Problem with importing the library
HeleneHemmer opened this issue · comments
Dear developing team,
I have a very basic problem. After succesfully installing Palantir with pip install palantir, I am not able to load the package into my notebook, instead I get the following error message:
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
Cell In[14], [line 1](vscode-notebook-cell:?execution_count=14&line=1)
----> [1](vscode-notebook-cell:?execution_count=14&line=1) import palantir
ModuleNotFoundError: No module named 'palantir'
My environment uses Python 3.9.19 and I already checked the installed dependencies, but they seem to be fine to me.
These are the conda-packages:
# Name Version Build Channel
absl-py 2.1.0 pyhd8ed1ab_0 conda-forge
anndata 0.10.7 pyhd8ed1ab_0 conda-forge
annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge
anyio 4.3.0 pyhd8ed1ab_0 conda-forge
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
array-api-compat 1.6 pyhd8ed1ab_0 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
backoff 2.2.1 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
blessed 1.19.1 pyhe4f9e05_2 conda-forge
brotli 1.1.0 hb547adb_1 conda-forge
brotli-bin 1.1.0 hb547adb_1 conda-forge
brotli-python 1.1.0 py39hb198ff7_1 conda-forge
bzip2 1.0.8 h93a5062_5 conda-forge
c-ares 1.28.1 h93a5062_0 conda-forge
ca-certificates 2024.2.2 hf0a4a13_0 conda-forge
cachecontrol 0.14.0 pyhd8ed1ab_0 conda-forge
cachecontrol-with-filecache 0.14.0 pyhd8ed1ab_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cellrank 2.0.4 pyhd8ed1ab_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py39he153c15_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
chex 0.1.83 pyhd8ed1ab_0 conda-forge
cleo 2.1.0 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
contextlib2 21.6.0 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py39h48c5dd5_0 conda-forge
crashtest 0.4.1 pyhd8ed1ab_0 conda-forge
croniter 1.4.1 pyhd8ed1ab_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cython 3.0.10 py39hf3050f2_0 conda-forge
dateutils 0.6.12 py_0 conda-forge
debugpy 1.8.1 py39hf3050f2_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
deepdiff 7.0.1 pyhd8ed1ab_0 conda-forge
distlib 0.3.8 pyhd8ed1ab_0 conda-forge
dm-tree 0.1.8 py39h386ad04_0 conda-forge
docrep 0.3.2 pyh44b312d_0 conda-forge
dulwich 0.21.7 py39h17cfd9d_0 conda-forge
et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
fastapi 0.110.3 pyhd8ed1ab_0 conda-forge
fcsparser 0.2.8 pyhdfd78af_0 bioconda
fftw 3.3.10 mpi_openmpi_haef8dc3_8 conda-forge
filelock 3.14.0 pyhd8ed1ab_0 conda-forge
flax 0.6.1 pyhd8ed1ab_1 conda-forge
fonttools 4.51.0 py39h17cfd9d_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
fsspec 2024.3.1 pyhca7485f_0 conda-forge
future 1.0.0 pyhd8ed1ab_0 conda-forge
get-annotations 0.1.2 pyhd8ed1ab_0 conda-forge
gmp 6.3.0 hebf3989_1 conda-forge
gmpy2 2.1.5 py39hd40a46f_0 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h5py 3.11.0 nompi_py39hd62a535_100 conda-forge
hdf5 1.14.3 mpi_openmpi_hdfb4f64_1 conda-forge
hypre 2.28.0 mpi_openmpi_haba3941_0 conda-forge
icu 73.2 hc8870d7_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib-resources 6.4.0 pyhd8ed1ab_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
inquirer 3.1.4 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.3 pyh3cd1d5f_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
itsdangerous 2.2.0 pyhd8ed1ab_0 conda-forge
jaraco.classes 3.4.0 pyhd8ed1ab_1 conda-forge
jax 0.4.13 pyhd8ed1ab_0 conda-forge
jaxlib 0.4.12 cpu_py39hdce1265_1 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
joblib 1.4.0 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.1 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py39h2804cbe_0 conda-forge
keyring 24.3.1 py39h2804cbe_0 conda-forge
kiwisolver 1.4.5 py39hbd775c9_1 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
lcms2 2.16 ha0e7c42_0 conda-forge
legacy-api-wrap 1.4 pyhd8ed1ab_1 conda-forge
lerc 4.0.0 h9a09cb3_0 conda-forge
libabseil 20230125.3 cxx17_h13dd4ca_0 conda-forge
libaec 1.1.3 hebf3989_0 conda-forge
libblas 3.9.0 22_osxarm64_openblas conda-forge
libbrotlicommon 1.1.0 hb547adb_1 conda-forge
libbrotlidec 1.1.0 hb547adb_1 conda-forge
libbrotlienc 1.1.0 hb547adb_1 conda-forge
libcblas 3.9.0 22_osxarm64_openblas conda-forge
libcurl 8.7.1 h2d989ff_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libdeflate 1.20 h93a5062_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h93a5062_2 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge
libgfortran5 13.2.0 hf226fd6_3 conda-forge
libgrpc 1.56.2 h9075ed4_1 conda-forge
libhwloc 2.10.0 default_h52d8fe8_1000 conda-forge
libiconv 1.17 h0d3ecfb_2 conda-forge
libjpeg-turbo 3.0.0 hb547adb_1 conda-forge
liblapack 3.9.0 22_osxarm64_openblas conda-forge
libllvm14 14.0.6 hd1a9a77_4 conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libopenblas 0.3.27 openmp_h6c19121_0 conda-forge
libpng 1.6.43 h091b4b1_0 conda-forge
libprotobuf 4.23.3 hf32f9b9_1 conda-forge
libptscotch 7.0.4 h820b06d_1 conda-forge
libscotch 7.0.4 hf7fe8bf_1 conda-forge
libsodium 1.0.18 h27ca646_1 conda-forge
libsqlite 3.45.3 h091b4b1_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libtiff 4.6.0 h07db509_3 conda-forge
libuv 1.48.0 h93a5062_0 conda-forge
libwebp-base 1.4.0 h93a5062_0 conda-forge
libxcb 1.15 hf346824_0 conda-forge
libxml2 2.12.6 h0d0cfa8_2 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
lightning 2.0.9.post0 pyhd8ed1ab_0 conda-forge
lightning-cloud 0.5.39 pyhd8ed1ab_0 conda-forge
lightning-utilities 0.11.2 pyhd8ed1ab_0 conda-forge
llvm-openmp 18.1.4 hbf6887a_0 conda-forge
llvmlite 0.42.0 py39h047a24b_1 conda-forge
loompy 3.0.6 py_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py39h17cfd9d_0 conda-forge
matplotlib 3.8.4 py39hdf13c20_0 conda-forge
matplotlib-base 3.8.4 py39hbab7938_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
metis 5.1.0 h13dd4ca_1007 conda-forge
ml-collections 0.1.1 pyhd8ed1ab_0 conda-forge
ml_dtypes 0.4.0 py39h47e51b9_0 conda-forge
more-itertools 10.2.0 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 h91ba8db_0 conda-forge
mpfr 4.2.1 h41d338b_1 conda-forge
mpi 1.0 openmpi conda-forge
mpi4py 3.1.6 py39h081f454_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.7 py39he9de807_0 conda-forge
mudata 0.2.3 pyhd8ed1ab_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
mumps-include 5.7.0 hce30654_1 conda-forge
mumps-mpi 5.7.0 hae04b0b_1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
natsort 8.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.4.20240210 h078ce10_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numba 0.59.1 py39h278f47c_0 conda-forge
numpy 1.26.4 py39h7aa2656_0 conda-forge
numpy_groupies 0.11.1 pyhd8ed1ab_0 conda-forge
numpyro 0.13.2 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.2 h9f1df11_0 conda-forge
openmpi 4.1.6 h526c993_101 conda-forge
openpyxl 3.1.2 py39h0f82c59_0 conda-forge
openssl 3.3.0 h0d3ecfb_0 conda-forge
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
optax 0.2.2 pyhd8ed1ab_0 conda-forge
ordered-set 4.1.0 pyhd8ed1ab_0 conda-forge
orjson 3.10.2 py39h8081647_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py39h47e51b9_0 conda-forge
parmetis 4.0.3 h6eb5794_1005 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
petsc 3.21.1 real_he8b5c48_101 conda-forge
petsc4py 3.21.1 real_h9f984d2_100 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.3.0 py39h3352c98_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pkginfo 1.10.0 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.1 pyhd8ed1ab_0 conda-forge
poetry 1.8.2 osx_pyh534df25_0 conda-forge
poetry-core 1.9.0 pyhd8ed1ab_0 conda-forge
poetry-plugin-export 1.7.1 pyhd8ed1ab_1 conda-forge
progressbar2 4.4.2 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
psutil 5.9.8 py39h17cfd9d_0 conda-forge
pthread-stubs 0.4 h27ca646_1001 conda-forge
ptscotch 7.0.4 hc1c4572_1 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 2.1.1 pyhd8ed1ab_0 conda-forge
pydantic-core 2.4.0 py39haff01fd_0 conda-forge
pygam 0.9.1 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pygpcca 1.0.4 pyhd8ed1ab_2 conda-forge
pyjwt 2.8.0 pyhd8ed1ab_1 conda-forge
pynndescent 0.5.12 pyhca7485f_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyproject_hooks 1.1.0 pyhd8ed1ab_0 conda-forge
pyro-api 0.1.2 pyhd8ed1ab_0 conda-forge
pyro-ppl 1.9.0 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.19 hd7ebdb9_0_cpython conda-forge
python-build 1.2.1 pyhd8ed1ab_0 conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-editor 1.0.4 py_0 conda-forge
python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge
python-installer 0.7.0 pyhd8ed1ab_0 conda-forge
python-multipart 0.0.9 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python-utils 3.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytorch 2.0.0 cpu_generic_py39hca7b873_1 conda-forge
pytorch-lightning 2.2.2 pyhd8ed1ab_0 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py39h0f82c59_1 conda-forge
pyzmq 26.0.2 py39hf4e74ac_0 conda-forge
rapidfuzz 3.8.1 py39hf3050f2_0 conda-forge
re2 2023.03.02 hc5e2d97_0 conda-forge
readchar 4.0.5 pyhd8ed1ab_0 conda-forge
readline 8.2 h92ec313_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
requests-toolbelt 1.0.0 pyhd8ed1ab_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
scalapack 2.2.0 h515df86_1 conda-forge
scanpy 1.10.1 pyhd8ed1ab_0 conda-forge
scikit-learn 1.1.3 py39h57c6424_1 conda-forge
scipy 1.13.0 py39hcc04109_0 conda-forge
scotch 7.0.4 hc1c4572_1 conda-forge
scvelo 0.3.2 pyhd8ed1ab_1 conda-forge
scvi-tools 1.1.2 pyhd8ed1ab_0 conda-forge
seaborn 0.13.2 hd8ed1ab_2 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sleef 3.5.1 h156473d_2 conda-forge
slepc 3.21.1 real_h3568378_100 conda-forge
slepc4py 3.21.1 real_h5096657_100 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sparse 0.15.1 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
starlette 0.37.2 pyhd8ed1ab_0 conda-forge
starsessions 1.3.0 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.1 py39h373d45f_0 conda-forge
stdlib-list 0.10.0 pyhd8ed1ab_0 conda-forge
suitesparse 5.10.1 h79486c6_3 conda-forge
superlu 5.2.2 hc615359_0 conda-forge
superlu_dist 8.2.1 h3dacc9e_1 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
tbb 2021.12.0 h2ffa867_0 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomlkit 0.12.4 pyha770c72_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
torchmetrics 1.3.2 pyhd8ed1ab_0 conda-forge
tornado 6.4 py39h17cfd9d_0 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
trove-classifiers 2024.4.10 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
umap-learn 0.5.5 py39h2804cbe_1 conda-forge
unicodedata2 15.1.0 py39h0f82c59_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
uvicorn 0.29.0 py39h2804cbe_0 conda-forge
virtualenv 20.26.1 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge
websockets 12.0 py39h17cfd9d_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
wrapt 1.16.0 py39h17cfd9d_0 conda-forge
xarray 2024.3.0 pyhd8ed1ab_0 conda-forge
xattr 1.1.0 py39h17cfd9d_0 conda-forge
xlrd 1.2.0 pyh9f0ad1d_1 conda-forge
xorg-libxau 1.0.11 hb547adb_0 conda-forge
xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zeromq 4.3.5 h5119023_3 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
This is what I installed with pip:
Package Version
----------------- -----------
anndata 0.10.7
annoy 1.17.3
array_api_compat 1.6
blosc2 2.6.2
cffi 1.16.0
click 8.1.7
contourpy 1.2.1
cycler 0.12.1
Cython 3.0.10
exceptiongroup 1.2.0
fcsparser 0.2.8
fonttools 4.51.0
h5py 3.10.0
igraph 0.11.4
imageio 2.34.0
jax 0.4.26
jaxlib 0.4.26
jaxopt 0.8.3
Jinja2 3.1.3
joblib 1.4.0
kiwisolver 1.4.5
lazy_loader 0.4
legacy-api-wrap 1.4
leidenalg 0.10.2
llvmlite 0.42.0
loompy 3.0.7
louvain 0.8.2
MarkupSafe 2.1.5
matplotlib 3.8.4
mellon 1.4.2
ml-dtypes 0.4.0
msgpack 1.0.8
natsort 8.4.0
ndindex 1.8
networkx 3.3
numba 0.59.1
numexpr 2.10.0
numpy 1.26.4
numpy-groupies 0.11.1
opt-einsum 3.3.0
packaging 24.0
palantir 1.3.3
pandas 2.2.1
patsy 0.5.6
pillow 10.3.0
pip 24.0
progressbar2 4.4.2
psutil 5.9.8
py-cpuinfo 9.0.0
pycparser 2.22
pygam 0.9.1
pynndescent 0.5.12
pyparsing 3.1.2
Pysa 0.3b5
pysam 0.22.1
python-dateutil 2.9.0.post0
python-utils 3.8.2
pytz 2024.1
scanpy 1.10.1
scikit-image 0.22.0
scikit-learn 1.4.2
scikit-misc 0.3.1
scipy 1.11.4
scvelo 0.3.2
seaborn 0.13.2
session_info 1.0.0
setuptools 65.5.0
setuptools-scm 8.0.4
six 1.16.0
statsmodels 0.14.1
stdlib-list 0.10.0
tables 3.9.2
texttable 1.7.0
threadpoolctl 3.4.0
tifffile 2024.2.12
tomli 2.0.1
tqdm 4.66.2
typing_extensions 4.11.0
tzdata 2024.1
tzlocal 5.2
umap-learn 0.5.6
Do you know what I am missing here? I tried to restart the kernel as well, but it did not help.
Thank you for helping me out!
Hi @HeleneHemmer,
Thank you for reporting! I am not sure this is a Palantir problem though. Coult you try running python -c "import palantir; print(palantir.__version__)" on the command line that you ran the pip freeze that reported that Palantir is installed. If this correctly reports the Palantir version then your notebook might not be set up to use the conda environment.
Please let me know what comes out and if you need help setting up a conda environment as a notebook kernel.
Hi @katosh
Thanks for your reply. I was travelling and could not respond earlier. I am fairly new to python environments and I might have set it up incorrectly. I will try again and let you know in case the issue persists 🙂
I recommend setting up your conda environment as a kernel to use in jupyter. To realize this, first enter the environment on the command line, and then run, e.g.,
conda install ipykernel # alternatively python -m pip install ipykernel
python -m ipykernel install --user --name $CONDA_DEFAULT_ENV --display-name "$CONDA_DEFAULT_ENV"This would setup a kernel that lives in the conda env and that is available in jupyter (refresh the jupyter server site in your browser so it shows up). You can find more details about installing kernels here https://ipython.readthedocs.io/en/latest/install/kernel_install.html
Yes, I think the issue was that I wanted to use Palantir in one of my environments but it was leading to a package conflict. I installed it in a clean environment now, and it works :)
Thanks for helping me out and explaining :)
Awesome! Glad it works now! :)