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bokulich-lab / q2-coordinates

methods for geographic mapping of qiime2 artifact data or metadata
BSD 3-Clause "New" or "Revised" License
2 stars 8 forks source link

Adding quadtrees and quadtree format to q2-coordinates under method quadtree #10

Closed zoechallacombe closed 3 years ago

zoechallacombe commented 4 years ago

Adding method for recursive sample division (into bins) by quadtrees based on latitude and longitude

nbokulich commented 4 years ago

thanks @zoechallacombe and @wasade ! I am really excited to see this PR!

@wasade please assign to me after you finish your review but just FYI my review may be a little delayed as I am between positions and moving soon-ish — if you want me to prioritize this or give a timeline (e.g., to coincide with the next QIIME 2 release) just let me know and I will do what I can.

@zoechallacombe if you have not already, could you please add a section to the tutorial in readme.md to describe and demonstrate the new action? Feel free to add new example data (or link to any large files elsewhere) if need. Thanks!

wasade commented 4 years ago

@nbokulich :+1: and good luck with the move!

nbokulich commented 3 years ago

Hi @zoechallacombe and @misialq looks like the discussion has gone quiet... what is the status of this PR?

misialq commented 3 years ago

Hey @zoechallacombe ! Thanks for replying to some of the comments. Not sure whether you are done with your updates - I don't see any new commits. Feel free to tag me here whenever you pushed your changes and are ready - I will have another look :) Thanks!

zoechallacombe commented 3 years ago

Hi @misialq, sorry about the silence, classes started again and I got a little behind on committing this stuff. Just added some fixes and new readme things, but it should be in a good place.

adamovanja commented 3 years ago

thanks a lot @zoechallacombe for adressing the changes. Currently the q2lint test is failing - since the headers in some files do not match the newest guidlines (q2_coordinates/qtrees.py, q2_coordinates/tests/test_quadtree.py and q2_coordinates/tests/test_quadtree_plugin.py). Replacing the current headers with the below one should resolve this easily: 

# ----------------------------------------------------------------------------
# Copyright (c) 2020, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
wasade commented 3 years ago

@zoechallacombe, please find a PR (https://github.com/zoechallacombe/q2-coordinates/pull/1) against your branch that resolves this final item from @adamovanja.