(!untested!) add Dockerfile, docker-compose, scripts. change dir struct.

.gitignore

@@ -1,4 +1,5 @@
-output
+/input/
+/output/
 examples
 
 # Byte-compiled / optimized / DLL files

Dockerfile

@@ -0,0 +1,24 @@
+FROM python:3
+
+ENV PYTHONUNBUFFERED 1
+ENV SHELL /bin/bash
+
+# ------------------------------------------
+# install necessary packages via apt-get:
+# ------------------------------------------
+RUN apt-get update && \
+	apt-get install -y --no-install-recommends \
+	graphicsmagick \
+	pandoc \
+	pandoc-citeproc \
+	curl \
+	texlive-xetex
+
+# this is supposed to save memory:
+RUN rm -rf /var/lib/apt/lists/*
+
+# ------------------------------------------
+# install python dependencies:
+# ------------------------------------------
+COPY requirements.txt "$INSTALL_DIR/"
+RUN pip install -r requirements.txt

docker-compose.yaml

@@ -0,0 +1,20 @@
+version: '3.7'
+
+services:
+
+  eoa_skripts:
+    build: .
+    image: ${IMAGE_NAME}
+    container_name: ${CONTAINER_NAME}
+    command: bash -c 'while :; do :; done & kill -STOP $$! && wait $$!'
+    volumes:
+      - ./${SRC_DIR}:${SRC_DIR_IN_CONTAINER}
+      - ./${INPUT_DIR}:${INPUT_DIR_IN_CONTAINER}
+      - ./${OUTPUT_DIR}:${OUTPUT_DIR_IN_CONTAINER}
+    working_dir: ${SRC_DIR_IN_CONTAINER}
+    environment:
+      - INPUT_DIR=${INPUT_DIR_IN_CONTAINER}
+      - OUTPUT_DIR=${OUTPUT_DIR_IN_CONTAINER}
+      - INSTALL_DIR=${SRC_DIR_IN_CONTAINER}
+    ports: []
+    user: ${USER}:${GROUP}

scripts/config/env.conf

@@ -0,0 +1,25 @@
+[config]
+
+###################################################
+# container names:
+###################################################
+
+IMAGE_NAME=eoa_skripts
+CONTAINER_NAME=eoa_skripts
+
+
+###################################################
+# volumes:
+###################################################
+
+SRC_DIR=src
+SRC_DIR_IN_CONTAINER=/eoa/skripts
+INPUT_DIR=input
+INPUT_DIR_IN_CONTAINER=/eoa/input
+OUTPUT_DIR=output
+OUTPUT_DIR_IN_CONTAINER=/eoa/output
+
+###################################################
+# user and group:
+# USER=$(id -u)
+# GROUP=$(id -g)

scripts/config/load_env.fish

@@ -0,0 +1,26 @@
+#!/bin/fish
+
+if not set -q SCRIPT_DIR
+	echo "ERROR in (status -m): \$SCRIPT_DIR is undefined!"
+	exit 1
+end
+set BASE_DIR "$SCRIPT_DIR/.."
+
+#######################################
+# actual script
+#######################################
+
+set RUNTIME_DIR "runtime_data"
+
+###################################################
+# export all these variables, so 
+# they can be referenced in the docker-compose.yaml
+###################################################
+
+# convert bash syntax to fish syntax:
+set commands (cat ./scripts/config/env.conf | grep -E --invert-match '^#|^[[:space:]]*$' | sed 's/^\(.*\)=\(.*\)/set -x \1 \2/' | sed 's/\$(/(/g')
+
+for cmd in $commands
+	echo "cmd: $cmd"
+	eval "$cmd"
+end

scripts/config/load_env.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+if [[ "$SCRIPT_DIR" == "" ]]; then
+	echo "ERROR in ./scripts/config/load_env.sh: \$SCRIPT_DIR is undefined!"
+	exit 1
+fi
+BASE_DIR="$SCRIPT_DIR/.."
+
+#######################################
+# actual script
+#######################################
+
+
+# these are the default settings used by all scripts:
+
+RUNTIME_DIR=runtime_data
+
+###################################################
+# export all these variables, so 
+# they can be referenced in the docker-compose.yaml
+###################################################
+set -a
+source $SCRIPT_DIR/config/env.conf
+set -a
+# (stop exporting variables)

scripts/exec_in_container.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+
+from utils.settings import BASE_DIR, load_config
+from utils.functions import exec_in_container
+
+from pathlib import Path
+import os
+
+if __name__ == '__main__':
+
+    from argparse import ArgumentParser
+
+    config = load_config()
+
+    parser = ArgumentParser(
+        description="open bash to the container, optionally exec CMD there"
+    )
+    parser.add_argument(
+        "CMD",
+        nargs='*',
+    )
+    args = parser.parse_args()
+
+    CMDS= \
+        (vars(args)['CMD'])
+
+    print( CMDS )
+
+    exec_in_container( 
+        *CMDS,
+        env=config
+    )

scripts/exit.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+
+from utils.settings import BASE_DIR, load_config
+
+from pathlib import Path
+import shutil
+import os
+
+def rm_dirs( config ):
+    path = Path( BASE_DIR, config['INPUT_DIR'] )
+    print( "removing dir '{}'".format( path ) )
+    shutil.rmtree(
+        path,
+        ignore_errors=True
+    )
+    # os.system('rm -rf "{}"'.format( path ))
+
+    path = Path( BASE_DIR, config['OUTPUT_DIR'] )
+    print( "removing dir '{}'".format( path ) )
+    shutil.rmtree(
+        path,
+        ignore_errors=True
+    )
+    # os.system('rm -rf "{}"'.format( path ))
+
+def rm_docker_env_file( config ):
+    path = Path(
+        BASE_DIR / ".env"
+    )
+    print( "removing '{}'".format( path ) )
+    path.unlink()
+
+if __name__ == '__main__':
+
+    from argparse import ArgumentParser
+
+    config = load_config()
+
+    parser = ArgumentParser(
+        description="clean up the repository"
+    )
+    parser.add_argument(
+        "--env-file",
+        action = "store_true"
+    )
+    parser.add_argument(
+        "--all",
+        action = "store_true"
+    )
+    args = parser.parse_args()
+
+    from stop import stop
+
+    stop( config )
+
+    rm_dirs( config )
+    if args.env_file or args.all:
+        rm_docker_env_file( config )

scripts/init.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+
+from utils.settings import BASE_DIR, load_config, create_docker_env_file
+from utils.functions import exec_in_container, run
+
+from pathlib import Path
+import shlex
+import shutil
+import pwd
+import os
+import subprocess
+from time import sleep
+
+BASE_DIR = Path( __file__ ).parent.parent
+DEP_DIR = BASE_DIR / "dependencies"
+
+
+SQLDB_WAIT_TIME=20
+
+def create_dir(dir):
+    print( "creating dir '{}'".format( dir ) )
+    Path(dir).mkdir(
+            parents = True,
+            exist_ok = True
+    )
+
+def copy_dir(src, dst):
+    print( "'{}' -> '{}'".format( src, dst ) )
+    if Path(dst).exists():
+        shutil.rmtree(
+            dst
+        )
+    shutil.copytree(
+            src=src,
+            dst=dst
+    )
+
+def create_dirs( config ):
+    create_dir(
+        BASE_DIR / config['INPUT_DIR']
+    )
+    create_dir(
+        BASE_DIR / config['OUTPUT_DIR']
+    )
+
+def install_git_dep(
+    repo_name,
+    repo_uri,
+    repo_hash,
+    init_script = None
+):
+    if (DEP_DIR / repo_name).exists():
+        shutil.rmtree( DEP_DIR / repo_name )
+
+    subprocess.check_call(
+        ["git", "clone", repo_uri, DEP_DIR / repo_name]
+    )
+    subprocess.check_call(
+        ["git", "checkout", repo_hash],
+        cwd = DEP_DIR / repo_name
+    )
+    if init_script is not None:
+        subprocess.check_call(
+            shlex.split( init_script ),
+            cwd = DEP_DIR / repo_name
+        )
+
+if __name__ == '__main__':
+
+    from argparse import ArgumentParser
+
+    parser = ArgumentParser(
+        description="initialize the repository: download git deps, create directories, etc"
+    )
+    parser.add_argument(
+        "--build",
+        action = "store_true"
+    )
+    args = parser.parse_args()
+
+    # orig_config_file -> env_file:
+    create_docker_env_file()
+
+    # load env_file:
+    config = load_config()
+
+    ## install git dependencies:
+    '''
+    install_git_dep(
+        repo_name = "eoa-publication-model",
+        repo_uri = "https://github.molgen.mpg.de/EditionOpenAccess/eoa-publication-model.git",
+        repo_hash = "d76a81feef1ebb708a90376d3f5a7eccb51807b0"
+    )
+    '''
+
+    create_dirs( config )
+
+    # rebuild docker image:
+    if args.build:
+        run(
+            env = config,
+            build = True,
+        )

scripts/run.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+
+from utils.settings import BASE_DIR, load_config
+from utils.functions import run
+
+import subprocess
+import shlex
+import os
+from time import sleep
+
+if __name__ == '__main__':
+
+    from argparse import ArgumentParser
+
+    config = load_config()
+
+    parser = ArgumentParser(
+        description="run the container"
+    )
+    parser.add_argument(
+        "--build",
+        action = "store_true"
+    )
+    parser.add_argument(
+        "CMD",
+        nargs="*"
+    )
+
+    args = parser.parse_args()
+
+    CMD= \
+        (vars(args)['CMD'])
+    run(
+        env=config,
+        build = args.build,
+        cmd=CMD
+    )

scripts/stop.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python3
+
+from utils.settings import BASE_DIR, load_config
+
+import subprocess
+import os
+
+
+def stop( env ):
+    # run application
+    subprocess.call(
+        "docker-compose down",
+        shell=True,
+        env=env
+    )
+
+if __name__ == '__main__':
+
+    from argparse import ArgumentParser
+
+    config = load_config()
+
+    parser = ArgumentParser(
+        description="stop the webserver"
+    )
+    args = parser.parse_args()
+
+    stop( config )