AttributeError: module 'pertpy.plot' has no attribute 'coda' #540
Description
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Hi,
i have started using scCODA and it was working normal while replication this tutorial (https://sccoda.readthedocs.io/en/latest/getting_started.html) ,
put when i tried to repicate the tutorial here https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/sccoda.html ( same one in best practices book), i get this error
sccoda_model = pt.tl.Sccoda()
AttributeError Traceback (most recent call last)
Cell In[71], line 1
----> 1 pt.pl.coda.effects_barplot(sim_results, "coda", "condition")
2 plt.show()
AttributeError: module 'pertpy.plot' has no attribute 'coda'
here is my environment installed packages , i just created a new environment and installed this
pip3 install torch ipykernel scanpy scipy numpy pandas altair pertpy
pip3 install tesnorflow
pip3 install ete3
pip3 install sccoda
Version information
oi had error with=["pybind11_abseil"]) so i did session_info.show(html=False, dependencies=True, excludes=["pybind11_abseil"])
altair 5.2.0
anndata 0.10.5.post1
matplotlib 3.8.3
mudata 0.2.3
numpy 1.26.4
pandas 2.2.0
pertpy 0.6.0
scanpy 1.9.8
sccoda 0.1.9
seaborn 0.13.2
session_info 1.0.0
tensorflow 2.15.0
torch 2.2.0+cu121
97d2165b493fecec79c65b5c6254dffd4e375528 NA
PIL 10.2.0
absl NA
adjustText 1.0.4
arviz 0.17.0
asttokens NA
astunparse 1.6.3
attr 23.2.0
attrs 23.2.0
certifi 2024.02.02
chardet 5.2.0
charset_normalizer 3.3.2
chex 0.1.85
cloudpickle 3.0.0
comm 0.2.1
contextlib2 NA
cycler 0.12.1
cython_runtime NA
dateutil 2.8.2
debugpy 1.8.1
decorator 5.1.1
decoupler 1.5.0
docrep 0.3.2
etils 1.5.2
exceptiongroup 1.2.0
executing 2.0.1
flatbuffers 23.5.26
flax 0.8.1
fsspec 2024.2.0
gast 0.5.4
google NA
h5py 3.10.0
idna 3.6
igraph 0.11.4
importlib_metadata NA
importlib_resources NA
ipykernel 6.29.2
ipywidgets 8.1.2
jax 0.4.24
jaxlib 0.4.24
jaxopt NA
jedi 0.19.1
jinja2 3.1.3
joblib 1.3.2
jsonschema 4.21.1
jsonschema_specifications NA
keras 2.15.0
kiwisolver 1.4.5
leidenalg 0.10.2
lightning 2.1.4
lightning_fabric 2.2.0.post0
lightning_utilities 0.10.1
llvmlite 0.42.0
markupsafe 2.1.5
matplotlib_inline 0.1.6
mizani 0.9.3
ml_collections NA
ml_dtypes 0.2.0
mpl_toolkits NA
msgpack 1.0.7
multipledispatch 0.6.0
natsort 8.4.0
numba 0.59.0
numpyro 0.13.2
opt_einsum v3.3.0
optax 0.1.9
ott 0.4.5
packaging 23.2
parso 0.8.3
patsy 0.5.6
pexpect 4.9.0
pkg_resources NA
platformdirs 4.2.0
plotnine 0.12.4
ply 3.11
prompt_toolkit 3.0.43
psutil 5.9.8
ptyprocess 0.7.0
pure_eval 0.2.2
pydev_ipython NA
pydevconsole NA
pydevd 2.9.5
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.17.2
pyomo 6.7.0
pyparsing 3.1.1
pyro 1.8.6
pytorch_lightning 2.2.0.post0
pytz 2024.1
referencing NA
requests 2.31.0
rich NA
rpds NA
scipy 1.12.0
scvi 1.1.0.post2
setuptools 69.1.0
six 1.16.0
sklearn 1.4.1.post1
skmisc 0.3.1
sparsecca 0.3.1
stack_data 0.6.3
statsmodels 0.14.1
stdlib_list 0.10.0
tensorboard 2.15.2
tensorflow_probability 0.23.0
termcolor NA
texttable 1.7.0
threadpoolctl 3.3.0
toolz 0.12.1
torchgen NA
torchmetrics 1.3.1
tornado 6.4
tqdm 4.66.2
traitlets 5.14.1
tree 0.1.8
typing_extensions NA
urllib3 2.2.1
wcwidth 0.2.13
wrapt 1.14.1
xarray 2024.2.0
xarray_einstats 0.7.0
yaml 6.0.1
zipp NA
zmq 25.1.2
zoneinfo NA
IPython 8.18.1
jupyter_client 8.6.0
jupyter_core 5.7.1
Python 3.9.16 (main, May 17 2023, 08:58:38) [GCC 9.2.0]
Linux-4.18.0-477.43.1.el8_8.x86_64-x86_64-with-glibc2.28
Session information updated at 2024-02-19 16:57