Adding apptainer support (#28)

[bendhouseart]

• Added .gitignore and README
• Updated README for formatting
• Adding apptainer scripts

---

[bendhouseart]

@kiwimarc Okay, maybe this is because I'm being difficult and running singularity/apptainer on Debian, but I'm unable to load the environment variables stored in my .env file via source. As a result the handler fails to start since the variable it's evaluating does not exist:

INFO:    instance started successfully
Waiting for Handler to be ready...
Starting UI container...
INFO:    Instance stats will not be available - requires cgroups v2 with systemd as manager.
/entrypoint.sh: line 6: [: ==: unary operator expected

INFO:    instance started successfully

[kiwimarc]

The problem is that Apptainer containers dont adopt the host environment variables
So this in entrypoint.sh at line 6, will not work:
if [ $BRAINLIFE_PRODUCTION == true ]; then

Because in run_apptainer.sh, it is missing something like:
--env "BRAINLIFE_PRODUCTION=$BRAINLIFE_PRODUCTION"

I can try to push an update and then you can test if it works :D

EDIT: I was wrong, maybe:

If you have environment variables set outside of your container, on the host, then by default they will be available inside the container. Except that:
An environment variable set on the host will be overridden by a variable of the same name that has been set either inside the container image, or via APPTAINERENV_ environment variables, or the --env and --env-file flags.
The PS1 shell prompt is reset for a container specific prompt.
The PATH environment variable will be modified to contain default values.
The LD_LIBRARY_PATH is modified to a default /.singularity.d/libs, that will include NVIDIA / ROCm libraries if applicable.

https://apptainer.org/docs/user/main/environment_and_metadata.html#environment-from-the-host

[kiwimarc]

@bendhouseart
Can you try to run this:

host> apptainer instance run --env "VITE_APIHOST=http://localhost:8082"  ui.sif ui ./start_ui.sh
host> apptainer shell instance://ui
Apptainer> echo $BRAINLIFE_PRODUCTION 

Just be sure that its the $BRAINLIFE_PRODUCTION variable that is missing

[bendhouseart]

Sorry, it's source that isn't behaving. When the environment variables are present on the host they are loaded into the container. This is very much a me problem with my Debian dev machine.

anthony@ip-10-0-1-167:~/ezbids$ cat .env
# Create/Copy this file as .env in the root of the project to set default environment variables

# insert your host name here, it should match your ssl certificate and/or the output
# of echo $HOSTNAME
SERVER_NAME=localhost

# Set the BRAINLIFE_PRODUCTION environment variable to true to use https"
# (this will launch the services on port 443) and run with nginx/production_nginx.conf"
# this will require providing the correct paths for the SSL_CERT_PATH, SSL_KEY_PATH and SSL_PASSWORD_PATH
# with false the UI will run on 3000"
BRAINLIFE_PRODUCTION=false

SSL_CERT_PATH=./nginx/ssl/sslcert.cert
SSL_KEY_PATH=./nginx/ssl/sslcert.key
SSL_PASSWORD_PATH=./nginx/ssl/sslpassword #if your key is not encrypted use an arbitrary path here

# Set the BRAINLIFE_AUTHENTICATION environment variable to true, if you're not running"
# this with brainlife don't use."
BRAINLIFE_AUTHENTICATION=false

# Set the BRAINLIFE_DEVELOPMENT enables additional debugging output and mounts 
# the ezbids repo/folder into the various containers default is false"
BRAINLIFE_DEVELOPMENT=false

# Define which profiles to use, e.g. set to COMPOSE_PROFILES=telemetry to enable telemetry 
COMPOSE_PROFILES=anthony@ip-10-0-1-167:~/ezbids$ source .env 
anthony@ip-10-0-1-167:~/ezbids$ env | grep BRAINLIFE
anthony@ip-10-0-1-167:~/ezbids$ 

I mentioned it earlier so that I'd be able to keep track of what was going on.

[melanieganz]

Hi @bendhouseart,
so right now Docker support is dead and we need the apptainer to work. The original apptainer by Marc worked here at NRU before you merged a lot of other stuff in. Can we revert to that stage and test here what is going on? What was all added beyond what Marc did in the apptainer branch?