Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -77,6 +77,14 @@
77	77
78	78	Next we shall create a virtual environment within this directory. Python 3 provides intrinsic support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows:
79	79
	80	+(% class="box errormessage" %)
	81	+(((
	82	+**Note:**
	83	+For older versions of Python 3, you might require to manually install `python3-venv` package before being able to run the below command. To install, run:
	84	+\\sudo apt-get install python3-venv
	85	+\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
	86	+)))
	87	+
80	80	(% class="box infomessage" %)
81	81	(((
82	82	**Screencast** - terminal
...	...	@@ -88,22 +88,68 @@
88	88	(% class="box infomessage" %)
89	89	(((
90	90	**Screencast** - file explorer
91		-\\<< show directory contents; especially lib/python3.9/site-packages >>
	99	+\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.9/site-packages >>
92	92	)))
93	93
94	94	As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we shall install various other packages, and you shall see that these would be reflected here.
95	95
	104	+To enter into this virtual environment, and thereby use its resources in isolation from other projects on your computer, we require to "activate" it. This is achieved by running the command:
	105	+
	106	+(% class="box infomessage" %)
	107	+(((
	108	+**Screencast** - terminal
	109	+\\(% style="color:#000000" %)source pynn_env/bin/activate
	110	+)))
	111	+
	112	+Notice how this changes the command prompt to show the name of your virtual environment. In our case, we had named it 'pynn_env', and this is now reflected as a prefix to the command prompt. This confirms that we are now in our new virtual environment.
	113	+
96	96	Now that we have our project's virtual environment setup, we are now ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. Alternatively, this would need to be done manually as described on the PyNN website. In this tutorial, we will adopt the easier approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
97	97
98		-We start here with the installation of Brian2.
	116	+We start here with the installation of Brian2. Brian2 can be installed simply using the pip command.
99	99
100	100	(% class="box infomessage" %)
101	101	(((
102		-**Screencast** - current state of editor
103		-\\
	120	+**Screencast** - terminal
	121	+\\(% style="color:#000000" %)pip install brian2
104	104	)))
105	105
	124	+This will install Brian2, along with all its dependencies such as 'cython', 'numpy', etc. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
106	106
	126	+(% class="box infomessage" %)
	127	+(((
	128	+**Screencast** - file explorer
	129	+\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
	130	+)))
	131	+
	132	+To confirm that we have properly installed Brian2 on our computer, we can test as follows:
	133	+
	134	+(% class="box infomessage" %)
	135	+(((
	136	+**Screencast** - terminal
	137	+\\(% style="color:#000000" %)python
	138	+\\import brian2
	139	+\\exit()
	140	+)))
	141	+
	142	+If there are no error messages here, and the import is successful, then we have completed installing Brian2.
	143	+
	144	+
	145	+We shall now move on to install the NEST simulator. Unlike Brian2, NEST is not a Python package and therefore its installation is a bit more involved. We shall install the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel.
	146	+
	147	+We first install the NEST module. Version 2.20 is currently supported by PyNN, and it is likely that other versions of NEST might have issues when used with the current version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself.
	148	+
	149	+(% class="box infomessage" %)
	150	+(((
	151	+**Screencast** - terminal
	152	+\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
	153	+sudo apt-get update
	154	+\\sudo apt-get install nest
	155	+)))
	156	+
	157	+At this point, we have installed the NEST module, but it is still not usable via Python. To do so, we next install PyNEST.
	158	+
	159	+
	160	+
107	107	(% class="box successmessage" %)
108	108	(((
109	109	**Slide** recap of learning objectives