Docs: fixed incorrect collapsing of Python API TOC.

conf.py

@@ -129,7 +129,9 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
+html_theme_options = {
+    "collapse_navigation" : False
+}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -264,6 +266,18 @@ def run_apidoc(_):
         with open(os.path.join(apidoc_dir, 'spirit.parameters.mmf.rst'), 'r') as generated_file:
             parameters_file.write(generated_file.read())
 
+    print("xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx")
+    print("xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx")
+    testfile = os.path.join(apidoc_dir, 'spirit.log.rst')
+    with open(testfile, 'r') as f:
+        print(f.read())
+    print("yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy")
+    print("yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy")
+    testfile = os.path.join(apidoc_dir, 'spirit.geometry.rst')
+    with open(testfile, 'r') as f:
+        print(f.read())
+    print("zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz")
+    print("zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz")
 
     if not os.path.exists(apidoc_dir):
         os.mkdir(apidoc_dir)

core/python/spirit/chain.py

@@ -1,6 +1,6 @@
 """
 Chain
---------------------
+====================
 
 Manipulate the chain of spin systems (also called images), e.g. add, remove or change active image.
 Get information, such as number of images or energies and reaction coordinates.

core/python/spirit/configuration.py

@@ -1,6 +1,6 @@
 """
 Configuration
---------------------
+====================
 
 Set various spin configurations, such as homogeneous domains, spirals or skyrmions.
 """

core/python/spirit/constants.py

@@ -1,6 +1,6 @@
 """
 Constants
---------------------
+====================
 """
 
 import spirit.spiritlib as spiritlib

core/python/spirit/geometry.py

@@ -1,6 +1,6 @@
 """
 Geometry
---------------------
+====================
 
 Change or get info on the current geometrical configuration, e.g.
 number of cells in the three crystal translation directions.

core/python/spirit/hamiltonian.py

@@ -1,6 +1,6 @@
 """
 Hamiltonian
---------------------
+====================
 
 Set the parameters of the Heisenberg Hamiltonian, such as external field or exchange interaction.
 """

core/python/spirit/htst.py

@@ -1,6 +1,6 @@
 """
 HTST
---------------------
+====================
 
 Harmonic transition state theory.
 

core/python/spirit/io.py

@@ -1,6 +1,6 @@
 """
 I/O
---------------------
+====================
 
 Read and write spin configurations, chains or eigenmodes.
 Vectorfields are generally written in the `OOMMF vector field (OVF) file format <http://math.nist.gov/oommf/doc/userguide12a5/userguide/OVF_2.0_format.html>`_.

core/python/spirit/log.py

@@ -1,6 +1,6 @@
 """
 Log
---------------------
+====================
 """
 
 import spirit.spiritlib as spiritlib

core/python/spirit/quantities.py

@@ -1,6 +1,6 @@
 """
 Quantities
---------------------
+====================
 """
 
 import spirit.spiritlib as spiritlib

core/python/spirit/simulation.py

@@ -1,6 +1,6 @@
 """
 Simulation
---------------------
+====================
 
 This module of Spirit is used to run and monitor iterative calculation methods.
 

core/python/spirit/state.py

@@ -1,6 +1,6 @@
 """
 State
---------------------
+====================
 
 The state contains the chain of spin systems (also called images).
 

core/python/spirit/system.py

@@ -1,6 +1,6 @@
 """
 System
---------------------
+====================
 """
 
 import spirit.spiritlib as spiritlib

core/python/spirit/transition.py

@@ -1,6 +1,6 @@
 """
 Transition
---------------------
+====================
 """
 
 import spirit.spiritlib as spiritlib