search

achtman-lab / GrapeTree

GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
https://genome.cshlp.org/content/28/9/1395
GNU General Public License v3.0
79 stars 27 forks source link

NumbaPendingDeprecationWarning type 'reflected list' found for argument 'a' of function 'contemporary' #100

Open peterjc opened 2 years ago

peterjc commented 2 years ago

Using one of your example input files under Linux Python 3.7:

$ pip freeze | grep grapetree 
grapetree==2.2
$ pip freeze | grep numba
numba==0.54.1
$ grapetree -p Grapetree_Agona.profile > Grapetree_Agona.profile.tree
/mnt/.../conda/lib/python3.7/site-packages/numba/core/ir_utils.py:2139: NumbaPendingDeprecationWarning: 
Encountered the use of a type that is scheduled for deprecation: type 'reflected list' found for argument 'a' of function 'contemporary'.

For more information visit https://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-reflection-for-list-and-set-types

File "/mnt/.../conda/lib/python3.7/site-packages/grapetree/module/MSTrees.py", line 35:
@jit(nopython=True)
def contemporary(a,b,c, n_loci) :
^

  warnings.warn(NumbaPendingDeprecationWarning(msg, loc=loc))
kjolley commented 1 year ago

Just upgraded our job server for PubMLST to the latest version of Ubuntu and now also experiencing this issue. Would be good to get a fix for this.