Setting up a SmartScope Development Environment

This section aims at describing the setup of a development environment for SmartScope.

1. First, install SmartScope using Docker or Podman

2. (Optional) Then, we suggest to make a fork of the repository.

3. Clone the dev branch from your fork or the main repository.

   ## Run this in the directory where smartscope is installed
   git clone https://github.com/NIEHS/SmartScope.git SmartScope-dev -b dev
   

4. Mount the source code as a volume to the smartscope container.

   Note

   This is the way to make modification possible and any change persistent.

   Warning

   The example below assumes that the source code was cloned in the installation directory

   version: "3"
   services:
     smartscope:
       image: ghcr.io/niehs/smartscope:dev
       user: 0:0 #This corresponds to the user running the smarscope.sh script
       volumes:
         - ./SmartScope-dev/:/opt/smartscope/
         # Example:
         # - /nfs/data/:/mnt/data/
         ######## ADD YOUR MICROSCOPES #########
         # The synthax from the microscope volumes is as follows:
         # - /path/to/where/serialem/will/write/files/:/mnt/your_scope_name_here/
         # Example:
         # - /mnt/gatan_Raid_X/smartscope/:/mnt/arctica/
   

5. (Optional) Set up fake scope mode as detailed here