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20 hours ago •
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ModuleNotFoundError: No module named 'Levenshtein'
Describe the bug upon loading scirpy I get the following error message. ModuleNotFoundError: No module named 'Levenshtein' checking for levenstein, resulted in it to be present: python-levenshtein 0.26.0 pyhd8ed1ab_0 conda-forge
To Reproduce mamba create --name scIRpy -c conda-forge -c bioconda scirpy jupyterlab mudata seaborn pandas -y
import mudata as md
import muon
import numpy as np, pandas as pd
import scanpy as sc, anndata as ad
import scirpy as ir
The full error:
ModuleNotFoundError Traceback (most recent call last)
Cell In[2], line 6
3 import numpy as np, pandas as pd
5 import scanpy as sc, anndata as ad
----> 6 import scirpy as ir
8 import yaml, os
9 import seaborn as sns
File /data/cephfs-1/work/groups/keller/users/steiertd_c/miniforge3/envs/UMscPy/lib/python3.12/site-packages/scirpy/__init__.py:3
1 from importlib.metadata import version
----> 3 from . import datasets, get, io, ir_dist, pl, pp, tl, util
5 __all__ = ["datasets", "get", "io", "ir_dist", "pl", "pp", "tl", "util"]
7 __version__ = version("scirpy")
File /data/cephfs-1/work/groups/keller/users/steiertd_c/miniforge3/envs/UMscPy/lib/python3.12/site-packages/scirpy/datasets/__init__.py:24
22 from scirpy.io._datastructures import AirrCell
23 from scirpy.io._io import _infer_locus_from_gene_names, _IOLogger
---> 24 from scirpy.pp import index_chains
25 from scirpy.util import _doc_params, _read_to_str, tqdm
27 HERE = Path(__file__).parent
File /data/cephfs-1/work/groups/keller/users/steiertd_c/miniforge3/envs/UMscPy/lib/python3.12/site-packages/scirpy/pp/__init__.py:3
1 from textwrap import dedent
----> 3 from scirpy.ir_dist import _ir_dist as ir_dist
5 from ._index_chains import index_chains
6 from ._merge_adata import merge_airr
File /data/cephfs-1/work/groups/keller/users/steiertd_c/miniforge3/envs/UMscPy/lib/python3.12/site-packages/scirpy/ir_dist/__init__.py:16
13 from scirpy.get import airr as get_airr
14 from scirpy.util import DataHandler, _doc_params, _is_na, deprecated
---> 16 from . import metrics
19 @deprecated(
20 "Due to added BCR support, this function has been renamed "
21 "to `sequence_dist`. The old version will be removed in a future release. "
22 )
23 def tcr_dist(*args, **kwargs):
24 return sequence_dist(*args, **kwargs)
File /data/cephfs-1/work/groups/keller/users/steiertd_c/miniforge3/envs/UMscPy/lib/python3.12/site-packages/scirpy/ir_dist/metrics.py:12
10 import scipy.sparse
11 import scipy.spatial
---> 12 from Levenshtein import distance as levenshtein_dist
13 from scanpy import logging
14 from scipy.sparse import coo_matrix, csr_matrix
ModuleNotFoundError: No module named 'Levenshtein'
Trying to import things from Levenshtein did not work with the same error.
Checked for importable packages with:
for dist in __import__('pkg_resources').working_set:
print (dist.project_name.replace('Python', ''))
Babel
Brotli
Cython
MarkupSafe
PySocks
PyYAML
Send2Trash
XlsxWriter
adjustText
airr
anndata
anyio
argon2-cffi
argon2-cffi-bindings
array-api-compat
arrow
asttokens
async-lru
attrs
awkward
awkward-cpp
beautifulsoup4
bleach
cached-property
certifi
cffi
charset-normalizer
colorama
comm
contourpy
cycler
debugpy
decorator
defusedxml
entrypoints
exceptiongroup
executing
fastjsonschema
fonttools
fqdn
fsspec
get-annotations
h11
h2
h5py
hpack
httpcore
httpx
hyperframe
idna
igraph
importlib-metadata
importlib-resources
ipykernel
ipython
isoduration
jedi
jinja2
joblib
json5
jsonpointer
jsonschema
jsonschema-specifications
jupyter-client
jupyter-core
jupyter-events
jupyter-lsp
jupyter-server
jupyter-server-terminals
jupyterlab
jupyterlab-pygments
jupyterlab-server
kiwisolver
legacy-api-wrap
llvmlite
lxml
matplotlib
matplotlib-inline
mistune
mudata
munkres
muon
natsort
nbclient
nbconvert
nbformat
nest-asyncio
networkx
nose
notebook-shim
numba
numpy
overrides
packaging
pandas
pandocfilters
parso
patsy
pexpect
pickleshare
pillow
pip
pkgutil-resolve-name
platformdirs
pooch
prometheus-client
prompt-toolkit
protobuf
psutil
ptyprocess
pure-eval
pycparser
pygments
pynndescent
pyparsing
python-dateutil
python-json-logger
python-pptx
pytz
pyzmq
referencing
requests
rfc3339-validator
rfc3986-validator
rpds-py
scanpy
scikit-learn
scipy
scirpy
seaborn
session-info
setuptools
six
sniffio
soupsieve
squarify
stack-data
statsmodels
stdlib-list
terminado
texttable
threadpoolctl
tinycss2
tomli
tornado
tqdm
traitlets
types-python-dateutil
typing-extensions
typing-utils
tzdata
umap-learn
uri-template
urllib3
wcwidth
webcolors
webencodings
websocket-client
wheel
yamlordereddictloader
zipp
zstandard
autocommand
backports.tarfile
inflect
jaraco.context
jaraco.functools
jaraco.text
more-itertools
ordered-set
typeguard
Expected behaviour No import error
System
- OS: Linux
- Python: python 3.12.7 hc5c86c4_0_cpython conda-forge
- Versions of libraries involved:
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
adjusttext 1.2.0 pyhd8ed1ab_0 conda-forge
airr 1.5.1 pyh7cba7a3_0 bioconda
anndata 0.10.8 pyhd8ed1ab_0 conda-forge
anyio 4.6.2.post1 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py312h66e93f0_5 conda-forge
arpack 3.9.1 nompi_h77f6705_101 conda-forge
array-api-compat 1.9 pyhd8ed1ab_0 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
awkward 2.6.8 pyhd8ed1ab_0 conda-forge
awkward-cpp 38 py312h68727a3_1 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.2 heb4867d_0 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
contourpy 1.3.0 py312h68727a3_2 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
debugpy 1.8.7 py312h2ec8cdc_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
executing 2.1.0 pyhd8ed1ab_0 conda-forge
fonttools 4.54.1 py312h66e93f0_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fsspec 2024.9.0 pyhff2d567_0 conda-forge
get-annotations 0.1.2 pyhd8ed1ab_0 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
h5py 3.12.1 nompi_py312hedeef09_100 conda-forge
hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.6 pyhd8ed1ab_0 conda-forge
httpx 0.27.2 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.5.0 pyha770c72_0 conda-forge
importlib_metadata 8.5.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.5 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 8.28.0 pyh707e725_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
json5 0.9.25 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py312h7900ff3_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab 4.2.5 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.7 py312h68727a3_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_1 conda-forge
legacy-api-wrap 1.4 pyhd8ed1ab_1 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
levenshtein 0.26.0 py312h2ec8cdc_2 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libblas 3.9.0 24_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcblas 3.9.0 24_linux64_openblas conda-forge
libcurl 8.10.1 hbbe4b11_0 conda-forge
libdeflate 1.22 hb9d3cd8_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.6.3 h5888daf_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgfortran 14.2.0 h69a702a_1 conda-forge
libgfortran-ng 14.2.0 h69a702a_1 conda-forge
libgfortran5 14.2.0 hd5240d6_1 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libhwloc 2.11.1 default_hecaa2ac_1000 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 24_linux64_openblas conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libpng 1.6.44 hadc24fc_0 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.46.1 hadc24fc_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libtiff 4.7.0 he137b08_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 he7c6b58_4 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
llvmlite 0.43.0 py312h374181b_1 conda-forge
markupsafe 3.0.1 py312h178313f_1 conda-forge
matplotlib-base 3.9.2 py312hd3ec401_1 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mudata 0.3.1 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
natsort 8.4.0 pyhd8ed1ab_0 conda-forge
nbclient 0.10.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 he02047a_1 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.4.1 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
numba 0.60.0 py312h83e6fd3_0 conda-forge
numpy 2.0.2 py312h58c1407_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.2 hb9d3cd8_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.3 py312hf9745cd_1 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 11.0.0 py312h7b63e92_0 conda-forge
pip 24.2 pyh8b19718_1 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge
pooch 1.8.2 pyhd8ed1ab_0 conda-forge
prometheus_client 0.21.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.48 pyha770c72_0 conda-forge
psutil 6.0.0 py312h66e93f0_2 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.13 pyhff2d567_0 conda-forge
pyparsing 3.2.0 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.7 hc5c86c4_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge
python-igraph 0.11.6 py312h3262465_2 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-levenshtein 0.26.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 5_cp312 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h66e93f0_1 conda-forge
pyzmq 26.2.0 py312hbf22597_3 conda-forge
qhull 2020.2 h434a139_5 conda-forge
rapidfuzz 3.10.0 py312h2ec8cdc_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.20.0 py312h12e396e_1 conda-forge
scanpy 1.10.3 pyhd8ed1ab_0 conda-forge
scikit-learn 1.5.2 py312h7a48858_1 conda-forge
scipy 1.14.1 py312h7d485d2_0 conda-forge
scirpy 0.18.0 pyhdfd78af_0 bioconda
seaborn 0.13.2 hd8ed1ab_2 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge
send2trash 1.8.3 pyh0d859eb_0 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
setuptools 75.1.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
squarify 0.4.3 py_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.4 py312hc0a28a1_0 conda-forge
stdlib-list 0.11.0 pyhd8ed1ab_0 conda-forge
tbb 2021.13.0 h84d6215_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
texttable 1.7.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.2 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py312h66e93f0_1 conda-forge
tqdm 4.66.5 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20241003 pyhff2d567_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024b hc8b5060_0 conda-forge
umap-learn 0.5.6 py312h7900ff3_1 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 24.8.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hb9d3cd8_1 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yamlordereddictloader 0.4.0 py_0 conda-forge
zeromq 4.3.5 h3b0a872_6 conda-forge
zipp 3.20.2 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py312hef9b889_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
