hometools..? - Githubissues

cistarsa commented 1 year ago

          Thanks for the update! I believe I've reinstalled all of the dependencies and pulled the newest version 0.2, but now I'm running into a "hometools" no module issue. I've tried to install this using the standard conda install and python pip to no avail. I see this in the func.py script, line 45 but nowhere else...?

Originally posted by @cistarsa in https://github.com/schneebergerlab/fixchr/issues/3#issuecomment-1404126183

cistarsa commented 1 year ago

test@zachary-Precision-7560:~/Desktop/$ pypisearch hometools No results

cistarsa commented 1 year ago

Thank you for pushing the newest update. However, now I'm getting an ImportError. I've installed the updates and gitcloned etc. but I'm getting a traceback error, am I missing something obvious here? Appreciate it.

2023-02-03 14:18:13,909 - fixchr - INFO - Reading alignments (fixchr.py:52)
Traceback (most recent call last):
  File "/home/test/miniconda3/bin/fixchr", line 4, in <module>
    __import__('pkg_resources').run_script('fixchr==0.2', 'fixchr')
  File "/home/test/miniconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 672, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/test/miniconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1479, in run_script
    exec(script_code, namespace, namespace)
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.2-py3.8.egg/EGG-INFO/scripts/fixchr", line 6, in <module>
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.2-py3.8.egg/fixchr/scripts/fixchr.py", line 108, in main
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.2-py3.8.egg/fixchr/scripts/fixchr.py", line 53, in fixchr
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.2-py3.8.egg/fixchr/scripts/func.py", line 446, in readcoords
  File "/home/test/miniconda3/lib/python3.8/site-packages/pandas/__init__.py", line 51, in <module>
    from pandas.core.api import (
  File "/home/test/miniconda3/lib/python3.8/site-packages/pandas/core/api.py", line 14, in <module>
    from pandas.core.algorithms import factorize, unique, value_counts
  File "/home/test/miniconda3/lib/python3.8/site-packages/pandas/core/algorithms.py", line 62, in <module>
    from pandas.core.indexers import validate_indices
  File "/home/test/miniconda3/lib/python3.8/site-packages/pandas/core/indexers/__init__.py", line 1, in <module>
    from pandas.core.indexers.utils import (
  File "/home/test/miniconda3/lib/python3.8/site-packages/pandas/core/indexers/utils.py", line 18, in <module>
    from pandas.util._exceptions import find_stack_level
ImportError: cannot import name 'find_stack_level' from 'pandas.util._exceptions' (/home/test/miniconda3/lib/python3.8/site-packages/pandas/util/_exceptions.py)

mnshgl0110 commented 1 year ago

Seems to be a pandas version issue. What version of pandas are you using? I tested fixchr with pandas 1.5.1, so that should work.

cistarsa commented 1 year ago

Thank you, I’ll 2x check this as soon as I can and get back to you!

On Mon, Feb 6, 2023 at 4:27 AM Manish Goel @.***> wrote:

Seems to be a pandas version issue. What version of pandas are you using? I tested fixchr with pandas 1.5.1, so that should work.

— Reply to this email directly, view it on GitHub https://github.com/schneebergerlab/fixchr/issues/4#issuecomment-1418771476, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE7FXO4ZQJVINFXXEV3NGMLWWC7XTANCNFSM6AAAAAAUGWTUNE . You are receiving this because you authored the thread.Message ID: @.***>

cistarsa commented 1 year ago

thank you, it worked with pandas 1.5.1!

schneebergerlab / fixchr

hometools..? #4