From b9840ba6126fe9c752daa7d6eeb6f8c102c0e3ba Mon Sep 17 00:00:00 2001
From: Maximilian Schmidt <max.schmidt@fz-juelich.de>
Date: Tue, 26 Jun 2018 18:41:54 +0900
Subject: [PATCH] Document infomap in README files and set default path to None
---
figures/Schmidt2018/README.md | 2 ++
figures/Schmidt2018_dyn/README.md | 2 ++
figures/Schmidt2018_dyn/helpers.py | 2 +-
3 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/figures/Schmidt2018/README.md b/figures/Schmidt2018/README.md
index 5780f29..45f6af7 100644
--- a/figures/Schmidt2018/README.md
+++ b/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`
diff --git a/figures/Schmidt2018_dyn/README.md b/figures/Schmidt2018_dyn/README.md
index 73f1c38..5cfc254 100644
--- a/figures/Schmidt2018_dyn/README.md
+++ b/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`.
diff --git a/figures/Schmidt2018_dyn/helpers.py b/figures/Schmidt2018_dyn/helpers.py
index b6fc713..9cb147b 100644
--- a/figures/Schmidt2018_dyn/helpers.py
+++ b/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'}
--
GitLab