Accurate requirements to setup the environment on Windows

[pbilinskyi]

Hi! First of all, thanks for creating this amazing model. Unfortunately, it was quite a challenge for me to setup the virtual environment. Maybe it has something to do with my operation system (Windows). I got into numerous dependency conflicts, but I resolved them and managed to set up the environment. I wanted to share my experience and help other people, who might encounter problems with environment.

OS: Windows Virtual environment tool: venv Python version: 3.7.9 pip version: 21.1.3

Now about packages and versions. First of all, you will need to install the jaxlib package from the wheel, using the custom file. The file can be found in the web. In requirements.txt add: jaxlib @ path/to/jaxlib-0.3.22-cp37-cp37m-win_amd64.whl

And requirements.txt:

absl-py==1.3.0
adjustText==0.8
aiohttp==3.8.4
aiosignal==1.3.1
anndata==0.8.0
async-timeout==4.0.2
asynctest==0.13.0
attrs==23.1.0
backcall==0.2.0
cached-property==1.5.2
cachetools==5.3.0
certifi==2023.5.7
charset-normalizer==3.1.0
chex==0.1.5
colorama==0.4.6
contextlib2==21.6.0
cycler==0.11.0
debugpy==1.6.7
decorator==5.1.1
dm-tree==0.1.8
docrep==0.3.2
entrypoints==0.4
et-xmlfile==1.1.0
etils==0.9.0
exceptiongroup==1.1.1
flax==0.6.4
fonttools==4.38.0
frozenlist==1.3.3
fsspec==2023.1.0
google-auth==2.18.0
google-auth-oauthlib==0.4.6
grpcio==1.54.0
h5py==3.8.0
idna==3.4
importlib-metadata==1.7.0
importlib-resources==5.12.0
iniconfig==2.0.0
ipykernel==6.16.2
ipython==7.34.0
ipywidgets==8.0.6
jax==0.3.25
jedi==0.18.2
joblib==1.2.0
jupyter-client==7.4.9
jupyter-core==4.12.0
jupyterlab-widgets==3.0.7
kiwisolver==1.4.4
llvmlite==0.39.1
Markdown==3.3.4
markdown-it-py==2.2.0
MarkupSafe==2.1.2
matplotlib==3.5.3
matplotlib-inline==0.1.6
mdurl==0.1.2
ml-collections==0.1.1
msgpack==1.0.5
mudata==0.2.1
multidict==6.0.4
multipledispatch==0.6.0
natsort==8.3.1
nest-asyncio==1.5.6
networkx==2.6.3
numba==0.56.4
numpy==1.21.6
numpyro==0.10.1
oauthlib==3.2.2
openpyxl==3.1.2
opt-einsum==3.3.0
optax==0.1.4
orbax==0.1.0
packaging==23.1
pandas==1.3.5
parso==0.8.3
patsy==0.5.3
pickleshare==0.7.5
Pillow==9.5.0
pluggy==1.0.0
prompt-toolkit==3.0.38
protobuf==3.20.3
psutil==5.9.5
pyasn1==0.5.0
pyasn1-modules==0.3.0
pyDeprecate==0.3.2
Pygments==2.15.1
pynndescent==0.5.7
pyparsing==3.0.9
pyro-api==0.1.2
pyro-ppl==1.8.4
pytest==7.3.1
python-dateutil==2.8.2
pytorch-lightning==1.7.7
pytz==2023.3
pywin32==306
PyYAML==6.0
pyzmq==25.0.2
requests==2.30.0
requests-oauthlib==1.3.1
rich==13.3.5
rsa==4.9
scanpy==1.9.3
scgen==2.1.0
scikit-learn==1.0.2
scipy==1.7.3
scvi-tools==0.19.0
seaborn==0.12.2
session-info==1.0.0
six==1.16.0
statsmodels==0.13.5
stdlib-list==0.8.0
tensorboard==2.11.2
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorstore==0.1.28
threadpoolctl==3.1.0
tomli==2.0.1
toolz==0.12.0
torch==1.13.1
torchmetrics==0.11.4
tornado==6.2
tqdm==4.65.0
traitlets==5.9.0
typing-extensions==4.5.0
umap-learn==0.5.3
urllib3==1.26.15
wcwidth==0.2.6
Werkzeug==2.2.3
widgetsnbextension==4.0.7
yarl==1.9.2
zipp==3.15.0