Updates setup.py to include minimum package requirements to run RABDAM

GarmanGroup · Sep 28, 2021 · 26149cb · 26149cb
1 parent dd163bd
commit 26149cb
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Showing 4 changed files with 16 additions and 14 deletions.
diff --git a/rabdam/Subroutines/CalculateBDamage.py b/rabdam/Subroutines/CalculateBDamage.py
@@ -372,7 +372,9 @@ def rabdam_dataframe(self, test=False):
                   '--USER INPUT-- type your choice and press RETURN\n'
                   'yes = continue RABDAM run\n'
                   'no = terminate RABDAM run\n')
-            owChoice = None
+            owChoice = None  # Change to yes for batch running to prevent user
+            # input being required
+            # owChoice = 'yes'
             while owChoice not in ['yes', 'no', 'y', 'n']:
                 if test is True:
                     owChoice = 'yes'

diff --git a/rabdam/Subroutines/output.py b/rabdam/Subroutines/output.py
@@ -358,7 +358,7 @@ def plot_Bnet_histogram(self, bnet_df, median, prot_or_na):
         x_min = min(bnet_df.BDAM.values) - (3*tail_width)
         x_max = max(bnet_df.BDAM.values) + (3*tail_width)
 
-        kde = gaussian_kde(dataset=bnet_df.BDAM.values, bw_method='scott', weights=None)
+        kde = gaussian_kde(dataset=bnet_df.BDAM.values, bw_method='scott')
         x_values = np.linspace(x_min, x_max, 100)
         y_values = kde(x_values)
         height = (x_values[-1]-x_values[0]) / (len(x_values)-1)
@@ -378,9 +378,9 @@ def plot_Bnet_histogram(self, bnet_df, median, prot_or_na):
                 total_area_RHS = total_area_RHS + area_RHS
 
         # Calculates area ratio (= Bnet)
-        ratio = total_area_RHS / total_area_LHS
+        kde_ratio = total_area_RHS / total_area_LHS
 
-        plt.annotate('Bnet = {:.1f}'.format(ratio),
+        plt.annotate('Bnet = {:.1f}'.format(kde_ratio),
                      xy=(max(x_values)*0.65, max(y_values)*0.9),
                      fontsize=10)
         plt.annotate('Median = {:.2f}'.format(median),
@@ -394,11 +394,11 @@ def plot_Bnet_histogram(self, bnet_df, median, prot_or_na):
             bnet_list.write('Bnet' + '\n')
             bnet_list.close()
         bnet_list = open('Logfiles/Bnet_{}.csv'.format(prot_or_na), 'a')
-        bnet_list.write('%s,%s\n' % (self.pdb_code, ratio))
+        bnet_list.write('%s,%s\n' % (self.pdb_code, kde_ratio))
         bnet_list.close()
 
         bnet_df = pd.DataFrame({'PDB': [self.pdb_code],
-                                'Bnet': [ratio]})
+                                'Bnet': [kde_ratio]})
         if os.path.isfile('Logfiles/Bnet_{}.pkl'.format(prot_or_na)):
             old_bnet_df = pd.read_pickle('Logfiles/Bnet_{}.pkl'.format(prot_or_na))
         else:

diff --git a/requirements.txt b/requirements.txt
@@ -1,8 +1,8 @@
 
-numpy
-matplotlib
-scipy
-seaborn
-pandas
+numpy >= 1.15.0
+matplotlib >= 2.2.0
+scipy >= 1.1.0
+seaborn >= 0.8.0
+pandas >= 0.24.1
 requests
 setuptools
diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
     packages=find_packages(),
     package_data={'rabdam': ['Subroutines/HTML_stylesheet.css',
                              'Subroutines/HTML_stylesheet.js']},
-    version='1.6.3',
+    version='1.6.4',
     description=('RABDAM: A program to identify and quantify specific '
                  'radiation damage within individual protein crystal '
                  'structures'),
@@ -22,8 +22,8 @@
     license='LGPL v3',
     keywords=['radiation damage', 'specific damage', 'atomic Bfactors',
               'atomic displacement parameters', 'BDamage', 'Bnet'],
-    install_requires=['numpy', 'matplotlib', 'scipy', 'seaborn', 'pandas',
-                      'requests', 'setuptools'],
+    install_requires=['numpy>=1.15.0', 'matplotlib>=2.2.0', 'scipy>=1.1.0',
+                      'seaborn>=0.8.0', 'pandas>=0.24.1', 'requests', 'setuptools'],
     classifiers=['Programming Language :: Python'],
     python_requires=('>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, '
                      '!=3.5.*, <4'),