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theislab / scCODA

A Bayesian model for compositional single-cell data analysis
BSD 3-Clause "New" or "Revised" License
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module 'pertpy.plot' has no attribute 'coda' #92

Closed Marwansha closed 4 months ago

Marwansha commented 4 months ago

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

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

johannesostner commented 4 months ago

Hi! The second tutorial is based on a complete reimplementation of scCODA in the pertpy package. I see that you already opened the same issue there, so I'll close this one