Try fix

kevinmicha · Dec 12, 2023 · 624fb5a · 624fb5a
1 parent 9af7bf7
commit 624fb5a
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/antipasti-env.yml b/antipasti-env.yml
@@ -15,7 +15,6 @@ dependencies:
   - umap-learn>=0.5.3
   - pip:
     - adabelief-pytorch>=0.2.1
-    - beautifulsoup4>=4.12.2
     - biopython>=1.79
     - opencv-python>=4.7.0.68
     - optuna>=3.1.1

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,9 +1,10 @@
 adabelief-pytorch>=0.2.1
-beautifulsoup4>=4.12.2
+biopython>=1.79
 coverage>=7.2.5
 matplotlib>=3.6.2
 numpy>=1.23.3
 opencv-python>=4.7.0.68
+optuna>=3.1.1
 pandas>=1.3.2
 pytest>=7.1.2
 requests>=2.28.2

diff --git a/setup.py b/setup.py
@@ -20,6 +20,6 @@ def run_tests(self):
     author_email='[email protected]',
     description='Deep Learning model that predicts the binding affinity of antibodies from their sequence and three-dimensional structure.',
     packages=['antipasti', 'antipasti.model', 'antipasti.preprocessing', 'antipasti.utils'],
-    install_requires=['adabelief-pytorch', 'beautifulsoup4', 'biopython', 'matplotlib', 'numpy', 'opencv-python', 'optuna', 'pandas', 'requests', 'scikit-learn', 'scipy', 'torch', 'torchmetrics', 'umap-learn'],
+    install_requires=['adabelief-pytorch', 'biopython', 'matplotlib', 'numpy', 'opencv-python', 'optuna', 'pandas', 'requests', 'scikit-learn', 'scipy', 'torch', 'torchmetrics', 'umap-learn'],
     cmdclass={'test': PyTest}
 )
diff --git a/tests/preprocessing_test.py b/tests/preprocessing_test.py
@@ -15,7 +15,7 @@ def setUp(self):
         self.pathological = ['5omm', '5i5k', '1uwx', '1mj7', '1qfw', '1qyg', '4ffz', '3ifl', '3lrh', '3pp4', '3ru8', '3t0w', '3t0x', '4fqr', '4gxu', '4jfx', '4k3h', '4jfz', '4jg0', '4jg1', '4jn2', '4o4y', '4qxt', '4r3s', '4w6y', '4w6y', '5ies', '5ivn', '5j57', '5kvd', '5kzp', '5mes', '5nmv', '5sy8', '5t29', '5t5b', '5vag', '3etb', '3gkz', '3uze', '3uzq', '4f9l', '4gqp', '4r2g', '5c6t', '3fku', '1oau', '1oay'] + ['4gqp', '3etb', '3gkz', '3uze', '3uzq', '3gm0', '4f9l', '6ejg', '6ejm', '1h8s', '5dfw', '6cbp', '4f9p', '5kov', '1dzb', '5j74', '5aaw', '3uzv', '5aam', '3ux9', '5a2j', '5a2k', '5a2i', '3fku', '5yy4', '3uyp', '5jyl', '1y0l', '1p4b', '3kdm', '4lar', '4ffy', '2ybr', '1mfa', '5xj3', '5xj4', '4kv5', '5vyf'] 
 
     def test_new_maps(self):
-        Preprocessing(data_path=self.data_path, structures_path=self.structures_path, scripts_path=self.scripts_path, df=self.df, pathological=self.pathological, renew_maps=True, renew_residues=False)
+        Preprocessing(data_path=self.data_path, structures_path=self.structures_path, scripts_path=self.scripts_path, df=self.df, pathological=self.pathological, renew_maps=True, renew_residues=True)
 
     def test_new_lengths(self):
         Preprocessing(data_path=self.data_path, structures_path=self.structures_path, scripts_path=self.scripts_path, df=self.df, pathological=self.pathological, renew_maps=False, renew_residues=True)
@@ -27,4 +27,4 @@ def test_contact_maps(self):
         Preprocessing(data_path=self.data_path, structures_path=self.structures_path, scripts_path=self.scripts_path, df=self.df, pathological=self.pathological, renew_maps=True, renew_residues=False, cmaps=True)
 
     def test_antigen_agnostic(self):
-        Preprocessing(data_path=self.data_path, structures_path=self.structures_path, scripts_path=self.scripts_path, df=self.df, pathological=self.pathological, renew_maps=True, renew_residues=False, ag_agnostic=True)
+        Preprocessing(data_path=self.data_path, structures_path=self.structures_path, scripts_path=self.scripts_path, df=self.df, pathological=self.pathological, renew_maps=True, renew_residues=True, ag_agnostic=True)