Some fixes

jgomezdans · Oct 29, 2018 · dfc6616 · dfc6616
1 parent d776820
commit dfc6616
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Showing 7 changed files with 20 additions and 88 deletions.
diff --git a/docs/.readthedocs.yml b/docs/.readthedocs.yml
diff --git a/docs/Makefile b/docs/Makefile
@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 SOURCEDIR     = .
-BUILDDIR      = ..
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/conf.py b/docs/conf.py
@@ -12,14 +12,11 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import os
-import sys
-sys.path.insert(0, os.path.abspath('.'))
-#sys.path.append(os.path.abspath('sphinxext'))
-
-sys.path.insert(0, os.path.abspath('../..'))
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir)))
-import matplotlib
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
 # -- Project information -----------------------------------------------------
 
 project = 'gp_emulator'
@@ -29,35 +26,9 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '1.6.5'
-
-try:
-    from gp_emulator import __version__ as version
-except ImportError:
-    pass
-else:
-    release = version
-
-# -- Hack for ReadTheDocs ------------------------------------------------------
-# This hack is necessary since RTD does not issue `sphinx-apidoc` before running
-# `sphinx-build -b html . _build/html`. See Issue:
-# https://github.com/rtfd/readthedocs.org/issues/1139
-# DON'T FORGET: Check the box "Install your project inside a virtualenv using
-# setup.py install" in the RTD Advanced Settings.
-
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
-if on_rtd:
-    import inspect
-    from sphinx import apidoc
-
-    __location__ = os.path.join(os.getcwd(), os.path.dirname(
-        inspect.getfile(inspect.currentframe())))
-
-    output_dir = os.path.join(__location__, "../docs/api")
-    module_dir = os.path.join(__location__, "../gp_emulator/")
-    cmd_line_template = "sphinx-apidoc -f -o {outputdir} {moduledir}"
-    cmd_line = cmd_line_template.format(outputdir=output_dir, moduledir=module_dir)
-    apidoc.main(cmd_line.split(" "))
+release = ''
+
+
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -67,22 +38,13 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [ 'matplotlib.sphinxext.mathmpl',
-            'matplotlib.sphinxext.plot_directive',
-                'sphinx.ext.autodoc',
-                'sphinx.ext.intersphinx',
-                'sphinx.ext.mathjax',
-                'sphinx.ext.ifconfig',
-                'sphinx.ext.viewcode'
+extensions = [
+    'matplotlib.sphinxext.plot_directive',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
 ]
 
-plot_include_source = True
-plot_html_show_source_link = False
-plot_html_show_formats = False
-plot_working_directory = '.'
-plot_rcparams = {
-    'figure.figsize': (10, 4)
-}
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -216,8 +178,3 @@
 
 
 # -- Extension configuration -------------------------------------------------
-
-# -- Options for intersphinx extension ---------------------------------------
-
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,5 +1,5 @@
 .. gp_emulator documentation master file, created by
-   sphinx-quickstart on Thu Sep 20 12:56:27 2018.
+   sphinx-quickstart on Mon Oct 29 16:05:31 2018.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
@@ -11,7 +11,7 @@ Welcome to gp_emulator's documentation!
    :caption: Contents:
 
    introduction.rst
-   module_docs.rst
+
 
 Indices and tables
 ==================

diff --git a/docs/module_docs.rst b/docs/module_docs.rst
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,4 +1,2 @@
 sphinxcontrib-napoleon
-matplotlib>2.0.0
-
-
+matplotlib>=2.0.0
diff --git a/gp_emulator/GaussianProcess.py b/gp_emulator/GaussianProcess.py
@@ -93,8 +93,8 @@ def _prepare_likelihood(self):
 
         exp_theta = np.exp(self.theta)
         # Calculation of the covariance matrix Q using theta
-        self.Z = dist.cdist(np.sqrt(expX[: (self.D)])*self.inputs,
-                            np.sqrt(expX[: (self.D)])*self.inputs,
+        self.Z = dist.cdist(np.sqrt(exp_theta[: (self.D)])*self.inputs,
+                            np.sqrt(exp_theta[: (self.D)])*self.inputs,
                             "sqeuclidean")
         self.Z = exp_theta[self.D] * np.exp(-0.5 * self.Z)
         self.Q = self.Z + exp_theta[self.D + 1] * np.eye(self.n)