diff --git a/README.md b/README.md index e995e4b1..ed4f13ad 100644 --- a/README.md +++ b/README.md @@ -25,8 +25,17 @@ The full set of dependencies for c302 can be installed with the following (see a pip install . owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json' -This will install c302 as well as all dependencies, including [pyNeuroML](https://github.com/NeuroML/pyNeuroML) and [owmeta](https://github.com/openworm/owmeta). +This will install c302 as well as [pyNeuroML](https://github.com/NeuroML/pyNeuroML) and [owmeta](https://github.com/openworm/owmeta). +To run the test.sh script, the Neuron simulator is also required, and should be installed as described [here](https://www.neuron.yale.edu/neuron/download). + +For Linux users, additional dependencies (OpenJDK 19 and Graphviz) are required to run the Usage Examples: + + sudo apt-get install openjdk-19-jdk graphviz + +Please note that Python3 is also required to run both the test.sh script and the Usage Examples. For convenience on Linux, it is recommended to install python-is-python3 prior to running the test.sh script. + + sudo apt-get install python-is-python3 #### Quick test @@ -42,7 +51,7 @@ To ensure everything is set up correctly try: To test all of the working features of the framework run [test.sh](https://raw.githubusercontent.com/openworm/CElegansNeuroML/master/CElegans/pythonScripts/c302/test.sh): - ./test.sh # or ./test3.sh if you use Python 3 + ./test.sh ### Docker image @@ -110,7 +119,7 @@ The other shows membrane potential for each neuron in the network. ![membrane potential](images/LEMS_MyNetwork-membranePotential.png) -To see the structure of the network, use pyNeuroML: +To see the structure of the network, use pyNeuroML (please note that Graphviz is required): pynml MyNetwork.net.nml -graph 4c # Try other options like 1, 2f, 5c for varying levels of detail diff --git a/test.sh b/test.sh index 3079e643..f6919554 100755 --- a/test.sh +++ b/test.sh @@ -1,9 +1,5 @@ set -ex -## Install - -python setup.py install - ## Test readers python -m c302.SpreadsheetDataReader