CostaLab · ruthvik07 · Apr 30, 2025 · Apr 30, 2025 · Apr 30, 2025 · Apr 30, 2025
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v4

diff --git a/dist/pycrosstalker-0.1.0-py3-none-any.whl b/dist/pycrosstalker-0.1.0-py3-none-any.whl
diff --git a/dist/pycrosstalker-0.1.0.tar.gz b/dist/pycrosstalker-0.1.0.tar.gz
diff --git a/docs/source/notebooks/output/LR_data.pkl b/docs/source/notebooks/output/LR_data.pkl
diff --git a/docs/source/notebooks/output/LR_data_final.pkl b/docs/source/notebooks/output/LR_data_final.pkl
diff --git a/docs/source/notebooks/pyCrossTalkeR.ipynb b/docs/source/notebooks/pyCrossTalkeR.ipynb
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -18,6 +18,10 @@ adjustText = "^1.2.0"
 scikit-learn = "^1.5.1"
 igraph = "^0.11.6"
 tqdm = "^4.66.5"
+attrs = "^25.3.0"
+plotly = "^6.0.1"
+sankeyflow = "^0.4.1"
+gprofiler-official = "1.0.0"
 
 [build-system]
 requires = ["poetry-core"]

diff --git a/requirements.txt b/requirements.txt
diff --git a/requirements_old.txt b/requirements_old.txt
diff --git a/tutorials/tests/R_data/graph_CTR.csv → test/R_data/graph_CTR.csv b/tutorials/tests/R_data/graph_CTR.csv → test/R_data/graph_CTR.csv
diff --git a/tutorials/tests/R_data/graph_CTR_ggi.csv → test/R_data/graph_CTR_ggi.csv b/tutorials/tests/R_data/graph_CTR_ggi.csv → test/R_data/graph_CTR_ggi.csv
diff --git a/tutorials/tests/R_data/graph_EXP.csv → test/R_data/graph_EXP.csv b/tutorials/tests/R_data/graph_EXP.csv → test/R_data/graph_EXP.csv
diff --git a/tutorials/tests/R_data/graph_EXP_ggi.csv → test/R_data/graph_EXP_ggi.csv b/tutorials/tests/R_data/graph_EXP_ggi.csv → test/R_data/graph_EXP_ggi.csv
diff --git a/tutorials/tests/R_data/graph_EXP_x_CTR.csv → test/R_data/graph_EXP_x_CTR.csv b/tutorials/tests/R_data/graph_EXP_x_CTR.csv → test/R_data/graph_EXP_x_CTR.csv
diff --git a/...tests/R_data/graph_EXP_x_CTR_filtered.csv → test/R_data/graph_EXP_x_CTR_filtered.csv b/...tests/R_data/graph_EXP_x_CTR_filtered.csv → test/R_data/graph_EXP_x_CTR_filtered.csv
diff --git a/...ials/tests/R_data/graph_EXP_x_CTR_ggi.csv → test/R_data/graph_EXP_x_CTR_ggi.csv b/...ials/tests/R_data/graph_EXP_x_CTR_ggi.csv → test/R_data/graph_EXP_x_CTR_ggi.csv
diff --git a/tutorials/tests/R_data/ranking_CTR.csv → test/R_data/ranking_CTR.csv b/tutorials/tests/R_data/ranking_CTR.csv → test/R_data/ranking_CTR.csv
diff --git a/tutorials/tests/R_data/ranking_CTR_ggi.csv → test/R_data/ranking_CTR_ggi.csv b/tutorials/tests/R_data/ranking_CTR_ggi.csv → test/R_data/ranking_CTR_ggi.csv
diff --git a/tutorials/tests/R_data/ranking_EXP.csv → test/R_data/ranking_EXP.csv b/tutorials/tests/R_data/ranking_EXP.csv → test/R_data/ranking_EXP.csv
diff --git a/tutorials/tests/R_data/ranking_EXP_ggi.csv → test/R_data/ranking_EXP_ggi.csv b/tutorials/tests/R_data/ranking_EXP_ggi.csv → test/R_data/ranking_EXP_ggi.csv
diff --git a/tutorials/tests/R_data/ranking_EXP_x_CTR.csv → test/R_data/ranking_EXP_x_CTR.csv b/tutorials/tests/R_data/ranking_EXP_x_CTR.csv → test/R_data/ranking_EXP_x_CTR.csv
diff --git a/...sts/R_data/ranking_EXP_x_CTR_filtered.csv → test/R_data/ranking_EXP_x_CTR_filtered.csv b/...sts/R_data/ranking_EXP_x_CTR_filtered.csv → test/R_data/ranking_EXP_x_CTR_filtered.csv
diff --git a/...ls/tests/R_data/ranking_EXP_x_CTR_ggi.csv → test/R_data/ranking_EXP_x_CTR_ggi.csv b/...ls/tests/R_data/ranking_EXP_x_CTR_ggi.csv → test/R_data/ranking_EXP_x_CTR_ggi.csv
diff --git a/tutorials/tests/R_data/stat_EXP_x_CTR.csv → test/R_data/stat_EXP_x_CTR.csv b/tutorials/tests/R_data/stat_EXP_x_CTR.csv → test/R_data/stat_EXP_x_CTR.csv
diff --git a/...als/tests/R_data/stat_EXP_x_CTR:MannU.csv → test/R_data/stat_EXP_x_CTR:MannU.csv b/...als/tests/R_data/stat_EXP_x_CTR:MannU.csv → test/R_data/stat_EXP_x_CTR:MannU.csv
diff --git a/...sts/R_data/stat_EXP_x_CTR_x_CTR:MannU.csv → test/R_data/stat_EXP_x_CTR_x_CTR:MannU.csv b/...sts/R_data/stat_EXP_x_CTR_x_CTR:MannU.csv → test/R_data/stat_EXP_x_CTR_x_CTR:MannU.csv
diff --git a/tutorials/tests/R_data/table_CTR.csv → test/R_data/table_CTR.csv b/tutorials/tests/R_data/table_CTR.csv → test/R_data/table_CTR.csv
diff --git a/tutorials/tests/R_data/table_EXP.csv → test/R_data/table_EXP.csv b/tutorials/tests/R_data/table_EXP.csv → test/R_data/table_EXP.csv
diff --git a/tutorials/tests/R_data/table_EXP_x_CTR.csv → test/R_data/table_EXP_x_CTR.csv b/tutorials/tests/R_data/table_EXP_x_CTR.csv → test/R_data/table_EXP_x_CTR.csv
diff --git a/..._/test_basic.cpython-313-pytest-7.4.4.pyc → ..._/test_basic.cpython-313-pytest-7.4.4.pyc b/..._/test_basic.cpython-313-pytest-7.4.4.pyc → ..._/test_basic.cpython-313-pytest-7.4.4.pyc
diff --git a/..._/test_basic.cpython-313-pytest-8.3.4.pyc → ..._/test_basic.cpython-313-pytest-8.3.4.pyc b/..._/test_basic.cpython-313-pytest-8.3.4.pyc → ..._/test_basic.cpython-313-pytest-8.3.4.pyc
diff --git a/..._with_R_data.cpython-313-pytest-8.3.4.pyc → ..._with_R_data.cpython-313-pytest-8.3.4.pyc b/..._with_R_data.cpython-313-pytest-8.3.4.pyc → ..._with_R_data.cpython-313-pytest-8.3.4.pyc
diff --git a/..._comparative.cpython-313-pytest-7.4.4.pyc → ..._comparative.cpython-313-pytest-7.4.4.pyc b/..._comparative.cpython-313-pytest-7.4.4.pyc → ..._comparative.cpython-313-pytest-7.4.4.pyc
diff --git a/..._comparative.cpython-313-pytest-8.3.4.pyc → ..._comparative.cpython-313-pytest-8.3.4.pyc b/..._comparative.cpython-313-pytest-8.3.4.pyc → ..._comparative.cpython-313-pytest-8.3.4.pyc
diff --git a/.../test_single.cpython-313-pytest-7.4.4.pyc → .../test_single.cpython-313-pytest-7.4.4.pyc b/.../test_single.cpython-313-pytest-7.4.4.pyc → .../test_single.cpython-313-pytest-7.4.4.pyc
diff --git a/.../test_single.cpython-313-pytest-8.3.4.pyc → .../test_single.cpython-313-pytest-8.3.4.pyc b/.../test_single.cpython-313-pytest-8.3.4.pyc → .../test_single.cpython-313-pytest-8.3.4.pyc
diff --git a/tutorials/tests/test_basic.py → test/test_basic.py b/tutorials/tests/test_basic.py → test/test_basic.py
@@ -3,7 +3,7 @@
 import pickle
 
 # Load data from pickle file
-with open("../output/LR_data.pkl", "rb") as f:
+with open("tutorials/output/LR_data.pkl", "rb") as f:
     data = pickle.load(f)
 
 def test_data_type():

diff --git a/tutorials/tests/test_check_with_R_data.py → test/test_check_with_R_data.py b/tutorials/tests/test_check_with_R_data.py → test/test_check_with_R_data.py
@@ -4,16 +4,16 @@
 import pandas as pd
 
 # Load data from pickle file
-with open("../output/LR_data.pkl", "rb") as f:
+with open("tutorials/output/LR_data.pkl", "rb") as f:
     data = pickle.load(f)
 
 print(f"\nTesting if data from pyCrossTalkeR is similar to data from CrossTalkeR")
 
 def test_check_table_data():
     # Load table data from R
-    data_R_CTR = pd.read_csv('R_data/table_CTR.csv')
-    data_R_EXP = pd.read_csv('R_data/table_EXP.csv')
-    data_R_EXP_x_CTR = pd.read_csv('R_data/table_EXP_x_CTR.csv')
+    data_R_CTR = pd.read_csv('test/R_data/table_CTR.csv')
+    data_R_EXP = pd.read_csv('test/R_data/table_EXP.csv')
+    data_R_EXP_x_CTR = pd.read_csv('test/R_data/table_EXP_x_CTR.csv')
 
     common_columns_CTR = data['tables']['CTR'].columns.intersection(data_R_CTR.columns)
     common_columns_EXP = data['tables']['EXP'].columns.intersection(data_R_EXP.columns)
@@ -37,7 +37,7 @@ def test_check_rankings_data():
     rankings_list = ['CTR', 'EXP', 'EXP_x_CTR', 'EXP_x_CTR_filtered', 'CTR_ggi', 'EXP_ggi', 'EXP_x_CTR_ggi']
     for ranking in rankings_list:
         # Load table data from R
-        ranking_R = pd.read_csv(f'R_data/ranking_{ranking}.csv')
+        ranking_R = pd.read_csv(f'test/R_data/ranking_{ranking}.csv')
         ranking_R = ranking_R.sort_values(by='nodes').reset_index(drop=True)
 
         ranking_py = data['rankings'][ranking].sort_values(by='nodes').reset_index(drop=True)
@@ -55,7 +55,7 @@ def test_check_graphs_data():
     graphs_list = ['CTR', 'EXP', 'EXP_x_CTR',  'EXP_x_CTR_filtered', 'CTR_ggi', 'EXP_ggi', 'EXP_x_CTR_ggi']
     for i, graph in enumerate(graphs_list):
         # Load table data from R
-        graph_R = pd.read_csv(f'R_data/graph_{graph}.csv')
+        graph_R = pd.read_csv(f'test/R_data/graph_{graph}.csv')
         graph_R_df = pd.DataFrame({
             "edge": graph_R['from'] + '-' + graph_R['to'],
             "LRScore": graph_R['LRScore'],
@@ -78,7 +78,7 @@ def test_check_graphs_data():
         print(f"{graph} graph data is similar")
 
 def test_check_stats_data():
-    stats_R = pd.read_csv('R_data/stat_EXP_x_CTR.csv')
+    stats_R = pd.read_csv('test/R_data/stat_EXP_x_CTR.csv')
     stats_R_df = pd.DataFrame({
         "cellpair": stats_R['columns_name'],
         "p_value": stats_R['p'],
@@ -96,7 +96,7 @@ def test_check_stats_data():
     print("\nEXP_x_CTR stats data is similar")
 
     for key in ['EXP', 'EXP_x_CTR']:
-        stats_mannu_R = pd.read_csv(f'R_data/stat_{key}_x_CTR:MannU.csv')
+        stats_mannu_R = pd.read_csv(f'test/R_data/stat_{key}_x_CTR:MannU.csv')
         stats_mannu_R_df = pd.DataFrame({
             "cellpair": stats_mannu_R['cellpair'],
             "p_value": stats_mannu_R['p'],

diff --git a/tutorials/tests/test_comparative.py → test/test_comparative.py b/tutorials/tests/test_comparative.py → test/test_comparative.py
diff --git a/tutorials/tests/test_single.py → test/test_single.py b/tutorials/tests/test_single.py → test/test_single.py
diff --git a/tutorials/output/LR_data.pkl b/tutorials/output/LR_data.pkl
diff --git a/tutorials/output/LR_data_final.pkl b/tutorials/output/LR_data_final.pkl
diff --git a/tutorials/pyCrossTalkeR.ipynb b/tutorials/pyCrossTalkeR.ipynb