Merge pull request #198 from dpploy/valmor

Docs update.
dpploy · Aug 2, 2019 · f65005f · f65005f
2 parents 419e3c8 + c50edd4
commit f65005f
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diff --git a/cortix/docs/build_docs.sh b/cortix/docs/build_docs.sh
@@ -19,38 +19,14 @@ sed -i -e 1,3d readme_converted.rst
 # Build docs for src directory
 sphinx-apidoc -o src_rst ../src
 
-# Build docs for src/utils subdirectory
-sphinx-apidoc -o src_rst/utils_rst ../src/utils
-
 # Build docs for support directory
 sphinx-apidoc -o support_rst ../support
 
-# Build docs for modulib directory
-sphinx-apidoc -o modulib_rst ../modulib
-
-# Build docs for pyplot subdirectory
-sphinx-apidoc -o modulib_rst/pyplot_rst ../modulib/pyplot
-
 # Build docs for examples directory
 sphinx-apidoc -o examples_rst ../examples
 
-# Build docs for console_run subdirectory
-sphinx-apidoc -o examples_rst/console_run_rst ../examples/console_run
-
-# Build docs for input subdirectory
-sphinx-apidoc -o examples_rst/input_rst ..examples/input
-
-# Build docs for modulib subdirectory
-sphinx-apidoc -o examples_rst/modulib_rst ../examples/modulib
-
-# Build docs for droplet subdirectory
-sphinx-apidoc -o examples_rst/modulib_rst/droplet_rst ../examples/modulib/droplet
-
 # Build docs for vortex subdirectory
-sphinx-apidoc -o examples_rst/modulib_rst/vortex_rst ../examples/modulib/vortex
-
-# Build docs for notebook_run subdirectory
-#sphinx-apidoc -o examples_rst/notebook_run_rst ../examples/notebook_run
+#sphinx-apidoc -o examples_rst/modulib_rst/vortex_rst ../examples/modulib/vortex
 
 # Make documentation
 make clean

diff --git a/cortix/docs/conf.py b/cortix/docs/conf.py
@@ -49,9 +49,19 @@
 #
 todo_include_todos=True
 #
+# vfda Thu 01 Aug 2019 07:14:56 PM EDT
+#
+# For docstrings to be semi-automatically used, the docstrings must of course be written 
+# in correct reStructuredText. You can then use all of the usual Sphinx markup in the 
+# docstrings, and it will end up correctly in the documentation.
+#
+#If you prefer NumPy or Google style docstrings over reStructuredText, you can also 
+# enable the napoleon extension. napoleon is a preprocessor that converts your 
+# docstrings to correct reStructuredText before autodoc processes them.
+#
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True
-napoleon_include_init_with_doc = False
+napoleon_include_init_with_doc = False  # include private functions "_func_name()"
 napoleon_include_private_with_doc = False
 napoleon_include_special_with_doc = True
 napoleon_use_admonition_for_examples = False

diff --git a/cortix/docs/contents.rst b/cortix/docs/contents.rst
@@ -7,6 +7,5 @@ Cortix Documentation
    :maxdepth: 2
 
    src_rst/modules
-   modulib_rst/modules
    examples_rst/modules
    support_rst/modules
diff --git a/cortix/docs/examples_rst/console_run_rst/main_executor.rst b/cortix/docs/examples_rst/console_run_rst/main_executor.rst
diff --git a/cortix/docs/examples_rst/console_run_rst/main_mpi.rst b/cortix/docs/examples_rst/console_run_rst/main_mpi.rst
diff --git a/cortix/docs/examples_rst/console_run_rst/main_pthread.rst b/cortix/docs/examples_rst/console_run_rst/main_pthread.rst
diff --git a/cortix/docs/examples_rst/console_run_rst/modules.rst b/cortix/docs/examples_rst/console_run_rst/modules.rst
diff --git a/cortix/docs/examples_rst/console_run_rst/wind_run.rst b/cortix/docs/examples_rst/console_run_rst/wind_run.rst
diff --git a/...mples_rst/console_run_rst/droplet_run.rst → cortix/docs/examples_rst/dataplot.rst b/...mples_rst/console_run_rst/droplet_run.rst → cortix/docs/examples_rst/dataplot.rst
@@ -1,7 +1,7 @@
-droplet\_run
-============
+dataplot module
+===============
 
-.. automodule:: droplet_run
+.. automodule:: dataplot
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/.../modulib_rst/pyplot_rst/cortix_driver.rst → cortix/docs/examples_rst/droplet.rst b/.../modulib_rst/pyplot_rst/cortix_driver.rst → cortix/docs/examples_rst/droplet.rst
@@ -1,7 +1,7 @@
-cortix\_driver
+droplet module
 ==============
 
-.. automodule:: cortix_driver
+.. automodule:: droplet
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/cortix/docs/examples_rst/input_rst/cortix_config.rst b/cortix/docs/examples_rst/input_rst/cortix_config.rst
diff --git a/cortix/docs/examples_rst/input_rst/modules.rst b/cortix/docs/examples_rst/input_rst/modules.rst
diff --git a/cortix/docs/examples_rst/modules.rst b/cortix/docs/examples_rst/modules.rst
@@ -2,8 +2,11 @@ examples
 ========
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 4
 
-   console_run_rst/modules
-   input_rst/modules
-   modulib_rst/modules
+   dataplot
+   droplet
+   dummy_module
+   plot_data
+   run_droplet
+   vortex
diff --git a/cortix/docs/examples_rst/modulib_rst/droplet_rst/cortix_driver.rst b/cortix/docs/examples_rst/modulib_rst/droplet_rst/cortix_driver.rst
diff --git a/cortix/docs/examples_rst/modulib_rst/droplet_rst/droplet.rst b/cortix/docs/examples_rst/modulib_rst/droplet_rst/droplet.rst
diff --git a/cortix/docs/examples_rst/modulib_rst/droplet_rst/modules.rst b/cortix/docs/examples_rst/modulib_rst/droplet_rst/modules.rst
diff --git a/cortix/docs/examples_rst/modulib_rst/modules.rst b/cortix/docs/examples_rst/modulib_rst/modules.rst
diff --git a/cortix/docs/examples_rst/modulib_rst/vortex_rst/cortix_driver.rst b/cortix/docs/examples_rst/modulib_rst/vortex_rst/cortix_driver.rst
diff --git a/cortix/docs/examples_rst/modulib_rst/vortex_rst/modules.rst b/cortix/docs/examples_rst/modulib_rst/vortex_rst/modules.rst
diff --git a/cortix/docs/examples_rst/run_droplet.rst b/cortix/docs/examples_rst/run_droplet.rst
@@ -0,0 +1,7 @@
+run\_droplet module
+===================
+
+.. automodule:: run_droplet
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/...les_rst/modulib_rst/vortex_rst/vortex.rst → cortix/docs/examples_rst/vortex.rst b/...les_rst/modulib_rst/vortex_rst/vortex.rst → cortix/docs/examples_rst/vortex.rst
diff --git a/cortix/docs/modulib_rst/modules.rst b/cortix/docs/modulib_rst/modules.rst
diff --git a/cortix/docs/modulib_rst/pyplot_rst/modules.rst b/cortix/docs/modulib_rst/pyplot_rst/modules.rst
diff --git a/cortix/docs/modulib_rst/pyplot_rst/pyplot.rst b/cortix/docs/modulib_rst/pyplot_rst/pyplot.rst
diff --git a/cortix/docs/modulib_rst/pyplot_rst/time_sequence.rst b/cortix/docs/modulib_rst/pyplot_rst/time_sequence.rst
diff --git a/cortix/docs/src_rst/module.rst b/cortix/docs/src_rst/module.rst
@@ -1,5 +1,5 @@
-module
-======
+module module
+=============
 
 .. automodule:: module
     :members:

diff --git a/cortix/docs/src_rst/modules.rst b/cortix/docs/src_rst/modules.rst
@@ -2,7 +2,7 @@ src
 ===
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 4
 
    cortix_main
    module

diff --git a/cortix/examples/droplet.py b/cortix/examples/droplet.py
@@ -15,12 +15,12 @@ class Droplet(Module):
     '''
     Droplet Cortix module used to model very simple fluid-particle interactions.
 
-    Ports
-    =====
-    external-flow: this is a port that exchanges data with any other module that
+    Note
+    ----
+    `external-flow`: this is a `port` that exchanges data with any other module that
     provides information about the flow outside the droplet.
 
-    visualization: this is a port that sends data to a visualization module.
+    `visualization`: this is a `port` that sends data to a visualization module.
     '''
 
     def __init__(self):

diff --git a/cortix/examples/plot_data.py b/cortix/examples/plot_data.py
@@ -1,6 +1,6 @@
 from cortix.src.module import Module
 from cortix.src.port import Port
-from cortix.util.dataplot import DataPlot
+from cortix.examples.dataplot import DataPlot
 from cortix.src.cortix_main import Cortix
 
 class PlotData(Module):

diff --git a/cortix/examples/vortex.py b/cortix/examples/vortex.py
@@ -19,9 +19,9 @@ class Vortex(Module):
     '''
     Vortex module used to model fluid flow using Cortix.
 
-    Ports
-    =====
-    Any port name and any number of ports are allowed.
+    Note
+    ----
+    Any `port` name and any number of ports are allowed.
     '''
 
     def __init__(self):

diff --git a/cortix/support/phase.py b/cortix/support/phase.py
@@ -144,6 +144,7 @@ def has_time_stamp(self, try_time_stamp):
         Parameters
         ----------
         try_time_stamp:
+
         Returns
         -------
 
@@ -161,8 +162,8 @@ def __get_time_unit(self):
         '''
         Returns the time unit of the `Phase.`
 
-        Paramers
-        --------
+        Parameters
+        ----------
         empty
 
         Returns
@@ -732,7 +733,7 @@ def WriteHTML(self, fileName):
         '''
         Convert the `Phase` container into an HTML file.
 
-        Paramters
+        Parameters
         ---------
         fileName: str