Integrating Doxygen/Breathe with TECA's rtd

doc/rtd/conf.py

@@ -24,12 +24,27 @@
 
 # -- General configuration ---------------------------------------------------
 
+# Run Doxygen to generate Doxygen's XML output for autodoc by Breathe
+import subprocess, os
+
+read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
+
+if read_the_docs_build:
+    subprocess.call('cd ../doxygen; doxygen', shell=True)
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'breathe'
 ]
 
+# Setup the breathe extension
+breathe_projects = {
+    "TECA": "../doxygen/xml"
+}
+breathe_default_project = "TECA"
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

doc/rtd/framework/alg.rst

@@ -0,0 +1,126 @@
+Algorithms
+==========
+
+Classes
+-------
+
+.. doxygenclass:: teca_2d_component_area
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_bayesian_ar_detect
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_binary_segmentation
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_cartesian_mesh_regrid
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_cartesian_mesh_source
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_component_area_filter
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_connected_components
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_dataset_diff
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_deeplabv3p_ar_detect::teca_deeplabv3p_ar_detect
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_integrated_vapor_transport
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_l2_norm
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_latitude_damper
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_normalize_coordinates
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_table_reduce
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_tc_candidates
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_tc_trajectory
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_tc_wind_radii
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_temporal_average
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_temporal_reduction::teca_temporal_reduction
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_vorticity
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+

doc/rtd/framework/core.rst

@@ -0,0 +1,45 @@
+CORE
+====
+
+.. doxygenclass:: teca_algorithm
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_binary_stream
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_dataset
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_index_executive
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_metadata
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_programmable_algorithm
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_variant_array
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+

doc/rtd/framework/data.rst

@@ -0,0 +1,42 @@
+DATA
+====
+
+Classes
+-------
+
+.. doxygenclass:: teca_array_collection
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_cartesian_mesh
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_curvilinear_mesh
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_mesh
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_table
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_uniform_cartesian_mesh
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+

doc/rtd/framework/framework.rst

@@ -0,0 +1,16 @@
+Framework
+=========
+
+TECA provides an extensive suite of algorithms and software utilities
+to build Climage Data Analysis pipelines
+for climate data analysis.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   alg
+   core
+   io
+   data
+   system

doc/rtd/framework/io.rst

@@ -0,0 +1,57 @@
+I/O
+===
+
+Classes
+-------
+
+.. doxygenclass:: teca_cartesian_mesh_reader
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_cartesian_mesh_writer
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_cf_reader
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_cf_writer
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_multi_cf_reader
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_table_reader
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+.. doxygenclass:: teca_table_writer
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+
+Namespaces
+----------
+
+.. doxygennamespace:: teca_file_util
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+

doc/rtd/framework/system.rst

@@ -0,0 +1,12 @@
+System
+======
+
+Namespaces
+----------
+
+.. doxygennamespace:: teca_system_interface
+   :members:
+   :protected-members:
+   :private-members:
+   :undoc-members:
+

doc/rtd/index.rst

@@ -22,3 +22,4 @@ largest scale on DOE HPC systems.
    applications
    python
    developer
+   framework/framework