rename to scBSP

YQ-Wang · Dec 7, 2023 · 0200738 · 0200738
1 parent f04126a
commit 0200738
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Showing 6 changed files with 13 additions and 13 deletions.
diff --git a/Makefile b/Makefile
@@ -18,7 +18,7 @@ test: clean
 
 # Target for running MyPy
 mypy: clean
-	@$(MYPY) bsp2/
+	@$(MYPY) scbsp/
 	@make clean_mypy_cache
 
 

diff --git a/README.md b/README.md
@@ -1,12 +1,12 @@
-# bsp2
-bsp2 is a specialized package designed for processing biological data, specifically in the analysis of gene expression and cell coordinates. It efficiently computes p-values for a given set of genes based on input matrices representing cell coordinates and gene expression data.
+# scBSP
+scBSP is a specialized package designed for processing biological data, specifically in the analysis of gene expression and cell coordinates. It efficiently computes p-values for a given set of genes based on input matrices representing cell coordinates and gene expression data.
 
 ## Installation
-`pip install "git+https://github.com/YQ-Wang/bsp2.git"`
+`pip install "git+https://github.com/YQ-Wang/scBSP.git"`
 
 ## Usage
 
-To use bsp2, you need to provide two primary inputs:
+To use scBSP, you need to provide two primary inputs:
 
 1. **Cell Coordinates Matrix (`input_sp_mat`)**: 
    - Format: Numpy array.
@@ -24,7 +24,7 @@ Additionally, you must specify the following parameters:
 ### Example
 
 ```python
-import bsp2
+import scbsp
 
 # Example data loading
 input_sp_mat = ...
@@ -35,9 +35,9 @@ d1 = ...
 d2 = ...
 
 # Calculate p-values
-p_values = bsp2.granp(input_sp_mat, input_exp_mat_raw, d1, d2)
+p_values = scbsp.granp(input_sp_mat, input_exp_mat_raw, d1, d2)
 ```
 
 ## Output
 
-The output of bsp2 is a list of p-values corresponding to the given genes.
+The output of scBSP is a list of p-values corresponding to the given genes.
diff --git a/bsp2/__init__.py → scbsp/__init__.py b/bsp2/__init__.py → scbsp/__init__.py
@@ -5,4 +5,4 @@
 """
 
 
-from bsp2.bsp2 import granp
+from scbsp.scbsp import granp
diff --git a/bsp2/bsp2.py → scbsp/scbsp.py b/bsp2/bsp2.py → scbsp/scbsp.py
diff --git a/setup.py b/setup.py
@@ -4,13 +4,13 @@
     long_description = f.read()
 
 setup(
-    name="bsp2",
+    name="scbsp",
     version="0.0.1",
     description="A package that efficiently computes p-values for a given set of genes based on input matrices representing cell coordinates and gene expression data",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    packages=["bsp2"],
-    url="https://github.com/YQ-Wang/bsp2",
+    packages=["scbsp"],
+    url="https://github.com/YQ-Wang/scBSP",
     author="Jinpu Li, Yiqing Wang",
     author_email="lijinp@health.missouri.edu, yiqing@wangemail.com",
     license="GPLv3",

diff --git a/test/test_bsp2.py → test/test_scbsp.py b/test/test_bsp2.py → test/test_scbsp.py
@@ -5,7 +5,7 @@
 from scipy.sparse import csr_matrix
 from scipy.sparse import random as sparse_random
 
-from bsp2.bsp2 import (
+from scbsp.scbsp import (
     _binary_distance_matrix_threshold,
     _scale_sparse_matrix,
     _spvars,
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,4 +5,4 @@
		"""


		from bsp2.bsp2 import granp
		from scbsp.scbsp import granp