fixed dependencies and updated setup.py

mortazavilab · Jul 6, 2023 · 612a0eb · 612a0eb
1 parent bacc2f4
commit 612a0eb
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Showing 3 changed files with 13 additions and 9 deletions.
diff --git a/setup.py b/setup.py
@@ -3,22 +3,22 @@
 setup(
   name = 'swan_vis',
   packages = ['swan_vis'],
-  version = 'v3.0',
+  version = 'v3.2',
   license='MIT',
   description = 'swan is a tool for visualizing and analyzing transcript isoforms',
   author = 'Fairlie Reese',
   author_email = 'fairlie.reese@gmail.com',
   url = 'https://github.com/mortazavilab/swan_vis/',
-  download_url='https://github.com/mortazavilab/swan_vis/archive/refs/tags/v3.0.tar.gz',
+  download_url='https://github.com/mortazavilab/swan_vis/archive/refs/tags/v3.2.tar.gz',
   keywords = ['swan', 'transcription', 'isoform', 'visualization'],
-  python_requires='>=3.6',
+  python_requires='>=3.8',
   install_requires=[
     'fpdf',
     'matplotlib',
     'scipy',
     'statsmodels>=0.12.2',
     'numpy',
-    'pandas>=1.1.0',
+    'pandas<2.0',
     'pytest',
     'networkx>=2.5',
     'tqdm',

diff --git a/swan_vis/utils.py b/swan_vis/utils.py
@@ -930,8 +930,10 @@ def get_die_gene_table(gene_df, conditions, rc):
 		return None, test_result
 
 	# compute isoform-level and gene-level delta pis
-	gene_df[cond1] = gene_df[cond1].astype(float)
-	gene_df[cond2] = gene_df[cond2].astype(float)
+	# gene_df[cond1] = gene_df[cond1].astype(float)
+	# gene_df[cond2] = gene_df[cond2].astype(float)
+	gene_df[cond1] = gene_df[cond1].values.to_dense().astype(np.float64)
+	gene_df[cond2] = gene_df[cond2].values.to_dense().astype(np.float64)
 	gene_df['dpi'] = gene_df[cond1] - gene_df[cond2]
 	test_result = 'testable'
 

diff --git a/tutorials/Analysis tools.ipynb b/tutorials/Analysis tools.ipynb
@@ -586,14 +586,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
+   "execution_count": 2,
+   "metadata": {
+    "tags": []
+   },
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Testing for DIE for each gene: 100%|██████████| 14684/14684 [03:50<00:00, 123.69it/s]"
+      "Testing for DIE for each gene: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 14684/14684 [02:54<00:00, 84.15it/s]\n"
      ]
     }
    ],