From 52de24c2410069b169858e6c4343576777ed19a8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Mar 2026 00:43:35 +0000
Subject: [PATCH 1/5] Initial plan


From 0b2b3326345ac419f49b0b2fe66c7eeea6e28780 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Mar 2026 02:23:54 +0000
Subject: [PATCH 2/5] Add warning for singularity/apptainer users with outdated
 eic-shell script

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .../eic/profile.d/z15_singularity_update.sh   | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 containers/eic/profile.d/z15_singularity_update.sh

diff --git a/containers/eic/profile.d/z15_singularity_update.sh b/containers/eic/profile.d/z15_singularity_update.sh
new file mode 100644
index 000000000..d69dbe320
--- /dev/null
+++ b/containers/eic/profile.d/z15_singularity_update.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+## Warn users running singularity/apptainer when their outer eic-shell script is outdated.
+## Users can upgrade by running `eic-shell --upgrade` outside the container.
+
+# Only run for interactive shells
+[[ $- == *i* ]] || return 0
+
+# Only run when inside singularity/apptainer
+if [ -z "${SINGULARITY_CONTAINER:-}" ] && [ -z "${APPTAINER_CONTAINER:-}" ]; then
+  return 0
+fi
+
+# Check if the outer eic-shell script is accessible
+_outer_eic_shell="${EIC_SHELL_PREFIX:-}/../eic-shell"
+if [ ! -f "$_outer_eic_shell" ]; then
+  unset _outer_eic_shell
+  return 0
+fi
+
+# Only warn if we have write access (meaning user can upgrade)
+if [ ! -w "$_outer_eic_shell" ]; then
+  unset _outer_eic_shell
+  return 0
+fi
+
+# Warn if the outer eic-shell script is older than 6 months (~180 days)
+if find "$_outer_eic_shell" -mtime +180 -print -quit 2>/dev/null | grep -q .; then
+  echo ""
+  echo "WARNING: Your eic-shell script appears to be more than 6 months old."
+  echo "         Consider upgrading by running outside the container:"
+  echo "           eic-shell --upgrade"
+  echo ""
+fi
+unset _outer_eic_shell

From 2ab6df8c185aeb15add0de99c14e9a083486423a Mon Sep 17 00:00:00 2001
From: Wouter Deconinck <wdconinc@gmail.com>
Date: Wed, 4 Mar 2026 08:30:21 -0600
Subject: [PATCH 3/5] fix: require EIC_SHELL_PREFIX (only
 singularity/apptainer)

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 containers/eic/profile.d/z15_singularity_update.sh | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/containers/eic/profile.d/z15_singularity_update.sh b/containers/eic/profile.d/z15_singularity_update.sh
index d69dbe320..ecb42f23b 100644
--- a/containers/eic/profile.d/z15_singularity_update.sh
+++ b/containers/eic/profile.d/z15_singularity_update.sh
@@ -11,8 +11,13 @@ if [ -z "${SINGULARITY_CONTAINER:-}" ] && [ -z "${APPTAINER_CONTAINER:-}" ]; the
   return 0
 fi
 
+# Require EIC_SHELL_PREFIX to be set; otherwise we cannot locate the outer eic-shell
+if [ -z "${EIC_SHELL_PREFIX:-}" ]; then
+  return 0
+fi
+
 # Check if the outer eic-shell script is accessible
-_outer_eic_shell="${EIC_SHELL_PREFIX:-}/../eic-shell"
+_outer_eic_shell="${EIC_SHELL_PREFIX}/../eic-shell"
 if [ ! -f "$_outer_eic_shell" ]; then
   unset _outer_eic_shell
   return 0

From c54d876f8ab08f2dc1eee7a48257d1be4b436a95 Mon Sep 17 00:00:00 2001
From: Wouter Deconinck <wdconinc@gmail.com>
Date: Wed, 4 Mar 2026 08:30:51 -0600
Subject: [PATCH 4/5] fix: allow sh/dash, avoid bashism

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 containers/eic/profile.d/z15_singularity_update.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/containers/eic/profile.d/z15_singularity_update.sh b/containers/eic/profile.d/z15_singularity_update.sh
index ecb42f23b..19152c422 100644
--- a/containers/eic/profile.d/z15_singularity_update.sh
+++ b/containers/eic/profile.d/z15_singularity_update.sh
@@ -4,7 +4,10 @@
 ## Users can upgrade by running `eic-shell --upgrade` outside the container.
 
 # Only run for interactive shells
-[[ $- == *i* ]] || return 0
+case "$-" in
+  *i*) ;;
+  *) return 0 ;;
+esac
 
 # Only run when inside singularity/apptainer
 if [ -z "${SINGULARITY_CONTAINER:-}" ] && [ -z "${APPTAINER_CONTAINER:-}" ]; then

From 828f23fbdd1232d3225a1e63c7bc242dcdf40b4f Mon Sep 17 00:00:00 2001
From: Wouter Deconinck <wdconinc@gmail.com>
Date: Wed, 4 Mar 2026 08:53:12 -0600
Subject: [PATCH 5/5] fix: use posix find and don't grep quiet

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 containers/eic/profile.d/z15_singularity_update.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/containers/eic/profile.d/z15_singularity_update.sh b/containers/eic/profile.d/z15_singularity_update.sh
index 19152c422..9d96258c2 100644
--- a/containers/eic/profile.d/z15_singularity_update.sh
+++ b/containers/eic/profile.d/z15_singularity_update.sh
@@ -33,7 +33,7 @@ if [ ! -w "$_outer_eic_shell" ]; then
 fi
 
 # Warn if the outer eic-shell script is older than 6 months (~180 days)
-if find "$_outer_eic_shell" -mtime +180 -print -quit 2>/dev/null | grep -q .; then
+if [ -n "$(find "$_outer_eic_shell" -mtime +180 -print 2>/dev/null)" ]; then
   echo ""
   echo "WARNING: Your eic-shell script appears to be more than 6 months old."
   echo "         Consider upgrading by running outside the container:"