Merge remote-tracking branch 'refs/remotes/origin/master'

smrt-model · Jan 24, 2018 · f4ac495 · f4ac495
2 parents b17be2b + 508c95a
commit f4ac495
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diff --git a/.gitignore b/.gitignore
@@ -61,7 +61,8 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+doc/build/
+doc/octave-workspace
 
 # PyBuilder
 target/

diff --git a/doc/rtd_requirements.txt b/doc/rtd_requirements.txt
@@ -0,0 +1,8 @@
+# These packages are needed for proper readthedocs import of documentation
+Sphinx==1.5.3
+numpy
+six
+xarray
+pandas
+scipy
+oct2py
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -21,6 +21,30 @@
 # sys.path.insert(0, os.path.abspath('source/'))
 sys.path.insert(0, os.path.abspath('../../smrt/'))
 
+# This allows readthedocs to find the submodules
+on_rtd = os.environ.get('READTHEDOCS') == 'True'
+if on_rtd:
+    # For DORT rtsolver:
+    import math
+    # For Autocorrelation microstructure_model:
+    import copy
+    # For everything:
+    import smrt
+
+# sphinxcontrib-restbuilder specific code
+# from https://pythonhosted.org/sphinxcontrib-restbuilder/
+rst_file_suffix = '.rst'
+rst_link_suffix = ''
+rst_line_width = 78
+rst_indent = 4
+def rst_file_transform(docname):
+    if docname == 'index':
+        docname = 'home'
+    return docname.title() + rst_file_suffix
+def rst_link_transform(docname):
+    if docname == 'index':
+        return 'wiki'
+    return 'wiki/' + docname.title()
 
 # -- General configuration ------------------------------------------------
 
@@ -31,6 +55,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
+
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.coverage',
@@ -73,9 +98,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0'
+version = u'1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'0'
+release = u'1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -135,17 +160,18 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'bizstyle'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-html_theme_options = {
-    "fixed_sidebar": "true",
-    "sidebar_collapse": "true",
-    "show_powered_by": "false"
-}
+# alabaster theme options
+#html_theme_options = {
+#    "fixed_sidebar": "true",
+#    "sidebar_collapse": "true",
+#    "show_powered_by": "false"
+#}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []

diff --git a/doc/source/modules.rst b/doc/source/modules.rst
@@ -0,0 +1,7 @@
+smrt
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   smrt
diff --git a/doc/source/smrt.atmosphere.rst b/doc/source/smrt.atmosphere.rst
@@ -0,0 +1,16 @@
+smrt.atmosphere package
+=======================
+
+.. automodule:: smrt.atmosphere
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+
+   smrt.atmosphere.simple_isotropic_atmosphere
+   smrt.atmosphere.test_atmosphere
+
diff --git a/doc/source/smrt.atmosphere.simple_isotropic_atmosphere.rst b/doc/source/smrt.atmosphere.simple_isotropic_atmosphere.rst
@@ -0,0 +1,7 @@
+smrt.atmosphere.simple_isotropic_atmosphere module
+==================================================
+
+.. automodule:: smrt.atmosphere.simple_isotropic_atmosphere
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.atmosphere.test_atmosphere.rst b/doc/source/smrt.atmosphere.test_atmosphere.rst
@@ -0,0 +1,7 @@
+smrt.atmosphere.test_atmosphere module
+======================================
+
+.. automodule:: smrt.atmosphere.test_atmosphere
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.error.rst b/doc/source/smrt.core.error.rst
@@ -0,0 +1,7 @@
+smrt.core.error module
+======================
+
+.. automodule:: smrt.core.error
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.fresnel.rst b/doc/source/smrt.core.fresnel.rst
@@ -0,0 +1,7 @@
+smrt.core.fresnel module
+========================
+
+.. automodule:: smrt.core.fresnel
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.globalconstants.rst b/doc/source/smrt.core.globalconstants.rst
@@ -0,0 +1,7 @@
+smrt.core.globalconstants module
+================================
+
+.. automodule:: smrt.core.globalconstants
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.layer.rst b/doc/source/smrt.core.layer.rst
@@ -0,0 +1,7 @@
+smrt.core.layer module
+======================
+
+.. automodule:: smrt.core.layer
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.model.rst b/doc/source/smrt.core.model.rst
@@ -0,0 +1,7 @@
+smrt.core.model module
+======================
+
+.. automodule:: smrt.core.model
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.plugin.rst b/doc/source/smrt.core.plugin.rst
@@ -0,0 +1,7 @@
+smrt.core.plugin module
+=======================
+
+.. automodule:: smrt.core.plugin
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.result.rst b/doc/source/smrt.core.result.rst
@@ -0,0 +1,7 @@
+smrt.core.result module
+=======================
+
+.. automodule:: smrt.core.result
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.rst b/doc/source/smrt.core.rst
@@ -0,0 +1,28 @@
+smrt.core package
+=================
+
+.. automodule:: smrt.core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+
+   smrt.core.error
+   smrt.core.fresnel
+   smrt.core.globalconstants
+   smrt.core.layer
+   smrt.core.model
+   smrt.core.plugin
+   smrt.core.result
+   smrt.core.sensitivity_study
+   smrt.core.sensor
+   smrt.core.snowpack
+   smrt.core.substrate
+   smrt.core.test_globalconstants
+   smrt.core.test_layer
+   smrt.core.test_sensor
+
diff --git a/doc/source/smrt.core.sensitivity_study.rst b/doc/source/smrt.core.sensitivity_study.rst
@@ -0,0 +1,7 @@
+smrt.core.sensitivity_study module
+==================================
+
+.. automodule:: smrt.core.sensitivity_study
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.sensor.rst b/doc/source/smrt.core.sensor.rst
@@ -0,0 +1,7 @@
+smrt.core.sensor module
+=======================
+
+.. automodule:: smrt.core.sensor
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.snowpack.rst b/doc/source/smrt.core.snowpack.rst
@@ -0,0 +1,7 @@
+smrt.core.snowpack module
+=========================
+
+.. automodule:: smrt.core.snowpack
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.substrate.rst b/doc/source/smrt.core.substrate.rst
@@ -0,0 +1,7 @@
+smrt.core.substrate module
+==========================
+
+.. automodule:: smrt.core.substrate
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.test_globalconstants.rst b/doc/source/smrt.core.test_globalconstants.rst
@@ -0,0 +1,7 @@
+smrt.core.test_globalconstants module
+=====================================
+
+.. automodule:: smrt.core.test_globalconstants
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.test_layer.rst b/doc/source/smrt.core.test_layer.rst
@@ -0,0 +1,7 @@
+smrt.core.test_layer module
+===========================
+
+.. automodule:: smrt.core.test_layer
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.core.test_sensor.rst b/doc/source/smrt.core.test_sensor.rst
@@ -0,0 +1,7 @@
+smrt.core.test_sensor module
+============================
+
+.. automodule:: smrt.core.test_sensor
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.commonfunc.rst b/doc/source/smrt.emmodel.commonfunc.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.commonfunc module
+==============================
+
+.. automodule:: smrt.emmodel.commonfunc
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.commontest.rst b/doc/source/smrt.emmodel.commontest.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.commontest module
+==============================
+
+.. automodule:: smrt.emmodel.commontest
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.dmrt_qca_shortrange.rst b/doc/source/smrt.emmodel.dmrt_qca_shortrange.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.dmrt_qca_shortrange module
+=======================================
+
+.. automodule:: smrt.emmodel.dmrt_qca_shortrange
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.dmrt_qcacp_shortrange.rst b/doc/source/smrt.emmodel.dmrt_qcacp_shortrange.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.dmrt_qcacp_shortrange module
+=========================================
+
+.. automodule:: smrt.emmodel.dmrt_qcacp_shortrange
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.dmrt_shortrange.rst b/doc/source/smrt.emmodel.dmrt_shortrange.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.dmrt_shortrange module
+===================================
+
+.. automodule:: smrt.emmodel.dmrt_shortrange
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.dmrt_test.rst b/doc/source/smrt.emmodel.dmrt_test.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.dmrt_test module
+=============================
+
+.. automodule:: smrt.emmodel.dmrt_test
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.effective_permittivity.rst b/doc/source/smrt.emmodel.effective_permittivity.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.effective_permittivity module
+==========================================
+
+.. automodule:: smrt.emmodel.effective_permittivity
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.iba.rst b/doc/source/smrt.emmodel.iba.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.iba module
+=======================
+
+.. automodule:: smrt.emmodel.iba
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.iba_original.rst b/doc/source/smrt.emmodel.iba_original.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.iba_original module
+================================
+
+.. automodule:: smrt.emmodel.iba_original
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.nonescattering.rst b/doc/source/smrt.emmodel.nonescattering.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.nonescattering module
+==================================
+
+.. automodule:: smrt.emmodel.nonescattering
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.prescribed_kskaeps.rst b/doc/source/smrt.emmodel.prescribed_kskaeps.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.prescribed_kskaeps module
+======================================
+
+.. automodule:: smrt.emmodel.prescribed_kskaeps
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/smrt.emmodel.rayleigh.rst b/doc/source/smrt.emmodel.rayleigh.rst
@@ -0,0 +1,7 @@
+smrt.emmodel.rayleigh module
+============================
+
+.. automodule:: smrt.emmodel.rayleigh
+    :members:
+    :undoc-members:
+    :show-inheritance: