Code

randomized svd draft#3008

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Draft

hanbin973 wants to merge 32 commits intotskit-dev:maintskit-dev/tskit:mainfrom hanbin973:rsvdhanbin973/tskit:rsvdCopy head branch name to clipboard

+454-1

Commits

Commits on Oct 3, 2024

• randomized svd draft

  hanbin973

  committed
  1f45245

Commits on Oct 4, 2024

• modified api remove scipy

  hanbin973

  committed
  e408ab3

Commits on Oct 7, 2024

• remove scipy

  hanbin973

  committed
  a176132

• correct docstring and comments

  hanbin973

  committed
  8c662c8

• space remove

  hanbin973

  committed
  aa13613

Commits on Oct 8, 2024

• rng to random seed

  hanbin973

  committed
  5bf405a

• add windows feature

  hanbin973

  committed
  6e415e5

Commits on Oct 11, 2024

• output shape change when windows=wholegnome

  hanbin973

  committed
  45ac61e

• make centre work with nodes

  hanbin973

  committed
  2cdb9dd

• remove redundant options from internal functions

  hanbin973

  committed
  1f194aa

Commits on Oct 13, 2024

• start at testing

  petrelharp

  committed
  fdc5842

• change variable name to n_* to num_*

  hanbin973

  committed
  c0a2854

• return range sketch matrix Q

  hanbin973

  committed
  667d60f

• fix random sketch option to handle None

  hanbin973

  committed
  36c10e9

• random_sketch needs windows specified

  hanbin973

  committed
  0ac88b8

• input checking for range_sketch to align with windows

  hanbin973

  committed
  a6fa8ab

• docstring change to reflect range_sketch

  hanbin973

  committed
  791c7da

Commits on Oct 14, 2024

• linting has a bug; when converting lambda to ordinary function definition, it omits return in the end of the function

  hanbin973

  committed
  2f4ce2b

Commits on Oct 17, 2024

• now output is a dataclass

  hanbin973

  committed
  be2f736

• docstring change

  hanbin973

  committed
  bcbbcf6

Commits on Oct 18, 2024

• change variable name of PCAResult class

  hanbin973

  committed
  1a8ff7a

• move internal function of PCA out

  hanbin973

  committed
  af16340

Commits on Oct 22, 2024

• function rearrangement

  hanbin973

  committed
  e81db15

Commits on Nov 15, 2024

• terminology change loaindgs -> factor

  hanbin973

  committed
  277cfc2

Commits on Nov 16, 2024

• time resolved feature

  hanbin973

  committed
  be715de

Commits on Nov 17, 2024

• Update python/tskit/trees.py

  Show description for d3e6c89
  

  hanbin973

  and

  petrelharp

  authored
  d3e6c89

• Update python/tskit/trees.py

  Show description for 49fe716
  

  hanbin973

  and

  petrelharp

  authored
  49fe716

• Update python/tskit/trees.py

  Show description for d217fc7
  

  hanbin973

  and

  petrelharp

  authored
  d217fc7

• Update python/tskit/trees.py

  Show description for 89e3b27
  

  hanbin973

  and

  petrelharp

  authored
  89e3b27

Commits on Nov 18, 2024

• remove comments; eigen_values -> eigenvalues

  hanbin973

  committed
  81cbecf

Commits on Nov 20, 2024

• support for subset of samples and individuals in a tree

  hanbin973

  committed
  7ca6452

Commits on Dec 18, 2024

• add time assertion

  hanbin973

  committed
  587409b