Fix doc (#258)

Author: dnerini

doc/requirements.txt

@@ -1,6 +1,5 @@
 # Additional requeriments related to the documentation build only
 sphinx
-numpydoc
 sphinxcontrib.bibtex
 sphinx_rtd_theme
 sphinx_gallery

doc/source/conf.py

@@ -30,7 +30,7 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.coverage",
     "sphinx.ext.mathjax",
-    "numpydoc",
+    "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
     "sphinx_gallery.gen_gallery",
 ]

doc/source/developer_guide/build_the_docs.rst

@@ -21,7 +21,7 @@ To install these packages activate your conda development environment and run::
 
 Then, to build the documentation, from the repo's root run::
 
-    `tox -e docs`
+    tox -e docs
 
 This will create a conda environment will all the necessary dependencies and the
 data needed to create the examples.

pysteps/verification/__init__.py

@@ -8,3 +8,4 @@
 from .plots import *
 from .probscores import *
 from .spatialscores import *
+from .salscores import *

pysteps/verification/salscores.py

@@ -50,7 +50,7 @@
 def sal(
     prediction,
     observation,
-    thr_factor=1 / 15,
+    thr_factor=0.067,  # default to 1/15 as in the reference paper
     thr_quantile=0.95,
     tstorm_kwargs=None,
 ):
@@ -94,9 +94,9 @@ def sal(
 
     See also
     --------
-    :py:func:`pysteps.verification.salscores.sal_structure`
-    :py:func:`pysteps.verification.salscores.sal_amplitude`
-    :py:func:`pysteps.verification.salscores.sal_location`
+    :py:func:`pysteps.verification.salscores.sal_structure`,
+    :py:func:`pysteps.verification.salscores.sal_amplitude`,
+    :py:func:`pysteps.verification.salscores.sal_location`,
     :py:mod:`pysteps.feature.tstorm`
     """
     prediction = np.copy(prediction)
@@ -143,9 +143,9 @@ def sal_structure(
 
     See also
     --------
-    :py:func:`pysteps.verification.salscores.sal`
-    :py:func:`pysteps.verification.salscores.sal_amplitude`
-    :py:func:`pysteps.verification.salscores.sal_location`
+    :py:func:`pysteps.verification.salscores.sal`,
+    :py:func:`pysteps.verification.salscores.sal_amplitude`,
+    :py:func:`pysteps.verification.salscores.sal_location`,
     :py:mod:`pysteps.feature.tstorm`
     """
     prediction_objects = _sal_detect_objects(
@@ -183,8 +183,8 @@ def sal_amplitude(prediction, observation):
 
     See also
     --------
-    :py:func:`pysteps.verification.salscores.sal`
-    :py:func:`pysteps.verification.salscores.sal_structure`
+    :py:func:`pysteps.verification.salscores.sal`,
+    :py:func:`pysteps.verification.salscores.sal_structure`,
     :py:func:`pysteps.verification.salscores.sal_location`
     """
     mean_obs = np.nanmean(observation)
@@ -228,9 +228,9 @@ def sal_location(
 
     See also
     --------
-    :py:func:`pysteps.verification.salscores.sal`
-    :py:func:`pysteps.verification.salscores.sal_structure`
-    :py:func:`pysteps.verification.salscores.sal_amplitude`
+    :py:func:`pysteps.verification.salscores.sal`,
+    :py:func:`pysteps.verification.salscores.sal_structure`,
+    :py:func:`pysteps.verification.salscores.sal_amplitude`,
     :py:mod:`pysteps.feature.tstorm`
     """
     return _sal_l1_param(prediction, observation) + _sal_l2_param(