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V2.0#96

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ckmah merged 86 commits intomasterYeoLab/bento-tools:masterfrom v2.0YeoLab/bento-tools:v2.0Copy head branch name to clipboardMay 3, 2023

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Commits

Commits on Jul 26, 2022

• wip

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Commits on Aug 16, 2022

• cleanup

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• simplify tensor decomposition for signature analysis

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• modularize counting neighbors

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• Merge branch 'colocation' of https://github.com/ckmah/bento-tools into colocation

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• modularize neighbor counting

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• simplify decomposition and use rasterio for shapes

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Commits on Aug 29, 2022

• cleanup diff plots

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• shape features

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• resolve merge conflicts

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Commits on Aug 31, 2022

• refactor sample features to be combinatorial, cleanup api

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Commits on Sep 15, 2022

• feature refactor

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Commits on Oct 11, 2022

• unstable

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Commits on Oct 18, 2022

• pretty colors

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Commits on Oct 26, 2022

• wip enrichment, embedding, plotting and more

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Commits on Oct 29, 2022

• wip start splitting up plot functions

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Commits on Nov 12, 2022

• wip many things

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Commits on Dec 13, 2022

• wip

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Commits on Jan 3, 2023

• reworked some api and updated rna flow method

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• add minisom dep

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Commits on Jan 11, 2023

• add robust CLR transform to flow; flowmap auto cluster flow embedding

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Commits on Jan 18, 2023

• remove clr from flow, add shape compositions, cleanup shape features, speedup spatial point indexing

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Commits on Feb 1, 2023

• cleanup flow, colocation, syncing utility functions

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Commits on Feb 9, 2023

• bugfixes

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Commits on Feb 10, 2023

• n_neighbors flow increase usability

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Commits on Feb 14, 2023

• Merge pull request #89 from ckmah/colocation

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• auto install poetry and dev bento-tools

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Commits on Feb 19, 2023

• bug fix for geopandas df IO of non-shapely objects

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Commits on Feb 20, 2023

• obs_stats use stripplots

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Commits on Feb 28, 2023

• geo format convert handle None

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• plotting improvements

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• flowmap polygons allow inner rings

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• plot flowmap elbow plot fast, cleanup imports

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• mistaken deleted code

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• build codespace container with poetry and package dev enabled

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• dependency cleanup

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• cleanup tools api

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• geometry cleanup

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• remove lock file from repo

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• more code cleanup

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Commits on Mar 1, 2023

• remove preprocessing module

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• rename flow to flux

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Commits on Mar 13, 2023

• cleanup savefig and add xia2019 gs

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• Pending changes exported from your codespace

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Commits on Mar 14, 2023

• Merge branch 'codespace-ckmah-supreme-robot-x97xw9gp56hvv7' into v2.0

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Commits on Mar 21, 2023

• extract pt registration fn

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• modularize enrichment fns

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• obs stats nucleus optional

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• fix cbars overlapping ticklabels

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  f5a4d5d

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• refactor plotting API

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• update deps

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• update api docs

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Commits on Mar 31, 2023

• inset colorbar

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• list full feature descriptions

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• bigfixes, colors, better default params, formatting, comments

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• update tests

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• revamp tutorials

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Commits on Apr 1, 2023

• mroe doc updates

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Commits on Apr 3, 2023

• fix fluxmap save fig

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• typechecking

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• cleanup and bump version

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• doc update

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Commits on Apr 4, 2023

• Merge branch 'master' into v2.0

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• Update python-package.yml

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• Update python-package.yml

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• Update python-package.yml

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• add install info for non-python deps

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• Merge branch 'v2.0' of github.com:ckmah/bento-tools into v2.0

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• typo

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• Merge pull request #97 from ckmah/ckmah-unit-tests

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• Update python-package.yml

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• cleanup test warnings

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• Merge branch 'v2.0' of github.com:ckmah/bento-tools into v2.0

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• Update python-package.yml

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Commits on Apr 5, 2023

• plotting tests

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• Merge branch 'v2.0' of github.com:ckmah/bento-tools into v2.0

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• syntax errors in tests

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Commits on Apr 24, 2023

• handle slicing metadata by type, ignore empty

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• hide obnoxious progress bars

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• features do not overwrite by default

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• fix typos

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• upgrade anndata to >=0.8

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Commits on Apr 27, 2023

• quantile plot handles nan values

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• features handle missing and recompute flag, add tests

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• fix typos, docs, explicit params

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Commits on May 1, 2023

• Merge pull request #98 from ckmah/bugfix-avery

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