theislab
Bootstrap not running
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Hi,
I've been trying to run "Distance.bootstrap(X, Y)" but I get the error: "AttributeError: 'Distance' object has no attribute 'bootstrap'". Any leads as to how to solve will be greatly appreciated.
Here my session_info
anndata 0.10.5.post1 gseapy 1.0.6 matplotlib 3.7.0 numpy 1.26.4 pandas 2.2.2 pertpy 0.7.0 phenograph 1.5.7 scanpy 1.9.8 scipy 1.11.4 seaborn 0.13.2 session_info 1.0.0 sklearn 1.1.3
Cython 3.0.8 PIL 10.2.0 absl NA adjustText 1.1.1 aiohttp 3.9.3 aiosignal 1.3.1 annotated_types 0.6.0 anyio NA appnope 0.1.4 arrow 1.3.0 arviz 0.18.0 asttokens NA attr 23.2.0 attrs 23.2.0 babel 2.14.0 backoff 2.2.1 blitzgsea NA bs4 4.12.3 certifi 2024.02.02 cffi 1.16.0 chardet 5.2.0 charset_normalizer 3.3.2 chex 0.1.85 click 8.1.7 comm 0.2.1 contextlib2 NA croniter NA custom_inherit 2.4.1 cycler 0.12.1 cython 3.0.8 cython_runtime NA dateutil 2.8.2 debugpy 1.8.1 decorator 5.1.1 decoupler 1.7.0 deepdiff 6.7.1 defusedxml 0.7.1 docrep 0.3.2 etils 1.6.0 executing 2.0.1 fastapi 0.109.2 fastjsonschema NA filelock 3.13.1 flax 0.8.1 fqdn NA frozenlist 1.4.1 fsspec 2024.2.0 h5py 3.10.0 idna 3.6 igraph 0.11.3 importlib_resources NA ipykernel 6.29.2 isoduration NA jax 0.4.30 jaxlib 0.4.30 jaxopt NA jedi 0.19.1 jinja2 3.0.3 joblib 1.3.2 json5 NA jsonpointer 2.4 jsonschema 4.21.1 jsonschema_specifications NA jupyter_events 0.9.0 jupyter_server 2.12.5 jupyterlab_server 2.25.2 kiwisolver 1.4.5 leidenalg 0.10.2 lightning 2.0.9.post0 lightning_cloud 0.5.64 lightning_fabric 2.2.0.post0 lightning_utilities 0.10.1 llvmlite 0.43.0 markupsafe 2.1.5 matplotlib_inline 0.1.6 ml_collections NA ml_dtypes 0.3.2 mpl_toolkits NA mpmath 1.3.0 msgpack 1.0.7 mudata 0.2.3 multidict 6.0.5 multipart 0.0.9 multipledispatch 0.6.0 natsort 8.4.0 nbformat 5.9.2 numba 0.60.0 numpyro 0.13.2 opt_einsum v3.3.0 optax 0.1.9 ordered_set 4.1.0 ott 0.4.6 overrides NA packaging 23.2 parso 0.8.3 patsy 0.5.6 pkg_resources NA platformdirs 4.2.0 ply 3.11 png 0.20220715.0 prometheus_client NA prompt_toolkit 3.0.43 psutil 5.9.8 pubchempy 1.0.4 pure_eval 0.2.2 pyarrow 16.1.0 pycparser 2.21 pydantic 2.1.1 pydantic_core 2.4.0 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.17.2 pynndescent 0.5.11 pyomo 6.7.3 pyparsing 3.1.1 pyro 1.8.6 pythonjsonlogger NA pytorch_lightning 2.2.0.post0 pytz 2024.1 pytz_deprecation_shim NA referencing NA reportlab 4.2.0 requests 2.31.0 rfc3339_validator 0.1.4 rfc3986_validator 0.1.1 rich NA rpds NA rpy2 3.5.12 scvi 1.1.0.post2 send2trash NA six 1.16.0 skmisc 0.3.1 sniffio 1.3.0 soupsieve 2.5 sparse 0.15.1 sparsecca 0.3.1 stack_data 0.6.3 starlette 0.36.3 statsmodels 0.14.1 sympy 1.12 texttable 1.7.0 threadpoolctl 3.2.0 toolz 0.12.1 torch 2.2.0 torchgen NA torchmetrics 1.3.1 tornado 6.4 toyplot 1.0.3 toytree 2.0.5 tqdm 4.66.4 traitlets 5.14.1 tree 0.1.8 typing_extensions NA tzlocal NA uri_template NA urllib3 2.0.7 uvicorn 0.27.1 wcwidth 0.2.13 webcolors 1.13 websocket 1.7.0 websockets 12.0 wrapt 1.16.0 xarray 2024.1.1 xarray_einstats 0.7.0 yaml 6.0.1 yarl 1.9.4 zmq 25.1.2
IPython 8.21.0 jupyter_client 8.6.0 jupyter_core 5.7.1 jupyterlab 4.1.1 notebook 7.1.0
Python 3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:38:07) [Clang 16.0.6 ] macOS-13.4-arm64-arm-64bit
Version information
No response
The example here:
https://pertpy.readthedocs.io/en/stable/usage/tools/pertpy.tools.Distance.html#pertpy.tools.Distance.bootstrap
works. Could you please provide more information on how you are running the code?
Thanks for your answer, sure, here what I'm trying to run: distance = pt.tl.Distance("wasserstein", obsm_key="X_pca") X = adatap.obsm["X_pca"][adatap.obs["condition"] == "2HR"] Y = adatap.obsm["X_pca"][adatap.obs["condition"] == "8HR"] dfd_variance = distance.bootstrap(X, Y)
Thanks!
I think it might be something related to installing the GitHub version...
pertpy 0.7.0
this is also not the latest version. Could you try installing the latest version with ``pip install -U pertpy`, please? I also advise you to use Python 3.10 or 3.11+
I just upgraded to 0.8 but still getting the "no attribute 'bootstrap'" error, do you recommend using python 3.10 to fix this?
Hi @aterceros! I wasn't able to reproduce your error either, everything works fine on my end. Yes, please try using python >= 3.10 and let me know if that resolves the issue. Also, you could try running our pertpy example for the bootstrap method to make sure we're running the same code:
adata = pt.dt.distance_example()
Distance = pt.tl.Distance(metric="edistance")
X = adata.obsm["X_pca"][adata.obs["perturbation"] == "p-sgCREB1-2"]
Y = adata.obsm["X_pca"][adata.obs["perturbation"] == "control"]
D = Distance.bootstrap(X, Y)
I'll close this issue for now. @aterceros, please feel free to reopen it if you're still facing the issue.
Sorry for the delay! I wasn't able to test on python 3.10 yet as I have some code running, but I can respond once I test this, thank you for your help!