From 437ae24802c461f2b247d25ac0d28b92bec8df86 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 17 Mar 2023 18:58:28 +0100
Subject: [PATCH 1/4] restore PATHs only after last run of pip installed eb

---
 EESSI-pilot-install-software.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index 09c35fbf4d..cfaf971189 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -177,10 +177,6 @@ else
     eb --install-latest-eb-release &> ${eb_install_out}
     check_exit_code $? "${ok_msg}" "${fail_msg}"
 
-    # restore origin $PATH and $PYTHONPATH values
-    export PATH=${ORIG_PATH}
-    export PYTHONPATH=${ORIG_PYTHONPATH}
-
     eb --search EasyBuild-${REQ_EB_VERSION}.eb | grep EasyBuild-${REQ_EB_VERSION}.eb > /dev/null
     if [[ $? -eq 0 ]]; then
         ok_msg="EasyBuild v${REQ_EB_VERSION} installed, alright!"
@@ -189,6 +185,10 @@ else
         check_exit_code $? "${ok_msg}" "${fail_msg}"
     fi
 
+    # restore origin $PATH and $PYTHONPATH values
+    export PATH=${ORIG_PATH}
+    export PYTHONPATH=${ORIG_PYTHONPATH}
+
     module avail easybuild/${REQ_EB_VERSION} &> ${ml_av_easybuild_out}
     if [[ $? -eq 0 ]]; then
         echo_green ">> EasyBuild module installed!"

From c9bf99c8e31a914fbc3f9708cfa7fa998dac4086 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 17 Mar 2023 12:42:05 +0100
Subject: [PATCH 2/4] attempt to fix issue #225

---
 create_tarball.sh | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 56ac8ab7ad..08dc4f4d7e 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -38,6 +38,7 @@ cd ${overlay_upper_dir}/versions/
 echo ">> Collecting list of files/directories to include in tarball via ${PWD}..."
 
 files_list=${tmpdir}/files.list.txt
+module_files_list=${tmpdir}/module_files.list.txt
 
 if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/.lmod ]; then
     # include Lmod cache and configuration file (lmodrc.lua),
@@ -49,12 +50,26 @@ if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules ]; then
     find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type f | grep -v '/\.wh\.' >> ${files_list}
     # module symlinks
     find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type l | grep -v '/\.wh\.' >> ${files_list}
+    # module files and symlinks
+    find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type f -o -type l \
+        | grep -v '/\.wh\.' | sed -e 's/.lua$//' | awk -F'/' '{printf "%s/%s\n", $(NF-1), $NF}' | sort | uniq \
+        >> ${module_files_list}
 fi
 if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software ]; then
     # installation directories
-    ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/*/* | grep -v '/\.wh\.' >> ${files_list}
+    # ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/*/* | grep -v '/\.wh\.' >> ${files_list}
+    for package_version in $(cat ${module_files_list}); do
+        echo "handling ${package_version}"
+        ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/${package_version} \
+            | grep -v '/\.wh\.' >> ${files_list}
+    done
 fi
 
+echo "wrote file list to ${files_list}"
+cat ${files_list}
+echo "wrote module file list to ${module_files_list}"
+cat ${module_files_list}
+
 topdir=${cvmfs_repo}/versions/
 
 echo ">> Creating tarball ${target_tgz} from ${topdir}..."

From 3b75f790edd4770b687a75fdf6fae06c4bddb728 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 17 Mar 2023 19:17:02 +0100
Subject: [PATCH 3/4] add comments, small improvements

---
 create_tarball.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 08dc4f4d7e..9381407d10 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -51,13 +51,12 @@ if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules ]; then
     # module symlinks
     find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type l | grep -v '/\.wh\.' >> ${files_list}
     # module files and symlinks
-    find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type f -o -type l \
+    find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules/all -type f -o -type l \
         | grep -v '/\.wh\.' | sed -e 's/.lua$//' | awk -F'/' '{printf "%s/%s\n", $(NF-1), $NF}' | sort | uniq \
         >> ${module_files_list}
 fi
 if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software ]; then
-    # installation directories
-    # ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/*/* | grep -v '/\.wh\.' >> ${files_list}
+    # installation directories but only those for which module files were created
     for package_version in $(cat ${module_files_list}); do
         echo "handling ${package_version}"
         ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/${package_version} \
@@ -65,6 +64,7 @@ if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software ]; then
     done
 fi
 
+# add a bit debug output
 echo "wrote file list to ${files_list}"
 cat ${files_list}
 echo "wrote module file list to ${module_files_list}"

From 610879e5415e01d71e3fea94f4d47e1262a83630 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 17 Mar 2023 22:13:21 +0100
Subject: [PATCH 4/4] improve handling of potentially non existing list files

---
 create_tarball.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 9381407d10..fd04a195cb 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -55,7 +55,7 @@ if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules ]; then
         | grep -v '/\.wh\.' | sed -e 's/.lua$//' | awk -F'/' '{printf "%s/%s\n", $(NF-1), $NF}' | sort | uniq \
         >> ${module_files_list}
 fi
-if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software ]; then
+if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software -a -r ${module_files_list} ]; then
     # installation directories but only those for which module files were created
     for package_version in $(cat ${module_files_list}); do
         echo "handling ${package_version}"
@@ -66,9 +66,9 @@ fi
 
 # add a bit debug output
 echo "wrote file list to ${files_list}"
-cat ${files_list}
+[ -r ${files_list} ] && cat ${files_list}
 echo "wrote module file list to ${module_files_list}"
-cat ${module_files_list}
+[ -r ${module_files_list} ] && cat ${module_files_list}
 
 topdir=${cvmfs_repo}/versions/