Last modified by adavison on 2022/10/04 13:53
From version 21.5
edited by shailesh
on 2021/10/06 13:11
Change comment: There is no comment for this version
To version 21.8
edited by shailesh
on 2021/10/06 14:04
Change comment: There is no comment for this version

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56 56  **Slide** listing prerequisites
57 57  )))
58 58  
59 -I shall be demonstrating the installation on a computer with Ubuntu 18.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS.
59 +I shall be demonstrating the installation on a computer with Ubuntu 18.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, the tutorial will focus only on Python 3, as Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I would be using Python 3.9.7 in this tutorial.
60 60  
61 61  (% class="box infomessage" %)
62 62  (((
63 -**Screencast** - blank document in editor
63 +**Screencast** - terminal
64 64  )))
65 65  
66 -We shall make use of virtualenv (virtual environment) in this tutorial. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects and thereby preventing unrequested changes in others, when any one of them is updated.
66 +We shall make use of virtual environments in this tutorial. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects and thereby preventing unrequested changes in others, when any one of them is updated.
67 67  
68 +We begin by creating a directory for our project.
69 +
68 68  (% class="box infomessage" %)
69 69  (((
70 -**Screencast** - current state of editor
71 -\\(% style="color:#000000" %)"""install and setup new virtualenv project"""(%%)
72 -\\(% style="color:#000000" %)sudo pip install virtualenv
73 -\\"""create a directory for project"""
74 -\\cd ~~
72 +**Screencast** - terminal
73 +\\(% style="color:#000000" %)cd ~~
75 75  mkdir pynn_project
76 76  cd pynn_project
77 -\\"""create a virtual environment for this project"""
78 -virtualenv pynn_env
79 79  )))
80 80  
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:
81 81  
80 +(% class="box infomessage" %)
81 +(((
82 +**Screencast** - terminal
83 +\\(% style="color:#000000" %)python -m venv pynn_env
84 +)))
82 82  
86 +A
87 +
88 +(% class="box infomessage" %)
89 +(((
90 +**Screencast** - file explorer
91 +\\<< show directory contents; especially site-packages >>
92 +)))
93 +
94 +
95 +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.
96 +
97 +We start here with the installation of Brian2.
98 +
99 +(% class="box infomessage" %)
100 +(((
101 +**Screencast** - current state of editor
102 +\\
103 +)))
104 +
105 +
83 83  (% class="box successmessage" %)
84 84  (((
85 85  **Slide** recap of learning objectives
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99 99  
100 100  (% class="wikigeneratedid" %)
101 101  For more information visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community.
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126 +
127 +(% class="wikigeneratedid" %)
128 +[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]