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maximilianh avatar maximilianh commented on July 30, 2024

from cellbrowser.

Jeltje avatar Jeltje commented on July 30, 2024

igraph isn't a dependency of scanpy:

pip show scanpy
Name: scanpy
Version: 1.3.2
Summary: Single-Cell Analysis in Python.
Home-page: http://github.com/theislab/scanpy
Author: Alex Wolf, Philipp Angerer, Davide Cittaro, Gokcen Eraslan, Fidel Ramirez, Tobias Callies
Author-email: [email protected]
License: BSD
Location: /home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages
Requires: numba, natsort, matplotlib, joblib, pandas, h5py, scipy, seaborn, networkx, tables, statsmodels, scikit-learn, anndata

So I pip installed it, but then I got

../../cellBrowser/src/cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o myscanpyout -n pbmc3k 2>&1 | tee cb.log
INFO:root:Creating myscanpyout
  File "../../cellBrowser/src/cbPyLib/cellbrowser.py", line 3267, in cbScanpyCli
    adata = cbScanpy(matrixFname, confFname, figDir, logFname)
  File "../../cellBrowser/src/cbPyLib/cellbrowser.py", line 3064, in cbScanpy
    sc.logging.print_versions()
  File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/scanpy/logging.py", line 180, in print_versions
    _print_versions_dependencies(['scanpy'] + _DEPENDENCIES_NUMERICS)
  File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/scanpy/logging.py", line 169, in _print_versions_dependencies
    imp = __import__(mod_name)
  File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/igraph/__init__.py", line 8, in <module>
    raise DeprecationWarning("To avoid name collision with the igraph project, "
cbScanpy $Id: 1e7c40a1801e210aa974d42ddb5ea5f4d3f225e6 $
Input file: filtered_gene_bc_matrices/hg19/matrix.mtx
Start time: 2018-10-12 10:22:04.242416
scanpy==1.3.2 anndata==0.6.11 numpy==1.14.6 scipy==1.1.0 pandas==0.23.4 scikit-learn==0.20.0 statsmodels==0.9.0 > /home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/igraph/__init__.py(8)<module>()
-> raise DeprecationWarning("To avoid name collision with the igraph project, "

It's a cliffhanger! It's listing the installed versions but not telling me what it wants.

Anyway, it then occurred to me you might have changed things since yesterday, so I pulled the latest.

../../cellBrowser/src/cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o myscanpyout -n pbmc3k 
Traceback (most recent call last):
  File "../../cellBrowser/src/cbScanpy", line 13, in <module>
    cellbrowser.cbScanpyCli()
  File "../../cellBrowser/src/cbPyLib/cellbrowser/cellbrowser.py", line 2950, in cbScanpyCli
    if options.init:
AttributeError: 'Values' object has no attribute 'init'

Can you let me know when you have tested the example on a clean system?

from cellbrowser.

maximilianh avatar maximilianh commented on July 30, 2024

from cellbrowser.

maximilianh avatar maximilianh commented on July 30, 2024

from cellbrowser.

maximilianh avatar maximilianh commented on July 30, 2024

from cellbrowser.

maximilianh avatar maximilianh commented on July 30, 2024

from cellbrowser.

maximilianh avatar maximilianh commented on July 30, 2024

Closing this one, too, as #11 was closed

from cellbrowser.

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