From 202c3ada1266cff2bb71c96e43d3c2117044e732 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 11:19:36 +0200
Subject: [PATCH 01/10] Make sure the full directory name is replaced in
 eb_hooks.py

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index 5ac2940..0376c3c 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -204,4 +204,4 @@ done
 sed -i "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/modules/EESSI/${EESSI_VERSION}.lua
 
 # replace EESSI version used in EasyBuild hooks
-sed -i "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/easybuild/eb_hooks.py
+sed -i "s@/eessi-<EESSI_VERSION>/@/eessi-${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/easybuild/eb_hooks.py

From bda6d6046369080c8eb09619cf93a9be64eb35fb Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 11:42:16 +0200
Subject: [PATCH 02/10] Compare files with placeholders removed

---
 install_scripts.sh | 33 ++++++++++++---------------------
 1 file changed, 12 insertions(+), 21 deletions(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index 0376c3c..d43a535 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -134,6 +134,9 @@ init_files=(
     minimal_eessi_env README.md test.py lmod_eessi_archdetect_wrapper.sh lmod_eessi_archdetect_wrapper_accel.sh
 
 )
+# make sure that scripts in init/ and scripts/ use correct EESSI version
+sed -i "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${TOPDIR}/init/eessi_defaults
+
 copy_files_by_list ${TOPDIR}/init ${INSTALL_PREFIX}/init "${init_files[@]}"
 
 # Copy for the init/arch_specs directory
@@ -152,12 +155,16 @@ copy_files_by_list ${TOPDIR}/init/Magic_Castle ${INSTALL_PREFIX}/init/Magic_Cast
 mc_files=(
    2023.06.lua
 )
+# replace EESSI version used in comments in EESSI module
+sed -i "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${TOPDIR}/init/modules/EESSI/${EESSI_VERSION}.lua
 copy_files_by_list ${TOPDIR}/init/modules/EESSI ${INSTALL_PREFIX}/init/modules/EESSI "${mc_files[@]}"
 
 # Copy for init/lmod directory
-init_script_files=(
-    bash zsh ksh fish csh    
-)
+init_script_files=$(ls ${TOPDIR}/init/lmod)
+# replace placeholder for default EESSI version in Lmod init scripts
+for shell in $init_script_files; do
+    sed -i "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${TOPDIR}/init/lmod/${shell}
+done
 copy_files_by_list ${TOPDIR}/init/lmod ${INSTALL_PREFIX}/init/lmod "${init_script_files[@]}"
 
 # Copy for the scripts directory
@@ -186,22 +193,6 @@ ${INSTALL_PREFIX}/scripts/gpu_support/nvidia/easystacks "${host_injections_easys
 hook_files=(
     eb_hooks.py
 )
-copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/init/easybuild "${hook_files[@]}"
-
-# replace version placeholders in scripts;
-# note: the commands below are always run, regardless of whether the scripts were changed,
-# but that should be fine (no changes are made if version placeholder is not present anymore)
-
-# make sure that scripts in init/ and scripts/ use correct EESSI version
-sed -i "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${INSTALL_PREFIX}/init/eessi_defaults
-
-# replace placeholder for default EESSI version in Lmod init scripts
-for shell in $(ls ${INSTALL_PREFIX}/init/lmod); do
-    sed -i "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${INSTALL_PREFIX}/init/lmod/${shell}
-done
-
-# replace EESSI version used in comments in EESSI module
-sed -i "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/modules/EESSI/${EESSI_VERSION}.lua
-
 # replace EESSI version used in EasyBuild hooks
-sed -i "s@/eessi-<EESSI_VERSION>/@/eessi-${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/easybuild/eb_hooks.py
+sed -i "s@/eessi-<EESSI_VERSION>/@/eessi-${EESSI_VERSION}/@g" ${TOPDIR}/eb_hooks.py
+copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/init/easybuild "${hook_files[@]}"

From 8f1f6ed86551fa760ad4145aeb1a7cafdedb8aa7 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 13:12:39 +0200
Subject: [PATCH 03/10] Make sure test step is using right EESSI version

---
 bot/test.sh | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/bot/test.sh b/bot/test.sh
index b615be0..168b0d5 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -151,12 +151,13 @@ EESSI_REPOS_CFG_DIR_OVERRIDE=$(cfg_get_value "repository" "repos_cfg_dir")
 export EESSI_REPOS_CFG_DIR_OVERRIDE=${EESSI_REPOS_CFG_DIR_OVERRIDE:-${PWD}/cfg}
 echo "bot/test.sh: EESSI_REPOS_CFG_DIR_OVERRIDE='${EESSI_REPOS_CFG_DIR_OVERRIDE}'"
 
-# determine pilot version to be used from .repository.repo_version in ${JOB_CFG_FILE}
-# here, just set & export EESSI_PILOT_VERSION_OVERRIDE
+# determine EESSI version to be used from .repository.repo_version in ${JOB_CFG_FILE}
+# here, just set & export EESSI_VERSION_OVERRIDE
 # next script (eessi_container.sh) makes use of it via sourcing init scripts
 # (e.g., init/eessi_defaults or init/minimal_eessi_env)
-export EESSI_PILOT_VERSION_OVERRIDE=$(cfg_get_value "repository" "repo_version")
-echo "bot/test.sh: EESSI_PILOT_VERSION_OVERRIDE='${EESSI_PILOT_VERSION_OVERRIDE}'"
+REPOSITORY_VERSION=$(cfg_get_value "repository" "repo_version")
+export EESSI_VERSION_OVERRIDE=${REPOSITORY_VERSION}
+echo "bot/build.sh: EESSI_VERSION_OVERRIDE='${EESSI_VERSION_OVERRIDE}'"
 
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down

From 140a20dcba513167fb65748e88a16b31d135857f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 13:43:48 +0200
Subject: [PATCH 04/10] Make trivial change to trigger deploy of file

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 4775bd4..552ba46 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -405,7 +405,7 @@ def parse_hook_zen4_module_only(ec, eprefix):
         env_varname = EESSI_IGNORE_ZEN4_GCC1220_ENVVAR
         # TODO: create a docs page to which we can refer for more info here
         # TODO: then update the link to the known issues page to the _specific_ issue
-        # Need to escape newline character so that the newline character actually ends up in the module file
+        # Need to escape the newline character so that the newline character actually ends up in the module file
         # (otherwise, it splits the string, and a 2-line string ends up in the modulefile, resulting in syntax error)
         errmsg = "EasyConfigs using toolchains based on GCCcore-12.2.0 are not supported for the Zen4 architecture.\\n"
         errmsg += "See https://www.eessi.io/docs/known_issues/eessi-<EESSI_VERSION>/#gcc-1220-and-foss-2022b-based-modules-cannot-be-loaded-on-zen4-architecture"

From 0b50d5b5eedd092e319b8cb1c3e9598e0701433c Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 14:02:35 +0200
Subject: [PATCH 05/10] Remove unnecessary space

---
 install_scripts.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index d43a535..4a52734 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -136,7 +136,6 @@ init_files=(
 )
 # make sure that scripts in init/ and scripts/ use correct EESSI version
 sed -i "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${TOPDIR}/init/eessi_defaults
-
 copy_files_by_list ${TOPDIR}/init ${INSTALL_PREFIX}/init "${init_files[@]}"
 
 # Copy for the init/arch_specs directory

From 2a287804b79ea7b1ba72d1c528a2d824dd81736b Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 14:14:16 +0200
Subject: [PATCH 06/10] Only retain the sed change if it is needed

---
 install_scripts.sh | 56 +++++++++++++++++++++++++++++++++++++---------
 1 file changed, 45 insertions(+), 11 deletions(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index 4a52734..d116a36 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -37,6 +37,30 @@ file_changed_in_pr() {
   ) && return 0 || return 1
 }
 
+sed_update_if_changed() {
+    # Usage: sed_update_if_changed 's/foo/bar/' file.txt
+    if [ "$#" -ne 2 ]; then
+        echo "Usage: sed_update_if_changed 'sed_command' file" >&2
+        return 1
+    fi
+
+    local sed_command="$1"
+    local file="$2"
+    local tmp_file="$(mktemp "${file}.XXXXXX")"
+
+    sed "$sed_command" "$file" > "$tmp_file" || {
+        rm -f "$tmp_file"
+        echo "sed command failed" >&2
+        return 1
+    }
+
+    if ! cmp -s "$file" "$tmp_file"; then
+        mv "$tmp_file" "$file"
+    else
+        rm -f "$tmp_file"
+    fi
+}
+
 compare_and_copy() {
     if [ "$#" -ne 2 ]; then
         echo "Usage of function: compare_and_copy <source_file> <destination_file>"
@@ -134,8 +158,6 @@ init_files=(
     minimal_eessi_env README.md test.py lmod_eessi_archdetect_wrapper.sh lmod_eessi_archdetect_wrapper_accel.sh
 
 )
-# make sure that scripts in init/ and scripts/ use correct EESSI version
-sed -i "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${TOPDIR}/init/eessi_defaults
 copy_files_by_list ${TOPDIR}/init ${INSTALL_PREFIX}/init "${init_files[@]}"
 
 # Copy for the init/arch_specs directory
@@ -154,16 +176,12 @@ copy_files_by_list ${TOPDIR}/init/Magic_Castle ${INSTALL_PREFIX}/init/Magic_Cast
 mc_files=(
    2023.06.lua
 )
-# replace EESSI version used in comments in EESSI module
-sed -i "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${TOPDIR}/init/modules/EESSI/${EESSI_VERSION}.lua
 copy_files_by_list ${TOPDIR}/init/modules/EESSI ${INSTALL_PREFIX}/init/modules/EESSI "${mc_files[@]}"
 
 # Copy for init/lmod directory
-init_script_files=$(ls ${TOPDIR}/init/lmod)
-# replace placeholder for default EESSI version in Lmod init scripts
-for shell in $init_script_files; do
-    sed -i "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${TOPDIR}/init/lmod/${shell}
-done
+init_script_files=(
+    bash zsh ksh fish csh    
+)
 copy_files_by_list ${TOPDIR}/init/lmod ${INSTALL_PREFIX}/init/lmod "${init_script_files[@]}"
 
 # Copy for the scripts directory
@@ -192,6 +210,22 @@ ${INSTALL_PREFIX}/scripts/gpu_support/nvidia/easystacks "${host_injections_easys
 hook_files=(
     eb_hooks.py
 )
-# replace EESSI version used in EasyBuild hooks
-sed -i "s@/eessi-<EESSI_VERSION>/@/eessi-${EESSI_VERSION}/@g" ${TOPDIR}/eb_hooks.py
 copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/init/easybuild "${hook_files[@]}"
+
+# replace version placeholders in scripts;
+# note: the commands below are always run, regardless of whether the scripts were changed,
+# but that should be fine (no changes are made if version placeholder is not present anymore)
+
+# make sure that scripts in init/ and scripts/ use correct EESSI version
+sed_update_if_changed "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${INSTALL_PREFIX}/init/eessi_defaults
+
+# replace placeholder for default EESSI version in Lmod init scripts
+for shell in $(ls ${INSTALL_PREFIX}/init/lmod); do
+    sed_update_if_changed "s/__EESSI_VERSION_DEFAULT__/${EESSI_VERSION}/g" ${INSTALL_PREFIX}/init/lmod/${shell}
+done
+
+# replace EESSI version used in comments in EESSI module
+sed_update_if_changed "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/modules/EESSI/${EESSI_VERSION}.lua
+
+# replace EESSI version used in EasyBuild hooks
+sed_update_if_changed "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/easybuild/eb_hooks.py

From b8c6600a2e18c1173deb8cbd8c04fa337c43440a Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 14:16:48 +0200
Subject: [PATCH 07/10] Use diff rather than cmp

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index d116a36..dc3356e 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -54,7 +54,7 @@ sed_update_if_changed() {
         return 1
     }
 
-    if ! cmp -s "$file" "$tmp_file"; then
+    if ! diff -q "$file" "$tmp_file" > /dev/null; then
         mv "$tmp_file" "$file"
     else
         rm -f "$tmp_file"

From 0afa994b6058510271f695f5be69f94846aab9ec Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 16 Jun 2025 14:20:26 +0200
Subject: [PATCH 08/10] Fix the original problem!

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index dc3356e..15675b2 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -228,4 +228,4 @@ done
 sed_update_if_changed "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/modules/EESSI/${EESSI_VERSION}.lua
 
 # replace EESSI version used in EasyBuild hooks
-sed_update_if_changed "s@/<EESSI_VERSION>/@/${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/easybuild/eb_hooks.py
+sed_update_if_changed "s@/eessi-<EESSI_VERSION>/@/eessi-${EESSI_VERSION}/@g" ${INSTALL_PREFIX}/init/easybuild/eb_hooks.py

From 4ca595fb19d52bcb0b2ee6a862e119c100eea51c Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 17 Jun 2025 12:29:04 +0200
Subject: [PATCH 09/10] Apply suggestions from code review

---
 install_scripts.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index 15675b2..adf9bca 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -55,7 +55,8 @@ sed_update_if_changed() {
     }
 
     if ! diff -q "$file" "$tmp_file" > /dev/null; then
-        mv "$tmp_file" "$file"
+        # Use cat to retain existing permissions, set umask to world readable in case the target file does not yet exist. 
+        (umask 022 && cat "$tmp_file" > "$file")
     else
         rm -f "$tmp_file"
     fi

From a8fc637f4658b410c5be1f1d70bc2409b07ab060 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 17 Jun 2025 12:49:20 +0200
Subject: [PATCH 10/10] Update install_scripts.sh

---
 install_scripts.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index adf9bca..cbe9bdb 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -57,9 +57,9 @@ sed_update_if_changed() {
     if ! diff -q "$file" "$tmp_file" > /dev/null; then
         # Use cat to retain existing permissions, set umask to world readable in case the target file does not yet exist. 
         (umask 022 && cat "$tmp_file" > "$file")
-    else
-        rm -f "$tmp_file"
     fi
+    # Remove the temporary file
+    rm -f "$tmp_file"
 }
 
 compare_and_copy() {