From c6f960ca8aabccf52921588f54e85595e05c36b5 Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Wed, 21 Feb 2024 11:47:35 +0100
Subject: [PATCH] (chore): remove wrapper

---
 .../tl/__init__.py                            |  2 +-
 src/multi_condition_comparisions/tl/de.py     |  2 +-
 .../tl/wrapper.py                             | 60 -------------------
 3 files changed, 2 insertions(+), 62 deletions(-)
 delete mode 100644 src/multi_condition_comparisions/tl/wrapper.py

diff --git a/src/multi_condition_comparisions/tl/__init__.py b/src/multi_condition_comparisions/tl/__init__.py
index 648a422..7bdce14 100644
--- a/src/multi_condition_comparisions/tl/__init__.py
+++ b/src/multi_condition_comparisions/tl/__init__.py
@@ -1 +1 @@
-from . import de, wrapper
+from . import de
diff --git a/src/multi_condition_comparisions/tl/de.py b/src/multi_condition_comparisions/tl/de.py
index 1b0c049..98c0af1 100644
--- a/src/multi_condition_comparisions/tl/de.py
+++ b/src/multi_condition_comparisions/tl/de.py
@@ -479,4 +479,4 @@ def _test_single_contrast(self, contrast: List[str], **kwargs) -> pd.DataFrame:
         # Convert results to pandas
         de_res = ro.conversion.rpy2py(ro.globalenv["de_res"])
 
-        return de_res.rename(columns={"PValue": "pvals", "logFC": "logfoldchanges", "FDR": "pvals_adj"})
+        return de_res.rename(columns={"PValue": "pvals", "logFC": "logfoldchanges", "FDR": "pvals_adj"})
\ No newline at end of file
diff --git a/src/multi_condition_comparisions/tl/wrapper.py b/src/multi_condition_comparisions/tl/wrapper.py
deleted file mode 100644
index 89ea92c..0000000
--- a/src/multi_condition_comparisions/tl/wrapper.py
+++ /dev/null
@@ -1,60 +0,0 @@
-from typing import List
-
-import numpy as np
-import pandas as pd
-import scanpy as sc
-from anndata import AnnData
-
-from multi_condition_comparisions.tl.de import BaseMethod
-
-def run_de(adata: AnnData, contrasts: str | List[str] | dict[str, np.ndarray],
-           method: str, design: str | np.ndarray | None = None,mask: str | None = None,layer: str | None = None, **kwargs):
-    '''
-    Wrapper function to run differential expression analysis.
-
-    Params:
-    ----------
-    adata
-        AnnData object, usually pseudobulked.
-    contrasts
-        Columns of .obs to perform contrasts with.
-    method
-        Method to perform DE.
-    design (optional)
-        Model design. Can be either a design matrix, a formulaic formula. If None, contrasts should be provided.
-    mask (optional)
-        A column in adata.var that contains a boolean mask with selected features.
-    layer (optional)
-        Layer to use in fit(). If None, use the X matrix.
-    **kwargs
-        Keyword arguments specific to the method implementation.
-    '''
-    
-    
-    ## TODO: Extract design matrix with Cond function
-    if design is not None:
-        design = np.array()
-        
-    ## TODO: Extract contrasts based on Cond function
-    if not isinstance(contrasts, dict):
-        contrasts = {} 
-
-    
-    ## TODO: Get pseudobulk adata with pseudobulk function
-    pb_adata = AnnData()
-    
-    ## Initialise object
-    pb_adata = BaseMethod(pb_adata, design, mask = mask, layer= layer)
-    
-    ## Fit model
-    pb_adata.fit(**kwargs)
-    
-    ## Test contrasts
-    de_res = pb_adata.test_contrasts(contrasts, **kwargs)
-
-    
-    ## TODO: Standardise column names
-    
-    
-    return de_res
-