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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
795 stars 214 forks source link

status of library? #762

Closed vsoch closed 2 weeks ago

vsoch commented 2 weeks ago

Hi there! :wave:

This looks like a beautiful library, and one I'd like to use (we have a tree based scheduler for HPC that would be well afforded by many of these visualizations) but I cloned the repository and was trying some examples out, and there are still print statements from Python 2. I had wanted to generate the bar chart alongside the tree example and was trying to start with cluster examples, but they look like they haven't been updated in many years.

So my question - what is the status of this library / plan for development? Thank you!

Rafiot commented 2 weeks ago

Have you looked at the ete4 branch? Or maybe the strint one, which seems to be the next one to be merged into ete4.

jhcepas commented 2 weeks ago

that's right! ete4 branch is the latest version we have in place. The sprint branch is the one we are using to advance with the final release of ETE v4.0, which will contain some syntax changes compared with current ete4.

dengzq1234 commented 2 weeks ago

Hi @Rafiot @vsoch! Yes at this moment I would reccommend you to try ete4 branch, you can find the tutorial here https://etetoolkit.github.io/ete/tutorial/

@vsoch as for you request, ete4 branch can already build the bar chart alongside the tree example, you can check here https://github.com/dengzq1234/ete4_gallery for some demo code. If you just need to annotate and visualize your metadata in very straight forward way, I would reccomend you to try https://github.com/compgenomicslab/TreeProfiler, which is a command-line tool designed for this purpose.

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Rafiot commented 2 weeks ago

Just a quick question while I'm thinking about it: do you have an rough timeframe regarding the release of v4.0?

jhcepas commented 2 weeks ago

we recently fixed a minimum set of features to make the official release (i.e. in pip, conda, etc), and I would say we are pretty close to tick all of them. So, my hope is to make it before xmas, unless @jordibc finds unexpected obstacles with any of the missing parts.

Rafiot commented 2 weeks ago

Sounds good, just keeping an eye on it for my weird use of ete and making sure I can easily upgrade.

vsoch commented 2 weeks ago

Awesome, thank you!