[mohab-elshamy]

Summary

This PR refactors AnalySim’s Docker deployment into a simpler, production-oriented Compose setup. It separates the ASP.NET Core backend, Angular/JupyterLite frontend, PostgreSQL database, one-shot migrations, backups, and Nginx/Certbot responsibilities into clear services, while keeping runtime configuration in a single .env file and persistent state under a user-configurable data directory.

Changes

• Splits deployment into dedicated PostgreSQL, backend, frontend/Nginx, migration, backup, and Certbot services.
• Adds separate Dockerfiles for the ASP.NET Core backend, Nginx frontend, and PostgreSQL backup service.
• Moves Angular and JupyterLite builds into the frontend/Nginx image.
• Keeps the backend image .NET-only and safe to publish without baked production secrets.
• Adds a one-shot EF Core migration container.
• Serves Angular/JupyterLite static files directly from Nginx and reverse-proxies /api/ to the backend.
• Simplifies runtime configuration to a single .env file.
• Keeps persistent data, backups, and certificates under a user-configurable ANALYSIM_DATA_ROOT.
• Updates deployment documentation and removes obsolete legacy Docker files.

Minimal Deploy Steps

cp .env.example .env
# edit .env: ANALYSIM_DATA_ROOT, domain, DB password/connection string, JWT secret, email settings

export ANALYSIM_DATA_ROOT=/path/to/persistent/analysim-data
mkdir -p "$ANALYSIM_DATA_ROOT"/{postgres/data,postgres/certs,backups,certbot/conf,certbot/www}

# add PostgreSQL TLS cert/key under:
# $ANALYSIM_DATA_ROOT/postgres/certs/server.crt
# $ANALYSIM_DATA_ROOT/postgres/certs/server.key

docker compose --env-file .env build
docker compose --env-file .env up -d

[cengique]

Thanks for providing such a comprehensive overhaul of the deployment system. I see many good features, but I also have some suggestions to fix.

I marked some suggestions specifically, but I got stuck in the first Docker run for getting the Let's Encrypt cert:

$ sudo docker run --rm      -v "$ANALYSIM_DATA_ROOT/certbot/conf:/etc/letsencrypt"      -v "$ANALYSIM_DATA_ROOT/certbot/www:/var/www/certbot"      certbot/certbot certonly      --webroot      --webroot-path /var/www/certbot      -d "localhost"
[sudo] password for cengiz: 
Unable to find image 'certbot/certbot:latest' locally
latest: Pulling from certbot/certbot
e6f31ffc071e: Pull complete 
9010581fffd4: Pull complete 
bfac9e75463e: Pull complete 
426f169c5b37: Pull complete 
500b30537bf5: Pull complete 
c37269114a8b: Pull complete 
5e4ba5eb6a5b: Pull complete 
0c77a7cefcb3: Pull complete 
f1e126553701: Pull complete 
bb95bb741cc3: Pull complete 
cc6a5902e005: Pull complete 
Digest: sha256:f70ad0adbb7e117f0fe42a63c553f28ea451edabc0148757b6efcd9735acaa20
Status: Downloaded newer image for certbot/certbot:latest
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Skipped user interaction because Certbot doesn't appear to be running in a terminal. You should probably include --non-interactive or --force-interactive on the command line.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Please read the Terms of Service at:
https://letsencrypt.org/documents/LE-SA-v1.8-July-06-2026.pdf
You must agree in order to register with the ACME server. Do you agree?
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
(Y)es/(N)o: An unexpected error occurred:
EOFError
Ask for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.

[cengique]

If we already provide the POSTGRES variables above, the connection string is redundant. Either remove this or the previous variables.

[cengique]

I thought these were under the data/ folder according to the README

[cengique]

isn't this the same as DOMAIN above? or is this only for local runs?

[cengique]

we may have more than one registration code

[cengique]

we may need some of these to be automatically created