weiyi-bitw / varnorm Goto Github PK

since recent change from hgvs to pyhgvs, it breaks when trying to install varnorm because pyhgvs is not available from pip.

It seems the package did not upgrade to python3 version. But Python3 will not be maintained soon, if still use python2 version package will incur security issue.
File "/py3_env/lib64/python3.7/site-packages/varnorm/varcharkey.py", line 116, in v2k
return unicode(rgChar + chromChar + startChar + endChar + altChar)
NameError: ("name 'unicode' is not defined", 'occurred at index 0')

The latest hgvs on pip is 0.4.13 which is not recent enough.
Thus one must intsall from https://github.com/counsyl/hgvs directly with git clone and setup.py.
This installs pyhgvs 0.9.4 which is sufficient.

Please update the setup.py

git diff
diff --git a/setup.py b/setup.py
index d0ff354..9fc3e2e 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@ setup(
     description='Variant normalization tool kit',
     long_description=open('README.md').read(),
     install_requires=[
-        "hgvs >= 0.8",
+        "pyhgvs >= 0.8",
         "pygr >= 0.8.2",
         "argparse >= 1.2.1"
     ]