Merge pull request #291 from nextstrain/opt_dependencies

setup.py: removed matplotlib, moved ipdb to dev. augur/frequency_esti…
nextstrain · Jul 2, 2019 · 108053e · 108053e
2 parents d1cf443 + 1163397
commit 108053e
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Showing 3 changed files with 37 additions and 24 deletions.
diff --git a/augur/frequency_estimators.py b/augur/frequency_estimators.py
@@ -726,7 +726,12 @@ def calc_confidence(self):
 
 
 def test_simple_estimator():
-    import matplotlib.pyplot as plt
+    try:
+        import matplotlib.pyplot as plt
+    except ImportError:
+        plot=False
+        print("Plotting requires a working matplotlib installation.")
+
     tps = np.sort(100 * np.random.uniform(size=500))
     freq_traj = [0.1]
     stiffness=100
@@ -755,7 +760,12 @@ def test_simple_estimator():
     return fe
 
 def test_nested_estimator():
-    import matplotlib.pyplot as plt
+    try:
+        import matplotlib.pyplot as plt
+    except ImportError:
+        plot=False
+        print("Plotting requires a working matplotlib installation.")
+
     tps = np.sort(100 * np.random.uniform(size=2000))
     freq_traj = [0.1]
     stiffness=1000

diff --git a/augur/titer_model.py b/augur/titer_model.py
@@ -502,26 +502,31 @@ def validate(self, plot=False, cutoff=0.0, validation_set = None, fname=None):
         model_performance['values'] = validation.values()
 
         self.validation = model_performance
+
         if plot:
-            import matplotlib.pyplot as plt
-            import seaborn as sns
-            fs=16
-            sns.set_style('darkgrid')
-            plt.figure()
-            ax = plt.subplot(111)
-            plt.plot([-1,6], [-1,6], 'k')
-            plt.scatter(actual, predicted)
-            plt.ylabel(r"predicted $\log_2$ distance", fontsize = fs)
-            plt.xlabel(r"measured $\log_2$ distance" , fontsize = fs)
-            ax.tick_params(axis='both', labelsize=fs)
-            plt.text(-2.5,6,'regularization:\nprediction error:\nR^2:', fontsize = fs-2)
-            plt.text(1.2,6, str(self.lam_drop)+'/'+str(self.lam_pot)+'/'+str(self.lam_avi)+' (HI/pot/avi)'
-                     +'\n'+str(round(model_performance['abs_error'], 2))+'/'+str(round(model_performance['rms_error'], 2))+' (abs/rms)'
-                     + '\n' + str(model_performance['r_squared']), fontsize = fs-2)
-            plt.tight_layout()
-
-            if fname:
-                plt.savefig(fname)
+            try:
+                import matplotlib.pyplot as plt
+                import seaborn as sns
+            except ImportError:
+                print("Plotting requires a working matplotlib and seaborn installation.")
+            else:
+                fs=16
+                sns.set_style('darkgrid')
+                plt.figure()
+                ax = plt.subplot(111)
+                plt.plot([-1,6], [-1,6], 'k')
+                plt.scatter(actual, predicted)
+                plt.ylabel(r"predicted $\log_2$ distance", fontsize = fs)
+                plt.xlabel(r"measured $\log_2$ distance" , fontsize = fs)
+                ax.tick_params(axis='both', labelsize=fs)
+                plt.text(-2.5,6,'regularization:\nprediction error:\nR^2:', fontsize = fs-2)
+                plt.text(1.2,6, str(self.lam_drop)+'/'+str(self.lam_pot)+'/'+str(self.lam_avi)+' (HI/pot/avi)'
+                         +'\n'+str(round(model_performance['abs_error'], 2))+'/'+str(round(model_performance['rms_error'], 2))+' (abs/rms)'
+                         + '\n' + str(model_performance['r_squared']), fontsize = fs-2)
+                plt.tight_layout()
+
+                if fname:
+                    plt.savefig(fname)
 
         return model_performance
 

diff --git a/setup.py b/setup.py
@@ -37,12 +37,9 @@
             "biopython >=1.73, ==1.*",
             "boto >=2.38, ==2.*",
             "cvxopt >=1.1.9, ==1.1.*",
-            "ipdb >=0.10.1",
             "jsonschema ==3.0.0a3",
-            "matplotlib >=2.0, ==2.*",
             "pandas >=0.23.4",
             "phylo-treetime >=0.5.6, ==0.5.*",
-            "seaborn >=0.9.0",
             "snakemake >=5.1.5, ==5.*"
         ],
         extras_require={
@@ -54,6 +51,7 @@
                 "sphinx-argparse >=0.2.5",
                 "sphinx-rtd-theme >=0.4.3",
                 "wheel >=0.32.3, ==0.32.*",
+                "ipdb >=0.10.1"
             ]
         },
         classifiers=[