Split embedded eic-shell heredocs into template files, assembled via Jinja2

.github/workflows/deploy.yml

@@ -22,6 +22,12 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Install Python dependencies
+        run: pip install jinja2
+
+      - name: Assemble standalone install.sh
+        run: python3 assemble.py . > install.sh.assembled && mv install.sh.assembled install.sh
+
       - name: Setup Pages
         uses: actions/configure-pages@v5
 

.gitignore

@@ -1,3 +1,4 @@
 .ipynb_checkpoints/
 Untitled.ipynb
 eic-shell
+__pycache__/

assemble.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+"""Assemble a standalone install.sh from the source install.sh and template files.
+
+The source install.sh generates each launcher script in two steps:
+  1. A variable-expanding heredoc writes a preamble with install-time values.
+  2. ``tail -n +2 "$SCRIPT_DIR/TEMPLATE" >> OUTPUT`` appends the template body
+     (skipping its ``#!/bin/bash`` shebang, which the preamble already provides).
+
+This assembler replaces step 2 with an equivalent inline heredoc so the result
+is a self-contained install.sh suitable for distribution (e.g., via curl | bash).
+
+Jinja2's FileSystemLoader is used to locate and read each template file cleanly.
+
+Usage:
+    python3 assemble.py [SOURCE_DIR]
+
+Output is written to stdout.
+"""
+
+import re
+import sys
+from pathlib import Path
+
+from jinja2 import Environment, FileSystemLoader
+
+
+def assemble(source_dir: Path) -> str:
+    env = Environment(
+        loader=FileSystemLoader(str(source_dir)),
+        keep_trailing_newline=True,
+    )
+
+    install_sh = (source_dir / 'install.sh').read_text()
+
+    # Remove the SCRIPT_DIR assignment line (not needed in the assembled version
+    # because all template file references are replaced by inline heredocs below).
+    install_sh = re.sub(r'SCRIPT_DIR=.*\n', '', install_sh, count=1)
+
+    # Replace each ``tail -n +2 "$SCRIPT_DIR/TEMPLATE" >> OUTPUT`` call with an
+    # inline heredoc containing the template body (all lines after the shebang).
+    def inline_template(match: re.Match) -> str:
+        indent = match.group('indent')
+        template_name = match.group('template')
+        output = match.group('output')
+
+        # Load the template file via Jinja2's FileSystemLoader.
+        template_source, _, _ = env.loader.get_source(env, template_name)
+        # Skip the first line (#!/bin/bash shebang); the preamble heredoc that
+        # precedes this call already provides the shebang in the assembled file.
+        parts = template_source.split('\n', 1)
+        template_body = parts[1].rstrip('\n') if len(parts) > 1 else ''
+
+        # Derive a safe heredoc closing marker from the template filename.
+        marker = template_name.upper().replace('-', '_').replace('.', '_')
+
+        return (
+            f"{indent}cat >> {output} << '{marker}'\n"
+            f"{template_body}\n"
+            f"{marker}"
+        )
+
+    install_sh = re.sub(
+        r'(?P<indent>[ \t]*)tail -n \+2 "\$SCRIPT_DIR/(?P<template>[^"]+)" >> (?P<output>\S+)',
+        inline_template,
+        install_sh,
+    )
+
+    # Validate: no $SCRIPT_DIR references should remain after assembly.
+    if '$SCRIPT_DIR/' in install_sh:
+        raise RuntimeError(
+            'Assembled install.sh still contains $SCRIPT_DIR/ references; '
+            'the assembly pattern may have drifted from the source.'
+        )
+
+    return install_sh
+
+
+if __name__ == '__main__':
+    source_dir = Path(sys.argv[1]) if len(sys.argv) > 1 else Path('.')
+    sys.stdout.write(assemble(source_dir))

eic-shell.docker

@@ -0,0 +1,81 @@
+#!/bin/bash
+
+## eic-shell Docker launcher
+## Install-time values are baked in by install.sh via a preamble prepended to this file.
+## The defaults below allow running this file directly for testing; override by
+## setting the corresponding environment variables before execution.
+: "${CONTAINER:=eic_xl}"
+: "${TMPDIR:=}"
+: "${VERSION:=nightly}"
+: "${PREFIX:=$PWD}"
+: "${DISABLE_CVMFS_USAGE:=}"
+: "${IMG:=eicweb/eic_xl:nightly}"
+: "${PLATFORM_FLAG:=}"
+: "${MOUNT:=}"
+
+function print_the_help {
+  echo "USAGE:  ./eic-shell [OPTIONS] [ -- COMMAND ]"
+  echo "OPTIONAL ARGUMENTS:"
+  echo "          -u,--upgrade    Upgrade the container to the latest version"
+  echo "          --noX           Disable X11 forwarding on macOS"
+  echo "          -h,--help       Print this message"
+  echo ""
+  echo "  Start the eic-shell containerized software environment (Docker version)."
+  echo ""
+  echo "EXAMPLES: "
+  echo "  - Start an interactive shell: ./eic-shell" 
+  echo "  - Upgrade the container:      ./eic-shell --upgrade"
+  echo "  - Execute a single command:   ./eic-shell -- <COMMAND>"
+  echo ""
+  exit
+}
+
+UPGRADE=
+NOX=
+while [ $# -gt 0 ]; do
+  key=$1
+  case $key in
+    -u|--upgrade)
+      UPGRADE=1
+      shift
+      ;;
+    --noX)
+      NOX=1
+      shift
+      ;;
+     -h|--help)
+      print_the_help
+      exit 0
+      ;;
+    --)
+      shift
+      break
+      ;;
+    *)
+      echo "ERROR: unknown argument: $key"
+      echo "use --help for more info"
+      exit 1
+      ;;
+  esac
+done
+
+if [ x${DISPLAY} == "x" ] ; then
+  echo "No X11 display detected, disabling X11"
+  NOX=1
+fi
+
+if [[ -n "$UPGRADE" ]]; then
+  echo "Upgrading eic-shell..."
+  docker pull ${IMG} || exit 1
+  echo "eic-shell upgrade successful"
+  exit 0
+fi
+
+if [ "$(uname -s)" = 'Darwin' ] && [[ -z "$NOX" ]]; then
+  nolisten=`defaults find nolisten_tcp | grep nolisten | head -n 1 | awk '{print $3}'|cut -b 1 `
+  [[ $nolisten -ne 0 ]] && echo "For X support: In XQuartz settings --> Security --> enable \"Allow connections from network clients\" and restart (should be only once)."
+  xhost +localhost
+  dispnum=`ps -e |grep Xquartz | grep listen | grep -v xinit |awk '{print $5}'`
+  XSTUFF="-e DISPLAY=host.docker.internal${dispnum} -v /tmp/.X11-unix:/tmp/.X11-unix"
+fi
+docker run ${PLATFORM_FLAG} ${MOUNT} ${XSTUFF} -w=$PWD -it --rm -e EIC_SHELL_PREFIX=${PREFIX}/local ${IMG} eic-shell "$@"

eic-shell.singularity

@@ -0,0 +1,112 @@
+#!/bin/bash
+
+## eic-shell Singularity launcher
+## Install-time values are baked in by install.sh via a preamble prepended to this file.
+## The defaults below allow running this file directly for testing; override by
+## setting the corresponding environment variables before execution.
+: "${ORGANIZATION:=eicweb}"
+: "${CONTAINER:=eic_xl}"
+: "${TMPDIR:=}"
+: "${VERSION:=nightly}"
+: "${PREFIX:=$PWD}"
+: "${DISABLE_CVMFS_USAGE:=}"
+: "${INSTALLED_SINGULARITY:=singularity}"
+: "${BINDPATH:=}"
+: "${INSTALLED_SIF:=}"
+
+function print_the_help {
+  echo "USAGE:  ./eic-shell [OPTIONS] [ -- COMMAND ]"
+  echo "OPTIONAL ARGUMENTS:"
+  echo "          -u,--upgrade       Upgrade the container to the latest version"
+  echo "          -n,--no-cvmfs      Disable check for local CVMFS when updating. (D: enabled)"
+  echo "          -c,--container     Container family (D: $CONTAINER) (requires cvmfs)"
+  echo "          -v,--version       Version to install (D: $VERSION) (requires cvmfs)"
+  echo "          -h,--help          Print this message"
+  echo ""
+  echo "  Start the eic-shell containerized software environment (Singularity version)."
+  echo ""
+  echo "ENVIRONMENT VARIABLES:"
+  echo "          SINGULARITY          Path to the singularity executable (D: $INSTALLED_SINGULARITY)"
+  echo "          SINGULARITY_OPTIONS  Additional options to pass to singularity exec (D: none)"
+  echo ""
+  echo "EXAMPLES: "
+  echo "  - Start an interactive shell: ./eic-shell" 
+  echo "  - Upgrade the container:      ./eic-shell --upgrade"
+  echo "  - Use different version:      ./eic-shell --version $(date +%y.%m).0-stable"
+  echo "  - Execute a single command:   ./eic-shell -- <COMMAND>"
+  echo "  - Use custom singularity:     SINGULARITY=/path/to/singularity ./eic-shell"
+  echo "  - Pass singularity options:   SINGULARITY_OPTIONS='--nv' ./eic-shell"
+  echo ""
+  exit
+}
+
+UPGRADE=
+
+while [ $# -gt 0 ]; do
+  key=$1
+  case $key in
+    -u|--upgrade)
+      UPGRADE=1
+      shift
+      ;;
+    -n|--no-cvmfs)
+      DISABLE_CVMFS_USAGE=true
+      shift
+      ;;
+    -c|--container)
+      CONTAINER=${2?Missing argument. Use --help for more info.}
+      export SIF=/cvmfs/singularity.opensciencegrid.org/${ORGANIZATION}/${CONTAINER}:${VERSION}
+      shift
+      shift
+      ;;
+    -v|--version)
+      VERSION=${2?Missing argument. Use --help for more info.}
+      export SIF=/cvmfs/singularity.opensciencegrid.org/${ORGANIZATION}/${CONTAINER}:${VERSION}
+      shift
+      shift
+      ;;
+    -h|--help)
+      print_the_help
+      exit 0
+      ;;
+    --)
+      shift
+      break
+      ;;
+    *)
+      echo "ERROR: unknown argument: $key"
+      echo "use --help for more info"
+      exit 1
+      ;;
+  esac
+done
+
+if [[ -n "$UPGRADE" ]]; then
+  echo "Upgrading eic-shell..."
+  if [ -z "$DISABLE_CVMFS_USAGE" -a -d /cvmfs/singularity.opensciencegrid.org/${ORGANIZATION}/${CONTAINER}:${VERSION} ]; then
+    echo ""
+    echo "Note: You cannot manually update the container as you are using the CVMFS version."
+    echo "      The container will automatically update every 24 hours."
+    echo "      You can override this by setting the '--no-cvmfs' flag, which will"
+    echo "      instantiate a local version."
+    echo "      This is only recommended for expert usage."
+    echo ""
+    echo "This will only upgrade the eic-shell script itself."
+    echo ""
+  fi
+  FLAGS="-p ${PREFIX} -v ${VERSION}"
+  if [[ -n "$TMPDIR" ]]; then
+    FLAGS="${FLAGS} -t ${TMPDIR}"
+  fi
+  if [[ -n "$DISABLE_CVMFS_USAGE" ]]; then
+    FLAGS="${FLAGS} --no-cvmfs"
+  fi
+  curl -L https://eic.github.io/eic-shell/install.sh \
+    | bash -s -- ${FLAGS}
+  echo "eic-shell upgrade successful"
+  exit 0
+fi
+
+export EIC_SHELL_PREFIX=${PREFIX}/local
+export SINGULARITY_BINDPATH=${BINDPATH}
+${SINGULARITY:-${INSTALLED_SINGULARITY}} exec ${SINGULARITY_OPTIONS:-} ${SIF:-${INSTALLED_SIF}} eic-shell "$@"