bdext 0.1.63__tar.gz → 0.1.65__tar.gz

{bdext-0.1.63 → bdext-0.1.65}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bdext
-Version: 0.1.63
+Version: 0.1.65
 Summary: Estimation of BDEISS-CT parameters from phylogenetic trees.
 Home-page: https://github.com/modpath/bdeissct
 Author: Anna Zhukova

{bdext-0.1.63 → bdext-0.1.65}/bdeissct_dl/bdeissct_model.py

@@ -7,7 +7,6 @@ RHO = 'rho'
 INFECTIOUS_TIME = 'd_I'
 REPRODUCTIVE_NUMBER = 'R'
 INFECTION_DURATION = 'd'
-SAMPLING_FRACTION = 'p'
 
 F_E = 'f_E'
 MU = 'mu'
@@ -129,5 +128,5 @@ for model in (BDEISSCT, BDEISSCT1, BDEISSCT2, BDEISSCT2000):
 
 
 
-CT_EPI_COLUMNS = [REPRODUCTIVE_NUMBER, INFECTION_DURATION, SAMPLING_FRACTION, LA, F_E, F_S, X_S, UPSILON, X_C]
-CT_RATE_COLUMNS = [PSI, RHO]
+CT_EPI_COLUMNS = [REPRODUCTIVE_NUMBER, LA, RHO, F_E, F_S, X_S, UPSILON, X_C]
+CT_RATE_COLUMNS = [PSI]

{bdext-0.1.63 → bdext-0.1.65}/bdeissct_dl/scaler_fitting.py

@@ -11,12 +11,11 @@ from bdeissct_dl.training import get_data_characteristics
 
 
 def fit_scalers(paths, x_indices, scaler_x=None):
-    # First pass: calculate mean and var
-    for path in paths:
+   for path in paths:
         df = pd.read_csv(path)
         if scaler_x:
             X = df.iloc[:, x_indices].to_numpy(dtype=float, na_value=0)
-            scaler_x.partial_fit(X)
+            scaler_x.fit(X)
 
 
 def main():

{bdext-0.1.63 → bdext-0.1.65}/bdeissct_dl/train_ct.py

@@ -74,8 +74,8 @@ def main():
 
     os.makedirs(params.model_path, exist_ok=True)
 
-    # R,d,p,f_E,f_S,X_S,upsilon,X_C,kappa,la are given
-    # psi,rho are to be predicted
+    # R,f_E,f_S,X_S,upsilon,X_C,kappa,la are given
+    # psi is to be predicted
 
     feature_columns = CT_EPI_COLUMNS
     target_columns = CT_RATE_COLUMNS
@@ -87,8 +87,8 @@ def main():
 
 
     x_indices, y_col2index = get_data_characteristics(paths=params.train_data,
-                                                                 feature_columns=feature_columns,
-                                                                 target_columns=target_columns)
+                                                      feature_columns=feature_columns,
+                                                      target_columns=target_columns)
 
     scaler_x = StandardScaler()
     fit_scalers(paths=params.train_data, x_indices=x_indices, scaler_x=scaler_x)

{bdext-0.1.63 → bdext-0.1.65}/bdext.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bdext
-Version: 0.1.63
+Version: 0.1.65
 Summary: Estimation of BDEISS-CT parameters from phylogenetic trees.
 Home-page: https://github.com/modpath/bdeissct
 Author: Anna Zhukova

{bdext-0.1.63 → bdext-0.1.65}/setup.py

@@ -9,12 +9,12 @@ setup(
     long_description_content_type='text/markdown',
     include_package_data=True,
     package_data={'bdeissct_dl': [os.path.join('..', 'README.md'),
-                            os.path.join('models', '*.keras'),
-                            os.path.join('models', '*.h5'),
-                            os.path.join('models', '*.json'),
-                            os.path.join('models', '*.txt'),
-                            os.path.join('models', '*.npy'),
-                            os.path.join('models', '*.gz'),
+                            # os.path.join('models', '*.keras'),
+                            # os.path.join('models', '*.h5'),
+                            # os.path.join('models', '*.json'),
+                            # os.path.join('models', '*.txt'),
+                            # os.path.join('models', '*.npy'),
+                            # os.path.join('models', '*.gz'),
                             os.path.join('..', 'LICENCE')]},
     classifiers=[
         'Development Status :: 4 - Beta',
@@ -24,7 +24,7 @@ setup(
         'Topic :: Software Development',
         'Topic :: Software Development :: Libraries :: Python Modules',
     ],
-    version='0.1.63',
+    version='0.1.65',
     description='Estimation of BDEISS-CT parameters from phylogenetic trees.',
     author='Anna Zhukova',
     author_email='anna.zhukova@pasteur.fr',