fix sphinx docs

.travis.yml

@@ -4,7 +4,7 @@ python:
   - "3.6"
   - "3.7"
 script:
-  - pip install -U sphinx
+  - pip install -U sphinx deprecated
   - sphinx-build -M html docs/ docs/_build/ -W  # Try building it before installing the rest, should work
   - pip install -U coveralls flaky pytest pytest-cov
   - pip install .

convoys/multi.py

@@ -1,4 +1,4 @@
-from deprecated import deprecated
+from deprecated.sphinx import deprecated
 import numpy
 from convoys import regression
 from convoys import single
@@ -41,8 +41,9 @@ def predict(self, group, *args, **kwargs):
     def rvs(self, group, *args, **kwargs):
         return self.base_model.rvs(self._get_x(group), *args, **kwargs)
 
-    @deprecated(version='0.1.8', reason='Use the `predict` method instead')
+    @deprecated(version='0.1.8', reason='Has been renamed to :meth:`predict`')
     def cdf(self, *args, **kwargs):
+        '''Returns the predicted values.'''
         return self.predict(*args, **kwargs)
 
 
@@ -68,8 +69,9 @@ def fit(self, G, B, T):
     def predict(self, group, t, *args, **kwargs):
         return self._group2model[group].predict(t, *args, **kwargs)
 
-    @deprecated(version='0.1.8', reason='Use the `predict` method instead')
+    @deprecated(version='0.1.8', reason='Has been renamed to :meth:`predict`')
     def cdf(self, *args, **kwargs):
+        '''Returns the predicted values.'''
         return self.predict(*args, **kwargs)
 
 

convoys/regression.py

@@ -1,7 +1,7 @@
 from convoys import autograd_scipy_monkeypatch  # NOQA
 import autograd
 from autograd_gamma import gammainc
-from deprecated import deprecated
+from deprecated.sphinx import deprecated
 import emcee
 import numpy
 from scipy.special import gammaincinv
@@ -311,8 +311,7 @@ def predict_posteriori(self, x, t, ci=None):
 
     def predict(self, x, t, ci=None):
         '''Returns the value of the cumulative distribution function
-        for a fitted model. TODO: this should probably be renamed
-        "predict" in the future to follow the scikit-learn convention.
+        for a fitted model.
 
         :param x: feature vector (or matrix)
         :param t: time
@@ -367,13 +366,14 @@ def rvs(self, x, n_curves=1, n_samples=1, T=None):
 
         return B, C
 
-    @deprecated(version='0.1.8', reason='Use the `predict` method instead')
+    @deprecated(version='0.1.8', reason='Has been renamed to :meth:`predict`')
     def cdf(self, *args, **kwargs):
+        '''Returns the predicted values.'''
         return self.predict(*args, **kwargs)
 
-    @deprecated(version='0.1.8',
-                reason='Use the `predict_posteriori` method instead')
+    @deprecated(version='0.1.8', reason='Has been renamed to :meth:`predict`')
     def cdf_posteriori(self, *args, **kwargs):
+        '''Returns the predicted values.'''
         return self.predict_posteriori(*args, **kwargs)
 
 

convoys/single.py

@@ -1,4 +1,4 @@
-from deprecated import deprecated
+from deprecated.sphinx import deprecated
 import numpy
 from scipy.special import expit, logit
 import scipy.stats
@@ -68,6 +68,7 @@ def _get_value_at(self, j, ci):
             return 1 - self._ss[j]
 
     def predict(self, t, ci=None):
+        '''Returns the predicted values.'''
         t = numpy.array(t)
         res = numpy.zeros(t.shape + (3,) if ci else t.shape)
         for indexes, value in numpy.ndenumerate(t):
@@ -79,6 +80,7 @@ def predict(self, t, ci=None):
                 res[indexes] = self._get_value_at(j, ci)
         return res
 
-    @deprecated(version='0.1.8', reason='Use the `predict` method instead')
+    @deprecated(version='0.1.8', reason='Has been renamed to :meth:`predict`')
     def cdf(self, *args, **kwargs):
+        '''Returns the predicted values.'''
         return self.predict(*args, **kwargs)