Docs

docs_sphinx/GUI/launching.rst

@@ -43,7 +43,7 @@ Installing phy 2.0
 
 If you want to use the phy GUI to visualize your results, you may need to install phy 2.0::
 
-    >> pip install colorcet pyopengl joblib
+    >> pip install colorcet pyopengl qtconsole requests traitlets tqdm joblib click mkdocs
     >> pip install --upgrade http://github.com/cortex-lab/phy/archive/dev.zip
     >> pip install --upgrade http://github.com/cortex-lab/phylib/archive/master.zip
 

docs_sphinx/introduction/install.rst

@@ -30,6 +30,14 @@ As an example for linux, just type::
     >> wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
     >> bash Miniconda-latest-Linux-x86_64.sh
 
+If you want, first, the best is to create a dedicated environment::
+
+    >> conda create -n circus python=3.6
+
+Then activate the environment::
+
+    >> conda activate circus
+
 Then install the software itself::
 
     >> conda install -c conda-forge -c anaconda -c spyking-circus spyking-circus
@@ -103,6 +111,8 @@ If you want to use the phy GUI to visualize your results, you may need to instal
     >> pip install --upgrade http://github.com/cortex-lab/phy/archive/dev.zip
     >> pip install --upgrade http://github.com/cortex-lab/phylib/archive/master.zip
 
+You can see more details on the `phy website <https://phy.readthedocs.io/en/latest/installation/>`_
+
 
 Home Directory
 --------------

docs_sphinx/introduction/mac.rst

@@ -5,17 +5,24 @@ Here are some detailed instructions:
 
     1. Install Anaconda_ (Python 2.7 or 3.5)
 
-    2. Install spiking-circus by executing::
+    2. The best is to create a dedicated environment to install the software, and activate it::
+
+        >> conda create -n circus python=3.6
+        >> conda activate circus
+
+    3. Install spiking-circus by executing::
 
         >> conda install -c conda-forge -c anaconda -c spyking-circus spyking-circus
     
-    3. If you prefer, you can use pip (this is equivalent to step 4)::
+    4. If you prefer, you can use pip (this is equivalent to step 3)::
     
         >> pip install spyking-circus
 
-    4. Here you are! Now run the code, for example::
+    5. Here you are! Now run the code, for example::
 
         >> spyking-circus pathtodata/data.dat -c 7
 
+If you want to install phy_ 2.0 as a visulization GUI, you can install it in the same environment (:doc:`see here for detailed instructions <../GUI/launching>` 
 
 .. _Anaconda: https://www.anaconda.com/distribution/
+.. _phy: https://github.com/cortex-lab/phy

docs_sphinx/introduction/windows.rst

@@ -5,23 +5,36 @@ Here are some detailed instructions:
 
     1. Install Anaconda_ (Python 2.7 or 3.5)
     2. Launched Anaconda's command line
-    3. Execute ``conda install -c anaconda mpi4py``
-    4. You should see the following message:
+    3. The best is to create a dedicated environment to install the software, and activate it::
+
+        >> conda create -n circus python=3.6
+        >> conda activate circus
+
+    4. Execute:: 
+
+        >> conda install -c anaconda mpi4py
+
+    5. You should see the following message:
         * mpi4py requires that Microsoft MPI 6 be installed on the host system. That is a system wide installation that is currently not available through conda. In order to successfully use mpi4py you must install Microsoft MPI and then append the bin directory of the MPI installation to your PATH environment variable. To install Microsoft MPI see MPIv10_
 
-    5. Install microsoft MPIv10_ (both .msi and .exe) as requested with the previous link
-    6. Add the mpi installation's bin directory to the path (``C:\program files\microsoft mpi\bin``)
-    7. Install spiking-circus by executing::
+    6. Install microsoft MPIv10_ (both .msi and .exe) as requested with the previous link
+    7. Add the mpi installation's bin directory to the path (``C:\program files\microsoft mpi\bin``)
+
+    8. Install spiking-circus by executing::
 
         >> conda install -c conda-forge -c anaconda -c spyking-circus spyking-circus
     
-    8. If you prefer, you can use pip (this is equivalent to step 7)::
+    9. If you prefer, you can use pip (this is equivalent to step 8)::
     
         >> pip install spyking-circus
 
-    9. Here you are! Now run the code, for example::
+    10. Here you are! Now run the code, for example::
 
         >> spyking-circus pathtodata/data.dat -c 7
 
+
+If you want to install phy_ 2.0 as a visulization GUI, you can install it in the same environment (:doc:`see here for detailed instructions <../GUI/launching>` 
+
 .. _Anaconda: https://www.anaconda.com/distribution/
-.. _MPIv10: https://www.microsoft.com/en-us/download/details.aspx?id=57467
+.. _MPIv10: https://www.microsoft.com/en-us/download/details.aspx?id=57467
+.. _phy: https://github.com/cortex-lab/phy