From 2518eca26ad7005775a5af0f6d3f033a4220aefa Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 4 Jul 2023 17:08:12 +0200
Subject: [PATCH 1/3] collections in overlays implemented

---
 Pmodules/modulecmd.bash.in | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index aca12cd..c31c661 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2909,8 +2909,11 @@ search_collection(){
 		_path=$(std::get_abspath "${_collection}")
 		return
 	fi
-	local _dirs2search=( "${UsrCollectionsDir}" "${SysCollectionsDir}" )
+	local _dirs2search=( "${UsrCollectionsDir}" )
 	local _dir
+	for _dir in "${UsedOverlays[@]}"; do
+		_dirs2search+=( "${_dir}" )
+	done
 	for _dir in "${_dirs2search[@]}"; do
 		if [[ -r "${_dir}/${_collection}" ]]; then
 			_path="${_dir}/${_collection}"
@@ -3001,7 +3004,7 @@ subcommand_savelist() {
 
 	get_collections() {
 		local -n _result="$1"
-		local -- _dir="$2"
+		local -n gc_dirs="$2"
 		shift 2
 		_result=()
 		local _pattern
@@ -3009,16 +3012,16 @@ subcommand_savelist() {
 		for _pattern in "$@"; do
 			while read _coll; do
 				_result+=( "${_coll}" )
-			done < <(find "${_dir}" -type f -ipath "*/${_pattern}" -printf "%P\n")
+			done < <(find "${gc_dirs[@]}" -type f -ipath "*/${_pattern}" -printf "%P\n")
 		done
 	}
 
 	print_collections() {
 		local -r prt_header="$1"
-		local -r prt_dir="$2"
+		local -n prt_dirs="$2"
 		shift 2
 		local -a prt_collections=()
-		get_collections prt_collections "${prt_dir}" "$@"
+		get_collections prt_collections prt_dirs "$@"
 
 		(( ${#prt_collections[@]} == 0 )) && return 0
 
@@ -3048,9 +3051,14 @@ subcommand_savelist() {
 	if (( ${#args[@]} == 0 )); then
 		args[0]='*'
 	fi
-	local -a collections=()
-	print_collections "User collections:"     "${UsrCollectionsDir}" "${args[@]}"
-	print_collections "\nSystem collections:" "${SysCollectionsDir}" "${args[@]}"
+	local -a _dirs=( "${UsrCollectionsDir[@]}" )
+	print_collections "User collections:"     _dirs "${args[@]}"
+	_dirs=()
+	local _ol
+	for _ol in "${UsedOverlays[@]}"; do
+		_dirs+=( "${OverlayInfo[${_ol}:inst_root]}/collections" )
+	done
+	print_collections "\nSystem collections:" _dirs "${args[@]}"
 }
 
 ##############################################################################
@@ -3092,7 +3100,7 @@ subcommand_saverm() {
 		search_collection collection "${collection}"
 		test -e "${collection}" || \
 			die_collection_doesnt_exist "${collection}"
-		rm -f "${collection}" 2>/dev/null || \
+		${rm} -f "${collection}" 2>/dev/null || \
 			die_removing_collection_failed "${collection}"
 	done
 }

From 14941fc8c39b1102889e1866ef4278f80e9ac049 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 4 Jul 2023 17:30:04 +0200
Subject: [PATCH 2/3] don't save Pmodules module in collection

---
 Pmodules/modulecmd.bash.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index c31c661..81f5fc7 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2879,6 +2879,7 @@ subcommand_save() {
 	IFS=':' read -a modules <<< "${LOADEDMODULES}"
 	local -- m=''
 	for m in "${modules[@]}"; do
+		[[ $m == Pmodules/* ]] && continue
 		s+="module load $m;\n"
 	done
 

From 460e6624f993326125db94847f6c9aff36ecab1b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 4 Jul 2023 17:31:24 +0200
Subject: [PATCH 3/3] modulecmd.bash.in: bugfix in search_collection

---
 Pmodules/modulecmd.bash.in | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 81f5fc7..06d213e 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2911,9 +2911,9 @@ search_collection(){
 		return
 	fi
 	local _dirs2search=( "${UsrCollectionsDir}" )
-	local _dir
-	for _dir in "${UsedOverlays[@]}"; do
-		_dirs2search+=( "${_dir}" )
+	local _ol
+	for _ol in "${UsedOverlays[@]}"; do
+		_dirs2search+=( "${OverlayInfo[${_ol}:inst_root]}/collections" )
 	done
 	for _dir in "${_dirs2search[@]}"; do
 		if [[ -r "${_dir}/${_collection}" ]]; then