From a0d0be210e9bc1c41bfdb599348a6460f310fea8 Mon Sep 17 00:00:00 2001
From: anushka255 <66816733+anushka255@users.noreply.github.com>
Date: Tue, 6 Aug 2024 11:48:44 -0400
Subject: [PATCH] minor update (#1)

 added pytest as dependency; added init file under test directory;  getting rid of glob from test
---
 environment.yml   | 10 +++++-----
 requirements.txt  |  1 +
 tests/__init__.py |  0
 tests/conftest.py | 19 +++++++++----------
 4 files changed, 15 insertions(+), 15 deletions(-)
 create mode 100644 tests/__init__.py

diff --git a/environment.yml b/environment.yml
index c5f4291..938dc27 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,10 +1,10 @@
 name: 'paste'
 
 channels:
-	- defaults
+    - defaults
 
 dependencies:
-	- python=3.8
-	- pip
-	- pip:
-		  - -r requirements.txt
\ No newline at end of file
+    - python=3.8
+    - pip
+    - pip:
+        - -r requirements.txt
diff --git a/requirements.txt b/requirements.txt
index f366f98..564b213 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,3 +5,4 @@ numpy
 scipy
 scikit-learn>=0.24.0
 IPython>=7.18.1
+pytest
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/conftest.py b/tests/conftest.py
index cdc9ff5..d6cc0ff 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,24 +1,23 @@
 from pathlib import Path
-
 import numpy as np
 import scanpy as sc
-import glob
 import pytest
 
 base_dir = Path(__file__).parent.parent
-data_folder = base_dir / "sample_data"
+data_dir = base_dir / "sample_data"
 
 
 @pytest.fixture(scope="session")
 def slices():
-    # Returns ann data object relating each slices
-    slice_files = glob.glob(f"{data_folder}/slice[0-9].csv")
-    coord_files = glob.glob(f"{data_folder}/slice[0-9]_coor.csv")
-
     slices = []
-    for slice, coord in zip(slice_files, coord_files):
-        _slice = sc.read_csv(Path(slice))
-        _slice.obsm["spatial"] = np.genfromtxt(coord, delimiter=",")
+    for i in range(1, 5):
+        # File path of slices and respective coordinates
+        s_fpath = Path(f"{data_dir}/slice{i}.csv")
+        c_fpath = Path(f"{data_dir}/slice{i}_coor.csv")
+
+        # Create ann data object of each slice and add other properties
+        _slice = sc.read_csv(s_fpath)
+        _slice.obsm["spatial"] = np.genfromtxt(c_fpath, delimiter=",")
         _slice.obsm["weights"] = np.ones((_slice.shape[0],)) / _slice.shape[0]
         slices.append(_slice)