From 3bd780e7d8de58cbf5df299acbdfecec14f69f58 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 14 Mar 2026 17:58:09 +0000
Subject: [PATCH 1/5] Initial plan


From 0ddc28d808fa3e56ccbc4babafa29f15e93be44a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 14 Mar 2026 18:17:32 +0000
Subject: [PATCH 2/5] Split embedded eic-shell heredocs into templates, use
 envsubst, add CI publish workflow

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .github/workflows/publish.yml        |  49 +++++++
 __pycache__/assemble.cpython-312.pyc | Bin 0 -> 2288 bytes
 assemble.py                          |  70 +++++++++
 eic-shell.docker                     |  75 ++++++++++
 eic-shell.singularity                | 107 ++++++++++++++
 install.sh                           | 206 ++-------------------------
 6 files changed, 314 insertions(+), 193 deletions(-)
 create mode 100644 .github/workflows/publish.yml
 create mode 100644 __pycache__/assemble.cpython-312.pyc
 create mode 100755 assemble.py
 create mode 100644 eic-shell.docker
 create mode 100644 eic-shell.singularity

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
new file mode 100644
index 0000000..e2f0e01
--- /dev/null
+++ b/.github/workflows/publish.yml
@@ -0,0 +1,49 @@
+name: Deploy GitHub Pages
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - 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
+
+      - name: Build with Jekyll
+        uses: actions/jekyll-build-pages@v1
+        with:
+          source: ./
+          destination: ./_site
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/__pycache__/assemble.cpython-312.pyc b/__pycache__/assemble.cpython-312.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..50983c87129899f7a188b675231fb41b9f7986a7
GIT binary patch
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diff --git a/assemble.py b/assemble.py
new file mode 100755
index 0000000..74d297b
--- /dev/null
+++ b/assemble.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+"""Assemble a standalone install.sh from the source install.sh and template files.
+
+This script replaces envsubst calls that read from external template files with
+equivalent inline heredoc-based calls, producing a self-contained install.sh
+suitable for distribution (e.g., via curl | bash).
+
+Usage:
+    python3 assemble.py [SOURCE_DIR]
+
+Output is written to stdout.
+"""
+
+import re
+import sys
+from pathlib import Path
+
+
+def assemble(source_dir: Path) -> str:
+    install_sh = (source_dir / 'install.sh').read_text()
+
+    # Remove the SCRIPT_DIR assignment line (not needed in assembled version)
+    install_sh = re.sub(
+        r'\nSCRIPT_DIR=.*\n',
+        '\n',
+        install_sh,
+    )
+
+    # Replace each envsubst call that reads from a $SCRIPT_DIR template file
+    # with an inline heredoc-based equivalent.
+    #
+    # Source pattern (single line):
+    #   envsubst 'VARS' < "$SCRIPT_DIR/TEMPLATE_FILE" > OUTPUT
+    #
+    # Assembled replacement:
+    #   envsubst 'VARS' > OUTPUT << 'HEREDOC_MARKER'
+    #   <template content>
+    #   HEREDOC_MARKER
+    def inline_template(match):
+        indent = match.group('indent')
+        variables = match.group('variables')
+        template_name = match.group('template')
+        output = match.group('output')
+
+        template_content = (source_dir / template_name).read_text()
+        # Normalize to exactly one trailing newline so the heredoc closing
+        # marker always appears on its own line
+        template_content = template_content.rstrip('\n') + '\n'
+        # Derive a safe heredoc marker from the template filename
+        marker = template_name.upper().replace('-', '_').replace('.', '_')
+
+        return (
+            f"{indent}envsubst '{variables}' > {output} << '{marker}'\n"
+            f"{template_content}"
+            f"{marker}"
+        )
+
+    install_sh = re.sub(
+        r'(?P<indent>[ \t]*)envsubst \'(?P<variables>[^\']+)\''
+        r' < "\$SCRIPT_DIR/(?P<template>[^"]+)" > (?P<output>\S+)',
+        inline_template,
+        install_sh,
+    )
+
+    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))
diff --git a/eic-shell.docker b/eic-shell.docker
new file mode 100644
index 0000000..d8dc29a
--- /dev/null
+++ b/eic-shell.docker
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+## capture environment setup for upgrades
+CONTAINER=${EICS_CONTAINER}
+TMPDIR=${EICS_TMPDIR}
+VERSION=${EICS_VERSION}
+PREFIX=${EICS_PREFIX}
+DISABLE_CVMFS_USAGE=${EICS_DISABLE_CVMFS_USAGE}
+
+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 [ ! -z ${UPGRADE} ]; then
+  echo "Upgrading eic-shell..."
+  docker pull ${EICS_IMG} || exit 1
+  echo "eic-shell upgrade successful"
+  exit 0
+fi
+
+if [ "$(uname -s)" = 'Darwin' ] && [ ! ${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 ${EICS_PLATFORM_FLAG} ${EICS_MOUNT} $XSTUFF -w=$PWD -it --rm -e EIC_SHELL_PREFIX=${EICS_PREFIX}/local ${EICS_IMG} eic-shell $@
diff --git a/eic-shell.singularity b/eic-shell.singularity
new file mode 100644
index 0000000..e28387a
--- /dev/null
+++ b/eic-shell.singularity
@@ -0,0 +1,107 @@
+#!/bin/bash
+
+## capture environment setup for upgrades
+ORGANIZATION=${EICS_ORGANIZATION}
+CONTAINER=${EICS_CONTAINER}
+TMPDIR=${EICS_TMPDIR}
+VERSION=${EICS_VERSION}
+PREFIX=${EICS_PREFIX}
+DISABLE_CVMFS_USAGE=${EICS_DISABLE_CVMFS_USAGE}
+
+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 "          -o,--organization  Organization (D: $ORGANIZATION) (requires cvmfs)"
+  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: detected during installation)"
+  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 [ ! -z ${UPGRADE} ]; then
+  echo "Upgrading eic-shell..."
+  if [ -z "$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 [ ! -z ${TMPDIR} ]; then
+    FLAGS="${FLAGS} -t ${TMPDIR}"
+  fi
+  if [ ! -z ${DISABLE_CVMFS_USAGE} ]; then
+    FLAGS="${FLAGS} --no-cvmfs"
+  fi
+  curl -L https://github.com/eic/eic-shell/raw/main/install.sh \
+    | bash -s -- ${FLAGS}
+  echo "eic-shell upgrade successful"
+  exit 0
+fi
+
+export EIC_SHELL_PREFIX=${EICS_PREFIX}/local
+export SINGULARITY_BINDPATH=${EICS_BINDPATH}
+${SINGULARITY:-${EICS_SINGULARITY}} exec ${SINGULARITY_OPTIONS:-} ${SIF:-${EICS_SIF}} eic-shell $@
diff --git a/install.sh b/install.sh
index 1881b68..6948c36 100755
--- a/install.sh
+++ b/install.sh
@@ -7,6 +7,8 @@
 ## with the $EIC_SHELL_PREFIX variable pointing
 ## to the $PREFIX/local directory
 
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
 ORGANIZATION="eicweb"
 CONTAINER="eic_xl"
 VERSION="nightly"
@@ -198,119 +200,14 @@ function install_singularity() {
 
   ## create a new top-level eic-shell launcher script
   ## that sets the EIC_SHELL_PREFIX and then starts singularity
-cat << EOF > eic-shell
-#!/bin/bash
-
-## capture environment setup for upgrades
-ORGANIZATION=$ORGANIZATION
-CONTAINER=$CONTAINER
-TMPDIR=$TMPDIR
-VERSION=$VERSION
-PREFIX=$PREFIX
-DISABLE_CVMFS_USAGE=${DISABLE_CVMFS_USAGE}
-
-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 "          -o,--organization  Organization (D: \$ORGANIZATION) (requires cvmfs)"
-  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: detected during installation)"
-  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 [ ! -z \${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 [ ! -z \${TMPDIR} ]; then
-    FLAGS="\${FLAGS} -t \${TMPDIR}"
-  fi
-  if [ ! -z \${DISABLE_CVMFS_USAGE} ]; then
-    FLAGS="\${FLAGS} --no-cvmfs"
-  fi
-  curl -L https://github.com/eic/eic-shell/raw/main/install.sh \
-    | bash -s -- \${FLAGS}
-  echo "eic-shell upgrade sucessful"
-  exit 0
-fi
-
-export EIC_SHELL_PREFIX=$PREFIX/local
-export SINGULARITY_BINDPATH=$BINDPATH
-\${SINGULARITY:-$SINGULARITY} exec \${SINGULARITY_OPTIONS:-} \${SIF:-$SIF} eic-shell \$@
-EOF
+  export EICS_ORGANIZATION="$ORGANIZATION" EICS_CONTAINER="$CONTAINER" EICS_TMPDIR="$TMPDIR" \
+    EICS_VERSION="$VERSION" EICS_PREFIX="$PREFIX" EICS_DISABLE_CVMFS_USAGE="${DISABLE_CVMFS_USAGE}" \
+    EICS_SINGULARITY="$SINGULARITY" EICS_BINDPATH="$BINDPATH" EICS_SIF="$SIF"
+  envsubst '${EICS_ORGANIZATION} ${EICS_CONTAINER} ${EICS_TMPDIR} ${EICS_VERSION} ${EICS_PREFIX} ${EICS_DISABLE_CVMFS_USAGE} ${EICS_SINGULARITY} ${EICS_BINDPATH} ${EICS_SIF}' < "$SCRIPT_DIR/eic-shell.singularity" > eic-shell
 
   chmod +x eic-shell
 
-  echo " - Created custom eic-shell excecutable"
+  echo " - Created custom eic-shell executable"
 }
 
 function install_docker() {
@@ -350,91 +247,14 @@ function install_docker() {
   fi
 
   ## create a new top-level eic-shell launcher script
-  ## that sets the EIC_SHELL_PREFIX and then starts singularity
-cat << EOF > eic-shell
-#!/bin/bash
-
-## capture environment setup for upgrades
-CONTAINER=$CONTAINER
-TMPDIR=$TMPDIR
-VERSION=$VERSION
-PREFIX=$PREFIX
-DISABLE_CVMFS_USAGE=${DISABLE_CVMFS_USAGE}
-
-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 [ ! -z \${UPGRADE} ]; then
-  echo "Upgrading eic-shell..."
-  docker pull $IMG || exit 1
-  echo "eic-shell upgrade sucessful"
-  exit 0
-fi
-EOF
-
-  if [ `uname -s` = 'Darwin' ]; then
-      echo 'if [ ! ${NOX} ]; then' >> eic-shell
-      echo ' nolisten=`defaults find nolisten_tcp | grep nolisten | head -n 1 | awk ' "'{print" '$3}'"'" '|cut -b 1 `' >> eic-shell
-      echo ' [[ $nolisten -ne 0 ]] && echo "For X support: In XQuartz settings --> Security --> enable \"Allow connections from network clients\" and restart (should be only once)."' >> eic-shell
-      ## getting the following single and double quotes, escapes and backticks right was a nightmare
-      ## But with a heredoc it was worse
-      echo '  xhost +localhost' >> eic-shell
-      echo '  dispnum=`ps -e |grep Xquartz | grep listen | grep -v xinit |awk ' "'{print" '$5}'"'" '`' >> eic-shell
-      echo '  XSTUFF="-e DISPLAY=host.docker.internal${dispnum} -v /tmp/.X11-unix:/tmp/.X11-unix"' >> eic-shell
-      echo 'fi' >> eic-shell
-  fi
-  echo "docker run $PLATFORM_FLAG $MOUNT \$XSTUFF -w=$PWD -it --rm -e EIC_SHELL_PREFIX=$PREFIX/local $IMG eic-shell \$@" >> eic-shell
+  ## that sets the EIC_SHELL_PREFIX and then starts docker
+  export EICS_CONTAINER="$CONTAINER" EICS_TMPDIR="$TMPDIR" EICS_VERSION="$VERSION" \
+    EICS_PREFIX="$PREFIX" EICS_DISABLE_CVMFS_USAGE="${DISABLE_CVMFS_USAGE}" \
+    EICS_IMG="$IMG" EICS_PLATFORM_FLAG="$PLATFORM_FLAG" EICS_MOUNT="$MOUNT"
+  envsubst '${EICS_CONTAINER} ${EICS_TMPDIR} ${EICS_VERSION} ${EICS_PREFIX} ${EICS_DISABLE_CVMFS_USAGE} ${EICS_IMG} ${EICS_PLATFORM_FLAG} ${EICS_MOUNT}' < "$SCRIPT_DIR/eic-shell.docker" > eic-shell
 
   chmod +x eic-shell
-  echo " - Created custom eic-shell excecutable"
+  echo " - Created custom eic-shell executable"
 }
 
 ## detect OS

From 978d38ddd962daa21e74ca7f3a934e76e26482cd Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 14 Mar 2026 18:17:47 +0000
Subject: [PATCH 3/5] Add __pycache__ to .gitignore and remove it from tracking

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .gitignore                           |   1 +
 __pycache__/assemble.cpython-312.pyc | Bin 2288 -> 0 bytes
 2 files changed, 1 insertion(+)
 delete mode 100644 __pycache__/assemble.cpython-312.pyc

diff --git a/.gitignore b/.gitignore
index 33eff7d..cf95cea 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 .ipynb_checkpoints/
 Untitled.ipynb
 eic-shell
+__pycache__/
diff --git a/__pycache__/assemble.cpython-312.pyc b/__pycache__/assemble.cpython-312.pyc
deleted file mode 100644
index 50983c87129899f7a188b675231fb41b9f7986a7..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 2288
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z(;Z05yO5N*7KD=9QB^3UOP$Vh4!ctwNx@q+sm|-ZJom7Undb^<iqnPLfqDLa?umJR
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zTyEc8NK{0=t-InAg7PMqfO0bfCoc}w0z7;b$DC^iBaPU_!i?F7`ta53vGBD+kyscH
z;l9{`W|bacIM0Ou>jP9DM4cVi@?$tQb|@0@Q3c*~c}iR#baL3U@VH*}t9F9!fdiYB
z&&L>3_A_z=UPS0V*s{8}ufW8--_g6AFLoT-P>vUs<KU5n(dQEC=v?Yr>?#L(%YoK%
zpkvc7bV$I!iYPztuX8Ir7aZZ92Hs$RpvVA~9jLYIv9Ozls*kE_3i`gPK4V>yw!;)@
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zZ!%Ju<dD!>$UX7({MsK`-T&>tgMqJ7Yuc0kcNRPE#g`I`iRBxMGe0YR-;b~F|KX#B
i(X!ybGy2KshR|6QIv1}jCri5{zX%5_A`<pg_4*gZeK~ai


From 42c57e16dea9fc4dba5077de995de680416aad33 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 14 Mar 2026 20:17:24 +0000
Subject: [PATCH 4/5] Integrate assemble step into deploy.yml, remove redundant
 publish.yml

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .github/workflows/deploy.yml  |  3 +++
 .github/workflows/publish.yml | 49 -----------------------------------
 2 files changed, 3 insertions(+), 49 deletions(-)
 delete mode 100644 .github/workflows/publish.yml

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 13421c0..e2f0e01 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -22,6 +22,9 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - 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
 
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
deleted file mode 100644
index e2f0e01..0000000
--- a/.github/workflows/publish.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-name: Deploy GitHub Pages
-
-on:
-  push:
-    branches: [main]
-  workflow_dispatch:
-
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
-# Allow only one concurrent deployment
-concurrency:
-  group: pages
-  cancel-in-progress: true
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - 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
-
-      - name: Build with Jekyll
-        uses: actions/jekyll-build-pages@v1
-        with:
-          source: ./
-          destination: ./_site
-
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
-
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v4

From c199be75322be90f56840d240d0098665ff5b796 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 14 Mar 2026 20:40:04 +0000
Subject: [PATCH 5/5] Replace envsubst/EICS_* with bash preamble + Jinja2
 assembly

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .github/workflows/deploy.yml |  3 ++
 assemble.py                  | 70 ++++++++++++++++++++----------------
 eic-shell.docker             | 26 ++++++++------
 eic-shell.singularity        | 37 ++++++++++---------
 install.sh                   | 33 ++++++++++++-----
 5 files changed, 105 insertions(+), 64 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index e2f0e01..1553222 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -22,6 +22,9 @@ 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
 
diff --git a/assemble.py b/assemble.py
index 74d297b..287eaad 100755
--- a/assemble.py
+++ b/assemble.py
@@ -1,9 +1,15 @@
 #!/usr/bin/env python3
 """Assemble a standalone install.sh from the source install.sh and template files.
 
-This script replaces envsubst calls that read from external template files with
-equivalent inline heredoc-based calls, producing a self-contained install.sh
-suitable for distribution (e.g., via curl | bash).
+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]
@@ -15,53 +21,57 @@
 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 assembled version)
-    install_sh = re.sub(
-        r'\nSCRIPT_DIR=.*\n',
-        '\n',
-        install_sh,
-    )
+    # 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 envsubst call that reads from a $SCRIPT_DIR template file
-    # with an inline heredoc-based equivalent.
-    #
-    # Source pattern (single line):
-    #   envsubst 'VARS' < "$SCRIPT_DIR/TEMPLATE_FILE" > OUTPUT
-    #
-    # Assembled replacement:
-    #   envsubst 'VARS' > OUTPUT << 'HEREDOC_MARKER'
-    #   <template content>
-    #   HEREDOC_MARKER
-    def inline_template(match):
+    # 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')
-        variables = match.group('variables')
         template_name = match.group('template')
         output = match.group('output')
 
-        template_content = (source_dir / template_name).read_text()
-        # Normalize to exactly one trailing newline so the heredoc closing
-        # marker always appears on its own line
-        template_content = template_content.rstrip('\n') + '\n'
-        # Derive a safe heredoc marker from the template filename
+        # 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}envsubst '{variables}' > {output} << '{marker}'\n"
-            f"{template_content}"
+            f"{indent}cat >> {output} << '{marker}'\n"
+            f"{template_body}\n"
             f"{marker}"
         )
 
     install_sh = re.sub(
-        r'(?P<indent>[ \t]*)envsubst \'(?P<variables>[^\']+)\''
-        r' < "\$SCRIPT_DIR/(?P<template>[^"]+)" > (?P<output>\S+)',
+        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
 
 
diff --git a/eic-shell.docker b/eic-shell.docker
index d8dc29a..f11466f 100644
--- a/eic-shell.docker
+++ b/eic-shell.docker
@@ -1,11 +1,17 @@
 #!/bin/bash
 
-## capture environment setup for upgrades
-CONTAINER=${EICS_CONTAINER}
-TMPDIR=${EICS_TMPDIR}
-VERSION=${EICS_VERSION}
-PREFIX=${EICS_PREFIX}
-DISABLE_CVMFS_USAGE=${EICS_DISABLE_CVMFS_USAGE}
+## eic-shell Docker launcher
+## Install-time values are baked in by install.sh via a preamble prepended to this file.
+## The defaults below allow running this file directly for testing; override by
+## setting the corresponding environment variables before execution.
+: "${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 ]"
@@ -58,18 +64,18 @@ if [ x${DISPLAY} == "x" ] ; then
   NOX=1
 fi
 
-if [ ! -z ${UPGRADE} ]; then
+if [[ -n "$UPGRADE" ]]; then
   echo "Upgrading eic-shell..."
-  docker pull ${EICS_IMG} || exit 1
+  docker pull ${IMG} || exit 1
   echo "eic-shell upgrade successful"
   exit 0
 fi
 
-if [ "$(uname -s)" = 'Darwin' ] && [ ! ${NOX} ]; then
+if [ "$(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 ${EICS_PLATFORM_FLAG} ${EICS_MOUNT} $XSTUFF -w=$PWD -it --rm -e EIC_SHELL_PREFIX=${EICS_PREFIX}/local ${EICS_IMG} eic-shell $@
+docker run ${PLATFORM_FLAG} ${MOUNT} ${XSTUFF} -w=$PWD -it --rm -e EIC_SHELL_PREFIX=${PREFIX}/local ${IMG} eic-shell "$@"
diff --git a/eic-shell.singularity b/eic-shell.singularity
index e28387a..ab0a0e5 100644
--- a/eic-shell.singularity
+++ b/eic-shell.singularity
@@ -1,19 +1,24 @@
 #!/bin/bash
 
-## capture environment setup for upgrades
-ORGANIZATION=${EICS_ORGANIZATION}
-CONTAINER=${EICS_CONTAINER}
-TMPDIR=${EICS_TMPDIR}
-VERSION=${EICS_VERSION}
-PREFIX=${EICS_PREFIX}
-DISABLE_CVMFS_USAGE=${EICS_DISABLE_CVMFS_USAGE}
+## 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 "          -o,--organization  Organization (D: $ORGANIZATION) (requires cvmfs)"
   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"
@@ -21,7 +26,7 @@ function print_the_help {
   echo "  Start the eic-shell containerized software environment (Singularity version)."
   echo ""
   echo "ENVIRONMENT VARIABLES:"
-  echo "          SINGULARITY        Path to the singularity executable (D: detected during installation)"
+  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: "
@@ -76,7 +81,7 @@ while [ $# -gt 0 ]; do
   esac
 done
 
-if [ ! -z ${UPGRADE} ]; then
+if [[ -n "$UPGRADE" ]]; then
   echo "Upgrading eic-shell..."
   if [ -z "$DISABLE_CVMFS_USAGE" -a -d /cvmfs/singularity.opensciencegrid.org/${ORGANIZATION}/${CONTAINER}:${VERSION} ]; then
     echo ""
@@ -90,18 +95,18 @@ if [ ! -z ${UPGRADE} ]; then
     echo ""
   fi
   FLAGS="-p ${PREFIX} -v ${VERSION}"
-  if [ ! -z ${TMPDIR} ]; then
+  if [[ -n "$TMPDIR" ]]; then
     FLAGS="${FLAGS} -t ${TMPDIR}"
   fi
-  if [ ! -z ${DISABLE_CVMFS_USAGE} ]; then
+  if [[ -n "$DISABLE_CVMFS_USAGE" ]]; then
     FLAGS="${FLAGS} --no-cvmfs"
   fi
-  curl -L https://github.com/eic/eic-shell/raw/main/install.sh \
+  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=${EICS_PREFIX}/local
-export SINGULARITY_BINDPATH=${EICS_BINDPATH}
-${SINGULARITY:-${EICS_SINGULARITY}} exec ${SINGULARITY_OPTIONS:-} ${SIF:-${EICS_SIF}} eic-shell $@
+export EIC_SHELL_PREFIX=${PREFIX}/local
+export SINGULARITY_BINDPATH=${BINDPATH}
+${SINGULARITY:-${INSTALLED_SINGULARITY}} exec ${SINGULARITY_OPTIONS:-} ${SIF:-${INSTALLED_SIF}} eic-shell "$@"
diff --git a/install.sh b/install.sh
index 6948c36..7e668b4 100755
--- a/install.sh
+++ b/install.sh
@@ -200,10 +200,19 @@ function install_singularity() {
 
   ## create a new top-level eic-shell launcher script
   ## that sets the EIC_SHELL_PREFIX and then starts singularity
-  export EICS_ORGANIZATION="$ORGANIZATION" EICS_CONTAINER="$CONTAINER" EICS_TMPDIR="$TMPDIR" \
-    EICS_VERSION="$VERSION" EICS_PREFIX="$PREFIX" EICS_DISABLE_CVMFS_USAGE="${DISABLE_CVMFS_USAGE}" \
-    EICS_SINGULARITY="$SINGULARITY" EICS_BINDPATH="$BINDPATH" EICS_SIF="$SIF"
-  envsubst '${EICS_ORGANIZATION} ${EICS_CONTAINER} ${EICS_TMPDIR} ${EICS_VERSION} ${EICS_PREFIX} ${EICS_DISABLE_CVMFS_USAGE} ${EICS_SINGULARITY} ${EICS_BINDPATH} ${EICS_SIF}' < "$SCRIPT_DIR/eic-shell.singularity" > eic-shell
+  cat > eic-shell << PREAMBLE
+#!/bin/bash
+ORGANIZATION="$ORGANIZATION"
+CONTAINER="$CONTAINER"
+TMPDIR="${TMPDIR:-}"
+VERSION="$VERSION"
+PREFIX="$PREFIX"
+DISABLE_CVMFS_USAGE="${DISABLE_CVMFS_USAGE:-}"
+INSTALLED_SINGULARITY="$SINGULARITY"
+BINDPATH="$BINDPATH"
+INSTALLED_SIF="$SIF"
+PREAMBLE
+  tail -n +2 "$SCRIPT_DIR/eic-shell.singularity" >> eic-shell
 
   chmod +x eic-shell
 
@@ -248,10 +257,18 @@ function install_docker() {
 
   ## create a new top-level eic-shell launcher script
   ## that sets the EIC_SHELL_PREFIX and then starts docker
-  export EICS_CONTAINER="$CONTAINER" EICS_TMPDIR="$TMPDIR" EICS_VERSION="$VERSION" \
-    EICS_PREFIX="$PREFIX" EICS_DISABLE_CVMFS_USAGE="${DISABLE_CVMFS_USAGE}" \
-    EICS_IMG="$IMG" EICS_PLATFORM_FLAG="$PLATFORM_FLAG" EICS_MOUNT="$MOUNT"
-  envsubst '${EICS_CONTAINER} ${EICS_TMPDIR} ${EICS_VERSION} ${EICS_PREFIX} ${EICS_DISABLE_CVMFS_USAGE} ${EICS_IMG} ${EICS_PLATFORM_FLAG} ${EICS_MOUNT}' < "$SCRIPT_DIR/eic-shell.docker" > eic-shell
+  cat > eic-shell << PREAMBLE
+#!/bin/bash
+CONTAINER="$CONTAINER"
+TMPDIR="${TMPDIR:-}"
+VERSION="$VERSION"
+PREFIX="$PREFIX"
+DISABLE_CVMFS_USAGE="${DISABLE_CVMFS_USAGE:-}"
+IMG="$IMG"
+PLATFORM_FLAG="$PLATFORM_FLAG"
+MOUNT="$MOUNT"
+PREAMBLE
+  tail -n +2 "$SCRIPT_DIR/eic-shell.docker" >> eic-shell
 
   chmod +x eic-shell
   echo " - Created custom eic-shell executable"