From 4248584eeb46e7f3a91a0bd78281e111468f042c Mon Sep 17 00:00:00 2001 From: Justin Hiemstra Date: Tue, 10 Oct 2023 20:27:43 +0000 Subject: [PATCH] Update CONTRIBUTING.md to include `pip` instructions --- CONTRIBUTING.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index ecefd7a5..8aa3b0fc 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -169,7 +169,8 @@ After completing this step, try running the Local Neighborhood algorithm through ```bash snakemake --cores 1 --configfile config/config.yaml ``` -Make sure to run the command inside the `spras` conda environment. +Make sure to run the command inside the `spras` conda environment. If installing via `pip` instead of using conda, install with the `-e` flag (the full command to run from the repo root is +`python -m pip install -e .`) so that Python picks up any changes you make. Omitting the `-e` flag will prevent your changes from being reflected unless you force re-install. As a workflow manager, Snakemake will consider the work described in the configuration file to be completed once the necessary output files have been written to the relevant output directory (`output` in the `config/config.yaml` configuration). That means that if you change your code and rerun the Snakemake command above, nothing may happen if the output files already exist.