Develop

.github/workflows/publish.yml

@@ -1,41 +1,41 @@
-name: Publish to PyPI
-
-on:
-  push:
-    branches:
-      - main
-    tags:
-      - "v*"
-
-jobs:
-  deploy:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-
-      - name: Install build dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install build twine
-
-      - name: Compile C++ code
-        run: |
-          cd vbi/models/cpp/_src
-          make
-
-      - name: Build package
-        run: python -m build
-
-      - name: Publish to PyPI
-        if: startsWith(github.ref, 'refs/tags/v')
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-        run: twine upload dist/*
+# name: Publish to PyPI
+
+# on:
+#   push:
+#     branches:
+#       - develop
+#     tags:
+#       - "v*"
+
+# jobs:
+#   deploy:
+#     runs-on: ubuntu-latest
+
+#     steps:
+#       - name: Checkout repository
+#         uses: actions/checkout@v4
+
+#       - name: Set up Python
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: "3.10"
+
+#       - name: Install build dependencies
+#         run: |
+#           python -m pip install --upgrade pip
+#           pip install build twine
+
+#       - name: Compile C++ code
+#         run: |
+#           cd vbi/models/cpp/_src
+#           make
+
+#       - name: Build package
+#         run: python -m build
+
+#       - name: Publish to PyPI
+#         if: startsWith(github.ref, 'refs/tags/v')
+#         env:
+#           TWINE_USERNAME: __token__
+#           TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+#         run: twine upload dist/*

MANIFEST.in

@@ -1,2 +1,3 @@
 include LICENSE
-graft docs
+graft docs
+graft vbi/models/cpp/_src

docs/API.rst

@@ -0,0 +1,71 @@
+.. raw:: html
+
+   <link rel="stylesheet" type="text/css" href="_static/custom.css">
+
+
+API and documentation
+=====================
+
+
+C++ models
+-------------------------
+
+
+vbi.models.cpp.jansen_rit
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.jansen_rit
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.km
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.km
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.mpr 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.mpr
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.vep 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.vep
+        :members:
+        :undoc-members:
+
+
+vbi.models.cpp.wc 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.wc
+        :members:
+        :undoc-members:
+
+
+Cupy models 
+-------------------------
+
+vbi.models.cupy.mpr 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.mpr
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.ghb
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.ghb
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.jansen_rit
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.jansen_rit
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.utils 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.utils
+        :members:
+        :undoc-members:

docs/_static/custom.css

@@ -0,0 +1,32 @@
+.color-title th {
+    color: rgb(131, 94, 179);
+}
+
+.color-caption caption {
+    color: rgb(139, 68, 206);
+}
+
+
+/* Change the color of module headers */
+.py.mod > .descclassname, .py.mod > .descname {
+    color: #FF5733; /* Orange */
+}
+
+/* Change the color of function signatures */
+.sig.sig-object.py {
+    color: #327219; /* Green */
+}
+
+/* Change the background color of code blocks */
+.highlight {
+    background-color: #F0F8FF; /* Light blue */
+}
+
+.section {
+    background-color: #f0f8ff; /* Light blue background for sections */
+}
+
+.descclassname, .descname {
+    color: #327219;  /* Green color for class and function names */
+}
+

docs/conf.py

@@ -31,6 +31,7 @@
 html_theme = 'nature'
 pygments_style = "colorful"
 add_function_parentheses = True
+html_static_path = ['_static']
 
 # html_theme = "bootstrap"
 # html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()

docs/index.rst

@@ -1,7 +1,24 @@
+.. raw:: html
+
+   <link rel="stylesheet" type="text/css" href="_static/custom.css">
+
+
 Virtual Brain Inference (VBI)
 ##############################
 
 
+.. image:: _static/vbi_log.png
+   :alt: VBI Logo
+   :width: 200px
+   :align: center
+
+Workflow
+========
+
+.. image:: _static/Fig1.png
+   :alt: VBI Logo
+   :width: 800px
+
 Installation
 ============
 
@@ -17,6 +34,13 @@ Installation
     # pip install -e .[all,dev,docs]
 
 
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   models
+
+
 Examples
 =========
 
@@ -32,10 +56,19 @@ Examples
    examples/mpr_sde_cupy
    examples/mpr_sde_numba
    examples/jansen_rit_sde_cpp
+   examples/jansen_rit_sde_cupy
    examples/ww_sde_torch_kong
    examples/ghb_sde_cupy
 
 
+
+.. toctree::
+    :maxdepth: 2
+    :caption: API Reference
+
+    API
+
+
 Indices and tables
 ==================
 
@@ -45,71 +78,3 @@ Indices and tables
 
 
 
-API and documentation
-=====================
-
-C++ models
--------------------------
-
-.. automodule:: vbi
-    :members:
-    :undoc-members:
-
-vbi.models.cpp.jansen_rit
--------------------------
-    .. automodule:: vbi.models.cpp.jansen_rit
-        :members:
-        :undoc-members:
-
-vbi.models.cpp.km
--------------------------
-    .. automodule:: vbi.models.cpp.km
-        :members:
-        :undoc-members:
-
-vbi.models.cpp.mpr 
--------------------------
-    .. automodule:: vbi.models.cpp.mpr
-        :members:
-        :undoc-members:
-
-vbi.models.cpp.vep 
--------------------------
-    .. automodule:: vbi.models.cpp.vep
-        :members:
-        :undoc-members:
-
-
-vbi.models.cpp.wc 
--------------------------
-    .. automodule:: vbi.models.cpp.wc
-        :members:
-        :undoc-members:
-
-
-Cupy models 
--------------------------
-
-vbi.models.cupy.mpr 
--------------------------
-    .. automodule:: vbi.models.cupy.mpr
-        :members:
-        :undoc-members:
-
-vbi.models.cupy.ghb
--------------------------
-    .. automodule:: vbi.models.cupy.ghb
-        :members:
-        :undoc-members:
-
-vbi.models.cupy.jansen_rit
-----------------------------
-    .. automodule:: vbi.models.cupy.jansen_rit
-        :members:
-        :undoc-members:
-
-vbi.models.cupy.utils 
--------------------------
-    .. automodule:: vbi.models.cupy.utils
-        :members:
-        :undoc-members: