Document infomap in README files and set default path to None

figures/Schmidt2018/README.md

@@ -12,6 +12,8 @@ Reproducing the figures requires some additional Python packages listed in `addi
 
 `pip install -r additional_requirements.txt`
 
+To produce Figure 7, an installation of the `infomap` package is required. Please follow the instructions on the website http://www.mapequation.org/code.html.
+
 If snakemake is installed, the figures can be produced by executing
 
 `snakemake`

figures/Schmidt2018_dyn/README.md

@@ -30,6 +30,8 @@ Reproducing the figures requires some additional Python packages listed in `addi
 
 The calculation of BOLD signals from the simulated firing rates for Fig. 8 requires an installation of R and the R library `neuRosim` (<https://cran.r-project.org/web/packages/neuRosim/index.html>).
 
+To produce Figure 8, an installation of the `infomap` package is required. Please follow the instructions on the website http://www.mapequation.org/code.html.
+
 ### Snakemake workflow
 
 The entire workflow from raw spike files till the final figures is defined in `Snakefile` and `Snakefile_preprocessing`. If snakemake is installed, the figures can be produced by executing `snakemake`.

figures/Schmidt2018_dyn/helpers.py

@@ -12,7 +12,7 @@ population_labels = ['2/3E', '2/3I', '4E', '4I', '5E', '5I', '6E', '6I']
 
 # This path determines the location of the infomap
 # installation and needs to be provided to execute the script for Fig. 7
-infomap_path = '/home/schmidt/opt/infomap'
+infomap_path = None
 
 tex_names = {'23': 'twothree', '4': 'four', '5': 'five', '6': 'six'}