23andme / bonsaitree Goto Github PK

Hello!
I noted in the README that focal IDs were said to be an optional input, and there was even an example with None as the input, but when I've tried to run either with =None as the example showed or with no argument at all for focal ID, I receive the message: "Exception: Focal ID must be a positive integer." If I do not have a desired focal ID, is the only option to choose one arbitrarily, or is there a way to avoid specifying one?

Hello. I'm getting the following error when I try to run the test (install test). I would greatly appreciate your help to debug this error. I also tried the troubleshooting suggestions (upgrading pip and making a virtual environment) and eventhough all the packages were installed, I'm still getting this error:

=============================== warnings summary ===============================
../miniconda/envs/bonsaitreeEnv/lib/python3.10/site-packages/_pytest/config/__init__.py:1233
  /tools/miniconda/envs/bonsaitreeEnv/lib/python3.10/site-packages/_pytest/config/__init__.py:1233: PytestConfigWarning: Unknown config option: config

    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")

bonsaitree/__init__.py:10
  /tools/bonsaitree/bonsaitree/__init__.py:10: Warning: Version not available for package bonsaitree.bonsaitree (is it installed?)
    warnings.warn("Version not available for package %s (is it installed?)" % __package__,

tests/test_bonsai.py::test_get_ibd_pattern_log_prob
  /tools/bonsaitree/tests/test_bonsai.py:504: RuntimeWarning: divide by zero encountered in log
    assert(result == (np.log(0),np.log(7/64)))

tests/test_bonsai.py::test_get_ibd_pattern_log_prob
  /tools/bonsaitree/tests/test_bonsai.py:508: RuntimeWarning: divide by zero encountered in log
    assert(result == (np.log(0),np.log(7/64)))

tests/test_bonsai.py: 20 warnings
  /tools/bonsaitree/tests/test_bonsai.py:1457: DeprecationWarning: Sampling from a set deprecated
  since Python 3.9 and will be removed in a subsequent version.
    sample_id_set = set(random.sample(all_ids, sample_size)) | {focal_id}

-- Docs: https://docs.pytest.org/en/stable/warnings.html
================== 38 passed, 24 warnings in 68.09s (0:01:08) ==================

Hi, after installing bonsaitree and passing the test successfully, I encoutered the following error when using it:

`Python 3.8.8 (default, Apr 13 2021, 19:58:26)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

from bonsaitree import bonsai
Traceback (most recent call last):
File "", line 1, in
File "", line 259, in load_module
File "/home/yh362/.local/lib/python3.8/site-packages/bonsaitree-0.1.dev14+g9df551b-py3.8-linux-x86_64.egg/bonsaitree/bonsai.py", line 13, in
File "", line 259, in load_module
File "/home/yh362/.local/lib/python3.8/site-packages/bonsaitree-0.1.dev14+g9df551b-py3.8-linux-x86_64.egg/bonsaitree/pedigree_object.py", line 9, in
ImportError: cannot import name 'deepcopy' from 'bonsaitree.copytools' (/home/yh362/.cache/Python-Eggs/bonsaitree-0.1.dev14+g9df551b-py3.8-linux-x86_64.egg-tmp/bonsaitree/copytools.cpython-38-x86_64-linux-gnu.so)

`

I am unsure what caused this. Hope you can provide some hints. Thanks!