start updating make files to new naming

doc/API/datatypes.rst

@@ -1,12 +1,12 @@
 Data Types
 ===================================
 
-.. autoclass:: whobpyt.datatypes.Recording
+.. autoclass:: whobpyt.datatypes.Timeseries
    :members:
    :undoc-members:
    :special-members: __init__
 
-.. autoclass:: whobpyt.datatypes.par
+.. autoclass:: whobpyt.datatypes.Parameter
    :members:
    :undoc-members:
    :special-members: __init__

doc/API/models.rst

@@ -1,27 +1,12 @@
 Models
 ===================================
 
-.. autoclass:: whobpyt.models.JansenRit.RNNJANSEN
-   :members: info, createIC, createDelayIC, setModelParameters, forward
+.. autoclass:: whobpyt.models.jansen_rit.JansenRitParams
+   :members: info, createIC, createDelayIC, setModelSCParameters, forward
    :undoc-members:
    :special-members: __init__
 
-.. autoclass:: whobpyt.models.RWW.RNNRWW
-   :members: info, createIC, setModelParameters, forward
-   :undoc-members:
-   :special-members: __init__
-
-.. autoclass:: whobpyt.models.RWWEI2.RWWEI2
-   :members: info, createIC, setModelParameters, forward
-   :undoc-members:
-   :special-members: __init__
-
-.. autoclass:: whobpyt.models.BOLD.BOLD_Layer
-   :members: info, createIC, setModelParameters, forward
-   :undoc-members:
-   :special-members: __init__
-
-.. autoclass:: whobpyt.models.EEG.EEG_Layer
-   :members: info, createIC, setModelParameters, forward
+.. autoclass:: whobpyt.models.wong_wang.ReducedWongWangModel
+   :members: info, createIC, createDelayIC, setModelSCParameters, forward
    :undoc-members:
    :special-members: __init__

doc/Makefile

@@ -9,7 +9,6 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-#SPHINXPROJ    = fooof
 SPHINXPROJ    = whobpyt
 SOURCEDIR     = .
 BUILDDIR      = _build
@@ -50,7 +49,6 @@ install:
 	#   --no-checkout just fetches the root folder without content
 	#   --depth 1 is a speed optimization since we don't need the history prior to the last commit
 	#   -b gh-pages fetches only the branch for the gh-pages
-	#git clone -b gh-pages --single-branch --no-checkout --depth 1 https://github.com/fooof-tools/fooof _build/gh_pages
 	git clone -b gh-pages --single-branch --no-checkout --depth 1 [email protected]:griffithslab/whobpyt _build/gh_pages
 	# A .nojekyll file tells Github pages to bypass Jekyll processing
 	touch _build/gh_pages/.nojekyll

requirements.txt

@@ -14,7 +14,7 @@ mne
 # Docs requirements
 sphinx
 #sphinx==3.1.1
-sphinx-gallery==0.8.1
+sphinx_gallery==0.8.1
 sphinx_rtd_theme #==0.5.0
 sphinx-tabs==1.3.0
 sphinx-copybutton==0.3.1

whobpyt/models/wong_wang/wong_wang.py

@@ -70,7 +70,7 @@ class ReducedWongWangModel(AbstractNeuralModel):
         A function that returns a dictionary with model information.
     createIC(self, ver)
         A function to return an initial state tensor for the model.
-    setModelParameters(self)
+    setModelSCParameters(self)
         A function that assigns model parameters as model attributes and also to assign parameters and hyperparameters for fitting, 
         so that the inherited Torch functionality can be used. 
         This practice may be replaced soon.