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Drop iPython dependency and simple print instead #188

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merged 3 commits into from
Oct 19, 2023
Merged

Drop iPython dependency and simple print instead #188

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5cb50c5
remove ipython requirement from setup.py
adamgayoso Oct 18, 2023
8861e31
Add ipython to docs requirements
adamgayoso Oct 18, 2023
8a31abf
Replace display with print
adamgayoso Oct 18, 2023
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1 change: 1 addition & 0 deletions docs/requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -13,3 +13,4 @@ sphinx_gallery==0.11.1
sphinx_autodoc_typehints
sphinxcontrib-bibtex==2.5.0
gitpython>=3.1.27
ipython
5 changes: 2 additions & 3 deletions pydeseq2/ds.py
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Expand Up @@ -8,7 +8,6 @@
import numpy as np
import pandas as pd
import statsmodels.api as sm # type: ignore
from IPython.display import display # type: ignore
from joblib import Parallel # type: ignore
from joblib import delayed # type: ignore
from joblib import parallel_backend # type: ignore
Expand Down Expand Up @@ -282,7 +281,7 @@ def summary(
f"Log2 fold change & Wald test p-value: "
f"{self.contrast[0]} {self.contrast[1]} vs {self.contrast[2]}"
)
display(self.results_df)
print(self.results_df)

def run_wald_test(self) -> None:
"""Perform a Wald test.
Expand Down Expand Up @@ -496,7 +495,7 @@ def lfc_shrink(self, coeff: Optional[str] = None) -> None:
f"{split_coeff[0]} {split_coeff[1]} vs {split_coeff[3]}"
)

display(self.results_df)
print(self.results_df)

def plot_MA(self, log: bool = True, save_path: Optional[str] = None, **kwargs):
"""
Expand Down
1 change: 0 additions & 1 deletion setup.py
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Expand Up @@ -28,7 +28,6 @@
packages=find_packages(exclude=["tests*"]),
install_requires=[
"anndata>=0.8.0",
"ipython",
"numpy>=1.23.0",
"pandas>=1.4.0",
"scikit-learn>=1.1.0",
Expand Down