz E. Beber (@Midnighter)
All current maintainers: (@Midnighter, @sofstam, @jfy133)
Package Name: taxpasta
One-Line Description of Package: TAXonomic Profile Aggregation and STAndardisation
Repository Link: https://github.com/taxprofiler/taxpasta
Version submitted: 0.2.1
Editor: @ctb
Reviewer 1: @snacktavish
Reviewer 2: @bluegenes
Archive: https://github.com/taxprofiler/taxpasta/releases/tag/0.4.0
JOSS DOI:
Version accepted: 0.4.0
Date accepted (month/day/year): 07/05/2023

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Description

The main purpose of taxpasta is to standardise taxonomic profiles created by a
range of bioinformatics tools. We call those tools taxonomic profilers. They
each come with their own particular, tabular output format. Across the profilers,
relative abundances can be reported in read counts, fractions, or percentages,
as well as any number of additional columns with extra information. We therefore
decided to take the lessons learnt to heart and provide
our own solution to deal with this pasticcio. With taxpasta you can ingest all
of those formats and, at a minimum, output taxonomy identifiers and their
integer counts.

Taxpasta can not only standardise profiles but also merge them across samples
for the same profiler into a single table. In future, we also intend to offer
methods for forming a consensus for the same sample analyzed by different
profilers.

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- [ ] Geospatial
- [ ] Education
- [ ] Pangeo

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

    Taxpasta is a tool for anyone working with taxonomic profiles from metagenomic sequencing experiments. Mostly that means ecologists, bioinformaticians, statisticians. Taxpasta's main application is to standardise profiles from a range of different tools. Having a singular format facilitates downstream analyses. Taxpasta is used, for example, in the upcoming taxprofiler pipeline implemented in nextflow. There, it also serves to combine the profiles of many samples into a single file.

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

    The BIOM format was created with the intention of standardizing a storage format for microbiome analyses. However, creating this format was entirely left to the user. Taxpasta conveniently knows how to read profiles from a range of tools and can also produce BIOM output.

    Some of the taxonomic profilers also come with scripts to convert their output into another format but none of them support such a wide range of tools as taxpasta does.

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[lwasser]

hey there 👋 @Midnighter welcome to pyopensci and thank you for this submission! i just wanted to say hello so you know that we see this submission and will be getting back to you shortly! i also am looking into forms for the submission template as well - many thanks for that suggestion! More soon!

[NickleDave]

Welcome @Midnighter @sofstam @jfy133!
I'm adding initial checks for this package.

Glad to see this as someone who develops a similar tool (for a different domain!).

Looks like most everything is there.

I do want to request one thing before we proceed with a review though:
can you please add at least one full tutorial?

Something like the "Examples" section in the Pynteny docs here (which also has a CLI interface): https://robaina.github.io/Pynteny/examples/example_cli/

(These docs were in place before we began the Pynteny review, which is why I'm providing them as an example of what we need to see before we start.)

I would suggest a sort of walkthrough of the main use case for taxpasta. This might be a simplified version of something you're using it for in research already.

I have provided some other feedback below but adding an initial tutorial is the only thing that's necessary at this time.

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.

• Installation The package can be installed from a community repository such as PyPI (preferred), and/or a community channel on conda (e.g. conda-forge, bioconda).
  • @Midnighter given the domain you're targeting, maybe it be good to publish a distribution package on bioconda and/or conda forge?
  • The package imports properly into a standard Python environment import package-name.
• Fit The package meets criteria for fit and overlap.
  • yes this is clearly a data munging package
• Documentation The package has sufficient online documentation to allow us to evaluate package function and scope without installing the package. This includes:
  • User-facing documentation that overviews how to install and start using the package.
    • I would strongly suggest adding a more general description of the package right at the top of the index page, that even a non-generalist (like me) can understand. What do people use taxonomic profiles for in your field? Why would it help me to be able to convert between formats? Links to Wikipedia pages, review articles, etc., would be helpful here. Ideally with a brief example of a table, like those shown in the command docs ("taxpasta is an interoperability tool for working with taxonomic profiles, that look something like this:"
    • There are install instructions but no real examples on the landing/index page. At a minimum the output of taxpasta -h could be shown and additionally a brief snippet. If the main usage is the CLI, then perhaps demos of usage could be shown with a tool like asciicinema
      • Also the output of taxpasta -h was truncated for me. See below. Not sure it would be clear to a new user what consensus and merge commands do because of the ellipsis. From the docs I guess this is because your cli package imports text from somewhere else? Is there a way to not truncate? Maybe just give a briefer summary?

$ taxpasta -h
Usage: taxpasta [OPTIONS] COMMAND [ARGS]...

  TAXonomic Profile Aggregation and STAndardisation

Options:
  --version                       Print only the current tool version and
                                  exit.
  -l, --log-level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
                                  Set the desired log level.  [default: INFO]
  --install-completion [bash|zsh|fish|powershell|pwsh]
                                  Install completion for the specified shell.
  --show-completion [bash|zsh|fish|powershell|pwsh]
                                  Show completion for the specified shell, to
                                  copy it or customize the installation.
  -h, --help                      Show this message and exit.

Commands:
  consensus    Form a consensus for the same sample but from different...
  merge        Standardise and merge two or more taxonomic profiles into...
  standardise  Standardise a taxonomic profile (alias: 'standardize').

• Short tutorials that help a user understand how to use the package and what it can do for them.
  • There are some snippet-like examples in documentation for commands of the command-line interface but I do not find more extensive tutorials
• API documentation (documentation for your code's functions, classes, methods and attributes): this includes clearly written docstrings with variables defined using a standard docstring format. We suggest using the Numpy docstring format.
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  • Contributing File The package has a CONTRIBUTING.md file that details how to install and contribute to the package.
    • @Midnighter is there a link to the CONTRIBUTING.rst in the README? I'm not finding it. If not, I'd suggest adding it.
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Editor comments

This is not required in checks but I would suggest adding example data to taxpasta.
Since you are working with tabular data that I'd guess can be failry lightweight, it should be relatively painless to add and it will really help people understand package usage. (Unless I'm wrong and the taxonomic profiles are like 100 MB each. In that case, see next paragraph.)
Again see the Pynteny example where they work with example data (not suggesting you need to add a download command but just showing you why built-in data is useful: https://robaina.github.io/Pynteny/examples/example_cli/#download-pgap-profile-hmm-database)

For my own library I just add the files directly to the package and then access with importlib.resources, see this issue: vocalpy/crowsetta#90
Some libraries have adopted the pooch library for data, e.g. scikit-image: https://scikit-image.org/docs/stable/api/skimage.data.html. Might be worth snooping their issues to help you figure out how to implement if you decide to adopt it.

[NickleDave]

Also @sofstam @jfy133 could you both please fill out the pre-review survey?
I have a reply for @Midnighter but not you I think.
https://forms.gle/F9mou7S3jhe8DMJ16
It's just a brief (5-10m) survey to help us understand how we're doing as an org. Thank you! 🙏

[Midnighter]

Hi @NickleDave,

Thank you for your review and comments. Adding a tutorial and improving the docs mostly makes sense to me. I will work on adding those.

The tables are indeed small, still I'm a little hesitant to distribute them with the package. However, pandas should be able to just load a table from a URL so that's maybe a way to go.

• Please note that taxpasta is already on bioconda https://bioconda.github.io/recipes/taxpasta/README.html#package-package%20'taxpasta' We need to document this, of course.
• I will also publish the package on Zenodo.

[jfy133]

Also @sofstam @jfy133 could you both please fill out the pre-review survey? I have a reply for @Midnighter but not you I think. https://forms.gle/F9mou7S3jhe8DMJ16 It's just a brief (5-10m) survey to help us understand how we're doing as an org. Thank you! pray

oops, sorry - from the second page most of the questions seemed to be about the package and I assume Moritz had already provided all that info.

I've filled it out, but left pretty much all the optional questions empty as either you have that info from Moritz, and/or submitting via pyOpenSci is Moritz' initative so I'm not that familiar/involved with python etc.

One comment though: I noticed that the options in your 'What background best describes you cultural identity?' question is extremely N. American focused. Unfortunately I don't have a good solution for you, but you may not be getting a particularly good overview of this - e.g. Asian spans half the world with many equally large sub-divisons as the Pacific Islanders, and also grouping 'Black' and African-American is also arguably unfair as they also can have a large difference in backgrounds/problems etc. For example see what official surveys from UK use: https://www.ethnicity-facts-figures.service.gov.uk/style-guide/ethnic-groups

[Midnighter]

@NickleDave regarding your comments on taxpasta -h the truncation is automatically created by typer. It looks better if you also install rich. I'll look into shortening the summaries such that they are not truncated by typer in the default view.

[NickleDave]

Thank you for your review and comments. Adding a tutorial and improving the docs mostly makes sense to me. I will work on adding those.

Great, thank you @Midnighter. Your other comments re: tables, bioconda, Zenodo, and the truncation all sound good. Would it be worth making rich a dependency so you don't have to special case typer behavior?

oops, sorry - from the second page most of the questions seemed to be about the package and I assume Moritz had already provided all that info.

I've filled it out, but left pretty much all the optional questions empty as either you have that info from Moritz, and/or submitting via pyOpenSci is Moritz' initative so I'm not that familiar/involved with python etc.

One comment though: I noticed that the options in your 'What background best describes you cultural identity?' question is extremely N. American focused.

Thank you @jfy133 I hear you and I will relay this to our executive director @lwasser. Your feedback is helpful; this is definitely a version 0.1 of the survey and I'm sure we can improve it to not be US-centric, and to encompass people who are core contributors to a project even if they are not primarily Python developers.

[Midnighter]

Would it be worth making rich a dependency so you don't have to special case typer behavior?

At the moment, it's an extra dependency that can be installed with taxpasta[rich]. (Come to think of it, we should document all of those.) The reason that it's not default is that where taxpasta originated, as a CLI tool for a nextflow pipeline, fancy terminal output is really not needed. We should definitely recommend installing that for interactive work, though.

[NickleDave]

where taxpasta originated, as a CLI tool for a nextflow pipeline, fancy terminal output is really not needed.

Understood!

Btw @Midnighter could I ask you to link this review issue on any issues you raise to make changes before review? By adding a link to the issue on the taxpasta repo, so that GitHub cross references them.

Just to help us track. Thank you 🙏

[Midnighter]

Dear @NickleDave,

We think that we've implemented everything that you've noticed. Please take another look and let us know your thoughts.

• There's now a detailed tutorial
• We've shortened the command summaries so hopefully they won't be truncated (except on extremely small windows).
• There's a short usage section right in the readme and on the docs' main page.
• Extras are documented.
• A number of other improvements to the documentation.

[NickleDave]

Hi @Midnighter I did check out these additions -- looks great!

Thank you for addressing all of those comments.
I will move ahead with finding an editor, will reply back here introducing them ASAP.

[NickleDave]

Hi again @Midnighter very happy to say that @ctb has very kindly agreed to take on the editor role for this review. Thanks for your patience while we found someone who knows your domain and the software community around it.

I will let @ctb take it from here and start tagging in reviewers.

[Midnighter]

I guess we'll have to add support for sourmash then 😆 Good to hear and I look forward to your review @ctb. Thank you for your time.

[ctb]

I guess we'll have to add support for sourmash then 😆 Good to hear and I look forward to your review @ctb. Thank you for your time.

welcome! ironically we have invested time in generating the same report formats as you, for other consumers of taxonomy, so I think we are well positioned to engage productively ;).

[lwasser]

Also @sofstam @jfy133 could you both please fill out the pre-review survey? I have a reply for @Midnighter but not you I think. https://forms.gle/F9mou7S3jhe8DMJ16 It's just a brief (5-10m) survey to help us understand how we're doing as an org. Thank you! pray

oops, sorry - from the second page most of the questions seemed to be about the package and I assume Moritz had already provided all that info.

I've filled it out, but left pretty much all the optional questions empty as either you have that info from Moritz, and/or submitting via pyOpenSci is Moritz' initative so I'm not that familiar/involved with python etc.

One comment though: I noticed that the options in your 'What background best describes you cultural identity?' question is extremely N. American focused. Unfortunately I don't have a good solution for you, but you may not be getting a particularly good overview of this - e.g. Asian spans half the world with many equally large sub-divisons as the Pacific Islanders, and also grouping 'Black' and African-American is also arguably unfair as they also can have a large difference in backgrounds/problems etc. For example see what official surveys from UK use: https://www.ethnicity-facts-figures.service.gov.uk/style-guide/ethnic-groups

hey y'all just wanted to note that i'm working on the survey questions being a LOT more inclusive. Many thanksf or your patience there and THANK YOU for calling this to our attention! It's very much american-centric

[ctb]

(finally got around to asking second reviewer; response soon :))

[ctb]

Editor comments

👋 Hi @bluegenes and @snacktavish! Thank you for volunteering to review
for pyOpenSci!

The following resources will help you complete your review:

1. Here is the reviewers guide. This guide contains all of the steps and information needed to complete your review.
2. Here is the review template that you will need to fill out and submit
   here as a comment, once your review is complete.

Please get in touch with any questions or concerns! Your review is due: April 21st, 2023.

Reviewers: @bluegenes @snacktavish
Due date: April 21, 2023.

[ctb]

ok, trying tagging in @bluegenes and @snacktavish again. Or do we need to invite them to this repo also?

[Midnighter]

FYI, we just released version 0.4.0 that wraps the changes from the reviews, as well as further issues discovered by users.

[ctb]

ok, here goes:

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🎉 taxpasta has been approved by pyOpenSci! Thank you @Midnighter for submitting and many thanks to @snacktavish @bluegenes 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 taxpasta. The badge should be [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/84).
• Please fill out the post-review survey. All maintainers and reviewers should fill this out.
• Add taxpasta to the pyOpenSci website. @Midnighter , please open a pr to update this file: to add your package and name to the list of contributors.
• @snacktavish @bluegenes 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!

It looks like you would like to submit this package to JOSS. Here are the next steps:

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🎉 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:

• Make sure that the maintainers filled out the post-review survey
• Invite the maintainers to submit a blog post highlighting their package. Feel free to use / adapt language found in this comment to help guide the author.
• Change the status tag of the issue to 6/pyOS-approved6 🚀🚀🚀.
• If the author submits to JOSS, please continue to update the labels for JOSS on this issue until the author is accepted (do not remove the 6/pyOS-approved label). Once accepted add the label 9/joss-approved to the issue. Skip this check if the package is not submitted to JOSS.

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[jfy133]

Added badge and confirm I've filled out the post-review survey!

[Kevin-Mattheus-Moerman]

@ctb @lwasser 👋 I am an editor for JOSS and processing the JOSS side of things. Can you clarify if this review is fully complete and this submission has passed review? The reason I ask is that many of the boxes ☝️ are not ticked.

[ctb]

Yes, it has passed review! At least one reviewer has checked all the criteria.

[Kevin-Mattheus-Moerman]

@ctb thanks for the reply. Note though that @NickleDave Editor in Chief checks set has unchecked boxes ☝️, and so does your Author Wrap Up Tasks and Editor Final Checks set. It seems to me like most of these can just be ticked? If so I think it would be best if your group makes a habit of ticking them (perhaps you still can now), so that somebody studying this review issue is not confused about the software/review lacking anything.

[ctb]

@ctb thanks for the reply. Note though that @NickleDave Editor in Chief checks set has unchecked boxes ☝️, and so does your Author Wrap Up Tasks and Editor Final Checks set. It seems to me like most of these can just be ticked? If so I think it would be best if your group makes a habit of ticking them (perhaps you still can now), so that somebody studying this review issue is not confused about the software/review lacking anything.

there are so many check boxes 😆

but also, I think:

Invite the maintainers to submit a blog post highlighting their package.

could maybe best happen after JOSS paper is available. Similarly,

If the author submits to JOSS...

I felt needed to wait until there was a JOSS issue. In addition, I don't think the authors have the ability to check off those boxes so it had to wait until THEY did the work and then I noticed that they had done so => check the boxes.

For the other checklist items like adding badges and so on, those were done after I signed off on the review and I don't get notified of PRs etc. referencing this issue so barring monitoring this issue manually or being tagged in on the PRs, I'm not sure how I would go about knowing I should check them off...

(I don't mean to be defensive - I am just explaining where we are and why, and confirming to myself that I had read the unchecked boxes and made the decision not to check them off yet, instead of missing them entirely, which was also certainly a possibility!)

[jfy133]

In addition, I don't think the authors have the ability to check off those boxes so it had to wait until THEY did the work and then I noticed that they had done so => check the boxes.

Correct, at least I was unable to tick of the boxes of what was meant to be our tasks (as authors)

[lwasser]

ahhhh ok lessons learned here that we need a way for authors to check their boxes AND/OR we need fewer of them . thank you all for the feedback!!! i hadn't considered that authors would NOT be able to check those author list boxes - we will have to come up with a better approach! i'm open to suggestions.

and it looks like taxpasta was accepted by JOSS - hooray. 🎉 🎉

[jfy133]

🎉 ! Thanks @lwasser !

[lwasser]

awesome! ok i'll close this issue now. Friends - if anyone from this review (reviewers, maintainers etc) is interested in joining our slack community please email me at leah at pyopensci.org or reply here if your email is available on your github and i can add you!! we'd love to have all of you there!

[Kevin-Mattheus-Moerman]

@lwasser One of the JOSS AEiCs here. Thanks for the great work with pyOpenSci.
On the checkboxes, yes I recommend a single set of checkboxes which are all ticked before acceptance in pyOpenSci. This way it is super clear that if they are all ticked things are completed/acceptable. This way people viewing the review issue do not get the wrong idea. If the authors cannot check them perhaps the editor can do it once completed. We sometimes have to do that with JOSS. Also, I believe just 1 reviewer complete the review here. Do you have guidelines/documentation on your policies on this somewhere for pyOpenSci? I would recommend that you adopt that at least 2 reviewers should complete the review. Thanks.