update setup/README to start jupyter from base environment

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`. 

setup.sh

@@ -1,12 +1,13 @@
+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
 unzip woodshole_new.zip
 mkdir woodshole
 mv woodshole_new/* woodshole
 rm woodshole_new.zip
-rm -r woodshole_new
+rm -r woodshole_new