From 143341c7fe0126a8100970e59e755bba8f7de771 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 28 Jan 2026 17:49:59 +0100
Subject: [PATCH 01/17] Make all shell initialisations more robust

---
 init/lmod/bash | 27 +++++++++++++++++----------
 init/lmod/csh  | 28 ++++++++++++++++++----------
 init/lmod/fish | 26 +++++++++++++++++---------
 init/lmod/ksh  | 28 ++++++++++++++++++----------
 init/lmod/zsh  | 28 ++++++++++++++++++----------
 5 files changed, 88 insertions(+), 49 deletions(-)

diff --git a/init/lmod/bash b/init/lmod/bash
index daba8351..7ca71b4f 100644
--- a/init/lmod/bash
+++ b/init/lmod/bash
@@ -3,17 +3,24 @@ EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
 # Choose an EESSI version
 EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Path to top-level module tree
-export MODULEPATH="${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-. "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash"
+# Now that we know our EESSI version let's not forget it
+export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
-if [ -z "$__Init_Default_Modules" ]; then
-   export __Init_Default_Modules=1;
+# ability to predefine elsewhere the default list
+LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
+export LMOD_SYSTEM_DEFAULT_MODULES
 
-   ## ability to predefine elsewhere the default list
-   LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
-   export LMOD_SYSTEM_DEFAULT_MODULES
-   module --initial_load --no_redirect restore
+if [ -z "$__Init_EESSI_Default_Modules" ]; then
+    export __Init_EESSI_Default_Modules=1;
+
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    unset __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    unset _ModuleTable001_
+    # Path to top-level module tree
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules"
+    . "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash"
+    module --initial_load --no_redirect restore
 else
-   module refresh
+    module reset
 fi
diff --git a/init/lmod/csh b/init/lmod/csh
index 2adb314c..0122981b 100644
--- a/init/lmod/csh
+++ b/init/lmod/csh
@@ -7,18 +7,26 @@ setenv EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
 if (! $?EESSI_VERSION) then
     set EESSI_VERSION = "${EESSI_VERSION_DEFAULT}"
 endif
-# Path to top-level module tree
-setenv MODULEPATH "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-source "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"
+# Now that we know our EESSI version let's not forget it
+setenv EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
-if (! $?__Init_Default_Modules ) then
-    setenv __Init_Default_Modules 1
+# ability to predefine elsewhere the default list
+if (! $?LMOD_SYSTEM_DEFAULT_MODULES) then
+    setenv LMOD_SYSTEM_DEFAULT_MODULES "EESSI/${EESSI_VERSION}"
+endif
+
+if (! $?__Init_EESSI_Default_Modules ) then
+    setenv __Init_EESSI_Default_Modules 1
+
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    unsetenv __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    unsetenv _ModuleTable001_
+    # Path to top-level module tree
+    setenv MODULEPATH "${EESSI_CVMFS_REPO}/init/modules"
+    source "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"
 
-    # ability to predefine elsewhere the default list
-    if (! $?LMOD_SYSTEM_DEFAULT_MODULES) then
-        setenv LMOD_SYSTEM_DEFAULT_MODULES "EESSI/${EESSI_VERSION}"
-    endif
     module --initial_load --no_redirect restore
 else
-    module refresh
+    module reset
 endif
diff --git a/init/lmod/fish b/init/lmod/fish
index 9e595441..2db34045 100644
--- a/init/lmod/fish
+++ b/init/lmod/fish
@@ -3,16 +3,24 @@ set EESSI_CVMFS_REPO (set -q EESSI_CVMFS_REPO; and echo "$EESSI_CVMFS_REPO"; or
 # Choose an EESSI version
 set EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
 set EESSI_VERSION (set -q EESSI_VERSION; and echo "$EESSI_VERSION"; or echo "$EESSI_VERSION_DEFAULT")
-# Path to top-level module tree
-set -x MODULEPATH "$EESSI_CVMFS_REPO"/versions/"$EESSI_VERSION"/init/modules
-. "$EESSI_CVMFS_REPO"/versions/"$EESSI_VERSION"/compat/linux/(uname -m)/usr/share/Lmod/init/fish
+# Now that we know our EESSI version let's not forget it
+set -x EESSI_VERSION_DEFAULT "$EESSI_VERSION"
 
-if test -z "$__Init_Default_Modules"
-	export __Init_Default_Modules=1;
+# ability to predefine elsewhere the default list
+set -x LMOD_SYSTEM_DEFAULT_MODULES (set -q LMOD_SYSTEM_DEFAULT_MODULE; and echo "$LMOD_SYSTEM_DEFAULT_MODULE"; or echo "EESSI/$EESSI_VERSION")
 
-	## ability to predefine elsewhere the default list
-	set -x LMOD_SYSTEM_DEFAULT_MODULES (set -q LMOD_SYSTEM_DEFAULT_MODULE; and echo "$LMOD_SYSTEM_DEFAULT_MODULE"; or echo "EESSI/$EESSI_VERSION")
-	module --initial_load --no_redirect restore
+if test -z "$__Init_EESSI_Default_Modules"
+    set -x __Init_EESSI_Default_Modules 1
+
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    set -e __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    set -e _ModuleTable001_
+    # Path to top-level module tree
+    set -x MODULEPATH "$EESSI_CVMFS_REPO"/init/modules
+    . "$EESSI_CVMFS_REPO"/versions/"$EESSI_VERSION"/compat/linux/(uname -m)/usr/share/Lmod/init/fish
+
+    module --initial_load --no_redirect restore
 else
-	module refresh
+    module reset
 end
diff --git a/init/lmod/ksh b/init/lmod/ksh
index ebf4c0ca..5be0cacd 100644
--- a/init/lmod/ksh
+++ b/init/lmod/ksh
@@ -3,17 +3,25 @@ EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
 # Choose an EESSI version
 EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Path to top-level module tree
-export MODULEPATH="${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-. "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/ksh"
+# Now that we know our EESSI version let's not forget it
+export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
-if [ -z "$__Init_Default_Modules" ]; then
-   export __Init_Default_Modules=1;
+## ability to predefine elsewhere the default list
+LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
+export LMOD_SYSTEM_DEFAULT_MODULES
+   
+if [ -z "$__Init_EESSI_Default_Modules" ]; then
+    export __Init_EESSI_Default_Modules=1;
 
-   ## ability to predefine elsewhere the default list
-   LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
-   export LMOD_SYSTEM_DEFAULT_MODULES
-   module --initial_load --no_redirect restore
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    unset __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    unset _ModuleTable001_
+    # Path to top-level module tree
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules"
+    . "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/ksh"
+
+    module --initial_load --no_redirect restore
 else
-   module refresh
+    module reset
 fi
diff --git a/init/lmod/zsh b/init/lmod/zsh
index dfdff0c7..f8abfbd0 100644
--- a/init/lmod/zsh
+++ b/init/lmod/zsh
@@ -3,17 +3,25 @@ EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
 # Choose an EESSI version
 EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Path to top-level module tree
-export MODULEPATH="${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/modules"
-. "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/zsh"
+# Now that we know our EESSI version let's not forget it
+export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
-if [ -z "$__Init_Default_Modules" ]; then
-   export __Init_Default_Modules=1;
+# ability to predefine elsewhere the default list
+LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
+export LMOD_SYSTEM_DEFAULT_MODULES
 
-   ## ability to predefine elsewhere the default list
-   LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
-   export LMOD_SYSTEM_DEFAULT_MODULES
-   module --initial_load --no_redirect restore
+if [ -z "$__Init_EESSI_Default_Modules" ]; then
+    export __Init_EESSI_Default_Modules=1;
+
+    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    unset __LMOD_REF_COUNT_MODULEPATH
+    # and clear out any memory Lmod might have
+    unset _ModuleTable001_
+    # Path to top-level module tree
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules"
+    . "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/zsh"
+
+    module --initial_load --no_redirect restore
 else
-   module refresh
+    module reset
 fi

From a428f6882558cf0596c77d8b314156d05f1168e4 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 28 Jan 2026 20:50:17 +0100
Subject: [PATCH 02/17] Fix typo and tests

---
 .github/workflows/scripts/test_init_scripts.sh | 2 +-
 init/lmod/csh                                  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index f543835c..979067f5 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -49,7 +49,7 @@ for shell in ${SHELLS[@]}; do
     assert_raises 'echo "${MODULE_SECTIONS[1]}" | grep -E "$PATTERN"'
 
     # TEST 3: Check if module overviews second section is the EESSI init module
-    assert "echo ${MODULE_SECTIONS[4]}" "/cvmfs/software.eessi.io/versions/$EESSI_VERSION/init/modules"
+    assert "echo ${MODULE_SECTIONS[4]}" "/cvmfs/software.eessi.io/init/modules"
 
     # TEST 4: Load EasyBuild module and check version
     # eb --version outputs: "This is EasyBuild 5.1.1 (framework: 5.1.1, easyblocks: 5.1.1) on host ..."
diff --git a/init/lmod/csh b/init/lmod/csh
index 0122981b..88771ad3 100644
--- a/init/lmod/csh
+++ b/init/lmod/csh
@@ -8,7 +8,7 @@ if (! $?EESSI_VERSION) then
     set EESSI_VERSION = "${EESSI_VERSION_DEFAULT}"
 endif
 # Now that we know our EESSI version let's not forget it
-setenv EESSI_VERSION_DEFAULT="$EESSI_VERSION"
+setenv EESSI_VERSION_DEFAULT "$EESSI_VERSION"
 
 # ability to predefine elsewhere the default list
 if (! $?LMOD_SYSTEM_DEFAULT_MODULES) then

From c3d3159bb66909131292649e9d216b01ecff0cca Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 28 Jan 2026 21:16:47 +0100
Subject: [PATCH 03/17] See where the error is

---
 .github/workflows/scripts/test_init_scripts.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index 979067f5..62d66959 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -47,6 +47,7 @@ for shell in ${SHELLS[@]}; do
     fi
     PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/modules/all"
     assert_raises 'echo "${MODULE_SECTIONS[1]}" | grep -E "$PATTERN"'
+    echo "${MODULE_SECTIONS[1]}" "$PATTERN"
 
     # TEST 3: Check if module overviews second section is the EESSI init module
     assert "echo ${MODULE_SECTIONS[4]}" "/cvmfs/software.eessi.io/init/modules"
@@ -72,6 +73,7 @@ for shell in ${SHELLS[@]}; do
     PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
     echo "$EASYBUILD_PATH" | grep -E "$PATTERN"
     assert_raises 'echo "$EASYBUILD_PATH" | grep -E "$PATTERN"'
+    echo "$EASYBUILD_PATH" "$PATTERN"
 
     # End Test Suite
     assert_end "source_eessi_$shell"

From 3692346bd1634a80ee1e63374304c035e7277eaa Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 29 Jan 2026 15:23:04 +0100
Subject: [PATCH 04/17] Add new capabilities and new tests

---
 .github/workflows/modules/append_module.lua   |  3 +++
 .github/workflows/modules/prepend_module.lua  |  3 +++
 .../workflows/scripts/test_init_scripts.sh    | 27 +++++++++++++++++++
 init/lmod/bash                                | 12 ++++++---
 init/lmod/csh                                 | 23 ++++++++++++----
 init/lmod/fish                                | 23 +++++++++++++---
 init/lmod/ksh                                 | 12 ++++++---
 init/lmod/zsh                                 | 12 ++++++---
 8 files changed, 94 insertions(+), 21 deletions(-)
 create mode 100644 .github/workflows/modules/append_module.lua
 create mode 100644 .github/workflows/modules/prepend_module.lua

diff --git a/.github/workflows/modules/append_module.lua b/.github/workflows/modules/append_module.lua
new file mode 100644
index 00000000..e45cb640
--- /dev/null
+++ b/.github/workflows/modules/append_module.lua
@@ -0,0 +1,3 @@
+setenv("INSIDE_GITHUB_ACTIONS", "true")
+-- Interfere with PATH so Lmod keeps a record
+prepend_path("PATH", "/snap/bin")
diff --git a/.github/workflows/modules/prepend_module.lua b/.github/workflows/modules/prepend_module.lua
new file mode 100644
index 00000000..e45cb640
--- /dev/null
+++ b/.github/workflows/modules/prepend_module.lua
@@ -0,0 +1,3 @@
+setenv("INSIDE_GITHUB_ACTIONS", "true")
+-- Interfere with PATH so Lmod keeps a record
+prepend_path("PATH", "/snap/bin")
diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index 62d66959..2e3a5a58 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -75,6 +75,33 @@ for shell in ${SHELLS[@]}; do
     assert_raises 'echo "$EASYBUILD_PATH" | grep -E "$PATTERN"'
     echo "$EASYBUILD_PATH" "$PATTERN"
 
+    # TEST 6 and 7: Check the various options (EESSI_SYSTEM_DEFAULT_MODULES_APPEND, EESSI_SYSTEM_DEFAULT_MODULES_APPEND, EESSI_EXTRA_MODULEPATH) all work
+    if [ "$shell" = "csh" ]; then
+      echo "setenv EESSI_SYSTEM_DEFAULT_MODULES_APPEND append_module" > ~/.cshrc
+      echo "setenv EESSI_SYSTEM_DEFAULT_MODULES_PREPEND prepend_module" >> ~/.cshrc
+      echo "setenv EESSI_EXTRA_MODULEPATH .github/workflows/modules" >> ~/.cshrc
+      echo "source init/lmod/$shell" >> ~/.cshrc
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'echo $MODULEPATH')
+    elif [ "$shell" = "fish" ]; then
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'set -x EESSI_SYSTEM_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_SYSTEM_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'set -x EESSI_SYSTEM_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_SYSTEM_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+    else
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_SYSTEM_DEFAULT_MODULES_APPEND=append_module ; export EESSI_SYSTEM_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'export EESSI_SYSTEM_DEFAULT_MODULES_APPEND=append_module ; export EESSI_SYSTEM_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+    fi
+    # escape the dots in ${EASYBUILD_VERSION}
+    LMOD_SYSTEM_DEFAULT_MODULES_PATTERN='^prepend_module:.*:append_module$'
+    echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" AND "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"
+    assert_raises 'echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" | grep -E "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"'
+    if [ "$shell" = "fish" ]; then
+      MODULEPATH_PATTERN='\.github/workflows/modules$'
+    else
+      MODULEPATH_PATTERN=':\.github/workflows/modules$'
+    fi
+    echo "$TEST_MODULEPATH" AND "$MODULEPATH_PATTERN"
+    assert_raises 'echo "$TEST_MODULEPATH" | grep -E "$MODULEPATH_PATTERN"'
+
     # End Test Suite
     assert_end "source_eessi_$shell"
   fi
diff --git a/init/lmod/bash b/init/lmod/bash
index 7ca71b4f..02e7d37a 100644
--- a/init/lmod/bash
+++ b/init/lmod/bash
@@ -6,20 +6,24 @@ EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 # Now that we know our EESSI version let's not forget it
 export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
-# ability to predefine elsewhere the default list
-LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
+# ability to predefine elsewhere the default list (with options to append or prepend)
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:+$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_SYSTEM_DEFAULT_MODULES_APPEND:+:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND}"
 export LMOD_SYSTEM_DEFAULT_MODULES
 
 if [ -z "$__Init_EESSI_Default_Modules" ]; then
     export __Init_EESSI_Default_Modules=1;
 
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    LMOD_EESSI_VERSION=${EESSI_VERSION/2023.06/2025.06}
+
     # If there is a local Lmod, make it forget about the system set MODULEPATH
     unset __LMOD_REF_COUNT_MODULEPATH
     # and clear out any memory Lmod might have
     unset _ModuleTable001_
     # Path to top-level module tree
-    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules"
-    . "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash"
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules${EESSI_EXTRA_MODULEPATH:+:$EESSI_EXTRA_MODULEPATH}"
+    . "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash"
     module --initial_load --no_redirect restore
 else
     module reset
diff --git a/init/lmod/csh b/init/lmod/csh
index 88771ad3..dddb1fbf 100644
--- a/init/lmod/csh
+++ b/init/lmod/csh
@@ -10,21 +10,34 @@ endif
 # Now that we know our EESSI version let's not forget it
 setenv EESSI_VERSION_DEFAULT "$EESSI_VERSION"
 
-# ability to predefine elsewhere the default list
-if (! $?LMOD_SYSTEM_DEFAULT_MODULES) then
-    setenv LMOD_SYSTEM_DEFAULT_MODULES "EESSI/${EESSI_VERSION}"
+# ability to predefine elsewhere the default list (with options to append or prepend)
+set LMOD_SYSTEM_DEFAULT_MODULES = "EESSI/$EESSI_VERSION"
+if ( $?EESSI_SYSTEM_DEFAULT_MODULES_PREPEND ) then
+    set LMOD_SYSTEM_DEFAULT_MODULES = "$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
 endif
+if ( $?EESSI_SYSTEM_DEFAULT_MODULES_APPEND ) then
+    set LMOD_SYSTEM_DEFAULT_MODULES = "$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND"
+endif
+setenv LMOD_SYSTEM_DEFAULT_MODULES "$LMOD_SYSTEM_DEFAULT_MODULES"
 
 if (! $?__Init_EESSI_Default_Modules ) then
     setenv __Init_EESSI_Default_Modules 1
 
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    set LMOD_EESSI_VERSION "$EESSI_VERSION:s/2023.06/2025.06/"
+
     # If there is a local Lmod, make it forget about the system set MODULEPATH
     unsetenv __LMOD_REF_COUNT_MODULEPATH
     # and clear out any memory Lmod might have
     unsetenv _ModuleTable001_
     # Path to top-level module tree
-    setenv MODULEPATH "${EESSI_CVMFS_REPO}/init/modules"
-    source "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"
+    set modulepath = "$EESSI_CVMFS_REPO/init/modules"
+    if ( $?EESSI_EXTRA_MODULEPATH && "$EESSI_EXTRA_MODULEPATH" != "" ) then
+        set modulepath = "$modulepath:$EESSI_EXTRA_MODULEPATH"
+    endif
+    setenv MODULEPATH "$modulepath"
+    source "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"
 
     module --initial_load --no_redirect restore
 else
diff --git a/init/lmod/fish b/init/lmod/fish
index 2db34045..742511c8 100644
--- a/init/lmod/fish
+++ b/init/lmod/fish
@@ -6,19 +6,34 @@ set EESSI_VERSION (set -q EESSI_VERSION; and echo "$EESSI_VERSION"; or echo "$EE
 # Now that we know our EESSI version let's not forget it
 set -x EESSI_VERSION_DEFAULT "$EESSI_VERSION"
 
-# ability to predefine elsewhere the default list
-set -x LMOD_SYSTEM_DEFAULT_MODULES (set -q LMOD_SYSTEM_DEFAULT_MODULE; and echo "$LMOD_SYSTEM_DEFAULT_MODULE"; or echo "EESSI/$EESSI_VERSION")
+# ability to predefine elsewhere the default list (with options to append or prepend)
+set LMOD_SYSTEM_DEFAULT_MODULES "EESSI/$EESSI_VERSION"
+if set -q EESSI_SYSTEM_DEFAULT_MODULES_PREPEND
+    set LMOD_SYSTEM_DEFAULT_MODULES "$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
+end
+if set -q EESSI_SYSTEM_DEFAULT_MODULES_APPEND
+    set LMOD_SYSTEM_DEFAULT_MODULES "$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND"
+end
+set -x LMOD_SYSTEM_DEFAULT_MODULES $LMOD_SYSTEM_DEFAULT_MODULES
 
 if test -z "$__Init_EESSI_Default_Modules"
     set -x __Init_EESSI_Default_Modules 1
 
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    set LMOD_EESSI_VERSION (string replace 2023.06 2025.06 -- $EESSI_VERSION)
+
     # If there is a local Lmod, make it forget about the system set MODULEPATH
     set -e __LMOD_REF_COUNT_MODULEPATH
     # and clear out any memory Lmod might have
     set -e _ModuleTable001_
     # Path to top-level module tree
-    set -x MODULEPATH "$EESSI_CVMFS_REPO"/init/modules
-    . "$EESSI_CVMFS_REPO"/versions/"$EESSI_VERSION"/compat/linux/(uname -m)/usr/share/Lmod/init/fish
+    set modulepath "$EESSI_CVMFS_REPO/init/modules"
+    if set -q EESSI_EXTRA_MODULEPATH; and test -n "$EESSI_EXTRA_MODULEPATH"
+        set modulepath "$modulepath:$EESSI_EXTRA_MODULEPATH"
+    end
+    set -x MODULEPATH $modulepath
+    . "$EESSI_CVMFS_REPO"/versions/"$LMOD_EESSI_VERSION"/compat/linux/(uname -m)/usr/share/Lmod/init/fish
 
     module --initial_load --no_redirect restore
 else
diff --git a/init/lmod/ksh b/init/lmod/ksh
index 5be0cacd..e497a75a 100644
--- a/init/lmod/ksh
+++ b/init/lmod/ksh
@@ -6,20 +6,24 @@ EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 # Now that we know our EESSI version let's not forget it
 export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
-## ability to predefine elsewhere the default list
-LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
+# ability to predefine elsewhere the default list (with options to append or prepend)
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:+$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_SYSTEM_DEFAULT_MODULES_APPEND:+:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND}"
 export LMOD_SYSTEM_DEFAULT_MODULES
    
 if [ -z "$__Init_EESSI_Default_Modules" ]; then
     export __Init_EESSI_Default_Modules=1;
 
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    LMOD_EESSI_VERSION=${EESSI_VERSION/2023.06/2025.06}
+
     # If there is a local Lmod, make it forget about the system set MODULEPATH
     unset __LMOD_REF_COUNT_MODULEPATH
     # and clear out any memory Lmod might have
     unset _ModuleTable001_
     # Path to top-level module tree
-    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules"
-    . "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/ksh"
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules${EESSI_EXTRA_MODULEPATH:+:$EESSI_EXTRA_MODULEPATH}"
+    . "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/ksh"
 
     module --initial_load --no_redirect restore
 else
diff --git a/init/lmod/zsh b/init/lmod/zsh
index f8abfbd0..869417b4 100644
--- a/init/lmod/zsh
+++ b/init/lmod/zsh
@@ -6,20 +6,24 @@ EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 # Now that we know our EESSI version let's not forget it
 export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
-# ability to predefine elsewhere the default list
-LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"EESSI/$EESSI_VERSION"}
+# ability to predefine elsewhere the default list (with options to append or prepend)
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:+$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_SYSTEM_DEFAULT_MODULES_APPEND:+:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND}"
 export LMOD_SYSTEM_DEFAULT_MODULES
 
 if [ -z "$__Init_EESSI_Default_Modules" ]; then
     export __Init_EESSI_Default_Modules=1;
 
+    # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
+    # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
+    LMOD_EESSI_VERSION=${EESSI_VERSION/2023.06/2025.06}
+
     # If there is a local Lmod, make it forget about the system set MODULEPATH
     unset __LMOD_REF_COUNT_MODULEPATH
     # and clear out any memory Lmod might have
     unset _ModuleTable001_
     # Path to top-level module tree
-    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules"
-    . "${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/zsh"
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules${EESSI_EXTRA_MODULEPATH:+:$EESSI_EXTRA_MODULEPATH}"
+    . "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/zsh"
 
     module --initial_load --no_redirect restore
 else

From 46c878f291d366636399eff68321f0db1ab4babd Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 29 Jan 2026 15:34:59 +0100
Subject: [PATCH 05/17] Try to fix csg

---
 init/lmod/csh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/init/lmod/csh b/init/lmod/csh
index dddb1fbf..3f911c73 100644
--- a/init/lmod/csh
+++ b/init/lmod/csh
@@ -11,12 +11,12 @@ endif
 setenv EESSI_VERSION_DEFAULT "$EESSI_VERSION"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
-set LMOD_SYSTEM_DEFAULT_MODULES = "EESSI/$EESSI_VERSION"
+set LMOD_SYSTEM_DEFAULT_MODULES="EESSI/$EESSI_VERSION"
 if ( $?EESSI_SYSTEM_DEFAULT_MODULES_PREPEND ) then
-    set LMOD_SYSTEM_DEFAULT_MODULES = "$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
+    set LMOD_SYSTEM_DEFAULT_MODULES="$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
 endif
 if ( $?EESSI_SYSTEM_DEFAULT_MODULES_APPEND ) then
-    set LMOD_SYSTEM_DEFAULT_MODULES = "$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND"
+    set LMOD_SYSTEM_DEFAULT_MODULES="$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND"
 endif
 setenv LMOD_SYSTEM_DEFAULT_MODULES "$LMOD_SYSTEM_DEFAULT_MODULES"
 
@@ -25,16 +25,16 @@ if (! $?__Init_EESSI_Default_Modules ) then
 
     # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
     # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
-    set LMOD_EESSI_VERSION "$EESSI_VERSION:s/2023.06/2025.06/"
+    set LMOD_EESSI_VERSION="$EESSI_VERSION:s/2023.06/2025.06/"
 
     # If there is a local Lmod, make it forget about the system set MODULEPATH
     unsetenv __LMOD_REF_COUNT_MODULEPATH
     # and clear out any memory Lmod might have
     unsetenv _ModuleTable001_
     # Path to top-level module tree
-    set modulepath = "$EESSI_CVMFS_REPO/init/modules"
+    set modulepath="$EESSI_CVMFS_REPO/init/modules"
     if ( $?EESSI_EXTRA_MODULEPATH && "$EESSI_EXTRA_MODULEPATH" != "" ) then
-        set modulepath = "$modulepath:$EESSI_EXTRA_MODULEPATH"
+        set modulepath="$modulepath:$EESSI_EXTRA_MODULEPATH"
     endif
     setenv MODULEPATH "$modulepath"
     source "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"

From 3a6c117924a71ac40721bded76eb5d6e4a42e51e Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 29 Jan 2026 15:59:07 +0100
Subject: [PATCH 06/17] csh has very short maximum length for envvar names,
 stick to <32 chars

---
 .../workflows/scripts/test_init_scripts.sh    | 14 ++++----
 init/lmod/bash                                |  2 +-
 init/lmod/csh                                 | 34 +++++++++++--------
 init/lmod/fish                                |  8 ++---
 init/lmod/ksh                                 |  2 +-
 init/lmod/zsh                                 |  2 +-
 6 files changed, 34 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index 2e3a5a58..a8d8652d 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -75,20 +75,20 @@ for shell in ${SHELLS[@]}; do
     assert_raises 'echo "$EASYBUILD_PATH" | grep -E "$PATTERN"'
     echo "$EASYBUILD_PATH" "$PATTERN"
 
-    # TEST 6 and 7: Check the various options (EESSI_SYSTEM_DEFAULT_MODULES_APPEND, EESSI_SYSTEM_DEFAULT_MODULES_APPEND, EESSI_EXTRA_MODULEPATH) all work
+    # TEST 6 and 7: Check the various options (EESSI_DEFAULT_MODULES_APPEND, EESSI_DEFAULT_MODULES_APPEND, EESSI_EXTRA_MODULEPATH) all work
     if [ "$shell" = "csh" ]; then
-      echo "setenv EESSI_SYSTEM_DEFAULT_MODULES_APPEND append_module" > ~/.cshrc
-      echo "setenv EESSI_SYSTEM_DEFAULT_MODULES_PREPEND prepend_module" >> ~/.cshrc
+      echo "setenv EESSI_DEFAULT_MODULES_APPEND append_module" > ~/.cshrc
+      echo "setenv EESSI_DEFAULT_MODULES_PREPEND prepend_module" >> ~/.cshrc
       echo "setenv EESSI_EXTRA_MODULEPATH .github/workflows/modules" >> ~/.cshrc
       echo "source init/lmod/$shell" >> ~/.cshrc
       TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'echo $LMOD_SYSTEM_DEFAULT_MODULES')
       TEST_MODULEPATH=$($shell -c 'echo $MODULEPATH')
     elif [ "$shell" = "fish" ]; then
-      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'set -x EESSI_SYSTEM_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_SYSTEM_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $LMOD_SYSTEM_DEFAULT_MODULES')
-      TEST_MODULEPATH=$($shell -c 'set -x EESSI_SYSTEM_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_SYSTEM_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
     else
-      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_SYSTEM_DEFAULT_MODULES_APPEND=append_module ; export EESSI_SYSTEM_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
-      TEST_MODULEPATH=$($shell -c 'export EESSI_SYSTEM_DEFAULT_MODULES_APPEND=append_module ; export EESSI_SYSTEM_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
     fi
     # escape the dots in ${EASYBUILD_VERSION}
     LMOD_SYSTEM_DEFAULT_MODULES_PATTERN='^prepend_module:.*:append_module$'
diff --git a/init/lmod/bash b/init/lmod/bash
index 02e7d37a..9cbec4f7 100644
--- a/init/lmod/bash
+++ b/init/lmod/bash
@@ -7,7 +7,7 @@ EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
-LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:+$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_SYSTEM_DEFAULT_MODULES_APPEND:+:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND}"
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
 export LMOD_SYSTEM_DEFAULT_MODULES
 
 if [ -z "$__Init_EESSI_Default_Modules" ]; then
diff --git a/init/lmod/csh b/init/lmod/csh
index 3f911c73..9c8f45d0 100644
--- a/init/lmod/csh
+++ b/init/lmod/csh
@@ -1,40 +1,46 @@
 # Choose an EESSI CVMFS repository
-if (! $?EESSI_CVMFS_REPO) then
+if ( ! $?EESSI_CVMFS_REPO) then
     set EESSI_CVMFS_REPO = "/cvmfs/software.eessi.io"
 endif
 # Choose an EESSI version
 setenv EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
-if (! $?EESSI_VERSION) then
+if ( ! $?EESSI_VERSION) then
     set EESSI_VERSION = "${EESSI_VERSION_DEFAULT}"
 endif
 # Now that we know our EESSI version let's not forget it
-setenv EESSI_VERSION_DEFAULT "$EESSI_VERSION"
+setenv EESSI_VERSION_DEFAULT "${EESSI_VERSION}"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
-set LMOD_SYSTEM_DEFAULT_MODULES="EESSI/$EESSI_VERSION"
-if ( $?EESSI_SYSTEM_DEFAULT_MODULES_PREPEND ) then
-    set LMOD_SYSTEM_DEFAULT_MODULES="$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
+set LMOD_SYSTEM_DEFAULT_MODULES="EESSI/${EESSI_VERSION}"
+if ( $?EESSI_DEFAULT_MODULES_PREPEND ) then
+    set LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND}:${LMOD_SYSTEM_DEFAULT_MODULES}"
 endif
-if ( $?EESSI_SYSTEM_DEFAULT_MODULES_APPEND ) then
-    set LMOD_SYSTEM_DEFAULT_MODULES="$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND"
+if ( $?EESSI_DEFAULT_MODULES_APPEND ) then
+    set LMOD_SYSTEM_DEFAULT_MODULES="${LMOD_SYSTEM_DEFAULT_MODULES}:${EESSI_DEFAULT_MODULES_APPEND}"
 endif
-setenv LMOD_SYSTEM_DEFAULT_MODULES "$LMOD_SYSTEM_DEFAULT_MODULES"
+setenv LMOD_SYSTEM_DEFAULT_MODULES "${LMOD_SYSTEM_DEFAULT_MODULES}"
 
-if (! $?__Init_EESSI_Default_Modules ) then
+if ( ! $?__Init_EESSI_Default_Modules ) then
     setenv __Init_EESSI_Default_Modules 1
 
     # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
     # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
-    set LMOD_EESSI_VERSION="$EESSI_VERSION:s/2023.06/2025.06/"
+    set LMOD_EESSI_VERSION="${EESSI_VERSION}"
+    if ( "${LMOD_EESSI_VERSION}" == "2023.06" ) then
+      set LMOD_EESSI_VERSION="2025.06"
+    endif
 
     # If there is a local Lmod, make it forget about the system set MODULEPATH
     unsetenv __LMOD_REF_COUNT_MODULEPATH
     # and clear out any memory Lmod might have
     unsetenv _ModuleTable001_
     # Path to top-level module tree
-    set modulepath="$EESSI_CVMFS_REPO/init/modules"
-    if ( $?EESSI_EXTRA_MODULEPATH && "$EESSI_EXTRA_MODULEPATH" != "" ) then
-        set modulepath="$modulepath:$EESSI_EXTRA_MODULEPATH"
+    set modulepath="${EESSI_CVMFS_REPO}/init/modules"
+    if ( $?EESSI_EXTRA_MODULEPATH ) then
+      # Now that we know it exists, check IF it is not empty
+      if ( "$EESSI_EXTRA_MODULEPATH" != "" ) then
+        set modulepath="${modulepath}:${EESSI_EXTRA_MODULEPATH}"
+      endif
     endif
     setenv MODULEPATH "$modulepath"
     source "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/`uname -m`/usr/share/Lmod/init/csh"
diff --git a/init/lmod/fish b/init/lmod/fish
index 742511c8..1e0ed23d 100644
--- a/init/lmod/fish
+++ b/init/lmod/fish
@@ -8,11 +8,11 @@ set -x EESSI_VERSION_DEFAULT "$EESSI_VERSION"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
 set LMOD_SYSTEM_DEFAULT_MODULES "EESSI/$EESSI_VERSION"
-if set -q EESSI_SYSTEM_DEFAULT_MODULES_PREPEND
-    set LMOD_SYSTEM_DEFAULT_MODULES "$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
+if set -q EESSI_DEFAULT_MODULES_PREPEND
+    set LMOD_SYSTEM_DEFAULT_MODULES "$EESSI_DEFAULT_MODULES_PREPEND:$LMOD_SYSTEM_DEFAULT_MODULES"
 end
-if set -q EESSI_SYSTEM_DEFAULT_MODULES_APPEND
-    set LMOD_SYSTEM_DEFAULT_MODULES "$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND"
+if set -q EESSI_DEFAULT_MODULES_APPEND
+    set LMOD_SYSTEM_DEFAULT_MODULES "$LMOD_SYSTEM_DEFAULT_MODULES:$EESSI_DEFAULT_MODULES_APPEND"
 end
 set -x LMOD_SYSTEM_DEFAULT_MODULES $LMOD_SYSTEM_DEFAULT_MODULES
 
diff --git a/init/lmod/ksh b/init/lmod/ksh
index e497a75a..d96285f6 100644
--- a/init/lmod/ksh
+++ b/init/lmod/ksh
@@ -7,7 +7,7 @@ EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
-LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:+$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_SYSTEM_DEFAULT_MODULES_APPEND:+:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND}"
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
 export LMOD_SYSTEM_DEFAULT_MODULES
    
 if [ -z "$__Init_EESSI_Default_Modules" ]; then
diff --git a/init/lmod/zsh b/init/lmod/zsh
index 869417b4..7738e3a7 100644
--- a/init/lmod/zsh
+++ b/init/lmod/zsh
@@ -7,7 +7,7 @@ EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
-LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:+$EESSI_SYSTEM_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_SYSTEM_DEFAULT_MODULES_APPEND:+:$EESSI_SYSTEM_DEFAULT_MODULES_APPEND}"
+LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
 export LMOD_SYSTEM_DEFAULT_MODULES
 
 if [ -z "$__Init_EESSI_Default_Modules" ]; then

From 785ae1386498229d4251588e51ea08b363484725 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 29 Jan 2026 16:05:15 +0100
Subject: [PATCH 07/17] Some fancy new runners available!

---
 .github/workflows/scripts/test_init_scripts.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index a8d8652d..5769a64f 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -45,7 +45,7 @@ for shell in ${SHELLS[@]}; do
     else
       MODULE_SECTIONS=($($shell -c "source init/lmod/$shell 2>/dev/null; module ov 2>&1 | grep -e '---'"))
     fi
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/modules/all"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3|intel/icelake)/modules/all"
     assert_raises 'echo "${MODULE_SECTIONS[1]}" | grep -E "$PATTERN"'
     echo "${MODULE_SECTIONS[1]}" "$PATTERN"
 
@@ -70,7 +70,7 @@ for shell in ${SHELLS[@]}; do
       EASYBUILD_PATH=$($shell -c "source init/lmod/$shell 2>/dev/null; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; which eb")
     fi
     # escape the dots in ${EASYBUILD_VERSION}
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3|intel/icelake)/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
     echo "$EASYBUILD_PATH" | grep -E "$PATTERN"
     assert_raises 'echo "$EASYBUILD_PATH" | grep -E "$PATTERN"'
     echo "$EASYBUILD_PATH" "$PATTERN"

From 61db94178daf3f3f0ebadf7eb3df425954441ae7 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 29 Jan 2026 16:10:22 +0100
Subject: [PATCH 08/17] Actually use the CPU override

---
 .github/workflows/tests_init_module.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tests_init_module.yml b/.github/workflows/tests_init_module.yml
index b4d31435..1cf0ac62 100644
--- a/.github/workflows/tests_init_module.yml
+++ b/.github/workflows/tests_init_module.yml
@@ -57,6 +57,7 @@ jobs:
 
       - name: Run tests for available shells
         run: |
+          export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}
           export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
           .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"

From dcce3405b818b9e41a28d8a0ee11eb281b7240d4 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 10:13:21 +0100
Subject: [PATCH 09/17] Use specific commit for assert.sh, also run tests on
 system with Lmod available

---
 .../workflows/scripts/test_init_scripts.sh    |  1 +
 .github/workflows/tests_init_module.yml       | 21 +++++++++++++++----
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index 5769a64f..21b94ea7 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -16,6 +16,7 @@ if [ ! -d assert.sh ]; then
   echo "assert.sh not cloned."
   echo ""
   echo "run \`git clone https://github.com/lehmannro/assert.sh.git\`"
+  echo "(see workflow file that calls this script for how to only clone specific commit if you are worried about security)"
   exit 1
 fi
 . assert.sh/assert.sh
diff --git a/.github/workflows/tests_init_module.yml b/.github/workflows/tests_init_module.yml
index 1cf0ac62..21747562 100644
--- a/.github/workflows/tests_init_module.yml
+++ b/.github/workflows/tests_init_module.yml
@@ -46,8 +46,13 @@ jobs:
             sed -i "s/__EESSI_VERSION_DEFAULT__/${{matrix.EESSI_VERSION}}/g" init/lmod/${shell}
           done
 
-      - name: Clone assert.sh script
-        run: git clone https://github.com/lehmannro/assert.sh.git
+      - name: Clone assert.sh at pinned commit
+        run: |
+          ASSERT_COMMIT_SHA=fe359e341670f1e8e86a3804ca00e5a3ebc30fa4
+          git clone --no-checkout https://github.com/lehmannro/assert.sh.git
+          cd assert.sh
+          git fetch --depth 1 origin $ASSERT_COMMIT_SHA
+          git checkout $ASSERT_COMMIT_SHA
 
       - name: Install missing shells
         run: |
@@ -55,10 +60,18 @@ jobs:
           sudo apt install zsh ksh fish tcsh
           echo "# INIT ZSH" > ~/.zshrc
 
-      - name: Run tests for available shells
+      - name: Run tests for available shells without system Lmod
         run: |
           export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}
           export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
           .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"
-
+      - name: Run tests for available shells with system Lmod
+        run: |
+          # We also want to perform the same test when there is an Lmod version available on the system
+          sudo apt install lmod
+          source /usr/share/lmod/lmod/init/bash
+          export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
+          export EESSI_VERSION=${{matrix.EESSI_VERSION}}
+          export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
+          .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"

From a97140abe64dda99e4dbebc67a4d611872922473 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 10:42:06 +0100
Subject: [PATCH 10/17] Don't clobber an existing .cshrc

---
 .github/workflows/scripts/test_init_scripts.sh | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index 21b94ea7..7d850904 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -29,9 +29,13 @@ for shell in ${SHELLS[@]}; do
   echo  RUNNING TESTS FOR SHELL: $shell
   echo = | awk 'NF += (OFS = $_) + 100'
   if [[ ! " ${TEST_SHELLS[*]} " =~ [[:space:]]${shell}[[:space:]] ]]; then
-    ### EXCEPTION FOR CSH ###
     echo -e "\033[33mWe don't now how to test the shell '$shell', PRs are Welcome.\033[0m" 
   else
+    if [ "$shell" = "csh" ]; then
+      # make sure our .cshrc is empty before we begin as we will clobber it
+      [ -f "~/.cshrc" ] && mv "~/.cshrc" "~/.cshrc_orig"
+    fi
+
     # TEST 1: Source Script and check Module Output
     expected="Module for EESSI/$EESSI_VERSION loaded successfully"
     assert "$shell -c 'source init/lmod/$shell' 2>&1 " "${expected}"
@@ -105,6 +109,12 @@ for shell in ${SHELLS[@]}; do
 
     # End Test Suite
     assert_end "source_eessi_$shell"
+
+    if [ "$shell" = "csh" ]; then
+      # Restore our .cshrc
+      [ -f "~/.cshrc_orig" ] && mv "~/.cshrc_orig" "~/.cshrc"
+    fi
+
   fi
 done
 

From d779b54aa42de413145eebcca452f324419dacd5 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 10:43:35 +0100
Subject: [PATCH 11/17] Add a sanity check to make sure module command works

---
 .github/workflows/tests_init_module.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tests_init_module.yml b/.github/workflows/tests_init_module.yml
index 21747562..d4d1f3b4 100644
--- a/.github/workflows/tests_init_module.yml
+++ b/.github/workflows/tests_init_module.yml
@@ -71,6 +71,7 @@ jobs:
           # We also want to perform the same test when there is an Lmod version available on the system
           sudo apt install lmod
           source /usr/share/lmod/lmod/init/bash
+          module avail
           export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}
           export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}

From d91ded8ca2b2fdc84f17ce4aa1c564599f467343 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 10:48:00 +0100
Subject: [PATCH 12/17] Set explicit MODULEPATH

---
 .github/workflows/tests_init_module.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tests_init_module.yml b/.github/workflows/tests_init_module.yml
index d4d1f3b4..902c31e3 100644
--- a/.github/workflows/tests_init_module.yml
+++ b/.github/workflows/tests_init_module.yml
@@ -71,6 +71,7 @@ jobs:
           # We also want to perform the same test when there is an Lmod version available on the system
           sudo apt install lmod
           source /usr/share/lmod/lmod/init/bash
+          export MODULEPATH=/usr/share/lmod/lmod/modulefiles
           module avail
           export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}

From fc13853360e357a0d379c95df759b71e7ef313a6 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 11:30:12 +0100
Subject: [PATCH 13/17] No quotes on ~

---
 .github/workflows/scripts/test_init_scripts.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index 7d850904..2cfe138e 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -33,7 +33,7 @@ for shell in ${SHELLS[@]}; do
   else
     if [ "$shell" = "csh" ]; then
       # make sure our .cshrc is empty before we begin as we will clobber it
-      [ -f "~/.cshrc" ] && mv "~/.cshrc" "~/.cshrc_orig"
+      [ -f ~/.cshrc ] && mv ~/.cshrc ~/.cshrc_orig
     fi
 
     # TEST 1: Source Script and check Module Output
@@ -112,7 +112,7 @@ for shell in ${SHELLS[@]}; do
 
     if [ "$shell" = "csh" ]; then
       # Restore our .cshrc
-      [ -f "~/.cshrc_orig" ] && mv "~/.cshrc_orig" "~/.cshrc"
+      [ -f ~/.cshrc_orig ] && mv ~/.cshrc_orig ~/.cshrc
     fi
 
   fi

From 7d621f10db92a15eea7c8e551db470b29659038c Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 11:36:28 +0100
Subject: [PATCH 14/17] Make test init script listen to
 EESSI_SOFTWARE_SUBDIR_OVERRIDE

---
 .github/workflows/scripts/test_init_scripts.sh | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index 2cfe138e..e775c632 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -11,6 +11,11 @@ if [ -z ${EXPECTED_EASYBUILD_VERSION} ]; then
   exit 1
 fi
 
+if [ -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
+  echo "\$EESSI_SOFTWARE_SUBDIR_OVERRIDE has to be set (e.g., x86_64/intel/haswell) so we can do well defined string comparison for the architecture."
+  exit 1
+fi
+
 # initialize assert framework
 if [ ! -d assert.sh ]; then
   echo "assert.sh not cloned."
@@ -50,7 +55,7 @@ for shell in ${SHELLS[@]}; do
     else
       MODULE_SECTIONS=($($shell -c "source init/lmod/$shell 2>/dev/null; module ov 2>&1 | grep -e '---'"))
     fi
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3|intel/icelake)/modules/all"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/modules/all"
     assert_raises 'echo "${MODULE_SECTIONS[1]}" | grep -E "$PATTERN"'
     echo "${MODULE_SECTIONS[1]}" "$PATTERN"
 
@@ -75,7 +80,7 @@ for shell in ${SHELLS[@]}; do
       EASYBUILD_PATH=$($shell -c "source init/lmod/$shell 2>/dev/null; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; which eb")
     fi
     # escape the dots in ${EASYBUILD_VERSION}
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3|intel/icelake)/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
     echo "$EASYBUILD_PATH" | grep -E "$PATTERN"
     assert_raises 'echo "$EASYBUILD_PATH" | grep -E "$PATTERN"'
     echo "$EASYBUILD_PATH" "$PATTERN"

From 78e286b84587776ded80e2412768ea1b08ee5339 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 11:38:46 +0100
Subject: [PATCH 15/17] Remove copy/pasted comment

---
 .github/workflows/scripts/test_init_scripts.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/scripts/test_init_scripts.sh b/.github/workflows/scripts/test_init_scripts.sh
index e775c632..509f71f4 100755
--- a/.github/workflows/scripts/test_init_scripts.sh
+++ b/.github/workflows/scripts/test_init_scripts.sh
@@ -100,7 +100,6 @@ for shell in ${SHELLS[@]}; do
       TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
       TEST_MODULEPATH=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
     fi
-    # escape the dots in ${EASYBUILD_VERSION}
     LMOD_SYSTEM_DEFAULT_MODULES_PATTERN='^prepend_module:.*:append_module$'
     echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" AND "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"
     assert_raises 'echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" | grep -E "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"'

From 4d9725682e6177d8f039d9101351c34bdb3fec39 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 16:20:41 +0100
Subject: [PATCH 16/17] Add licence and more extensive documentation

---
 init/lmod/bash | 67 ++++++++++++++++++++++++++++++++++++++++++++------
 init/lmod/csh  | 45 +++++++++++++++++++++++----------
 init/lmod/fish | 29 +++++++++++++++++++---
 init/lmod/ksh  | 25 ++++++++++++++++---
 init/lmod/zsh  | 25 ++++++++++++++++---
 5 files changed, 159 insertions(+), 32 deletions(-)

diff --git a/init/lmod/bash b/init/lmod/bash
index 9cbec4f7..15dbdf8b 100644
--- a/init/lmod/bash
+++ b/init/lmod/bash
@@ -1,12 +1,62 @@
+#!/usr/bin/env bash
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Assumptions:
+# - EESSI accessible under $EESSI_CVMFS_REPO or /cvmfs/software.eessi.io
+#   - expected to be true as this file is also meant to be shipped under that location
+#   - Lmod must the shipped in the repository in the correct location
+#
+# Options:
+# - The script listens to environment variables so that it can be silently configured by a site
+#   - EESSI_CVMFS_REPO: perform the initialisation from a respository other than /cvmfs/software.eessi.io
+#   - EESSI_VERSION: loads a specific EESSI version ignoring the default in the file
+#   - EESSI_DEFAULT_MODULES_PREPEND: environment variable allows you to prepend modules to the defaults (loaded last)
+#   - EESSI_DEFAULT_MODULES_APPEND: environment variable allows you to append modules to the defaults (loaded first)
+#   - EESSI_EXTRA_MODULEPATH: environment variable allows a site to append to MODULEPATH (lower priority than EESSI MODULEPATH)
+#
+# Other options that can be set to influence the end result:
+# - The EESSI module also listens to environment variables so that it can be silently configured by a site
+#   - EESSI_MODULE_FAMILY_NAME: use the value of the environment variable to set an Lmod family for the EESSI module
+#   - EESSI_MODULE_STICKY: make the EESSI module sticky
+#   - EESSI_MODULE_UPDATE_PS1: have the EESSI module update PS1 to give a prompt that is prepended with "{EESSI/...} "
+#
+# Effects:
+# - Should always succeed
+# - Initialises Lmod from specific version of EESSI
+#   - Clobbers any existing Lmod configuration
+#   - Some special environment variables that are internal to Lmod (__LMOD_REF_COUNT_MODULEPATH and
+#     _ModuleTable001_) are used to force a hard reset of an existing Lmod installation. This
+#     approach may be brittle.
+# - Then loads module EESSI/... to initialise EESSI
+#   - use `module show EESSI/...` to see the environment variables set by the EESSI module
+#
+# Reverting the effects:
+# - EESSI initialisation via `module unload EESSI/...`
+# - Lmod initialisation cannot be undone
+
 # Choose an EESSI CVMFS repository
 EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
-# Choose an EESSI version
-EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
+
+# Choose an EESSI version (the default is only used if the EESSI_VERSION environment variable is not provided)
+EESSI_VERSION_DEFAULT="${__EESSI_VERSION_USED_FOR_INIT:-__EESSI_VERSION_DEFAULT__}"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Now that we know our EESSI version let's not forget it
-export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
+# On the first run we want to record the EESSI version used for init as an environment variable so that if a different
+# version of this script is called (e.g, for a a different EESSI version) it retains a memory which EESSI
+# version was actually used in the initialisation. This is useful as __Init_EESSI_Default_Modules used below will
+# be defined on the first call and Lmod initialisation will not happen twice.
+# This sets the value only on first execution, if the variable already exists in the environment
+# the original value is retained.
+export __EESSI_VERSION_USED_FOR_INIT="${__EESSI_VERSION_USED_FOR_INIT:-${EESSI_VERSION}}"
 
-# ability to predefine elsewhere the default list (with options to append or prepend)
+# Ability to predefine elsewhere the default list of modules to load (colon separated):
+# - EESSI_DEFAULT_MODULES_PREPEND environment variable allows you to prepend modules (loaded last)
+# - EESSI_DEFAULT_MODULES_APPEND environment variable allows you to append modules (loaded first)
 LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
 export LMOD_SYSTEM_DEFAULT_MODULES
 
@@ -17,11 +67,14 @@ if [ -z "$__Init_EESSI_Default_Modules" ]; then
     # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
     LMOD_EESSI_VERSION=${EESSI_VERSION/2023.06/2025.06}
 
-    # If there is a local Lmod, make it forget about the system set MODULEPATH
+    # Lmod may have been initialised so we need to clear some internal variables to allow for a full reset
+    # - make it forget about the system set MODULEPATH
     unset __LMOD_REF_COUNT_MODULEPATH
-    # and clear out any memory Lmod might have
+    # - and clear out any memory Lmod might have
     unset _ModuleTable001_
+
     # Path to top-level module tree
+    # - EESSI_EXTRA_MODULEPATH environment variable allows a site to append to MODULEPATH (lower priority than EESSI MODULEPATH)
     export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules${EESSI_EXTRA_MODULEPATH:+:$EESSI_EXTRA_MODULEPATH}"
     . "${EESSI_CVMFS_REPO}/versions/${LMOD_EESSI_VERSION}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash"
     module --initial_load --no_redirect restore
diff --git a/init/lmod/csh b/init/lmod/csh
index 9c8f45d0..a10836d1 100644
--- a/init/lmod/csh
+++ b/init/lmod/csh
@@ -1,22 +1,41 @@
+#!/usr/bin/env csh
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
 if ( ! $?EESSI_CVMFS_REPO) then
     set EESSI_CVMFS_REPO = "/cvmfs/software.eessi.io"
 endif
-# Choose an EESSI version
-setenv EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
-if ( ! $?EESSI_VERSION) then
-    set EESSI_VERSION = "${EESSI_VERSION_DEFAULT}"
+
+# Choose an EESSI version (default is used if EESSI_VERSION is not provided)
+if ( ! $?__EESSI_VERSION_USED_FOR_INIT ) then
+    set EESSI_VERSION_DEFAULT = "__EESSI_VERSION_DEFAULT__"
+else
+    set EESSI_VERSION_DEFAULT = "$__EESSI_VERSION_USED_FOR_INIT"
+endif
+if ( ! $?EESSI_VERSION ) then
+    set EESSI_VERSION = "$EESSI_VERSION_DEFAULT"
+endif
+# On first run, record the EESSI version used for init as an environment variable.
+# We use setenv to ensure it is available to child processes (equivalent to export).
+if ( ! $?__EESSI_VERSION_USED_FOR_INIT ) then
+    setenv __EESSI_VERSION_USED_FOR_INIT "$EESSI_VERSION"
 endif
-# Now that we know our EESSI version let's not forget it
-setenv EESSI_VERSION_DEFAULT "${EESSI_VERSION}"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
-set LMOD_SYSTEM_DEFAULT_MODULES="EESSI/${EESSI_VERSION}"
+set LMOD_SYSTEM_DEFAULT_MODULES = "EESSI/${EESSI_VERSION}"
 if ( $?EESSI_DEFAULT_MODULES_PREPEND ) then
-    set LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND}:${LMOD_SYSTEM_DEFAULT_MODULES}"
+    set LMOD_SYSTEM_DEFAULT_MODULES = "${EESSI_DEFAULT_MODULES_PREPEND}:${LMOD_SYSTEM_DEFAULT_MODULES}"
 endif
 if ( $?EESSI_DEFAULT_MODULES_APPEND ) then
-    set LMOD_SYSTEM_DEFAULT_MODULES="${LMOD_SYSTEM_DEFAULT_MODULES}:${EESSI_DEFAULT_MODULES_APPEND}"
+    set LMOD_SYSTEM_DEFAULT_MODULES = "${LMOD_SYSTEM_DEFAULT_MODULES}:${EESSI_DEFAULT_MODULES_APPEND}"
 endif
 setenv LMOD_SYSTEM_DEFAULT_MODULES "${LMOD_SYSTEM_DEFAULT_MODULES}"
 
@@ -25,9 +44,9 @@ if ( ! $?__Init_EESSI_Default_Modules ) then
 
     # Lmod version in 2023.06 has a problem with newer Lmod caches, so let's stick to more recent Lmod
     # (has no effect except on Lmod itself, and compatible caches are still created/supported by EESSI)
-    set LMOD_EESSI_VERSION="${EESSI_VERSION}"
+    set LMOD_EESSI_VERSION = "${EESSI_VERSION}"
     if ( "${LMOD_EESSI_VERSION}" == "2023.06" ) then
-      set LMOD_EESSI_VERSION="2025.06"
+      set LMOD_EESSI_VERSION = "2025.06"
     endif
 
     # If there is a local Lmod, make it forget about the system set MODULEPATH
@@ -35,11 +54,11 @@ if ( ! $?__Init_EESSI_Default_Modules ) then
     # and clear out any memory Lmod might have
     unsetenv _ModuleTable001_
     # Path to top-level module tree
-    set modulepath="${EESSI_CVMFS_REPO}/init/modules"
+    set modulepath = "${EESSI_CVMFS_REPO}/init/modules"
     if ( $?EESSI_EXTRA_MODULEPATH ) then
       # Now that we know it exists, check IF it is not empty
       if ( "$EESSI_EXTRA_MODULEPATH" != "" ) then
-        set modulepath="${modulepath}:${EESSI_EXTRA_MODULEPATH}"
+        set modulepath = "${modulepath}:${EESSI_EXTRA_MODULEPATH}"
       endif
     endif
     setenv MODULEPATH "$modulepath"
diff --git a/init/lmod/fish b/init/lmod/fish
index 1e0ed23d..881e6262 100644
--- a/init/lmod/fish
+++ b/init/lmod/fish
@@ -1,10 +1,31 @@
+#!/usr/bin/env fish
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
 set EESSI_CVMFS_REPO (set -q EESSI_CVMFS_REPO; and echo "$EESSI_CVMFS_REPO"; or echo "/cvmfs/software.eessi.io")
+
 # Choose an EESSI version
-set EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
-set EESSI_VERSION (set -q EESSI_VERSION; and echo "$EESSI_VERSION"; or echo "$EESSI_VERSION_DEFAULT")
-# Now that we know our EESSI version let's not forget it
-set -x EESSI_VERSION_DEFAULT "$EESSI_VERSION"
+if not set -q __EESSI_VERSION_USED_FOR_INIT
+    set EESSI_VERSION_DEFAULT "__EESSI_VERSION_DEFAULT__"
+else
+    set EESSI_VERSION_DEFAULT "$__EESSI_VERSION_USED_FOR_INIT"
+end
+if not set -q EESSI_VERSION
+    set EESSI_VERSION "$EESSI_VERSION_DEFAULT"
+end
+
+# Record version used for init; -x exports it to the environment
+if not set -q __EESSI_VERSION_USED_FOR_INIT
+    set -x __EESSI_VERSION_USED_FOR_INIT "$EESSI_VERSION"
+end
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
 set LMOD_SYSTEM_DEFAULT_MODULES "EESSI/$EESSI_VERSION"
diff --git a/init/lmod/ksh b/init/lmod/ksh
index d96285f6..37c3caff 100644
--- a/init/lmod/ksh
+++ b/init/lmod/ksh
@@ -1,10 +1,27 @@
+#!/usr/bin/env ksh
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
 EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
-# Choose an EESSI version
-EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
+
+# Choose an EESSI version (the default is only used if the EESSI_VERSION environment variable is not provided)
+EESSI_VERSION_DEFAULT="${__EESSI_VERSION_USED_FOR_INIT:-__EESSI_VERSION_DEFAULT__}"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Now that we know our EESSI version let's not forget it
-export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
+# On the first run we want to record the EESSI version used for init as an environment variable so that if a different
+# version of this script is called (e.g, for a a different EESSI version) it retains a memory which EESSI
+# version was actually used in the initialisation. This is useful as __Init_EESSI_Default_Modules used below will
+# be defined on the first call and Lmod initialisation will not happen twice.
+# This sets the value only on first execution, if the variable already exists in the environment
+# the original value is retained.
+export __EESSI_VERSION_USED_FOR_INIT="${__EESSI_VERSION_USED_FOR_INIT:-${EESSI_VERSION}}"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
 LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"
diff --git a/init/lmod/zsh b/init/lmod/zsh
index 7738e3a7..f7c0fc25 100644
--- a/init/lmod/zsh
+++ b/init/lmod/zsh
@@ -1,10 +1,27 @@
+#!/usr/bin/env zsh
+
+# SPDX-License-Identifier: GPL-2.0-only
+# Copyright (C) 2020-2026 EESSI contributors
+#
+# EESSI - European Environment for Scientific Software Installations
+#
+# This file is a template for initialising EESSI via Lmod for the environment indicated by the shebang.
+#
+# Please refer to the reference bash implementation for full documentation, only minimal comments are included here
+
 # Choose an EESSI CVMFS repository
 EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
-# Choose an EESSI version
-EESSI_VERSION_DEFAULT="__EESSI_VERSION_DEFAULT__"
+
+# Choose an EESSI version (the default is only used if the EESSI_VERSION environment variable is not provided)
+EESSI_VERSION_DEFAULT="${__EESSI_VERSION_USED_FOR_INIT:-__EESSI_VERSION_DEFAULT__}"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
-# Now that we know our EESSI version let's not forget it
-export EESSI_VERSION_DEFAULT="$EESSI_VERSION"
+# On the first run we want to record the EESSI version used for init as an environment variable so that if a different
+# version of this script is called (e.g, for a a different EESSI version) it retains a memory which EESSI
+# version was actually used in the initialisation. This is useful as __Init_EESSI_Default_Modules used below will
+# be defined on the first call and Lmod initialisation will not happen twice.
+# This sets the value only on first execution, if the variable already exists in the environment
+# the original value is retained.
+export __EESSI_VERSION_USED_FOR_INIT="${__EESSI_VERSION_USED_FOR_INIT:-${EESSI_VERSION}}"
 
 # ability to predefine elsewhere the default list (with options to append or prepend)
 LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"

From 30a8f7c56606bf0b9a4659b07eb1af50fb2fcea8 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 30 Jan 2026 16:36:09 +0100
Subject: [PATCH 17/17] Add some additional comments to the bash script

---
 init/lmod/bash | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/init/lmod/bash b/init/lmod/bash
index 15dbdf8b..2110400d 100644
--- a/init/lmod/bash
+++ b/init/lmod/bash
@@ -44,6 +44,8 @@
 EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO:-/cvmfs/software.eessi.io}"
 
 # Choose an EESSI version (the default is only used if the EESSI_VERSION environment variable is not provided)
+# (Note: in the repository which is home to this file a template value __EESSI_VERSION_DEFAULT__ is present in
+#  the line below which is replaced within our deployment pipeline.)
 EESSI_VERSION_DEFAULT="${__EESSI_VERSION_USED_FOR_INIT:-__EESSI_VERSION_DEFAULT__}"
 EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 # On the first run we want to record the EESSI version used for init as an environment variable so that if a different
@@ -54,7 +56,13 @@ EESSI_VERSION="${EESSI_VERSION:-${EESSI_VERSION_DEFAULT}}"
 # the original value is retained.
 export __EESSI_VERSION_USED_FOR_INIT="${__EESSI_VERSION_USED_FOR_INIT:-${EESSI_VERSION}}"
 
-# Ability to predefine elsewhere the default list of modules to load (colon separated):
+# LMOD_SYSTEM_DEFAULT_MODULES are used by Lmod to load a default set of modules in the scenario
+# - where we initialise Lmod (the if part of the clause below)
+# - where we reset Lmod (the else part of the clause below)
+# This means that if we call this script twice we will get the same end result: an Lmod installation
+# with a set of default modules loaded.
+#
+# We also allow the ability to predefine elsewhere the default list of modules to load (colon separated):
 # - EESSI_DEFAULT_MODULES_PREPEND environment variable allows you to prepend modules (loaded last)
 # - EESSI_DEFAULT_MODULES_APPEND environment variable allows you to append modules (loaded first)
 LMOD_SYSTEM_DEFAULT_MODULES="${EESSI_DEFAULT_MODULES_PREPEND:+$EESSI_DEFAULT_MODULES_PREPEND:}EESSI/$EESSI_VERSION${EESSI_DEFAULT_MODULES_APPEND:+:$EESSI_DEFAULT_MODULES_APPEND}"