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John-P / wsic

Whole Slide image (WSI) conversion for brightfield histology images
MIT License
32 stars 4 forks source link

Issue installing with pip #151

Open Abdol opened 4 months ago

Abdol commented 4 months ago

Description

I have tried installing the package with pip, following the docs. Despite the package being successfully installed according to pip, when I run wsic from the terminal I get a missing dependency error. This shouldn't normally happen because I expect dependency to be installed with the pip command unless otherwise mentioned in the docs.

What I Did

Installing with pip:

$ pip install wsic
Collecting wsic
  Downloading wsic-0.9.0-py2.py3-none-any.whl (118 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.8/118.8 kB 6.9 MB/s eta 0:00:00
Requirement already satisfied: zarr in ./miniconda3/lib/python3.9/site-packages (from wsic) (2.14.2)
Requirement already satisfied: numpy in ./miniconda3/lib/python3.9/site-packages (from wsic) (1.26.4)
Requirement already satisfied: asciitree in ./miniconda3/lib/python3.9/site-packages (from zarr->wsic) (0.3.3)
Requirement already satisfied: numcodecs>=0.10.0 in ./miniconda3/lib/python3.9/site-packages (from zarr->wsic) (0.12.1)
Requirement already satisfied: fasteners in ./miniconda3/lib/python3.9/site-packages (from zarr->wsic) (0.19)
Installing collected packages: wsic
Successfully installed wsic-0.9.0

Trying wsic

$ wsic
Traceback (most recent call last):
  File "/home/USER/miniconda3/bin/wsic", line 5, in <module>
    from wsic.cli import main
  File "/home/USER/miniconda3/lib/python3.9/site-packages/wsic/__init__.py", line 7, in <module>
    from . import codecs, magic, metadata, multiproc, readers, typedefs, writers
  File "/home/USER/miniconda3/lib/python3.9/site-packages/wsic/readers.py", line 9, in <module>
    import xarray as xr
ModuleNotFoundError: No module named 'xarray'

Update 1

When trying to manually install xarray after getting the above error message, I get a similar dependency error concerning dask:

$ wsic
Traceback (most recent call last):
  File "/home/u2271662/miniconda3/envs/wsic/bin/wsic", line 5, in <module>
    from wsic.cli import main
  File "/home/USER/miniconda3/envs/wsic/lib/python3.9/site-packages/wsic/__init__.py", line 7, in <module>
    from . import codecs, magic, metadata, multiproc, readers, typedefs, writers
  File "/home/USER/miniconda3/envs/wsic/lib/python3.9/site-packages/wsic/writers.py", line 34, in <module>
    from wsic.tile_iterators import DaskTileIterator
  File "/home/USER/miniconda3/envs/wsic/lib/python3.9/site-packages/wsic/tile_iterators.py", line 11, in <module>
    import dask.distributed as daskd
ModuleNotFoundError: No module named 'dask'
****

Update 2

Installing from source did not fix the problem, too.