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Hierarchical Clustering Algorithms

License: Other

Python 78.35% C 13.44% Cython 8.21%

clustering hierarchical-clustering python

hcluster's People

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cjferba fpierfed resurgo-genetics rama-jpmc afcarl 2016102050016 yikaill leeliuhuan fjsj francisfuzz fagan2888 atif-github-venture renchanghow sailfish009 scriptkiddi hirnimeshrampuresoftware odidev stjordanis arpitjain799

hcluster's Issues

Deprecation warning due to invalid escape sequences

Deprecation warnings are raised due to invalid escape sequences. This can be fixed by using raw strings or escaping the literals. pyupgrade also helps in automatic conversion : https://github.com/asottile/pyupgrade/

find . -iname '*.py' | grep -Ev 'test.py' | xargs -P4 -I{} python3.8 -Wall -m py_compile {}
./hcluster/distance.py:1648: DeprecationWarning: invalid escape sequence \c
  '(k \choose 2)=n)!') % name)
./hcluster/distance.py:1652: DeprecationWarning: invalid escape sequence \c
  'be a k such that (k \choose 2)=n)!')

set up CI

Copy tests for distance from scipy

Remove scipy dependencies

update readme

The Readme should be expanded to include:

installation
testing
team / credits
errors / bugs
copyright / license

Add support to release Linux AArch64 wheels

Problem

On aarch64, ‘pip install dedupe-hcluster’ build the wheels from source code and then installs it. It requires the user to have a development environment installed on his system. Also, it takes more time to build the wheels than downloading and extracting the wheels from PyPI.

Resolution

On aarch64, ‘pip install dedupe-hcluster’ should download the wheels from PyPI.

@derekeder, Please let me know your interest in releasing aarch64 wheels. I can help with this.

Remove scipy specific documentation

ImportError: cannot import name '_distance_wrap' on v0.3.3

Started getting this error after the latest version bump:

/usr/local/lib/python3.6/site-packages/dedupe/__init__.py:6: in <module>
--
  | from dedupe._init import *  # noqa
  | /usr/local/lib/python3.6/site-packages/dedupe/_init.py:1: in <module>
  | from dedupe.api import StaticDedupe, Dedupe  # noqa: F401
  | /usr/local/lib/python3.6/site-packages/dedupe/api.py:27: in <module>
  | import dedupe.clustering as clustering
  | /usr/local/lib/python3.6/site-packages/dedupe/clustering.py:12: in <module>
  | import hcluster
  | /usr/local/lib/python3.6/site-packages/hcluster/__init__.py:1: in <module>
  | from .hierarchy import *
  | /usr/local/lib/python3.6/site-packages/hcluster/hierarchy.py:175: in <module>
  | from . import distance
  | /usr/local/lib/python3.6/site-packages/hcluster/distance.py:73: in <module>
  | from . import _distance_wrap
  | E   ImportError: cannot import name '_distance_wrap'

This is running on Python 3.6.5.

Catch hcluster up with scipy.

Fix setup.py for standalone

hcluster.cophenet can't handle big data

https://gist.github.com/fgregg/7f275e030f509fdb26a1

Let's make a simpler case for reproducing bug.

syntax error

` SyntaxError: Missing parentheses in call to 'print'. Did you mean print("No paths in the python path contain numpy/arrayobject.h")?

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-pxq8nc0h/hcluster/
`

Got this when installing hcluster..

Bring in distance in from scipy

https://github.com/scipy/scipy/blob/master/scipy/spatial/distance.py