Installation issue #60
Comments
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Hi @josenimo, can you try using a more recent version of python and pytorch? So, if you don't have particular reasons for which you have to install python v3.8 and pytorch v1.12, I would suggest you to install at least python v3.10 and the latest version of pytorch. Let me know! |
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Hey @marcovarrone, mamba create -n cellcharter_v4 python=3.10 pytorch
pip install scarches
pip install cellcharterAt the pip install cellcharter I got the following pip ERROR: ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
schpl 1.0.5 requires pandas<2,>=1.1.2, but you have pandas 2.2.3 which is incompatible.So there is still a bit of an issue. For the sake of trying I tried to run the tutorial commands, the lightning import worked, however it failed again at the model import (see traceback below) model import traceback---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[8], line 2
1 # model = cc.tl.TRVAE.load('./tutorial_models/codex_mouse_spleen_trvae', adata, map_location='cpu')
----> 2 model = cc.tl.TRVAE.load('./tutorial_models/codex_mouse_spleen_trvae', adata, map_location='cpu')
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v4/lib/python3.10/site-packages/cellcharter/tl/_trvae.py:172, in TRVAE.load(cls, dir_path, adata, map_location)
169 elif not os.path.exists(adata_path) and load_adata:
170 raise ValueError("Save path contains no saved anndata and no adata was passed.")
--> 172 attr_dict, model_state_dict, var_names = cls._load_params(dir_path, map_location=map_location)
174 # Overwrite adata with new genes
175 adata = _validate_var_names(adata, var_names)
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v4/lib/python3.10/site-packages/scarches/models/base/_base.py:131, in BaseMixin._load_params(cls, dir_path, map_location)
128 varnames_path = os.path.join(dir_path, "var_names.csv")
130 try:
--> 131 with open(setup_dict_path, "rb") as handle:
132 attr_dict = pickle.load(handle)
133 # This catches the following error:
134 # RuntimeError: Attempting to deserialize object on a CUDA device
135 # but torch.cuda.is_available() is False.
136 # If you are running on a CPU-only machine, please use torch.load with
137 # map_location=torch.device('cpu') to map your storages to the CPU.
FileNotFoundError: [Errno 2] No such file or directory: './tutorial_models/codex_mouse_spleen_trvae/attr.pkl'happy to provide more feedback if needed. I guess I need to find the right combination of packages.. For the sake of completeness here is the list of all packages: # packages in environment at [/opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v4](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v4):
#
# Name Version Build Channel
absl-py 2.1.0 pypi_0 pypi
affine 2.4.0 pypi_0 pypi
aiobotocore 2.5.4 pypi_0 pypi
aiohappyeyeballs 2.4.3 pypi_0 pypi
aiohttp 3.11.7 pypi_0 pypi
aioitertools 0.12.0 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
anndata 0.10.9 pypi_0 pypi
anyio 4.6.2.post1 pypi_0 pypi
appnope 0.1.4 pypi_0 pypi
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
array-api-compat 1.9.1 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
async-lru 2.0.4 pypi_0 pypi
async-timeout 5.0.1 pypi_0 pypi
attrs 24.2.0 pypi_0 pypi
babel 2.16.0 pypi_0 pypi
beautifulsoup4 4.12.3 pypi_0 pypi
bleach 6.2.0 pypi_0 pypi
botocore 1.31.17 pypi_0 pypi
bzip2 1.0.8 h99b78c6_7 conda-forge
ca-certificates 2024.8.30 hf0a4a13_0 conda-forge
cellcharter 0.3.2 pypi_0 pypi
certifi 2024.8.30 pypi_0 pypi
cffi 1.17.1 pypi_0 pypi
charset-normalizer 3.4.0 pypi_0 pypi
chex 0.1.87 pypi_0 pypi
click 8.1.7 pypi_0 pypi
click-plugins 1.1.1 pypi_0 pypi
cligj 0.7.2 pypi_0 pypi
cloudpickle 3.1.0 pypi_0 pypi
colorcet 3.1.0 pypi_0 pypi
comm 0.2.2 pypi_0 pypi
contourpy 1.3.1 pypi_0 pypi
cpython 3.10.15 py310hd8ed1ab_2 conda-forge
cycler 0.12.1 pypi_0 pypi
dask 2024.11.2 pypi_0 pypi
dask-expr 1.1.19 pypi_0 pypi
dask-image 2024.5.3 pypi_0 pypi
datashader 0.16.3 pypi_0 pypi
debugpy 1.8.9 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
distributed 2024.11.2 pypi_0 pypi
docrep 0.3.2 pypi_0 pypi
etils 1.10.0 pypi_0 pypi
exceptiongroup 1.2.2 pypi_0 pypi
executing 2.1.0 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
fastjsonschema 2.20.0 pypi_0 pypi
filelock 3.16.1 pyhd8ed1ab_0 conda-forge
flax 0.10.2 pypi_0 pypi
fonttools 4.55.0 pypi_0 pypi
fqdn 1.5.1 pypi_0 pypi
frozenlist 1.5.0 pypi_0 pypi
fsspec 2023.6.0 pypi_0 pypi
gdown 5.2.0 pypi_0 pypi
geopandas 1.0.1 pypi_0 pypi
gmp 6.3.0 h7bae524_2 conda-forge
gmpy2 2.1.5 py310heb17c8b_2 conda-forge
grpcio 1.68.0 pypi_0 pypi
h11 0.14.0 pypi_0 pypi
h5py 3.12.1 pypi_0 pypi
httpcore 1.0.7 pypi_0 pypi
httpx 0.27.2 pypi_0 pypi
humanize 4.11.0 pypi_0 pypi
idna 3.10 pypi_0 pypi
igraph 0.11.8 pypi_0 pypi
imageio 2.36.0 pypi_0 pypi
importlib-metadata 8.5.0 pypi_0 pypi
importlib-resources 6.4.5 pypi_0 pypi
inflect 7.4.0 pypi_0 pypi
ipykernel 6.29.5 pypi_0 pypi
ipython 8.29.0 pypi_0 pypi
ipywidgets 8.1.5 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jax 0.4.35 pypi_0 pypi
jaxlib 0.4.35 pypi_0 pypi
jedi 0.19.2 pypi_0 pypi
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
jmespath 1.0.1 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
json5 0.9.28 pypi_0 pypi
jsonpointer 3.0.0 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2024.10.1 pypi_0 pypi
jupyter 1.1.1 pypi_0 pypi
jupyter-client 8.6.3 pypi_0 pypi
jupyter-console 6.6.3 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
jupyter-events 0.10.0 pypi_0 pypi
jupyter-lsp 2.2.5 pypi_0 pypi
jupyter-server 2.14.2 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyterlab 4.2.6 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.27.3 pypi_0 pypi
jupyterlab-widgets 3.0.13 pypi_0 pypi
kiwisolver 1.4.7 pypi_0 pypi
lazy-loader 0.4 pypi_0 pypi
legacy-api-wrap 1.4 pypi_0 pypi
leidenalg 0.10.2 pypi_0 pypi
libabseil 20240722.0 cxx17_hf9b8971_1 conda-forge
libblas 3.9.0 25_osxarm64_openblas conda-forge
libcblas 3.9.0 25_osxarm64_openblas conda-forge
libcxx 19.1.4 ha82da77_0 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
liblapack 3.9.0 25_osxarm64_openblas conda-forge
libopenblas 0.3.28 openmp_hf332438_1 conda-forge
libprotobuf 5.28.2 h8f0b736_0 conda-forge
libsqlite 3.47.0 hbaaea75_1 conda-forge
libtorch 2.5.1 cpu_generic_h61b979d_3 conda-forge
libuv 1.49.2 h7ab814d_0 conda-forge
libzlib 1.3.1 h8359307_2 conda-forge
lightning 2.4.0 pypi_0 pypi
lightning-utilities 0.11.9 pypi_0 pypi
llvm-openmp 19.1.4 hdb05f8b_0 conda-forge
llvmlite 0.43.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
markdown 3.7 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 3.0.2 py310h5799be4_0 conda-forge
matplotlib 3.8.4 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
matplotlib-scalebar 0.8.1 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
mistune 3.0.2 pypi_0 pypi
ml-collections 1.0.0 pypi_0 pypi
ml-dtypes 0.5.0 pypi_0 pypi
more-itertools 10.5.0 pypi_0 pypi
mpc 1.3.1 h8f1351a_1 conda-forge
mpfr 4.2.1 hb693164_3 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack 1.1.0 pypi_0 pypi
mudata 0.3.1 pypi_0 pypi
multidict 6.1.0 pypi_0 pypi
multipledispatch 1.0.0 pypi_0 pypi
multiscale-spatial-image 1.0.1 pypi_0 pypi
muon 0.1.7 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
nbclient 0.10.0 pypi_0 pypi
nbconvert 7.16.4 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ncurses 6.5 h7bae524_1 conda-forge
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.4.2 pyh267e887_2 conda-forge
newick 1.0.0 pypi_0 pypi
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 7.2.2 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
numba 0.60.0 pypi_0 pypi
numcodecs 0.13.1 pypi_0 pypi
numpy 1.26.4 pypi_0 pypi
numpyro 0.15.3 pypi_0 pypi
ome-zarr 0.9.0 pypi_0 pypi
omnipath 1.0.8 pypi_0 pypi
openssl 3.4.0 h39f12f2_0 conda-forge
opt-einsum 3.4.0 pypi_0 pypi
optax 0.2.4 pypi_0 pypi
orbax-checkpoint 0.10.0 pypi_0 pypi
overrides 7.7.0 pypi_0 pypi
packaging 24.2 pypi_0 pypi
pandas 2.2.3 pypi_0 pypi
pandocfilters 1.5.1 pypi_0 pypi
param 2.1.1 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
partd 1.4.2 pypi_0 pypi
patsy 1.0.1 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
pillow 11.0.0 pypi_0 pypi
pims 0.7 pypi_0 pypi
pip 24.3.1 pyh8b19718_0 conda-forge
platformdirs 4.3.6 pypi_0 pypi
pooch 1.8.2 pypi_0 pypi
prometheus-client 0.21.0 pypi_0 pypi
prompt-toolkit 3.0.48 pypi_0 pypi
propcache 0.2.0 pypi_0 pypi
protobuf 5.28.3 pypi_0 pypi
psutil 6.1.0 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.3 pypi_0 pypi
pyarrow 18.0.0 pypi_0 pypi
pycparser 2.22 pypi_0 pypi
pyct 0.5.0 pypi_0 pypi
pygments 2.18.0 pypi_0 pypi
pynndescent 0.5.13 pypi_0 pypi
pyogrio 0.10.0 pypi_0 pypi
pyparsing 3.2.0 pypi_0 pypi
pyproj 3.7.0 pypi_0 pypi
pyro-api 0.1.2 pypi_0 pypi
pyro-ppl 1.9.1 pypi_0 pypi
pysocks 1.7.1 pypi_0 pypi
python 3.10.15 hdce6c4c_2_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-json-logger 2.0.7 pypi_0 pypi
python_abi 3.10 5_cp310 conda-forge
pytorch 2.5.1 cpu_generic_py310hf6af900_3 conda-forge
pytorch-lightning 2.4.0 pypi_0 pypi
pytz 2024.2 pypi_0 pypi
pyyaml 6.0.2 pypi_0 pypi
pyzmq 26.2.0 pypi_0 pypi
rasterio 1.4.2 pypi_0 pypi
readline 8.2 h92ec313_1 conda-forge
referencing 0.35.1 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rich 13.9.4 pypi_0 pypi
rpds-py 0.21.0 pypi_0 pypi
s3fs 2023.6.0 pypi_0 pypi
scanpy 1.10.4 pypi_0 pypi
scarches 0.6.1 pypi_0 pypi
schpl 1.0.5 pypi_0 pypi
scikit-image 0.24.0 pypi_0 pypi
scikit-learn 1.5.2 pypi_0 pypi
scipy 1.14.1 pypi_0 pypi
scvi-tools 1.2.0 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
send2trash 1.8.3 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 75.6.0 pyhff2d567_0 conda-forge
shapely 2.0.6 pypi_0 pypi
simplejson 3.19.3 pypi_0 pypi
six 1.16.0 pypi_0 pypi
sknw 0.15 pypi_0 pypi
sleef 3.7 h8391f65_2 conda-forge
slicerator 1.1.0 pypi_0 pypi
sniffio 1.3.1 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
soupsieve 2.6 pypi_0 pypi
sparse 0.15.4 pypi_0 pypi
spatial-image 1.1.0 pypi_0 pypi
spatialdata 0.2.5.post0 pypi_0 pypi
spatialdata-plot 0.2.7 pypi_0 pypi
squidpy 1.6.2 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
statsmodels 0.14.4 pypi_0 pypi
stdlib-list 0.11.0 pypi_0 pypi
sympy 1.13.3 pyh2585a3b_104 conda-forge
tblib 3.0.0 pypi_0 pypi
tensorboard 2.18.0 pypi_0 pypi
tensorboard-data-server 0.7.2 pypi_0 pypi
tensorstore 0.1.68 pypi_0 pypi
terminado 0.18.1 pypi_0 pypi
texttable 1.7.0 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2024.9.20 pypi_0 pypi
tinycss2 1.4.0 pypi_0 pypi
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.1.0 pypi_0 pypi
toolz 1.0.0 pypi_0 pypi
torchgmm 0.1.2 pypi_0 pypi
torchmetrics 1.6.0 pypi_0 pypi
tornado 6.4.2 pypi_0 pypi
tqdm 4.67.0 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
typeguard 4.4.1 pypi_0 pypi
types-python-dateutil 2.9.0.20241003 pypi_0 pypi
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024.2 pypi_0 pypi
umap-learn 0.5.7 pypi_0 pypi
uri-template 1.3.0 pypi_0 pypi
urllib3 1.26.20 pypi_0 pypi
validators 0.34.0 pypi_0 pypi
wcwidth 0.2.13 pypi_0 pypi
webcolors 24.11.1 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.8.0 pypi_0 pypi
werkzeug 3.1.3 pypi_0 pypi
wheel 0.45.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.13 pypi_0 pypi
wrapt 1.17.0 pypi_0 pypi
xarray 2024.3.0 pypi_0 pypi
xarray-dataclasses 1.8.0 pypi_0 pypi
xarray-datatree 0.0.15 pypi_0 pypi
xarray-schema 0.0.3 pypi_0 pypi
xarray-spatial 0.4.0 pypi_0 pypi
xz 5.2.6 h57fd34a_0 conda-forge
yarl 1.18.0 pypi_0 pypi
zarr 2.18.3 pypi_0 pypi
zict 3.0.0 pypi_0 pypi
zipp 3.21.0 pypi_0 pypi |
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Now the packages look great! The Regarding the notebook error, it's my bad, I have to make the documentation clearer. In alternative, the quickest solution is just to download the 3 files of the trVAE model from the GitHub page and place them in the appropriate directory. |
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hey @marcovarrone I have some general questions about usage of cellcharter, where would you prefer to discuss these? Intuitively I went to image.sc but it seems there is nothing there, and also not in scverse (btw we are starting a spatial proteomics group). I guess we could also zoom :) |
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Perfect @josenimo! I enabled "Discussions" in the repository. |
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Actually I am reopening it as a reminder to change the notebooks and documentation |
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In that case I can report that sq.pl.spatial_scatter(
adata,
color='sample',
library_key='sample',
img=None,
title=['BALBc-3'],
size=2500,
connectivity_key='spatial_connectivities',
edges_width=0.3,
legend_loc=None,
crop_coord=(900000, 900000, 1700000, 1700000 ),
library_id=['BALBc-3']
)runs into an error because can't find adata.obsm['spatial_connectivities'] If you need any testers let me know :) |
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Did you run |
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I did not, hehe, my bad, now it works! |
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This is slowly becoming a tutorial troubleshooting thread 😅 My kernel crashes when reaching the gmm.fit(adata, use_rep='X_cellcharter')I get: With a very useless jupyter log about how it failed, any tips here? |
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No problem! |
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I did, to understand the elements and stuff, as predicted by tutorial: I am on a MacOS Sonoma, M2 Pro, 16GB Memory. |
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The installation is not working as expected, and I am not able to run tutorial imports correctly (especifically lightning).
I think that I am not able to get a stable env going, any help for a MacOS would be super appreciated :)
If I ignore that requirement, I can continue with the tutorial until:
Here I get that scarches is not installed
If i try
import scarchesthis happens:import scarches error
Here is my very long traceback of installing the environment:
https://gist.github.com/josenimo/b694b7edf7822ae0bbd9eac768ec294c
Version information
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