Get both sets of sphinx docs rendering properly

API docs had an issue with the theme, and the rtd docs are now pointing
at the updating API docs.

.github/workflows/test-overall.yml

@@ -127,3 +127,4 @@ jobs:
         UPLOAD_SCIKITS_ODES_API_DOCS: ${{ github.repository == 'bmcage/odes' && 'true' || 'false' }}
         GITHUB_ACTOR: ${{ secrets.GITHUB_ACTOR }}
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        API_DOCS_OUT_DIR: /tmp/new_sundials_docs

apidocs/api.rst → apidocs/api/compat.rst

@@ -1,9 +1,10 @@
-Lower Level API
-===============
+scikits.odes
+============
 
 scikits.odes
 ------------
 .. automodule:: scikits.odes
+    :members:
 
 scikits.odes.ode
 ----------------

apidocs/api/core.rst

@@ -0,0 +1,5 @@
+scikits-odes-core
+-----------------
+
+.. automodule:: scikits_odes_core
+    :members:

apidocs/api/daepack.rst

@@ -0,0 +1,12 @@
+scikits-odes-daepack
+====================
+
+.. scikits_odes_daepack.ddaspkint
+.. ------------------------------
+.. .. automodule:: scikits_odes_daepack.ddaspkint
+..     :members:
+.. 
+.. scikits_odes_daepack.lsodiint
+.. -----------------------------
+.. .. automodule:: scikits_odes_daepack.lsodiint
+..     :members:

apidocs/api/index.rst

@@ -0,0 +1,11 @@
+Lower Level API
+===============
+
+.. toctree::
+   :maxdepth: 2
+
+   core
+   daepack
+   sundials
+   main
+   compat

apidocs/api/main.rst

@@ -0,0 +1,23 @@
+scikits-odes
+============
+
+scikits_odes
+------------
+.. automodule:: scikits_odes
+    :members:
+
+scikits_odes.ode
+----------------
+.. automodule:: scikits_odes.ode
+    :members:
+
+scikits_odes.dae
+----------------
+.. automodule:: scikits_odes.dae
+    :members:
+
+scikits_odes.dopri5
+--------------------
+.. automodule:: scikits_odes.dopri5
+    :members:
+

apidocs/api/sundials.rst

@@ -0,0 +1,17 @@
+scikits-odes-sundials
+=====================
+
+scikits_odes_sundials
+---------------------
+.. automodule:: scikits_odes_sundials
+    :members:
+
+scikits_odes_sundials.cvode
+---------------------------
+.. automodule:: scikits_odes_sundials.cvode
+    :members:
+
+scikits_odes_sundials.ida
+-------------------------
+.. automodule:: scikits_odes_sundials.ida
+    :members:

apidocs/conf.py

@@ -113,7 +113,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'alabaster'
 
 # 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
@@ -145,11 +145,11 @@
 html_static_path = ['_static']
 
 # from https://rackerlabs.github.io/docs-rackspace/tools/rtd-tables.html
-html_context = {
-    'css_files': [
-        '_static/theme_overrides.css',  # override wide tables in RTD theme
-        ],
-     }
+#html_context = {
+#    'css_files': [
+#        '_static/theme_overrides.css',  # override wide tables in RTD theme
+#        ],
+#     }
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

apidocs/index.rst

@@ -1,8 +1,3 @@
-.. Odes documentation master file, created by
-   sphinx-quickstart on Tue Feb  2 13:13:32 2016.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 Welcome to the ODES scikit API Documentation
 ============================================
 
@@ -15,12 +10,12 @@ For other versions of the API documentation, see https://bmcage.github.io/odes.
 Contents:
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 4
 
    ode
    dae
    sundials
-   api
+   api/index
 
 Indices and tables
 ==================

apidocs/requirements.txt

@@ -1,4 +1,4 @@
 sphinx>=1.4
-sphinx_rtd_theme
+sphinx-rtd-theme
 sphinxcontrib-jquery
 docs-versions-menu

apidocs/sundials.rst

@@ -5,17 +5,19 @@ Selecting Precision
 -------------------
 Sundials can be built with different precisions (currently `'single'` which maps
 to C `'float'`; `'double'` (the default) which maps to C `'double'`; and
-`'extended'` which maps to C `'long double'`), and scikits.odes supports using
-whichever precision Sundials is built with. To take advantage of this, you must
-first have sundials built and installed with the desired precision setting.
-
-Once you have done this, build scikits.odes against this particular version of
-sundials (see the main documentation for how to do this). scikits.odes will
-automatically detect the precision, and store this in a variable called
+`'extended'` which maps to C `'long double'`), and scikits-odes-sundials
+supports using whichever precision Sundials is built with. To take advantage of
+this, you must first have sundials built and installed with the desired
+precision setting.
+
+Once you have done this, build scikits-odes-sundials against this particular
+version of sundials (see the main documentation for how to do this).
+scikits-odes-sundials will automatically detect the precision, and store this in
+a variable called
 :py:const:`DTYPE`. :py:const:`DTYPE` should be accessed from
-:py:mod:`scikits.odes.sundials` (other modules may have :py:const:`DTYPE`
-defined, but :py:mod:`scikits.odes.sundials` should be preferred). Additionally
-:py:const:`scikits.odes.sundials.precision` contains the precision setting found
+:py:mod:`scikits_odes_sundials` (other modules may have :py:const:`DTYPE`
+defined, but :py:mod:`scikits_odes_sundials` should be preferred). Additionally
+:py:const:`scikits_odes_sundials.precision` contains the precision setting found
 by scikits.odes.
 
 To use :py:const:`DTYPE`, treat it as a numpy dtype; use it whenever you need to

apidocs/upload_api_docs.sh

@@ -3,6 +3,7 @@
 set -ex
 
 if [ "true" = "$UPLOAD_SCIKITS_ODES_API_DOCS" ]; then
+    cd /tmp
     # Clone gh-pages
     git clone --branch gh-pages https://github.com/bmcage/odes gh-pages
     # Run rsync

docs/conf.py

@@ -48,7 +48,7 @@
         'https://docs.scipy.org/doc/scipy/', None
     ),
     'apidocs': (
-        'https://bmcage.github.io/odes/dev', None
+        'https://bmcage.github.io/odes/master/', None
     ),
 }
 

packages/scikits-odes-core/src/scikits_odes_core/__init__.py

@@ -8,7 +8,7 @@ class DaeBase:
 
     Parameters
     ----------
-    Rfn :
+    Rfn : function
         residual function
     options : mapping
         Additional options for initialization, solver dependent
@@ -186,8 +186,8 @@ class OdeBase:
     ----------
     Rfn : function
         A function which computes the required derivatives. The signature
-        should be ``func(t, y, y_dot, *args, **kwargs)``. Note that *args and
-        **kwargs handling are solver dependent.
+        should be ``func(t, y, y_dot, *args, **kwargs)``. Note that ``*args``
+        and ``**kwargs`` handling are solver dependent.
 
     options : mapping
         Additional options for initialization, solver dependent