From 29b3c034c116dfeb2a531005ea67e070311b50eb Mon Sep 17 00:00:00 2001 From: Maximilian Schmidt <max.schmidt@fz-juelich.de> Date: Tue, 5 Jun 2018 16:17:10 +0900 Subject: [PATCH] Remove R from requirements, add correlation_toolbox and add instructions for R to README --- figures/Schmidt2018_dyn/README.md | 2 ++ figures/Schmidt2018_dyn/additional_requirements.txt | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/figures/Schmidt2018_dyn/README.md b/figures/Schmidt2018_dyn/README.md index 64fdd94..73f1c38 100644 --- a/figures/Schmidt2018_dyn/README.md +++ b/figures/Schmidt2018_dyn/README.md @@ -28,6 +28,8 @@ Reproducing the figures requires some additional Python packages listed in `addi `pip install -r additional_requirements.txt` +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>). + ### 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/additional_requirements.txt b/figures/Schmidt2018_dyn/additional_requirements.txt index 8489ecf..fe439da 100644 --- a/figures/Schmidt2018_dyn/additional_requirements.txt +++ b/figures/Schmidt2018_dyn/additional_requirements.txt @@ -1,5 +1,5 @@ statsmodels -R networkx pyx python-louvain +-e git+https://github.com/mschmidt87/correlation-toolbox.git@enh/add_setup_file#egg=correlation-toolbox -- GitLab