Update docs with install steps for Windows OS

_modules/goo/cell.html

@@ -216,6 +216,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

_modules/goo/division.html

@@ -216,6 +216,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

_modules/goo/force.html

@@ -216,6 +216,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

_modules/goo/reloader.html

@@ -216,6 +216,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

_modules/goo/simulator.html

@@ -216,6 +216,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

_modules/goo/utils.html

@@ -216,6 +216,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

_modules/index.html

@@ -216,6 +216,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

_sources/getting_started/installation.rst.txt

@@ -38,17 +38,21 @@ Dependencies
 .. _mathutils: https://pypi.org/project/mathutils/
 .. _scipy: https://pypi.org/project/scipy/
 
-Install Dependencies in Blender
--------------------------------
+
+Install dependencies in Blender
+================================
+
+MacOS/Linux
+------------
 
 Blender comes with its own Python interpreter, which is isolated from the system's Python environment. 
 Goo requires a few additional Python packages that need to be installed directly into Blender's Python environment. 
 
-To install Goo's dependencies: 
+To install Goo's dependencies from the terminal: 
 
 1. Find the paths of the Blender executable and its Python interpreter.
 
-   For macOS, it is usually in the Applications folder, e.g., `/Applications/Blender.app/Contents/MacOS/Blender` and `/Applications/Blender.app/Contents/Resources/3.6/python/bin/python3.10`. For Windows, it is usually in the Program Files folder.
+   For macOS, it is usually in the Applications folder, e.g., `/Applications/Blender.app/Contents/MacOS/Blender` and `/Applications/Blender.app/Contents/Resources/3.6/python/bin/python3.10`.
 
 2. Create a new environment using Blender's Python interpreter:
 
@@ -79,3 +83,50 @@ To install Goo's dependencies:
    .. code-block:: bash
 
       /Applications/Blender.app/Contents/MacOS/Blender
+
+
+Windows
+------------
+
+Blender comes with its own Python interpreter, which is isolated from the system's Python environment. 
+Goo requires a few additional Python packages that need to be installed directly into Blender's Python environment. 
+
+To install Goo's dependencies from a terminal: 
+
+1. Find the paths of the Blender executable and its Python interpreter.
+
+   For Windows, it is usually in the Program Files, e.g., `C:\\Program Files\\Blender Foundation\\Blender 4.1\\Blender.exe` and `C:\\Program Files\\Blender Foundation\\Blender 4.1\\4.1\python\\bin\\python.exe`.
+
+2. Create a new virtual environment using Blender's Python interpreter:
+
+   .. code-block:: bash
+
+      C:\\Program Files\\Blender Foundation\\Blender 4.1\\4.1\\python\\bin\\python.exe -m venv .blender_env
+
+
+3. Activate the environment:
+
+   .. code-block:: bash
+
+      .blender_env\\Scripts\\activate
+
+4. Install the dependencies:
+
+   .. code-block:: bash
+
+      C:\\Program Files\\Blender Foundation\\Blender 4.1\\4.1\\python\\bin\\python.exe -m pip install setuptools numpy scipy sphinx sphinx_copybutton furo typing_extensions
+
+5. Check that the dependencies are installed:
+
+   .. code-block:: bash
+
+      C:\\Program Files\\Blender Foundation\\Blender 4.1\\4.1\\python\\bin\\python.exe -m pip list
+
+6. Launch Blender from within the activated virtual environment:
+
+   .. code-block:: bash
+
+       C:\\Program Files\\Blender Foundation\\Blender 3.3\\Blender.exe
+
+
+Blender supports virtual environment and the installed packages will be available to use for scripting in Blender. 

credits/credits_and_citation.html

@@ -217,6 +217,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

developer_guide/developers.html

@@ -217,6 +217,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../getting_started/blender_on_o2.html">Running Goo on O2</a></li>

genindex.html

@@ -215,6 +215,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul>
 <li class="toctree-l1"><a class="reference internal" href="getting_started/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="getting_started/installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="getting_started/learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="getting_started/example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="getting_started/blender_on_o2.html">Running Goo on O2</a></li>
@@ -429,12 +430,16 @@ <h2>D</h2>
 </li>
         <li><a href="user_guide/goo.cell.html#goo.cell.CellType.default_celltype">default_celltype() (goo.cell.CellType static method)</a>
 </li>
-        <li><a href="user_guide/goo.molecule.html#goo.molecule.DiffusionSystem.diffuse">diffuse() (goo.molecule.DiffusionSystem method)</a>
-</li>
-        <li><a href="user_guide/goo.handler.html#goo.handler.DiffusionHandler">DiffusionHandler (class in goo.handler)</a>
+        <li><a href="user_guide/goo.handler.html#goo.handler.DiffusionHandler.diffuse">diffuse() (goo.handler.DiffusionHandler method)</a>
+
+        <ul>
+          <li><a href="user_guide/goo.molecule.html#goo.molecule.DiffusionSystem.diffuse">(goo.molecule.DiffusionSystem method)</a>
 </li>
+        </ul></li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="user_guide/goo.handler.html#goo.handler.DiffusionHandler">DiffusionHandler (class in goo.handler)</a>
+</li>
         <li><a href="user_guide/goo.molecule.html#goo.molecule.DiffusionSystem">DiffusionSystem (class in goo.molecule)</a>
 </li>
         <li><a href="user_guide/goo.force.html#goo.force.Force.disable">disable() (goo.force.Force method)</a>
@@ -700,8 +705,6 @@ <h2>M</h2>
         </ul></li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="user_guide/goo.handler.html#goo.handler.MolecularSensingHandler">MolecularSensingHandler (class in goo.handler)</a>
-</li>
         <li><a href="user_guide/goo.molecule.html#goo.molecule.Molecule">Molecule (class in goo.molecule)</a>
 </li>
         <li><a href="user_guide/goo.molecule.html#goo.molecule.DiffusionSystem.molecules">molecules (goo.molecule.DiffusionSystem property)</a>
@@ -801,6 +804,8 @@ <h2>R</h2>
         <li><a href="user_guide/goo.handler.html#goo.handler.Colorizer.RANDOM">RANDOM (goo.handler.Colorizer attribute)</a>
 </li>
         <li><a href="user_guide/goo.handler.html#goo.handler.RandomMotionHandler">RandomMotionHandler (class in goo.handler)</a>
+</li>
+        <li><a href="user_guide/goo.handler.html#goo.handler.DiffusionHandler.read_molecular_signal">read_molecular_signal() (goo.handler.DiffusionHandler method)</a>
 </li>
         <li><a href="user_guide/goo.cell.html#goo.cell.Cell.recenter">recenter() (goo.cell.Cell method)</a>
 </li>
@@ -821,11 +826,11 @@ <h2>R</h2>
         <li><a href="user_guide/goo.simulator.html#goo.simulator.Simulator.render">render() (goo.simulator.Simulator method)</a>
 </li>
         <li><a href="user_guide/goo.reloader.html#goo.reloader.reset_modules">reset_modules() (in module goo.reloader)</a>
-</li>
-        <li><a href="user_guide/goo.reloader.html#goo.reloader.reset_scene">reset_scene() (in module goo.reloader)</a>
 </li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="user_guide/goo.reloader.html#goo.reloader.reset_scene">reset_scene() (in module goo.reloader)</a>
+</li>
         <li><a href="user_guide/goo.division.html#goo.division.DivisionHandler.run">run() (goo.division.DivisionHandler method)</a>
 
         <ul>
@@ -844,14 +849,10 @@ <h2>R</h2>
           <li><a href="user_guide/goo.handler.html#goo.handler.GrowthPIDHandler.run">(goo.handler.GrowthPIDHandler method)</a>
 </li>
           <li><a href="user_guide/goo.handler.html#goo.handler.Handler.run">(goo.handler.Handler method)</a>
-</li>
-          <li><a href="user_guide/goo.handler.html#goo.handler.MolecularSensingHandler.run">(goo.handler.MolecularSensingHandler method)</a>
 </li>
           <li><a href="user_guide/goo.handler.html#goo.handler.RandomMotionHandler.run">(goo.handler.RandomMotionHandler method)</a>
 </li>
           <li><a href="user_guide/goo.handler.html#goo.handler.RemeshHandler.run">(goo.handler.RemeshHandler method)</a>
-</li>
-          <li><a href="user_guide/goo.molecule.html#goo.molecule.DiffusionSystem.run">(goo.molecule.DiffusionSystem method)</a>
 </li>
           <li><a href="user_guide/goo.simulator.html#goo.simulator.Simulator.run">(goo.simulator.Simulator method)</a>
 </li>
@@ -911,6 +912,10 @@ <h2>S</h2>
         <li><a href="user_guide/goo.force.html#goo.force.Force.shape">shape (goo.force.Force property)</a>
 </li>
         <li><a href="user_guide/goo.cell.html#goo.cell.SimpleType">SimpleType (class in goo.cell)</a>
+</li>
+        <li><a href="user_guide/goo.molecule.html#goo.molecule.DiffusionSystem.simulate">simulate() (goo.molecule.DiffusionSystem method)</a>
+</li>
+        <li><a href="user_guide/goo.handler.html#goo.handler.DiffusionHandler.simulate_diffusion">simulate_diffusion() (goo.handler.DiffusionHandler method)</a>
 </li>
         <li><a href="user_guide/goo.simulator.html#goo.simulator.Simulator">Simulator (class in goo.simulator)</a>
 </li>
@@ -973,10 +978,10 @@ <h2>U</h2>
   <table style="width: 100%" class="indextable genindextable"><tr>
     <td style="width: 33%; vertical-align: top;"><ul>
         <li><a href="user_guide/goo.handler.html#goo.handler.ForceDist.UNIFORM">UNIFORM (goo.handler.ForceDist attribute)</a>
-</li>
-        <li><a href="user_guide/goo.handler.html#goo.handler.DiffusionHandler.update_cell_concentration">update_cell_concentration() (goo.handler.DiffusionHandler method)</a>
 </li>
         <li><a href="user_guide/goo.molecule.html#goo.molecule.DiffusionSystem.update_concentration">update_concentration() (goo.molecule.DiffusionSystem method)</a>
+</li>
+        <li><a href="user_guide/goo.handler.html#goo.handler.DiffusionHandler.update_molecular_signal">update_molecular_signal() (goo.handler.DiffusionHandler method)</a>
 </li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>

getting_started/blender_on_o2.html

@@ -217,6 +217,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Running Goo on O2</a></li>

getting_started/example_scripts.html

@@ -217,6 +217,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="blender_on_o2.html">Running Goo on O2</a></li>

getting_started/hardware.html

@@ -217,6 +217,7 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html#install-dependencies-in-blender">Install dependencies in Blender</a></li>
 <li class="toctree-l1"><a class="reference internal" href="learning_resources.html">Learning resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="example_scripts.html">Example scripts</a></li>
 <li class="toctree-l1"><a class="reference internal" href="blender_on_o2.html">Running Goo on O2</a></li>