Merge branch '0.9.0'

README.md

@@ -6,8 +6,8 @@
 # PyRates
 PyRates is a framework for neural modeling and simulations, developed by Richard Gast and Daniel Rose at the Max Planck Institute of Human Cognitive and Brain Sciences, Leipzig, Germany. 
 
-Basic features:
----------------
+## Basic features:
+
 - Different backends: `Numpy` for fast simulations of small- to medium-sized networks. `Tensorflow` for efficient parallelization on GPUs/CPUs, `Fortran` for parameter continuations.
 - Each model is internally represented by a `networkx` graph of nodes and edges, with the former representing the model units (i.e. single cells, cell populations, ...) and the latter the information transfer between them. In principle, this allows to implement any kind of dynamic neural system that can be expressed as a graph via PyRates.
 - Solutions of initial value problems via different numerical solvers (e.g. full interface to `scipy.integrate.solve_ivp`)
@@ -21,16 +21,31 @@ Basic features:
 - Model configuration and simulation can be done within a few lines of code.  
 - Various templates for rate-based population models are provided that can be used for neural network simulations imediatly.
 
-Installation
-------------
+## Installation
+
 PyRates can be installed via the `pip` command. We recommend to use `Anaconda` to create a new python environment with Python >= 3.6 and then simply run the following line from a terminal with the environment being activated:
 ```
 pip install pyrates
 ```
-Alternatively, it is possible to clone this repository and run the following line from the directory in which the repository was cloned:
+
+You can install optional (non-default) packages by specifying one or more options in brackets, e.g.:
+```
+pip install pyrates[tf,plot]
+```
+
+Available options are `tf`, `plot`, `proc`, `cluster`, `numba` and `all`. 
+The latter includes all optional packages.
+
+Alternatively, it is possible to clone this repository and run one of the following lines 
+from the directory in which the repository was cloned:
 ```
 python setup.py install
 ```
+or
+```
+pip install .[<options>]
+```
+
 Finally, a singularity container of the most recent version of this software can be found [here](https://singularity.gwdg.de/containers/3).
 This container provides a stand-alone version of PyRates including all necessary Python tools to be run, independent of local operating systems. 
 To be able to use this container, you need to install [Singularity](https://singularity.lbl.gov/) on your local machine first.

pyrates/backend/numpy_backend.py

@@ -1388,7 +1388,7 @@ def add_input_layer(self, inputs: list, T: float, continuous=True) -> NumpyVar:
                 time = np.linspace(0, T, inputs[0][0].shape[0])
 
                 for (inp, target_var, idx) in inputs:
-                    in_name = f"{inp.short_name}_inp" if hasattr(inp, 'short_name') else "var_inp"
+                    in_name = f"{inp.short_name}_inp" if hasattr(inp, 'short_name') else f"{target_var.short_name}_inp"
                     if len(inp.shape) > 1:
                         inp = inp.squeeze()
                     f = interp1d(time, inp, axis=0, copy=False, kind='linear')