Getting started

Welcome to teili!

To start using teili, follow the instructions below and see our tutorials.

Prepare a virtual environment

Before we can install teili we encourage to set up a virtual environment using anaconda (or miniconda). Make sure you have installed conda.

  • Create a virtual environment using conda

conda create --name <myenv> python=3.7

Note

Replace <myenv> with the desired name for your virtual environment

Note

If you want to use CTXCTL add the particular python version to the conda environment

conda create --name <myenv> python=3.7.1

  • Activate your conda environment

source activate <myenv>

Install latest stable release of teili

For installing the latest stable release run the following command

pip install teili
python -m teili.tools.generate_teiliApps

The first command will install teili and all its dependencies. The second command generates a teiliApps directory in your home folder. This folder contains a selection of neuron and synapse models, tutorials, as well as unit tests. Please run the unit tests to check if everything is working as expected by

cd ~/teiliApps
python -m unittest discover unit_tests/

Attention

Running the unit_tests will output a lot of Warnings to your terminal. This, however, does not mean that the unit_tests failed as we need to generate and kill test plots. As long as the last line states: Ran 78 tests in 93.373s OK Everything is good.

You are good to go.

Note

If you find yourself seeing an warning as shown below consider updating pyqtgraph to the current development version using pip install git+https://github.com/pyqtgraph/pyqtgraph@develop

Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/home/you/miniconda3/envs/teili_test/lib/python3.6/site-packages/pyqtgraph/__init__.py", line 312, in cleanup
    if isinstance(o, QtGui.QGraphicsItem) and isQObjectAlive(o) and o.scene() is None:
ReferenceError: weakly-referenced object no longer exists

In case you want the latest stable version of teili you refer to our repository The following steps are only required, if you need the most recent stable version/unstable developments for your simulations. If you do not require the latest version please proceed to tutorials.

Install latest development version of teili

  • To get the most recent version of teili you can either clone the repository as shown below or download the tar.gz file.

git clone https://gitlab.com/neuroinf/teili.git

Note

If you have set up git properly you can use of course git clone git@gitlab.com:neuroinf/teili.git

Note

For the latest development version of teili please checkout the dev branch: git checkout dev.

  • Navigate to the parent folder containing the cloned repository or the downloaded tar.gz file and install teili using pip (make sure you activated your virtual environment).

# Point pip to the location of the setup.py
pip install teili/
# or point pip to the downloaded tar.gz file
pip install teili*.tar.gz

Note

Note that the path provided in the install command needs to point to the folder which contains the setup.py file. When using the source files the teiliApps directory is generated automically.

The setup.py will by default create a folder in your home directory called teiliApps. This folder contains a selection of neuron and synapse models, tutorials, as well as unit tests. Please run the unit tests to check if everything is working as expected by

cd ~/teiliApps
python -m unittest discover unit_tests/

You are good to go!

Note

Due to pyqtgraph the unit tests will print warnings, as we generate and close figures to test the functionality of teili. These warning are normal. As longer as no Error is returned, everything is behaving as expected.

If you want to change the location of teiliApps, you can do so by moving the folder manually.

The installation instructions above will install all requirements and dependencies. It will also build pre-defined neuron and synapse models and place them in teiliApps/equations/. Make sure you checkout our tutorials.

Re-building models after installation

Note

By default models are generated during installation. Only if you accidentally deleted them manually you need to rebuild models.

By default the models will be placed in teiliApps/equations/. If you want to place them at a different location follow the instructions below:

source activate <myenv>
python

from teili import neuron_models, synapse_models
neuron_models.main("/path/to/my/equations/")
synapse_models.main("/path/to/my/equations/")

Attention

You need to specify the absolute path. So use /home/<YOU>/your_custom_path/, rather than ~/your_custom_path/.

Note, that the following folder structure is generated in the specified location: /path/to/my/equations/teiliApps/equations/. If you simply call the classes without a path the equations will be placed in ~/teiliApps/equations/. Have a look at our tutorials to see how to use teili and which features it provides to you.