From e3567342056fccc69775dacfaa7a06db4fdfe545 Mon Sep 17 00:00:00 2001 From: Larissa Heinrich Date: Fri, 25 Aug 2023 13:40:10 +0000 Subject: [PATCH] update setup/README to start jupyter from base environment --- README.md | 28 ++-------------------------- setup.sh | 5 +++-- 2 files changed, 5 insertions(+), 28 deletions(-) diff --git a/README.md b/README.md index 36e80d8..d6c493e 100644 --- a/README.md +++ b/README.md @@ -5,31 +5,7 @@ Run the shell script: ``` -./setup.sh +source setup.sh ``` -Activate the environment: -``` -conda activate 06_instance_segmentation -``` - -Start jupyter (you can use jupyter-notebook if you'd prefer, however jupyter-lab has some nice cell collapsing and is structured more similar to an IDE): - -``` -jupyter-lab -``` - -If running remotely (i.e through an ssh tunnel instead of no machine) call no -browser from your remote machine: - -``` -jupyter-lab --no-browser -``` - -And then set up a tunnel from your local machine (adjust port accordingly): - -``` -ssh -NL 8888:localhost:8888 username@hostname -``` - -...and continue with the instructions in the notebook. +Start jupyter-lab, select the `06_instance_segmentation` kernel and follow the instructions in the notebook `exercise.ipynb`. diff --git a/setup.sh b/setup.sh index 15a8f45..d167cd0 100755 --- a/setup.sh +++ b/setup.sh @@ -1,7 +1,8 @@ +mamba activate base echo -e "\n creating mamba env... \n" mamba env create -f environment.yml jupyter nbextension enable --py widgetsnbextension -mamba activate 06_instance_segmentation +mamba activate base echo -e "\n downloading data...\n" aws s3 cp "s3://dl-at-mbl-2023-data/woodshole_new.zip" "." --no-sign-request @@ -9,4 +10,4 @@ unzip woodshole_new.zip mkdir woodshole mv woodshole_new/* woodshole rm woodshole_new.zip -rm -r woodshole_new \ No newline at end of file +rm -r woodshole_new