diff --git a/_preprocessing/prepare_input_datasets.py b/_preprocessing/prepare_input_datasets.py index 54fd514..e42fffc 100644 --- a/_preprocessing/prepare_input_datasets.py +++ b/_preprocessing/prepare_input_datasets.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:conda-2023-atlas-protocol] # language: python diff --git a/_preprocessing/subsample_luca.py b/_preprocessing/subsample_luca.py index 2530a7b..548a654 100644 --- a/_preprocessing/subsample_luca.py +++ b/_preprocessing/subsample_luca.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:.conda-pircher-sc-integrate2] # language: python diff --git a/docs/notebooks/01_merge.py b/docs/notebooks/01_merge.py index 6027503..da1654a 100644 --- a/docs/notebooks/01_merge.py +++ b/docs/notebooks/01_merge.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # --- # %% [markdown] diff --git a/docs/notebooks/02_qc.py b/docs/notebooks/02_qc.py index 67122bd..a614c71 100644 --- a/docs/notebooks/02_qc.py +++ b/docs/notebooks/02_qc.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:conda-2023-atlas-protocol] # language: python diff --git a/docs/notebooks/03_seed_annotation.py b/docs/notebooks/03_seed_annotation.py index 7cac5a2..d9ff0d5 100644 --- a/docs/notebooks/03_seed_annotation.py +++ b/docs/notebooks/03_seed_annotation.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:conda-2023-atlas-protocol] # language: python diff --git a/docs/notebooks/04_integrate_scvi.py b/docs/notebooks/04_integrate_scvi.py index a58880e..1a0c015 100644 --- a/docs/notebooks/04_integrate_scvi.py +++ b/docs/notebooks/04_integrate_scvi.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # --- # %% [markdown] diff --git a/docs/notebooks/05_cell_type_annotation.py b/docs/notebooks/05_cell_type_annotation.py index 2e7c9b8..95a9ab7 100644 --- a/docs/notebooks/05_cell_type_annotation.py +++ b/docs/notebooks/05_cell_type_annotation.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:conda-2023-atlas-protocol] # language: python diff --git a/docs/notebooks/06_differential_expression.py b/docs/notebooks/06_differential_expression.py index 427d9ca..a3d6069 100644 --- a/docs/notebooks/06_differential_expression.py +++ b/docs/notebooks/06_differential_expression.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:conda-2023-atlas-protocol] # language: python diff --git a/docs/notebooks/09_compositional.py b/docs/notebooks/09_compositional.py index 30935c9..b640375 100644 --- a/docs/notebooks/09_compositional.py +++ b/docs/notebooks/09_compositional.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:conda-2023-atlas-protocol] # language: python diff --git a/docs/notebooks/10_bulk_integration.py b/docs/notebooks/10_bulk_integration.py index f70a4f8..686fad6 100644 --- a/docs/notebooks/10_bulk_integration.py +++ b/docs/notebooks/10_bulk_integration.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: Python [conda env:conda-2023-atlas-protocol] # language: python diff --git a/docs/notebooks/10_functional_analysis.py b/docs/notebooks/10_functional_analysis.py index d0dd710..cd05072 100644 --- a/docs/notebooks/10_functional_analysis.py +++ b/docs/notebooks/10_functional_analysis.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: 'SSH apollo-15 apollo-15: mmCD45' # language: '' diff --git a/docs/notebooks/15_cell_cell_communication.py b/docs/notebooks/15_cell_cell_communication.py index 47b88f4..f0b3cda 100644 --- a/docs/notebooks/15_cell_cell_communication.py +++ b/docs/notebooks/15_cell_cell_communication.py @@ -5,7 +5,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.15.0 +# jupytext_version: 1.16.1 # kernelspec: # display_name: atlas_protocol # language: python diff --git a/src/atlas_protocol_scripts/tl/_cell2cell.py b/src/atlas_protocol_scripts/tl/_cell2cell.py index 205f928..fb48a08 100644 --- a/src/atlas_protocol_scripts/tl/_cell2cell.py +++ b/src/atlas_protocol_scripts/tl/_cell2cell.py @@ -2,6 +2,7 @@ Focuses on differential cellphonedb analysis between conditions. """ + from typing import Literal import altair as alt