Added Docker files

.dockerignore

+/etl/credentials/db_credentials*.yml
+/etl/stg/archive/*
+/etl/prs/fits/cubes/*
+/etl/prs/fits/moments/*
+/etl/prs/fits/ratios/*
+/etl/prs/fits/grids/*
+/etl/mdl/radmc_files/*
+/etl/mdl/scratches/*
+/etl/prs/output/*
+/etl/*.sif
\ No newline at end of file

Dockerfile

+FROM python:3.9-slim
+
+
+# STEP 1) Setting up environment
+# apt packages
+RUN apt-get update && \
+    apt-get --yes upgrade && \
+    apt-get install --yes libgomp1 && \
+    apt-get install --yes postgresql-client && \
+    apt-get install --yes --reinstall build-essential && \
+    apt-get -y install curl vim less nano git && \
+    apt-get -y install zip unzip && \
+    apt-get clean
+
+WORKDIR /usr/src/etl
+RUN python -m pip install --upgrade pip
+COPY etl/requirements.txt .
+RUN pip install -r requirements.txt
+
+RUN mkdir /sak_user
+# RUN /usr/sbin/usermod -d /sak_user root
+RUN HOME=/sak_user
+COPY documentation/radmc3d_install.sh .
+RUN chmod 755 radmc3d_install.sh
+RUN HOME=/sak_user;./radmc3d_install.sh
+ENV PATH="/sak_user/bin:${PATH}"
+ENV PYTHONPATH="/sak_user/bin/python:${PYTHONPATH}"
+RUN chmod 755 /sak_user/bin/radmc3d
+
+# STEP 2) Bundling app
+COPY etl .
+
+CMD python main.py
\ No newline at end of file

apptainer.def

+Bootstrap: docker
+From: postgres:14.1-alpine
+
+%environment
+export POSTGRES_DB=$DB_NAME
+export POSTGRES_USER=$DB_USER
+export POSTGRES_PASSWORD=$DB_PASS

create_apptainer_image_file.sh

+rm swiss_army_knife_latest.sif
+singularity pull --disable-cache docker://git.ia2.inaf.it:5050/andrea.giannetti/swiss_army_knife
+

docker-compose.yaml

+version: '3.8'
+services:
+  db:
+    image: postgres:14.1-alpine
+    container_name: db_container_sak
+    restart: always
+    environment:
+      - POSTGRES_DB=$DB_NAME
+      - POSTGRES_USER=$DB_USER
+      - POSTGRES_PASSWORD=$DB_PASS
+    ports:
+      - '31000:5432'
+    volumes:
+      - db:/var/lib/postgresql/data
+    networks:
+      - sak_network
+
+  etl:
+    build:
+      dockerfile: Dockerfile
+    container_name: 'etl_sak'
+    image: 'sak_etl'
+    depends_on:
+      - db
+    stdin_open: true
+    tty: true
+    networks:
+      - sak_network
+    volumes:
+      - ./etl:/usr/src/etl
+volumes:
+  db:
+    driver: local
+networks:
+  sak_network:
+    name: 'sak_app_network'
\ No newline at end of file

documentation/radmc3d_install.sh

+#!/bin/bash
+# Set PYCHARM_HOME, INSTALL_DEPENDENCIES environment variable
+PYCHARM_HOME=${PYCHARM_HOME:=$HOME}
+INSTALL_DEPENDENCIES="${INSTALL_DEPENDENCIES:=true}"
+echo $PYCHARM_HOME
+cd $PYCHARM_HOME
+export RADMC_HOME=$PYCHARM_HOME/radmc3d-2.0
+if [[ ! -d "$RADMC_HOME" ]]
+then
+    echo RADMC not found, cloning into "$(pwd)"
+    git clone https://github.com/dullemond/radmc3d-2.0.git
+fi
+
+if $INSTALL_DEPENDENCIES
+then
+    apt-get install -y gfortran
+fi
+
+cd $RADMC_HOME/src
+make
+echo "y\n y\n"| make install
+
+# Add this to the .bashrc configuration file (or equivalent)
+export PATH=$HOME/bin:$PATH
+export PYTHONPATH=$HOME/bin/python:$PYTHONPATH
+
+cd $RADMC_HOME/python/radmc3dPy
+python setup.py install