From f5aaff58421d21af353eeff0b3b9d26c9a1b3f41 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 22 Apr 2021 09:35:12 +0200
Subject: [PATCH 01/94] libmodules.tcl: some unconditional debug output removed

---
 Pmodules/libmodules.tcl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Pmodules/libmodules.tcl b/Pmodules/libmodules.tcl
index 3a830d3..12690a9 100644
--- a/Pmodules/libmodules.tcl
+++ b/Pmodules/libmodules.tcl
@@ -21,7 +21,6 @@ if {[info exists env(PMODULES_DEBUG)] && $env(PMODULES_DEBUG)} {
 	proc debug {msg} {}
 }
 
-puts stderr "loading libmodules"
 debug "loading libmodules"
 
 proc _pmodules_parse_pmodules_env { } {

From bfc754efa1830ee687c25f08a9591c3146c59dd2 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 22 Apr 2021 09:37:56 +0200
Subject: [PATCH 02/94] tcllib added, version set to 1.1.1

---
 build                | 8 ++++----
 config/versions.conf | 3 ++-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/build b/build
index 3495bcb..5a3d960 100755
--- a/build
+++ b/build
@@ -356,12 +356,12 @@ pmodules::compile() {
 		build bash
 	fi
 
-	if [[ ! -f "${PMODULES_HOME}/sbin/find" ]] || [[ ${opt_force} == 'yes' ]]; then
-		build findutils
+	if [[ ! -e "${PMODULES_HOME}/${UTILBIN_DIR}/tclsh" ]] || [[ ${opt_force} == 'yes' ]]; then
+		build Tcl
 	fi
 
-	if [[ ! -e "${PMODULES_HOME}/sbin/tclsh" ]] || [[ ${opt_force} == 'yes' ]]; then
-		build Tcl
+	if [[ ! -e "${PMODULES_HOME}/lib/tcllib1.20" ]] || [[ ${opt_force} == 'yes' ]]; then
+		build tcllib
 	fi
 
 	if [[ ! -e "${PMODULES_HOME}/libexec/modulecmd.bin" ]] || [[ ${opt_force} == 'yes' ]]; then
diff --git a/config/versions.conf b/config/versions.conf
index 37deb08..f106cbc 100644
--- a/config/versions.conf
+++ b/config/versions.conf
@@ -4,5 +4,6 @@ findutils	4.7.0
 getopt		1.1.6
 gettext		0.21
 modules		3.2.10.1
-Pmodules	1.1.0
+Pmodules	1.1.1
 Tcl		8.6.10
+tcllib		1.20

From a53bf42479c8c4d39664785838f7d72f590bb565 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 22 Apr 2021 09:41:06 +0200
Subject: [PATCH 03/94] modulecmd: use IFS saved as the beginning for restoring

---
 Pmodules/modulecmd.bash.in | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index cd7afdc..ed2c61d 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -476,10 +476,9 @@ subcommand_load() {
 		         "No module specified"
 	fi
 
-        local saved_IFS="${IFS}";
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${saved_IFS}
+	IFS=${__IFS}
 
         local m=''
 	for m in "${args[@]}"; do
@@ -900,10 +899,9 @@ get_available_modules() {
 #               if no modulefile could be found
 #       
 find_module() {
-	local saved_IFS=${IFS}; 
 	IFS=':'
 	local -a dirs=($3)
-	IFS=${saved_IFS}
+	IFS=${__IFS}
 	local -r module="$4"
 
         for dir in "${dirs[@]}"; do
@@ -1519,10 +1517,9 @@ unuse directory|group|release...
 
 subcommand_unuse() {
         local -r subcommand='unuse'
-        local saved_IFS=${IFS};
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${saved_IFS}
+	IFS=${__IFS}
 
         unuse() {
                 unuse_overlay() {
@@ -2275,10 +2272,9 @@ subcommand_search() {
 		shift
 	done
 	if [[ -z "${src_prefix}" ]]; then
-		local saved_IFS="${IFS}";
 		IFS=':'
 		local -a src_prefix=(${PMODULES_OVERLAYS})
-		IFS=${saved_IFS}
+		IFS=${__IFS}
 	fi
 
 	if [[ "${opt_use_releases}" == ":" ]]; then

From a415cdc1367e3d4ac6731ca7a3c40e2a35fca5b4 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 22 Apr 2021 09:44:03 +0200
Subject: [PATCH 04/94] modulecmd: follow links in find cmd

---
 Pmodules/modulecmd.bash.in | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index ed2c61d..bc25b65 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -870,7 +870,7 @@ get_available_modules() {
 			                mods+=( "${mod}" ${release} "${dir}/${mod}" )
                                         dict[${mod}]=1
 				fi
-		        done < <(${find} ${entries} \
+		        done < <(${find} -L ${entries} \
 					 \( -type f -o -type l \) \
 					 -not -name ".*" \
                                          -ipath "${module}*")
@@ -913,7 +913,7 @@ find_module() {
                         # a version number has been specified. But we still might
                         # have the same module/version with different use flags.
                         # Releases we ignore in this case.
-                        modules=$(${find} "${dir}" -type f -not -name ".*" \
+                        modules=$(${find} -L "${dir}" -type f -not -name ".*" \
                                        -ipath "${dir}/${module}*" \
                                           | cut -b${col}-)
                         for mod in "${modules[@]}"; do
@@ -936,7 +936,7 @@ find_module() {
                         # difficult. We have to load the newest version taking
                         # the used releases and flags into account.
                         (( col += ${#module} + 1 ))
-                        modules=( $(${find} "${dir}" -type f -not -name ".*" \
+                        modules=( $(${find} -L "${dir}" -type f -not -name ".*" \
                                          -ipath "${dir}/${module}/*"  \
                                             | cut -b${col}- \
                                             | sort -rV ) )
@@ -1182,7 +1182,7 @@ compute_group_depth () {
         local group=${dir%/*}
         local group=${group##*/}
         [[ -n "${GroupDepths[${group}]}" ]] && return 0
-	local -i depth=$(${find} "${dir}" -depth \( -type f -o -type l \) \
+	local -i depth=$(${find} -L "${dir}" -depth \( -type f -o -type l \) \
                           -printf "%d" -quit 2>/dev/null)
 	(( depth-=2 ))
 	# if a group doesn't contain a modulefile, depth is negativ

From 5661f69169b24768dae9968eac2ac58b12df9789 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 22 Apr 2021 09:45:39 +0200
Subject: [PATCH 05/94] modulecmd: get_available_modules(): bugfix

- it was expected that all modules are in an overlay. This is wrong. a
  user may add a modulefile directory with module use DIR.
---
 Pmodules/modulecmd.bash.in | 40 ++++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 17 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index bc25b65..70b2079 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -846,26 +846,32 @@ get_available_modules() {
 					"${dir}" \
 					"${mod}"
 				[[ :${releases}: =~ ${release} ]] || continue
-				#
-				# add to list of available modules, if
-				# - first time found by name only
-				# - in same overlay as first found
-				# - new version and not hidden by overlay
-				local name="${mod%/*}"
 				local add='no'
-				if [[ -z "${modulenames[${name}]}" ]]; then
-					if [[ "${Overlays[$overlay]}" == 'h' ]]; then
-						modulenames[${name}]="${overlay}"
-					else
-						modulenames[${name}]='0'
+				if [[ -n "${overlay}" ]]; then
+					# module is in an overlay
+					#
+					# add to list of available modules, if
+					# - first time found by name only
+					# - in same overlay as first found
+					# - new version and not hidden by overlay
+					local name="${mod%/*}"
+					if [[ -z "${modulenames[${name}]}" ]]; then
+						if [[ "${Overlays[$overlay]}" == 'h' ]]; then
+							modulenames[${name}]="${overlay}"
+						else
+							modulenames[${name}]='0'
+						fi
+						add='yes'
+					elif [[ "${modulenames[${name}]}" == "${overlay}" ]]; then
+						add='yes'
+					elif [[ "${modulenames[${name}]}" == '0'  ]] \
+						     && [[ -z ${dict[${mod}]} ]]; then
+						add='yes'
 					fi
+				else
+					# module is NOT in an overlay
 					add='yes'
-				elif [[ "${modulenames[${name}]}" == "${overlay}" ]]; then
-					add='yes'
-				elif [[ "${modulenames[${name}]}" == '0'  ]] \
-					     && [[ -z ${dict[${mod}]} ]]; then
-					add='yes'
-                                fi
+				fi
 				if [[ "${add}" == 'yes' ]]; then
 			                mods+=( "${mod}" ${release} "${dir}/${mod}" )
                                         dict[${mod}]=1

From b62841239c67b28fec49ee53977fc5e46037dbdc Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 22 Apr 2021 09:48:27 +0200
Subject: [PATCH 06/94] modulecmd: bugfix in use/unuse overlay

- Since Pmodules itself can be loaded as module, it must be possible
  to add/remove overlays if no modules are loaded or only a Pmodules
  module.
---
 Pmodules/modulecmd.bash.in | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 70b2079..020f225 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1323,7 +1323,7 @@ subcommand_use() {
 
 	use () {
                 use_overlay() {
-			if [[ -n "${_LMFILES_}" ]]; then
+			if [[ -n "${_LMFILES_}" ]] && [[ ${LOADEDMODULES} != Pmodules/* ]]; then
 				std::die 3 "%s %s: %s -- %s" \
 					 "${CMD}" "${subcommand}" \
 					 "overlays can be added as long as no modules are loaded!" \
@@ -1529,12 +1529,11 @@ subcommand_unuse() {
 
         unuse() {
                 unuse_overlay() {
-		        [[ -n "${_LMFILES_}" ]] && \
-				std::die 3 "%s %s: %s -- %s" \
+			if [[ -n "${_LMFILES_}" ]] && [[ ${LOADEDMODULES} != Pmodules/* ]]; then				std::die 3 "%s %s: %s -- %s" \
 					 "${CMD}" "${subcommand}" \
-					 "overlays can be removed as long as modules are loaded!" \
+					 "overlays can NOT be removed as long as modules are loaded!" \
 					 "${overlay}"
-
+			fi
 			overlay=${overlay%:*}  # ignore any modifier
 			overlay=${overlay%/} # remove trailing '/' if there is one
                         [[ -d "${overlay}" ]] || \

From 7ddd9b0ed78f71a8ee0d1c115f44f765133d0f4e Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 22 Apr 2021 09:51:19 +0200
Subject: [PATCH 07/94] modulecmd: bugfix in initializing env. variable needed
 for overlays.

- if we switch from a Pmodules version without overlay support to a
  Pmodule version with, some environment variables must be initialzed.
---
 Pmodules/modulecmd.bash.in | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 020f225..297a87b 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2608,8 +2608,30 @@ if [[ -z "${Subcommands[${subcommand}]}" ]]; then
 	std::die 1 "${CMD}: unknown sub-command -- ${subcommand}"
 fi
 
+_init_overlay_map() {
+	local overlay
+	for overlay in "${!Overlays[@]}"; do
+		local group
+		for group in ${UsedGroups//:/ }; do
+			local dir="${overlay}/${group}/${PMODULES_MODULEFILES_DIR}"
+			if [[ -d "${dir}" ]]; then
+				MapDirsToOverlays[${dir}]=${overlay}
+			fi
+		done
+	done
+}
+
 if [[ -n ${PMODULES_ENV} ]]; then
 	eval "$("${base64}" -d <<< "${PMODULES_ENV}" 2>/dev/null)"
+	# if we load a Pmodules version with overlay support,
+	# PMODULES_OVERLAYS might not be set. Since libmodules.tcl
+	# reads PMODULES_ENV we have to save the environment.
+	if [[ -z "${PMODULES_OVERLAYS}" ]]; then
+		declare -g PMODULES_OVERLAYS="${PMODULES_ROOT}"
+		declare -Ag Overlays=([${PMODULES_ROOT}]="0")
+		_init_overlay_map
+		save_env
+	fi
 else
 	pmodules_init
 fi

From 15fb22e4c8e5e3907d4c2f98cb009caaead89fc4 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:02:53 +0200
Subject: [PATCH 08/94] build script: commented out lines to build coreutils
 removed

---
 build | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/build b/build
index 5a3d960..cdd6ac4 100755
--- a/build
+++ b/build
@@ -338,10 +338,6 @@ pmodules::compile() {
 	echo "  root of Pmodules environment: ${prefix}"
 	echo "  Pmodule prefix:               ${PMODULES_HOME}"
 
-	#if [[ ! -f "${PMODULES_HOME}/${UTILBIN_DIR}/base64" ]] || [[ ${opt_force} == 'yes' ]]; then
-	#	build coreutils
-	#fi
-
 	if [[ "${OS}" == 'Darwin' ]]; then
 		if [[ ! -f "${PMODULES_HOME}/${UTILBIN_DIR}/getopt" ]] || [[ ${opt_force} == 'yes' ]]; then
 			build getopt

From 0b8059efac4e6fcc1cfa3cf469e3be8e754aa148 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:05:09 +0200
Subject: [PATCH 09/94] libmodules.tcl: refactor some variable names, review

- name of dictionary of overlay renamed from Overlays to OverlayDict
- get list of overlays from PMODULES_ENV (OverlayList),
  PMODULES_OVERLAYS has been removed
---
 Pmodules/libmodules.tcl | 52 ++++++++++++++++++++++++++---------------
 1 file changed, 33 insertions(+), 19 deletions(-)

diff --git a/Pmodules/libmodules.tcl b/Pmodules/libmodules.tcl
index 12690a9..d886a90 100644
--- a/Pmodules/libmodules.tcl
+++ b/Pmodules/libmodules.tcl
@@ -3,7 +3,7 @@
 # switch/swap
 # unload modules if parent removed
 #
-package require base64
+
 
 if {[info exists env(PMODULES_DEBUG)] && $env(PMODULES_DEBUG)} {
 	proc debug {msg} {
@@ -23,14 +23,27 @@ if {[info exists env(PMODULES_DEBUG)] && $env(PMODULES_DEBUG)} {
 
 debug "loading libmodules"
 
+package require base64
+
+set ::MODULEFILES_DIR "modulefiles"
+
 proc _pmodules_parse_pmodules_env { } {
+        debug "enter"
 	foreach line [split [base64::decode $::env(PMODULES_ENV)] "\n"] {
-		if { ![regexp -- {.* -[aA] (.*)=\((.*)\)} $line -> name value] } {
+		if { ![regexp -- {.* -[aAx]* (.*)=\((.*)\)} $line -> name value] } {
 			continue
 		}
 		switch $name {
-			Overlays {
-				array set ::Overlays [regsub -all  {[]=[]} $value " "]
+			OverlayDict {
+				array set ::OverlayDict [regsub -all  {[]=[]} $value " "]
+			}
+		        OverlayList {
+			        array set tmp [regsub -all  {[]=[]} $value " "]
+  			        set ::OverlayList {}
+				set l [lsort [array names tmp]]
+			        foreach k $l {
+				        lappend ::OverlayList $tmp($k)
+			        }
 			}
 		}
 	}
@@ -55,20 +68,23 @@ proc module-addgroup { group } {
         debug "mode=[module-info mode]"
 	if { [module-info mode load] } {
 		array set overlayed_groups {}
-		foreach overlay [lreverse_n $::PmodulesOverlays 1] {
+		foreach overlay [lreverse_n $::OverlayList 1] {
 			debug "overlay=$overlay"
 			if {![info exists overlayed_groups($group)]}	{
+				debug "group=$group"
+				debug "::variant=$::variant"
 				set dir [file join \
 					     $overlay \
 					     $group \
-					     $::PmodulesModulfilesDir \
+					     $::MODULEFILES_DIR \
 					     {*}$::variant]
 				if { [file isdirectory $dir] } {
+					debug "prepend $dir to MODULEPATH "
 					prepend-path MODULEPATH $dir
 				}
 			}
 			# don't add if overlayed
-			if { [string compare $::Overlays($overlay) "g"] == 0 } {
+			if { [string compare $::OverlayDict($overlay) "g"] == 0 } {
 				# get groups in this overlay
 				set dirs [glob -directory $overlay -type d {[A-Z]*}]
 				foreach dir $dirs {
@@ -76,9 +92,8 @@ proc module-addgroup { group } {
 				}
 			}
                 }
+		debug "end foreach"
 		prepend-path UsedGroups $group
-		debug "mode=load: new MODULEPATH=$env(MODULEPATH)"
-		debug "mode=load: new UsedGroups=$env(UsedGroups)"
 	} elseif { [module-info mode remove] } {
 		set GROUP [string toupper $group]
 		debug "mode=remove: hierarchical group '${GROUP}'"
@@ -99,11 +114,11 @@ proc module-addgroup { group } {
 			debug "mode=remove: no orphan modules to unload"
 		}
 		debug "mode=remove: $env(MODULEPATH)"
-                foreach overlay $::PmodulesOverlays {
+                foreach overlay $::OverlayList {
                         set dir [file join \
                                      $overlay \
                                      $group \
-                                     $::PmodulesModulfilesDir \
+                                     $::MODULEFILES_DIR \
                                      {*}$::variant]
                         remove-path MODULEPATH $dir
                 }
@@ -136,7 +151,6 @@ proc lreverse_n { list n } {
         set res
 }
 
-debug "test"
 #
 # set standard environment variables
 #
@@ -291,15 +305,15 @@ proc ModulesHelp { } {
 # intialize global vars
 # Modulefile is something like
 #
-#   ${PMODULES_ROOT}/group/${PMODULES_MODULEFILES_DIR}/name/version
+#   ${PMODULES_ROOT}/group/modulefiles/name/version
 # or
-#   ${PMODULES_ROOT}/group/${PMODULES_MODULEFILES_DIR}/X1/Y1/name/version
+#   ${PMODULES_ROOT}/group/modulefiles/X1/Y1/name/version
 # or
-#   ${PMODULES_ROOT}/group/${PMODULES_MODULEFILES_DIR}/X1/Y1//X2/Y2/name/version
+#   ${PMODULES_ROOT}/group/modulefiles/X1/Y1//X2/Y2/name/version
 #
 proc _find_overlay { modulefile_components } {
-        debug "_is_in_overlay"
-        foreach overlay $::PmodulesOverlays  {
+        debug "_find_overlay()"
+        foreach overlay $::OverlayList  {
                 debug "$overlay"
                 if { [string range $overlay end end] == "/" } {
                         set overlay [string range $overlay 0 end-1]
@@ -314,6 +328,7 @@ proc _find_overlay { modulefile_components } {
                         return $overlay_components
                 }
         }
+        debug "not found"
         return {}
 }
 
@@ -332,8 +347,6 @@ proc _pmodules_init_global_vars { } {
 	global	variant
 	global	PREFIX		# prefix of package
 
-	set	::PmodulesOverlays	[split $::env(PMODULES_OVERLAYS) ':']
-        set	::PmodulesModulfilesDir	$::env(PMODULES_MODULEFILES_DIR)
         set	modulefile_components	[file split $::ModulesCurrentModulefile]
 
         set     overlay_components [_find_overlay ${modulefile_components}]
@@ -360,6 +373,7 @@ proc _pmodules_init_global_vars { } {
 	debug "group of module $name: $group"
 }
 
+
 if { [info exists ::whatis] } {
 	module-whatis	"$whatis"
 }

From ef1d10aa3d6506a0945816013c38b640624a6234 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:17:52 +0200
Subject: [PATCH 10/94] modulecmd.bash.in: unset IFS instead of restoring a
 default

---
 Pmodules/modulecmd.bash.in | 24 ++++++++++--------------
 1 file changed, 10 insertions(+), 14 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 297a87b..63d8f71 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -47,9 +47,8 @@ fi
 
 declare verbosity_lvl=${PMODULES_VERBOSITY:-'verbose'}
 
-# we use newline as internal field separator
-IFS=$' \t\n'
-declare -r __IFS=${IFS}	# used to restore IFS
+# use default IFS
+unset IFS
 
 shopt -s nullglob
 
@@ -478,7 +477,7 @@ subcommand_load() {
 
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${__IFS}
+	unset IFS
 
         local m=''
 	for m in "${args[@]}"; do
@@ -494,7 +493,7 @@ subcommand_load() {
 
 			IFS=':'
 			local -a toks=($m)
-			IFS=${__IFS}
+			unset IFS
 			local group=''
 			local release=''
 			if is_group "${toks[0]}"; then
@@ -1141,11 +1140,9 @@ subcommand_avail() {
 	if (( ${#pattern[@]} == 0 )); then
 	        pattern+=( '' )
 	fi
-        local -a modulepath
 	IFS=':'
-	modulepath=(${MODULEPATH})
-	IFS=${__IFS}
-        
+	local -a modulepath=(${MODULEPATH})
+	unset IFS
         local overlay=''
         local group=''
         local -A modulepath_of_group
@@ -1249,7 +1246,7 @@ subcommand_use() {
         local -r subcommand='use'
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${__IFS}
+	unset IFS
         local add2path_func='std::append_path'
 
         group_is_used() {
@@ -1525,8 +1522,7 @@ subcommand_unuse() {
         local -r subcommand='unuse'
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${__IFS}
-
+	unset IFS
         unuse() {
                 unuse_overlay() {
 			if [[ -n "${_LMFILES_}" ]] && [[ ${LOADEDMODULES} != Pmodules/* ]]; then				std::die 3 "%s %s: %s -- %s" \
@@ -2186,12 +2182,12 @@ subcommand_search() {
 					# get dependencies encoded in directory name
 					local deps=()
 					local -i j
-					IFS='/'
+					IFS='/'   # note: IFS is used to concat in the for loop!
 					local toks=( ${modulefile} )
 					for ((j = -depth-2; j < -2; j += 2)); do
 						deps+=( "${toks[*]: $j:2}" );
 					done
-					IFS=${__IFS}
+					unset IFS
 				fi
 				
 				echo ${name} ${release} ${group} ${modulefile} \

From 6674333728eeb854abff82dc59e438c3300a48dc Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:23:31 +0200
Subject: [PATCH 11/94] modulecmd.bash.in: call logger via variable with full
 path

---
 Pmodules/modulecmd.bash.in | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 63d8f71..9592945 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -22,6 +22,10 @@ declare -r sort
 awk=$(PATH=/bin:/usr/bin /usr/bin/which awk)
 declare -r awk
 rm=$(PATH=/bin:/usr/bin /usr/bin/which rm)
+declare -r rm
+logger=$(PATH=/bin:/usr/bin /usr/bin/which logger)
+declare -r logger
+
 if [[ $(uname -s) == 'Darwin' ]]; then
 	declare -r getopt="${libexecdir}/getopt"
 	declare -r find="${libexecdir}/find"
@@ -624,7 +628,7 @@ subcommand_load() {
                            [[ ${release} != stable ]]; then
 		        std::info "%s" "${msg}"
 		fi
-		logger "${msg}"
+		${logger} -t Pmodules "${msg}"
 	done
 	# fix LOADEDMODULES
 	LOADEDMODULES="${_LMFILES_}"

From 3eb18304436cfe1067f6e3d5a86f351b8c19cf6f Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:26:42 +0200
Subject: [PATCH 12/94] modulecmd.bash.in: save_env(): no need to export
 UsedGroups

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

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 9592945..1752c24 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -112,6 +112,7 @@ save_env() {
 	local s=$(typeset -p ${vars[@]})
 	declare -g PMODULES_ENV=$( "${base64}" --wrap=0 <<< "$s" )
 	export_env 'PMODULES_ENV'
+	unset UsedGroups
 }
 
 trap 'save_env ' EXIT

From a75e766cbc0a3b5c133a5c24eb51e31284d06a1f Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:29:21 +0200
Subject: [PATCH 13/94] modulecmd.bash.in: get_release(): redirect release file
 to upvar

---
 Pmodules/modulecmd.bash.in | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 1752c24..e319b7c 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -144,8 +144,7 @@ get_release() {
 	local -r releasefile="${modulefile%/*}/.release-${modulefile##*/}"
 	if [[ -r ${releasefile} ]]; then
 		# read releasefile, remove empty lines, spaces etc
-		local -r data=$( < "${releasefile}" )
-		std::upvar $1 "${data}"
+		std::upvar $1 $( < "${releasefile}" )
 	else
 		std::upvar $1 'unstable'
 	fi

From f9430563e58a849c49cfb587e9df441ec10eb573 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:34:55 +0200
Subject: [PATCH 14/94] modulecmd.bash.in: cleanup

---
 Pmodules/modulecmd.bash.in | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index e319b7c..390fb2e 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -178,7 +178,7 @@ find_overlay () {
         local group="${path#${overlay}/}"
         group=${group%%/*}
         std::upvar $2 "${group}"
-        return 0
+	return 0
 }
 
 module_is_loaded() {
@@ -302,10 +302,6 @@ subcommand_load() {
 	local prefix=''
 	local m=''
 
-	IFS=':'
-	local -a modulepath=(${MODULEPATH})
-	IFS=${__IFS}
-
 	#
 	# Test whether a given module is available.
 	# The passed module-name can be

From 376be20d35fe716f1b0487cd7ac51c78624c135b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:35:52 +0200
Subject: [PATCH 15/94] modulecmd.bash.in: reset_modulepath() must be global

---
 Pmodules/modulecmd.bash.in | 33 ++++++++++++++++++---------------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 390fb2e..cb2da82 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1715,6 +1715,24 @@ subcommand_refresh() {
         subcommand_generic0 'refresh' "$@"
 }
 
+#
+# help function, used during initialization and for purging all modules
+#
+reset_modulepath() {
+	MODULEPATH=''
+	local group
+	local overlay
+	for overlay in "${!OverlayDict[@]}"; do
+		for group in ${PMODULES_DEFAULT_GROUPS}; do
+			local dir="${overlay}/${group}/${PMODULES_MODULEFILES_DIR}"
+			if [[ -d "${dir}" ]]; then
+				std::prepend_path MODULEPATH "${dir}"
+				Dir2OverlayMap[${dir}]=${overlay}
+			fi
+		done
+	done
+}
+
 pmodules_init() {
 	declare -gx LOADEDMODULES=''
 	declare -gx _LMFILES_=''
@@ -1735,21 +1753,6 @@ pmodules_init() {
 		g_env_must_be_saved='yes'
 	}
 
-	reset_modulepath() {
-		MODULEPATH=''
-		local group
-		local overlay
-		for overlay in "${!Overlays[@]}"; do
-			for group in ${PMODULES_DEFAULT_GROUPS}; do
-				local dir="${overlay}/${group}/${PMODULES_MODULEFILES_DIR}"
-				if [[ -d "${dir}" ]]; then
-					std::prepend_path MODULEPATH "${dir}"
-					MapDirsToOverlays[${dir}]=${overlay}
-				fi
-			done
-		done
-	}
-
 	reset_used_releases() {
 		declare -g  UsedReleases=''
 		for r in ${PMODULES_DEFAULT_RELEASES//:/ }; do

From 05aa3d0e4237acfa21ec0a086d349592a711ed1e Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:37:54 +0200
Subject: [PATCH 16/94] modulecmd.bash.in: new global function
 get_overlay_of_moduledir()

---
 Pmodules/modulecmd.bash.in | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index cb2da82..d16ca62 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -117,6 +117,19 @@ save_env() {
 
 trap 'save_env ' EXIT
 
+get_overlay_of_moduledir() {
+	local "$1"
+	local -r moduledir=$2
+
+	if [[ ! -v Dir2OverlayMap[${moduledir}] ]]; then
+		for overlay in "${OverlayList[@]}" 'other'; do
+			[[ ${moduledir} == ${overlay}/* ]] && break
+		done
+		Dir2OverlayMap[${moduledir}]="${overlay}"
+	fi
+	std::upvar $1 "${Dir2OverlayMap[${moduledir}]}"
+}
+
 #
 # get release of module
 # Note:

From cc7b4b10cd351eaabd5d134df63fa3c4e43c6fbb Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:40:41 +0200
Subject: [PATCH 17/94] modulecmd.bash.in: is_group(): upvar with $1 must be
 declared local

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

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index d16ca62..40c14a3 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -431,6 +431,7 @@ subcommand_load() {
 	# hierarchical depth of a group must always be the same.
 	#
 	is_group () {
+		local "$1"
 		find_an_overlay_providing_group () {
 			local "$1"
 			local -r group="$2/${PMODULES_MODULEFILES_DIR}"

From 0751e9c7435e6fa411e27f1254af0e40fc846bee Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:45:05 +0200
Subject: [PATCH 18/94] modulecnd.bash.in: find_module(): changes in arguments
 $3 and $4

- $3 is now the module to load
- $4 is now an array of the splitted MODULEPATH
---
 Pmodules/modulecmd.bash.in | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 40c14a3..aa37ae7 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -563,7 +563,7 @@ subcommand_load() {
 			fi
 		fi # handle extended module names
                 local release=''
-                find_module current_modulefile release "${MODULEPATH}" "${m}"
+                find_module current_modulefile release "${m}" "${modulepath[@]}"
                 if [[ -z ${current_modulefile} ]]; then
 			local text=''
 			get_load_hints text
@@ -902,8 +902,8 @@ get_available_modules() {
 # find module(file) to load. Input arguments are
 #       $1      upvar: return module file
 #       $2      upvar: return module release
-#       $3      a modulepath (usually MODULEPATH)
-#       $4      module to load
+#       $3      module to load
+#       $4      a modulepath (usually MODULEPATH)
 #
 # The module name can be
 #       name
@@ -918,10 +918,10 @@ get_available_modules() {
 #               if no modulefile could be found
 #       
 find_module() {
-	IFS=':'
-	local -a dirs=($3)
-	IFS=${__IFS}
-	local -r module="$4"
+	local "$1"
+	local "$2"
+	local -r module="$3"
+	local -a dirs=("${@:4}")
 
         for dir in "${dirs[@]}"; do
                 test -d "${dir}" || continue

From bf030e81b5279681ed06d440bdaf916371f9e8ec Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:47:59 +0200
Subject: [PATCH 19/94] modulecmd.bash.in: subcommand_load(): update
 Dir2OverlayMap

- after loading a module the dictionary mapping a directory to an
  overlay must be updated if a new hierarchical group was added
---
 Pmodules/modulecmd.bash.in | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index aa37ae7..7e28f24 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -646,7 +646,9 @@ subcommand_load() {
 	while read dir; do
 		[[ "${dir: -1}" == "/" ]] || dir+="/"
 		LOADEDMODULES="${LOADEDMODULES//${dir}}"
+		get_overlay_of_moduledir overlay "${dir}"
 	done <<< "${MODULEPATH//:/$'\n'}"
+        g_env_must_be_saved='yes'
 	export_env 'LOADEDMODULES'
 }
 

From dc52066b7ec689012cc476f5a6561757f1105011 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:51:40 +0200
Subject: [PATCH 20/94] modulecmd.bash.in: improve readable of module avail

---
 Pmodules/modulecmd.bash.in | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 7e28f24..3e5fdd4 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1084,14 +1084,15 @@ subcommand_avail() {
 	human_readable_output() {
 		output_header "$1"
 
-		local -i column=$cols
-		local -i colsize=16
+		local -a available_modules=()
+		local mod=''
+		local -i max_length=1
 		for ((i=0; i<${#mods[@]}; i+=3)); do
 			if [[ ${verbosity_lvl} == 'verbose' ]]; then
 			        local  release=${mods[i+1]}
 			        case ${mods[i+1]} in
 					stable )
-						mod=${mods[i]}
+						mod="${mods[i]}"
 						;;
 					* )
 						mod="${mods[i]}(${release:0:1})"
@@ -1100,9 +1101,17 @@ subcommand_avail() {
 			else
 				mod=${mods[i]}
 			fi
+			local -i n=${#mod}
+			(( n > max_length )) && (( max_length=n ))
+			available_modules+=("${mod}")
+		done
+		IFS=$'\n' available_modules=($(sort <<<"${available_modules[*]}"))
+		unset IFS
+		local -i span=$(( max_length / 16 + 1 ))	# compute column size
+		local -i colsize=$(( span * 16 ))		# as multiple of 16
+		local -i column=$cols				# force a line-break
+		for mod in "${available_modules[@]}"; do
 			local -i len=${#mod}
-			local -i span=$(( len / 16 + 1 ))
-			local -i colsize=$(( span * 16 ))
 			if (( column+len >= cols )); then
 			        printf -- "\n" 1>&2
 				column=0

From 1932db23d0c1e526b7cdb38577d034fd1eff6c29 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:54:29 +0200
Subject: [PATCH 21/94] modulecmd.bash.in: sub.._avail(): use variable
 reference not dict

using a variable reference makes it possible to pass an array to
get_available_modules() insteas a colon separated string
---
 Pmodules/modulecmd.bash.in | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 3e5fdd4..0443ed7 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1170,26 +1170,27 @@ subcommand_avail() {
 	unset IFS
         local overlay=''
         local group=''
-        local -A modulepath_of_group
         local -a groups=()
         for dir in "${modulepath[@]}"; do
                 group='other'
                 find_overlay overlay group "${dir}"
-                if [[ ${modulepath_of_group[${group}]} ]]; then
-                           modulepath_of_group[${group}]+=:${dir}
-                else
-                        modulepath_of_group[${group}]=${dir}
-                        groups+=( "${group}" )
-                fi
+		if [[ -v modulepath_${group} ]]; then
+			path+=("${dir}")
+		else
+			typeset -a modulepath_${group}="${dir}"
+			typeset -n path=modulepath_${group}
+			groups+=("${group}")
+		fi
         done
-        local string
-	for string in "${pattern[@]}"; do
+        local p
+	for p in  "${pattern[@]}"; do
                 for group in "${groups[@]}"; do
+			declare -n path=modulepath_${group}
 			get_available_modules \
 				mods \
-                                "${string}" \
+                                "${p}" \
                                 "${opt_use_releases}" \
-				"${modulepath_of_group[${group}]}"
+				"${path[@]}"
 
 			[[ ${#mods[@]} == 0 ]] && continue
 

From 624b2757ffbbfd05f7dd65a0c6379361ff1bddc4 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 00:58:42 +0200
Subject: [PATCH 22/94] modulecmd.bash.in: subcommand_unuse(): cleanup

---
 Pmodules/modulecmd.bash.in | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 0443ed7..c632c2d 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1551,7 +1551,8 @@ subcommand_unuse() {
 	unset IFS
         unuse() {
                 unuse_overlay() {
-			if [[ -n "${_LMFILES_}" ]] && [[ ${LOADEDMODULES} != Pmodules/* ]]; then				std::die 3 "%s %s: %s -- %s" \
+			if [[ -n "${_LMFILES_}" ]] && [[ ${LOADEDMODULES} != Pmodules/* ]]; then
+				std::die 3 "%s %s: %s -- %s" \
 					 "${CMD}" "${subcommand}" \
 					 "overlays can NOT be removed as long as modules are loaded!" \
 					 "${overlay}"

From ad8a02cdcf95d63454cd88cff3625fde6d634e14 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 01:01:21 +0200
Subject: [PATCH 23/94] modulecmd.bash.in: bug fixed in looping over overlays

- the order of overlays is important, we have to use an array instead
  of a dictionary
- PMODULES_OVERLAYS renamed to OverlayList which is now an array and
  exported in PMODULES_ENV
- MapDirsToOverlays renamed to Dir2OverlayMap
- dictionary Overlays renamed to OverlayDict
---
 Pmodules/modulecmd.bash.in | 105 +++++++++++++++++++------------------
 1 file changed, 55 insertions(+), 50 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index c632c2d..000bf01 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -57,7 +57,7 @@ unset IFS
 shopt -s nullglob
 
 declare -A GroupDepths='()'
-declare -A MapDirsToOverlays='()'
+declare -A Dir2OverlayMap='()'
 declare    Shell=''
 declare -A Subcommands
 declare -A Options
@@ -106,8 +106,8 @@ save_env() {
         local vars=( GroupDepths UsedReleases UseFlags UsedGroups )
         vars+=( PMODULES_DEFAULT_GROUPS PMODULES_DEFINED_RELEASES )
         vars+=( PMODULES_DEFAULT_RELEASES )
-        vars+=( PMODULES_OVERLAYS )
-        vars+=( Overlays MapDirsToOverlays)
+        vars+=( OverlayList )
+        vars+=( OverlayDict Dir2OverlayMap)
 
 	local s=$(typeset -p ${vars[@]})
 	declare -g PMODULES_ENV=$( "${base64}" --wrap=0 <<< "$s" )
@@ -133,8 +133,8 @@ get_overlay_of_moduledir() {
 #
 # get release of module
 # Note:
-# - the release of a module outside ${Overlays[@]} is always 'stable'
-# - the release of a module inside ${Overlays[@]} without a 
+# - the release of a module outside ${OverlayDict[@]} is always 'stable'
+# - the release of a module inside ${OverlayDict[@]} without a
 #   coresponding release file is always 'unstable'
 #
 # Args:
@@ -147,7 +147,14 @@ get_release() {
 	local -r moduledir=$2
 	local -r name=$3
 	local -r modulefile="$2/$3"
-        
+
+	local overlay
+	get_overlay_of_moduledir overlay "${moduledir}"
+
+	if [[ "${overlay}" == 'other' ]]; then
+		std::upvar $1 'stable'
+		return
+	fi
         #
         # In an overlay the name of the module-file is something like
         #   dir/modulefiles/name/version
@@ -180,14 +187,12 @@ find_overlay () {
         local "$1"
         local "$2"
         local -r path=$3
-        local overlay=${MapDirsToOverlays[${path}]}
-	if [[ -z "${overlay}" ]]; then
-		for overlay in "${!Overlays[@]}" 'ZZZZZZ'; do
-			[[ ${path}/ =~ ^${overlay}/ ]] && break
-		done
-		[[ "${overlay}" == 'ZZZZZZ' ]] && return 1
-	fi
+        local overlay=${Dir2OverlayMap[${path}]}
+	get_overlay_of_moduledir overlay "${path}"
         std::upvar $1 "${overlay}"
+
+	[[ "${overlay}" == 'other' ]] && return 1
+
         local group="${path#${overlay}/}"
         group=${group%%/*}
         std::upvar $2 "${group}"
@@ -436,7 +441,7 @@ subcommand_load() {
 			local "$1"
 			local -r group="$2/${PMODULES_MODULEFILES_DIR}"
 			local overlay
-			for overlay in "${!Overlays[@]}"; do
+			for overlay in "${OverlayList[@]}"; do
 				if [[ -d "${overlay}/${group}" ]]; then
 					std::upvar $1 "${overlay}"
 					return 0
@@ -548,9 +553,9 @@ subcommand_load() {
 				MODULEPATH=""
 				modulepath=()
 				group+="${PMODULES_MODULEFILES_DIR}"
-                                for overlay in "${!Overlays[@]}"; do
-                                        MODULEPATH+=":${overlay}/${group}/"
-				        modulepath+=( ${MODULEPATH} )
+                                for overlay in "${OverlayList[@]}"; do
+                                        MODULEPATH="${overlay}/${group}/:${MODULEPATH}"
+				        modulepath=( "${overlay}/${group}/" "${modulepath[@]}" )
                                 done
 			fi
 			if [[ -n ${release} ]]; then
@@ -871,7 +876,7 @@ get_available_modules() {
 					# - new version and not hidden by overlay
 					local name="${mod%/*}"
 					if [[ -z "${modulenames[${name}]}" ]]; then
-						if [[ "${Overlays[$overlay]}" == 'h' ]]; then
+						if [[ "${OverlayDict[$overlay]}" == 'h' ]]; then
 							modulenames[${name}]="${overlay}"
 						else
 							modulenames[${name}]='0'
@@ -1322,9 +1327,9 @@ subcommand_use() {
                 local overlay
 		std::info ''
                 std::info "Used overlays:"
-                for overlay in "${!Overlays[@]}"; do
+                for overlay in "${OverlayList[@]}"; do
 			local hiding=''
-			[[ "${Overlays[${overlay}]}" != '0' ]] && hiding=' (hiding)'
+			[[ "${OverlayDict[${overlay}]}" != '0' ]] && hiding=' (hiding)'
                         std::info "\t${overlay}${hiding}"
                 done
 
@@ -1377,7 +1382,7 @@ subcommand_use() {
                                          "${CMD}" "${subcommand}" \
                                          "is not an overlay directory" \
                                          "${overlay}"
-                        if [[ -n "${Overlays[${overlay}]}" ]]; then
+                        if [[ -n "${OverlayDict[${overlay}]}" ]]; then
                                 std::info "%s %s: %s -- %s" \
                                           "${CMD}" "${subcommand}" \
                                           "overlay already in use" \
@@ -1394,7 +1399,7 @@ subcommand_use() {
                                         dir+="${group}/${PMODULES_MODULEFILES_DIR}"
                                         [[ -d "${dir}" ]] || continue  # no
 					
-					for dir in "${!Overlays[@]}"; do
+					for dir in "${OverlayList[@]}"; do
 						dir+="/${group}/${PMODULES_MODULEFILES_DIR}"
 						std::remove_path MODULEPATH "${dir}"
 					done
@@ -1406,28 +1411,28 @@ subcommand_use() {
                                 dir+="${group}/${PMODULES_MODULEFILES_DIR}"
                                 if [[ -d "${dir}" ]]; then
                                         std::prepend_path MODULEPATH "${dir}"
-					MapDirsToOverlays[${dir}]=${overlay}
+					Dir2OverlayMap[${dir}]=${overlay}
                                 fi
                         done
 
-                        Overlays[${overlay}]=${modifier}
-                        PMODULES_OVERLAYS+=":${overlay}"
-                        export_env PMODULES_OVERLAYS
+                        OverlayDict[${overlay}]=${modifier}
+                        OverlayList=( "${overlay}" "${OverlayList[@]}" )
+                        export_env OverlayList
                         g_env_must_be_saved='yes'
-	                scan_groups "${!Overlays[@]}"
+	                scan_groups "${OverlayList[@]}"
                         local group
                 }
 
                 use_group() {
 			std::append_path UsedGroups "$1"
                         local overlay group
-                        for overlay in "${!Overlays[@]}"; do
+                        for overlay in "${OverlayList[@]}"; do
                                 for group in ${UsedGroups//:/ }; do
                                         local dir="${overlay}/"
                                         dir+="${group}/${PMODULES_MODULEFILES_DIR}"
                                         if [[ -d "${dir}" ]]; then
                                                 std::prepend_path MODULEPATH "${dir}"
-						MapDirsToOverlays[${dir}]=${overlay}
+						Dir2OverlayMap[${dir}]=${overlay}
                                         fi
                                 done
                         done
@@ -1486,7 +1491,7 @@ subcommand_use() {
 
                 local dir="$(cd "${arg}" && pwd)"
                 local overlay
-                for overlay in "${!Overlays[@]}"; do
+                for overlay in "${OverlayList[@]}"; do
                         if [[ ${dir}/ =~ ^${overlay}/ ]]; then
                                 # dir is in one of our used overlays
 			        std::die 3 "%s %s: %s -- %s" \
@@ -1569,7 +1574,7 @@ subcommand_unuse() {
                                          "${CMD}" "${subcommand}" \
                                          "cannot remove root overlay" \
                                          "${overlay}"
-                        [[ -z ${Overlays[${overlay}]} ]] && \
+                        [[ -z ${OverlayDict[${overlay}]} ]] && \
                                 std::die 3 "%s %s: %s -- %s" \
                                          "${CMD}" "${subcommand}" \
                                          "not an used overlay" \
@@ -1584,17 +1589,20 @@ subcommand_unuse() {
                                         dir+="${group}/${PMODULES_MODULEFILES_DIR}"
                                         [[ -d "${dir}" ]] || continue  # no
 					
-					for dir in "${!Overlays[@]}"; do
+					for dir in "${OverlayList[@]}"; do
 						dir+="/${group}/${PMODULES_MODULEFILES_DIR}"
 						std::remove_path MODULEPATH "${dir}"
 					done
 				done
 			fi
 
-                        unset "Overlays[${overlay}]"
-                        std::remove_path PMODULES_OVERLAYS "${overlay}"
+                        unset "OverlayDict[${overlay}]"
+			local i
+			for i in "${!OverlayList[@]}"; do
+				[[ ${OverlayList[i]} == ${overlay} ]] && unset 'OverlayList[i]'
+			done
                         g_env_must_be_saved='yes'
-                        export_env PMODULES_OVERLAYS
+                        export_env OverlayList
                         local dir
                         for dir in "${modulepath[@]}"; do
                                 if [[ "${dir}" =~ "${overlay}" ]]; then
@@ -1613,7 +1621,7 @@ subcommand_unuse() {
                         fi
                         std::remove_path UsedGroups "${arg}"
                         local overlay
-                        for overlay in "${!Overlays[@]}"; do
+                        for overlay in "${OverlayList[@]}"; do
                                 local dir="${overlay}/${arg}/${PMODULES_MODULEFILES_DIR}"
 			        std::remove_path MODULEPATH "${dir}"
                         done
@@ -1662,7 +1670,7 @@ subcommand_unuse() {
 
                 local dir="$(cd "${arg}" && pwd)"
                 local overlay
-                for overlay in "${!Overlays[@]}"; do
+                for overlay in "${OverlayList[@]}"; do
                         if [[ ${dir}/ =~ ^${overlay}/ ]]; then
                                 # dir is in one of our used overlays
 			        std::die 3 "%s %s: %s -- %s" \
@@ -1764,8 +1772,8 @@ pmodules_init() {
 	declare -gx LOADEDMODULES=''
 	declare -gx _LMFILES_=''
 
-        declare -Ag Overlays=([${PMODULES_ROOT}]="0")
-        declare -gx PMODULES_OVERLAYS="${PMODULES_ROOT}"
+        declare -Ag OverlayDict=([${PMODULES_ROOT}]="0")
+        declare -ag OverlayList=( "${PMODULES_ROOT}" )
 	declare -g  UsedGroups=''
 	declare -gx MODULEPATH=''
 	declare -Ag GroupDepths='()'
@@ -1817,7 +1825,6 @@ pmodules_init() {
         reset_used_releases
         init_manpath
         export_env \
-                PMODULES_OVERLAYS \
                 LOADEDMODULES \
                 _LMFILES_ \
                 MODULEPATH \
@@ -2303,9 +2310,7 @@ subcommand_search() {
 		shift
 	done
 	if [[ -z "${src_prefix}" ]]; then
-		IFS=':'
-		local -a src_prefix=(${PMODULES_OVERLAYS})
-		IFS=${__IFS}
+		local -a src_prefix=( "${OverlayList[@]}" )
 	fi
 
 	if [[ "${opt_use_releases}" == ":" ]]; then
@@ -2636,12 +2641,12 @@ fi
 
 _init_overlay_map() {
 	local overlay
-	for overlay in "${!Overlays[@]}"; do
+	for overlay in "${!OverlayDict[@]}"; do
 		local group
 		for group in ${UsedGroups//:/ }; do
 			local dir="${overlay}/${group}/${PMODULES_MODULEFILES_DIR}"
 			if [[ -d "${dir}" ]]; then
-				MapDirsToOverlays[${dir}]=${overlay}
+				Dir2OverlayMap[${dir}]=${overlay}
 			fi
 		done
 	done
@@ -2650,11 +2655,11 @@ _init_overlay_map() {
 if [[ -n ${PMODULES_ENV} ]]; then
 	eval "$("${base64}" -d <<< "${PMODULES_ENV}" 2>/dev/null)"
 	# if we load a Pmodules version with overlay support,
-	# PMODULES_OVERLAYS might not be set. Since libmodules.tcl
+	# OverlayList might not be set. Since libmodules.tcl
 	# reads PMODULES_ENV we have to save the environment.
-	if [[ -z "${PMODULES_OVERLAYS}" ]]; then
-		declare -g PMODULES_OVERLAYS="${PMODULES_ROOT}"
-		declare -Ag Overlays=([${PMODULES_ROOT}]="0")
+	if [[ -z "${OverlayList}" ]]; then
+		declare -ag OverlayList=( "${PMODULES_ROOT}" )
+		declare -Ag OverlayDict=([${PMODULES_ROOT}]="0")
 		_init_overlay_map
 		save_env
 	fi
@@ -2663,7 +2668,7 @@ else
 fi
 
 if (( ${#GroupDepths[@]} == 0 )); then
-	scan_groups "${!Overlays[@]}"
+	scan_groups "${!OverlayDict[@]}"
 fi
 
 declare options

From aa4140631ce3159f115e331d591e26965dd1f175 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 10:52:12 +0200
Subject: [PATCH 24/94] tcllib added to repo

---
 Tools/tcllib/build | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100755 Tools/tcllib/build

diff --git a/Tools/tcllib/build b/Tools/tcllib/build
new file mode 100755
index 0000000..af189fe
--- /dev/null
+++ b/Tools/tcllib/build
@@ -0,0 +1,5 @@
+#!/usr/bin/env modbuild
+
+pbuild::set_download_url "https://core.tcl-lang.org/tcllib/uv/$P-$V.tar.xz"
+#uild::install_docfiles 'license.terms' 'README.md'
+

From a0420cc73fe611baaa139646da088e57bb7e2024 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 10:53:07 +0200
Subject: [PATCH 25/94] modulecmd.bash.in: save_env() requires an argument now

PMODULES_ENV will be compiles and exported if save_env() is called
with $1 != 'no'
---
 Pmodules/modulecmd.bash.in | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 000bf01..420cd30 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -102,7 +102,7 @@ export_env() {
 declare g_env_must_be_saved='no'
 
 save_env() {
-        [[ ${g_env_must_be_saved} == 'no' ]] && return 0
+        [[ "$1" == 'no' ]] && return 0
         local vars=( GroupDepths UsedReleases UseFlags UsedGroups )
         vars+=( PMODULES_DEFAULT_GROUPS PMODULES_DEFINED_RELEASES )
         vars+=( PMODULES_DEFAULT_RELEASES )
@@ -115,7 +115,7 @@ save_env() {
 	unset UsedGroups
 }
 
-trap 'save_env ' EXIT
+trap 'save_env ${g_env_must_be_saved}' EXIT
 
 get_overlay_of_moduledir() {
 	local "$1"

From 1b43ccbe21228548dd7e5e486c2445a69f074209 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 10:56:00 +0200
Subject: [PATCH 26/94] modulecmd.bash.in: bugfix in initialization of overlays

the variables required for overlays were not initialized in a proper
way if we switch from a Pmodules version without overlay support
---
 Pmodules/modulecmd.bash.in | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 420cd30..c2ac3ee 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2639,7 +2639,9 @@ if [[ -z "${Subcommands[${subcommand}]}" ]]; then
 	std::die 1 "${CMD}: unknown sub-command -- ${subcommand}"
 fi
 
-_init_overlay_map() {
+_init_overlay_vars() {
+	declare -ag OverlayList=( "${PMODULES_ROOT}" )
+	declare -Ag OverlayDict=([${PMODULES_ROOT}]="0")
 	local overlay
 	for overlay in "${!OverlayDict[@]}"; do
 		local group
@@ -2650,6 +2652,7 @@ _init_overlay_map() {
 			fi
 		done
 	done
+	save_env 'yes'
 }
 
 if [[ -n ${PMODULES_ENV} ]]; then
@@ -2658,10 +2661,7 @@ if [[ -n ${PMODULES_ENV} ]]; then
 	# OverlayList might not be set. Since libmodules.tcl
 	# reads PMODULES_ENV we have to save the environment.
 	if [[ -z "${OverlayList}" ]]; then
-		declare -ag OverlayList=( "${PMODULES_ROOT}" )
-		declare -Ag OverlayDict=([${PMODULES_ROOT}]="0")
-		_init_overlay_map
-		save_env
+		_init_overlay_vars
 	fi
 else
 	pmodules_init

From 4ed8961fc17f6fc8e20f4b74bee49bcecab79caa Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 10:58:53 +0200
Subject: [PATCH 27/94] modulecmd.bash.in: bug fixed in purge sub-cmd

---
 Pmodules/modulecmd.bash.in | 61 ++++++++++++++++++++++++++++++++++----
 1 file changed, 55 insertions(+), 6 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index c2ac3ee..af165f3 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1845,6 +1845,13 @@ USAGE:
 '
 
 subcommand_purge() {
+	#
+	# unload all loaded modules
+	#
+	# Note:
+	#     If a Pmodule module is loaded, it will *not* be
+	#     unloaded! 
+	#
         local -r subcommand='purge'
 	local -a args=()
 	while (( $# > 0)); do
@@ -1865,13 +1872,55 @@ subcommand_purge() {
                          "${CMD}" "${subcommand}" \
                          "no arguments allowd"
         fi
-	# we cannot unset PMODULES_HOME, otherwise the module function
-	# would fail.
-	local saved_home="${PMODULES_HOME}"
-	"${modulecmd}" "${Shell}" "${subcommand}"
+
+	# is a Pmodule module loaded?
+	# if yes, save name in variable 'pmodule'
+	local pmodule=''
+	IFS=':'
+	local -a lmfiles=($_LMFILES_)
+	unset IFS
+	for f in "${lmfiles[@]}"; do
+		if [[ $f == */${PMODULES_MODULEFILES_DIR}/Pmodules/* ]]; then
+			pmodule="${f##*/${PMODULES_MODULEFILES_DIR}/}"
+			break;
+		fi
+	done
+
+	# run module purge
+	# since we might have to reload a Pmodules module, we cannot
+	# just run 'modulecmd ${Shell} purge'
+	local tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
+		|| std::die 1 "Oops: unable to create tmp file!"
+	local output=$("${modulecmd}" 'bash' 'purge' 2> "${tmpfile}")
+
+	local error=$( < "${tmpfile}")
+	if [[ "${error}" =~ ":ERROR:" ]]; then
+                local s=${error%%$'\n'*}
+                local error_txt='failed'
+		std::die 3 "%s %s: %s" \
+                         "${CMD}" "${subcommand}" \
+                         "${error_txt}"
+        fi
+        if [[ "${Shell}" == "sh" ]]; then
+		# for sh-like shells just echo 
+                echo "${output}"
+        else
+		# re-run with right shell
+                "${modulecmd}" "${Shell}" 'purge'
+        fi
+	eval "${output}"
+	if [[ -n "${error}" ]]; then
+                echo "${error}" 1>&2
+	fi
+
         reset_modulepath
-        reset_used_groups
-	PMODULES_HOME="${saved_home}"
+	if [[ -n "${pmodule}" ]]; then
+		# reload a previously loaded Pmodule module
+		# stderr is redirected to /dev/null, otherwise
+		# we may get output like
+		# 'unstable module has been loaded'
+		subcommand_load "${pmodule}" 2> /dev/null
+	fi
 	
 	export_env MODULEPATH PMODULES_HOME
 }

From 077cf0c4be45343f4f9c58f3951c26898b4aaeeb Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 11:46:13 +0200
Subject: [PATCH 28/94] modulecmd: bugfix in save_env()

Unsetting 'UsedGroups' the way we did doesn't work, revert this change
---
 Pmodules/modulecmd.bash.in | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index af165f3..dc3700a 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -112,7 +112,6 @@ save_env() {
 	local s=$(typeset -p ${vars[@]})
 	declare -g PMODULES_ENV=$( "${base64}" --wrap=0 <<< "$s" )
 	export_env 'PMODULES_ENV'
-	unset UsedGroups
 }
 
 trap 'save_env ${g_env_must_be_saved}' EXIT

From 23cbb4210e8a14751d62181cce7d6f76cfea4b97 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 11:49:45 +0200
Subject: [PATCH 29/94] modulecmd: sub-cmd purge: reset MODUEPATH to used
 groups

The sub-command purge should not remove used groups from MODULEPATH
---
 Pmodules/modulecmd.bash.in | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index dc3700a..cb19df5 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1757,7 +1757,7 @@ reset_modulepath() {
 	local group
 	local overlay
 	for overlay in "${!OverlayDict[@]}"; do
-		for group in ${PMODULES_DEFAULT_GROUPS}; do
+		for group in ${UsedGroups//:/ }; do
 			local dir="${overlay}/${group}/${PMODULES_MODULEFILES_DIR}"
 			if [[ -d "${dir}" ]]; then
 				std::prepend_path MODULEPATH "${dir}"
@@ -1912,7 +1912,6 @@ subcommand_purge() {
                 echo "${error}" 1>&2
 	fi
 
-        reset_modulepath
 	if [[ -n "${pmodule}" ]]; then
 		# reload a previously loaded Pmodule module
 		# stderr is redirected to /dev/null, otherwise
@@ -1920,6 +1919,7 @@ subcommand_purge() {
 		# 'unstable module has been loaded'
 		subcommand_load "${pmodule}" 2> /dev/null
 	fi
+        reset_modulepath
 	
 	export_env MODULEPATH PMODULES_HOME
 }

From c44f393ef26101e5667704ae43b2c039465419cd Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 14:21:16 +0200
Subject: [PATCH 30/94] modulecmd: improved handling of tmp file(s)

A tmp file is now created at the very beginning for all subcommands
where a tmp file is needed. The file is removed in the _exit()
function which is registered via trap.
---
 Pmodules/modulecmd.bash.in | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index cb19df5..f3e8d88 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -114,7 +114,12 @@ save_env() {
 	export_env 'PMODULES_ENV'
 }
 
-trap 'save_env ${g_env_must_be_saved}' EXIT
+_exit() {
+	save_env "${g_env_must_be_saved}"
+	${rm} -f "${tmpfile}"
+}
+
+trap '_exit' EXIT
 
 get_overlay_of_moduledir() {
 	local "$1"
@@ -597,8 +602,6 @@ subcommand_load() {
 			test -r "${prefix}/.dependencies" && load_dependencies "$_"
                 fi
 
-		local tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
-			|| std::die 1 "Oops: unable to create tmp file!"
 		local output=$("${modulecmd}" 'bash' ${opts} 'load' \
                                               "${current_modulefile}" 2> "${tmpfile}")
 
@@ -1888,8 +1891,6 @@ subcommand_purge() {
 	# run module purge
 	# since we might have to reload a Pmodules module, we cannot
 	# just run 'modulecmd ${Shell} purge'
-	local tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
-		|| std::die 1 "Oops: unable to create tmp file!"
 	local output=$("${modulecmd}" 'bash' 'purge' 2> "${tmpfile}")
 
 	local error=$( < "${tmpfile}")
@@ -2181,8 +2182,6 @@ subcommand_search() {
                         func_print_line='print_line_csv'
                 }
 
-                local -r tmpfile=$1
-
                 if [[ "${opt_print_modulefiles}" == 'yes' ]]; then
                         print_modulefiles
                 elif [[ "${opt_print_csv}" == 'yes' ]]; then
@@ -2220,8 +2219,6 @@ subcommand_search() {
 	search () {
 		local -r module=$1
 		# write results to a temporary file for later processing
-		local -r tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
-			|| std::die 1 "Oops: unable to create tmp file!"
 		local group
 		# loop over all groups
 		for group in "${!GroupDepths[@]}"; do
@@ -2279,8 +2276,7 @@ subcommand_search() {
                                      ${deps[@]} >> "${tmpfile}"
 			done
 		done
-		print_result "${tmpfile}"
-		${rm} -f "${tmpfile}"
+		print_result
 	}
 
 	while (( $# > 0 )); do
@@ -2719,6 +2715,13 @@ if (( ${#GroupDepths[@]} == 0 )); then
 	scan_groups "${!OverlayDict[@]}"
 fi
 
+case ${subcommand} in
+	load|purge|search )
+		declare -r tmpfile=$( ${mktemp} /tmp/Pmodules.XXXXXX ) \
+			|| std::die 1 "Oops: unable to create tmp file!"
+		;;
+esac
+
 declare options
 options=$( "${getopt}" ${Options[${subcommand}]} -- -- "${opts[@]}" "$@" ) \
         || print_help "${subcommand}"

From 9e6566636b35316baa7057b3d85320c0bafb19b7 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 18:51:29 +0200
Subject: [PATCH 31/94] modulecmd: bugfix in use/unuse overlays

---
 Pmodules/modulecmd.bash.in | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index f3e8d88..5d98ad6 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1353,7 +1353,7 @@ subcommand_use() {
 
 	use () {
                 use_overlay() {
-			if [[ -n "${_LMFILES_}" ]] && [[ ${LOADEDMODULES} != Pmodules/* ]]; then
+			if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
 				std::die 3 "%s %s: %s -- %s" \
 					 "${CMD}" "${subcommand}" \
 					 "overlays can be added as long as no modules are loaded!" \
@@ -1558,7 +1558,7 @@ subcommand_unuse() {
 	unset IFS
         unuse() {
                 unuse_overlay() {
-			if [[ -n "${_LMFILES_}" ]] && [[ ${LOADEDMODULES} != Pmodules/* ]]; then
+			if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
 				std::die 3 "%s %s: %s -- %s" \
 					 "${CMD}" "${subcommand}" \
 					 "overlays can NOT be removed as long as modules are loaded!" \

From d23fdf930a523796de8562dfb91a76cccd9b6ef1 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 18:52:58 +0200
Subject: [PATCH 32/94] Pmodule modulefile: remove Pmodules bin dir from PATH

in some cases it might happen that we have a Pmodules bin directory
in PATH. This has to be removed if we load a Pmodule module.
---
 Pmodules/modulefile | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/Pmodules/modulefile b/Pmodules/modulefile
index 65aa4c1..2a9311d 100644
--- a/Pmodules/modulefile
+++ b/Pmodules/modulefile
@@ -8,3 +8,15 @@ module-maintainer	"Achim Gsell <achim.gsell@psi.ch>"
 module-help	"
 Pmodules are a hierarchical module environment based on Environment Modules.
 "
+
+#
+# It might be that '${PMODULES_ROOT}/Tools/Pmodules/VERSION' is in PATH.
+# Why? With older version the PATH might have been set without loading
+# a module.
+#
+if { [module-info mode load] } {
+    set PATH ":$::env(PATH):"
+    if { [regexp -- {.*:(.*/Pmodules/[^:]*):} $PATH -> str] } {
+    	remove-path PATH $str
+    }
+}

From 47b5fae59b0f59f5ae13fb338c678006ea3ce018 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 29 Apr 2021 17:54:25 +0200
Subject: [PATCH 33/94] modbuild: better support for build modules in overlays

A new configuration file has been added to map human readable overlay
names to the corresponding directory. The overlay can be specified
with the --overlay option. The passed string can be either a name or a
directory. If a name is passed, this name must map to directory in the
configuration file ${PMODULES_ROOT}/config/overlays.conf. The name is
also used as to select the variant files 'files/variants.name'. The
selection of variant files can be overriden with the --system
option.
---
 Pmodules/libpbuild.bash |  6 ++--
 Pmodules/modbuild.in    | 62 +++++++++++++++++++++++++++++++++++------
 2 files changed, 57 insertions(+), 11 deletions(-)

diff --git a/Pmodules/libpbuild.bash b/Pmodules/libpbuild.bash
index 526d9c3..944eeab 100644
--- a/Pmodules/libpbuild.bash
+++ b/Pmodules/libpbuild.bash
@@ -764,12 +764,12 @@ pbuild::make_all() {
 		fi
 
 		modulefile_dir=$(join_by '/' \
-					 "${overlay}/${GROUP}/${PMODULES_MODULEFILES_DIR}" \
+					 "${overlay_dir}/${GROUP}/${PMODULES_MODULEFILES_DIR}" \
 					 "${names[@]}" \
 					 "${module_name}")
 		modulefile_name="${modulefile_dir}/${module_version}"
 		
-		PREFIX="${overlay}/${GROUP}/${module_name}/${module_version}"
+		PREFIX="${overlay_dir}/${GROUP}/${module_name}/${module_version}"
 		local -i i=0
 		for ((i=${#names[@]}-1; i >= 0; i--)); do
 			PREFIX+="/${names[i]}"
@@ -1479,7 +1479,7 @@ pbuild.bootstrap() {
 
 	MODULECMD=$(which true)
 	GROUP='Tools'
-	PREFIX="${overlay}/${GROUP}/Pmodules/${PMODULES_VERSION}"
+	PREFIX="${overlay_dir}/${GROUP}/Pmodules/${PMODULES_VERSION}"
 
 	C_INCLUDE_PATH="${PREFIX}/include"
 	CPLUS_INCLUDE_PATH="${PREFIX}/include"
diff --git a/Pmodules/modbuild.in b/Pmodules/modbuild.in
index 4827218..a992d9a 100755
--- a/Pmodules/modbuild.in
+++ b/Pmodules/modbuild.in
@@ -154,7 +154,7 @@ declare         opt_verbose='no'
 # array collecting all modules specified on the command line via '--with=module'
 declare -a      opt_with_modules=()
 
-declare         overlay=''
+declare         opt_overlay_name_or_dir=''
 
 
 parse_args() {
@@ -259,10 +259,10 @@ parse_args() {
 			opt_update_modulefiles='yes'
 			;;
                 --overlay )
-                        overlay=$2
+                        opt_overlay_name_or_dir=$2
                         ;;
                 --overlay=* )
-                        overlay=${1/*=}
+                        opt_overlay_name_or_dir=${1/*=}
                         ;;
                 -- )
                         :
@@ -366,7 +366,6 @@ build_modules() {
                 fi
 	done
 
-        
         local variants=()
         local variants_files=()
         for f in "${files[@]}"; do
@@ -408,15 +407,64 @@ build_modules() {
         done
 }
 
+declare -r OVERLAY_CONF="${PMODULES_ROOT}/${PMODULES_CONFIG_DIR}/overlays.conf"
+
+get_overlay_name_and_dir() {
+	local "$1"
+	local "$2"
+	if [[ -r "${OVERLAY_CONF}" ]]; then
+		local toks=()
+		while read -a toks; do
+			if [[ ${toks[0]} == $3 ]] || [[ ${toks[1]} == $3 ]]; then
+				std::upvar $1  "${toks[0]}"
+				std::upvar $2  "${toks[1]}"
+				return 0
+			fi
+		done < "${OVERLAY_CONF}"
+	fi
+	return 1
+}
+
 #.............................................................................
 # main
 
 parse_args "$@"
 
-if [[ -z "${opt_system}" ]]; then
-        opt_system=$(std::get_os_release)
+#
+# --overlay=name
+#    lookup overlay directory, system name equivalent to overlay name
+# --overlay=name --system=sysname
+#    lookup name, use given system name
+# --overlay=dir
+#    use given overlay dir and default system name
+# --system=name
+#    lookup name, set overlay_dir of found confi
+declare overlay_name=''
+declare overlay_dir=''
+if [[ -n "${opt_overlay_name_or_dir}" ]]; then
+	if ! get_overlay_name_and_dir overlay_name overlay_dir "${opt_overlay_name_or_dir}"; then
+		# not found in config
+		if [[ ${opt_overlay_name_or_dir:0:1} == / ]]; then
+			overlay_dir="${opt_overlay_name_or_dir}"
+		else
+			std::die 1 "Invalid overlay name -- ${opt_overlay_name_or_dir}"
+		fi
+	fi
+	if [[ -z "${opt_system}" ]] && [[ -n "${overlay_name}" ]]; then
+		opt_system="${overlay_name}"
+	fi
+elif [[ -n "${opt_system}" ]]; then
+	get_overlay_name_and_dir overlay_name overlay_dir "${opt_system}" || :
 fi
 
+[[ -z "${overlay_name}" ]] && overlay_name='unknown'
+[[ -z "${overlay_dir}" ]] && overlay_dir="${PMODULES_ROOT}"
+[[ -z "${opt_system}" ]] && opt_system=$(std::get_os_release)
+
+echo overlay_name=$overlay_name
+echo overlay_dir=$overlay_dir
+echo opt_system=$opt_system
+
 pbuild.jobs "${opt_jobs}"
 pbuild.force_rebuild "${opt_force_rebuild}"
 pbuild.build_target "${opt_build_target}"
@@ -441,8 +489,6 @@ fi
 source "${opt_build_config}" || \
         std::die 3 "Oops: Cannot source configuration file -- '$_'"
 
-[[ -z "${overlay}" ]] && overlay=${PMODULES_ROOT}
-
 # :FIXME: should go dist files to
 #         ${PMODULES_ROOT}/var/distfiles
 #         or

From 80728b8a6a557b3157e5b6d0c9690766f2f3f489 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 29 Apr 2021 18:10:55 +0200
Subject: [PATCH 34/94] modulecmd: tag log messages with 'Pmodules'

---
 Pmodules/modulecmd.bash.in | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 8501996..ee4e922 100755
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -22,6 +22,10 @@ declare -r sort
 awk=$(PATH=/bin:/usr/bin /usr/bin/which awk)
 declare -r awk
 rm=$(PATH=/bin:/usr/bin /usr/bin/which rm)
+declare -r rm
+logger=$(PATH=/bin:/usr/bin /usr/bin/which logger)
+declare -r logger
+
 if [[ $(uname -s) == 'Darwin' ]]; then
 	declare -r getopt="${libexecdir}/getopt"
 	declare -r find="${libexecdir}/find"
@@ -556,7 +560,7 @@ subcommand_load() {
                            [[ ${release} != stable ]]; then
 		        std::info "%s" "${msg}"
 		fi
-		logger "${msg}"
+		${logger} -t Pmodules "${msg}"
 	done
 	# fix LOADEDMODULES
 	LOADEDMODULES="${_LMFILES_}"

From a970be1cf3b2a91b8ab829fd38983a55c037c8a9 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 29 Apr 2021 18:47:01 +0200
Subject: [PATCH 35/94] modulecmd: don't remove a loaded Pmodules module with
 module purge

Removing a Pmodule module with module purge has some unwanted
side-effects. It is not required to have modulecmd in a directory of
PATH. If you user explicitly loads a Pmodules module the bin directory
of the Pmodule module is added to the PATH. A Pmodules module might be
loaded for two reasons. First to change the Pmodules version, second
to make the build system available. If we remove a Pmodules module
with module purge the build systems is getting unavailable again. This
is confusing for the user.
---
 Pmodules/modulecmd.bash.in | 68 +++++++++++++++++++++++++++++++++-----
 1 file changed, 60 insertions(+), 8 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index ee4e922..744d64c 100755
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1320,7 +1320,7 @@ reset_modulepath() {
 	MODULEPATH=''
         local group
         local root="${PMODULES_ROOT}"
-        for group in ${PMODULES_DEFAULT_GROUPS}; do
+	for group in ${UsedGroups//:/ }; do
                 local dir="${root}/${group}/${PMODULES_MODULEFILES_DIR}"
                 [[ -d "${dir}" ]] && std::prepend_path MODULEPATH "${dir}"
         done
@@ -1395,6 +1395,13 @@ USAGE:
 '
 
 subcommand_purge() {
+	#
+	# unload all loaded modules
+	#
+	# Note:
+	#     If a Pmodule module is loaded, it will *not* be
+	#     unloaded! 
+	#
         local -r subcommand='purge'
 	local -a args=()
 	while (( $# > 0)); do
@@ -1411,21 +1418,66 @@ subcommand_purge() {
 		shift
 	done
         if (( ${#args[@]} > 0 )); then
-	        std::die 3 "%s %s: %s\n" \
+	        std::die 3 "%s %s: %s" \
                          "${CMD}" "${subcommand}" \
                          "no arguments allowd"
         fi
-	# we cannot unset PMODULES_HOME, otherwise the module function
-	# would fail.
-	local saved_home="${PMODULES_HOME}"
-	"${modulecmd}" "${Shell}" "${subcommand}"
+
+	# is a Pmodule module loaded?
+	# if yes, save name in variable 'pmodule'
+	local pmodule=''
+	IFS=':'
+	local -a lmfiles=($_LMFILES_)
+	unset IFS
+	for f in "${lmfiles[@]}"; do
+		if [[ $f == */${PMODULES_MODULEFILES_DIR}/Pmodules/* ]]; then
+			pmodule="${f##*/${PMODULES_MODULEFILES_DIR}/}"
+			break;
+		fi
+	done
+
+	# run module purge
+	# since we might have to reload a Pmodules module, we cannot
+	# just run 'modulecmd ${Shell} purge'
+	local tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
+                || std::die 1 "Oops: unable to create tmp file!\n"
+
+	local output=$("${modulecmd}" 'bash' 'purge' 2> "${tmpfile}")
+
+	local error=$( < "${tmpfile}")
+	${rm} "${tmpfile}"
+	if [[ "${error}" =~ ":ERROR:" ]]; then
+                local s=${error%%$'\n'*}
+                local error_txt='failed'
+		std::die 3 "%s %s: %s" \
+                         "${CMD}" "${subcommand}" \
+                         "${error_txt}"
+        fi
+        if [[ "${Shell}" == "sh" ]]; then
+		# for sh-like shells just echo 
+                echo "${output}"
+        else
+		# re-run with right shell
+                "${modulecmd}" "${Shell}" 'purge'
+        fi
+	eval "${output}"
+	if [[ -n "${error}" ]]; then
+                echo "${error}" 1>&2
+	fi
+
+	if [[ -n "${pmodule}" ]]; then
+		# reload a previously loaded Pmodule module
+		# stderr is redirected to /dev/null, otherwise
+		# we may get output like
+		# 'unstable module has been loaded'
+		subcommand_load "${pmodule}" 2> /dev/null
+	fi
         reset_modulepath
-        reset_used_groups
-	PMODULES_HOME="${saved_home}"
 	
 	export_env MODULEPATH PMODULES_HOME
 }
 
+
 ##############################################################################
 #
 # list [-hlt]

From c55404a798237f5599784d64ef16d90b95f3e791 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 29 Apr 2021 19:29:42 +0200
Subject: [PATCH 36/94] modulecmd: better tmp file handling

A global tmp file is created if the sub-command is 'load', 'purge' or
'search' and removed in the exit function.
---
 Pmodules/modulecmd.bash.in | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 744d64c..124c95d 100755
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -102,7 +102,7 @@ export_env() {
 declare g_env_must_be_saved='no'
 
 save_env() {
-        [[ ${g_env_must_be_saved} == 'no' ]] && return 0
+        [[ $1 == 'no' ]] && return 0
         local vars=( GroupDepths UsedReleases UseFlags UsedGroups )
         vars+=( PMODULES_DEFAULT_GROUPS PMODULES_DEFINED_RELEASES )
         vars+=( PMODULES_DEFAULT_RELEASES )
@@ -112,7 +112,12 @@ save_env() {
 	export_env 'PMODULES_ENV'
 }
 
-trap 'save_env ' EXIT
+_exit() {
+	save_env "${g_env_must_be_saved}"
+	${rm} -f "${tmpfile}"
+}
+
+trap '_exit' EXIT
 
 #
 # get release of module
@@ -515,8 +520,6 @@ subcommand_load() {
                         test -r "${prefix}/.info" && cat "$_" 1>&2
 			test -r "${prefix}/.dependencies" && load_dependencies "$_"
 		fi
-		local tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
-                    || std::die 1 "Oops: unable to create tmp file!\n"
 		local output=$("${modulecmd}" 'bash' ${opts} 'load' \
                                               "${current_modulefile}" 2> "${tmpfile}")
 
@@ -1439,9 +1442,6 @@ subcommand_purge() {
 	# run module purge
 	# since we might have to reload a Pmodules module, we cannot
 	# just run 'modulecmd ${Shell} purge'
-	local tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
-                || std::die 1 "Oops: unable to create tmp file!\n"
-
 	local output=$("${modulecmd}" 'bash' 'purge' 2> "${tmpfile}")
 
 	local error=$( < "${tmpfile}")
@@ -1774,8 +1774,6 @@ subcommand_search() {
 	search () {
 		local -r module=$1
 		# write results to a temporary file for later processing
-		local -r tmpfile=$( "${mktemp}" /tmp/Pmodules.XXXXXX ) \
-			|| std::die 1 "Oops: unable to create tmp file!"
 		local group
 		# loop over all groups
 		for group in "${!GroupDepths[@]}"; do
@@ -2251,6 +2249,13 @@ if (( ${#GroupDepths[@]} == 0 )); then
 	scan_groups "${PMODULES_ROOT}"
 fi
 
+case ${subcommand} in
+	load|purge|search )
+		declare -r tmpfile=$( ${mktemp} /tmp/Pmodules.XXXXXX ) \
+			|| std::die 1 "Oops: unable to create tmp file!"
+		;;
+esac
+
 declare options
 options=$( "${getopt}" ${Options[${subcommand}]} -- -- "${opts[@]}" "$@" ) \
         || print_help "${subcommand}"

From 2747861b523b7ca8e9464469f303951a1bb3d876 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 30 Apr 2021 15:23:44 +0200
Subject: [PATCH 37/94] modmanage: shebang fixed

---
 Pmodules/modmanage.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modmanage.bash.in b/Pmodules/modmanage.bash.in
index 9a59809..acf750d 100755
--- a/Pmodules/modmanage.bash.in
+++ b/Pmodules/modmanage.bash.in
@@ -1,4 +1,4 @@
-#!@PMODULES_HOME@/sbin/bash
+#!@BASH@ --noprofile
 
 # we have to unset CDPATH, otherwise 'cd' prints the directoy!
 unset CDPATH

From 291039084b55d981e3a7122a70c58723989fa23c Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 30 Apr 2021 15:24:13 +0200
Subject: [PATCH 38/94] modmanage: hardcode CMD

---
 Pmodules/modmanage.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modmanage.bash.in b/Pmodules/modmanage.bash.in
index acf750d..1f74361 100755
--- a/Pmodules/modmanage.bash.in
+++ b/Pmodules/modmanage.bash.in
@@ -4,7 +4,7 @@
 unset CDPATH
 
 # used for some output only
-declare -r  CMD=$(basename "$0")
+declare -r  CMD='modmanage'
 
 declare -r  mydir=$(cd $(dirname "$0") && pwd)
 declare -r  prefix=$(dirname "${mydir}")

From 8c4d911fa5bda535c3a6aaf461ff4566de3303db Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 30 Apr 2021 15:27:46 +0200
Subject: [PATCH 39/94] modmanage: don't use PATH to find commands

---
 Pmodules/modmanage.bash.in | 66 ++++++++++++++++++++++++--------------
 1 file changed, 42 insertions(+), 24 deletions(-)

diff --git a/Pmodules/modmanage.bash.in b/Pmodules/modmanage.bash.in
index 1f74361..62727e3 100755
--- a/Pmodules/modmanage.bash.in
+++ b/Pmodules/modmanage.bash.in
@@ -6,17 +6,37 @@ unset CDPATH
 # used for some output only
 declare -r  CMD='modmanage'
 
-declare -r  mydir=$(cd $(dirname "$0") && pwd)
-declare -r  prefix=$(dirname "${mydir}")
+dirname=$(PATH=/bin:/usr/bin which dirname)
+declare -r dirname
+uname=$(PATH=/bin:/usr/bin which uname)
+declare -r uname
+mkdir=$(PATH=/bin:/usr/bin which mkdir)
+declare -r mkdir
+rsync=$(PATH=/bin:/usr/bin which rsync)
+declare -r rsync
+rm=$(PATH=/bin:/usr/bin /usr/bin/which rm)
+declare -r rm
+
+if [[ $(${uname} -s) == 'Darwin' ]]; then
+	declare -r getopt="${libexecdir}/getopt"
+	declare -r find="${libexecdir}/find"
+else
+	getopt=$(PATH=/bin:/usr/bin /usr/bin/which getopt)
+	declare -r getopt
+	find=$(PATH=/bin:/usr/bin /usr/bin/which find)
+	declare -r find
+fi
+
+
+declare -r  mydir=$(cd $(${dirname} "$0") && pwd)
+declare -r  prefix=$(${dirname} "${mydir}")
 declare -r  bindir="${prefix}/bin"
-declare -r  sbindir="${prefix}/sbin"
 declare -r  libdir="${prefix}/lib"
 declare -r  libexecdir="${prefix}/libexec"
 
-source "${libdir}/libstd.bash"
-source "${libdir}/libpmodules.bash"
 
-PATH="${sbindir}:${bindir}:${PATH}"
+source "${libdir}/libstd.bash"
+
 
 _exit () {
 	std::die 1 "Interrupted..."
@@ -205,7 +225,7 @@ get_module_prefix() {
 #	$1: relative module file path
 #
 get_releasefile_name() {
-	echo "$(dirname "$1")/.release-$(basename "$1")"
+	echo "$(${dirname} "$1")/.release-$(basename "$1")"
 }
 
 ##############################################################################
@@ -234,8 +254,8 @@ sync_module() {
 
 	# install/update module
 	if [[ ! -d "${target_prefix}/${rel_module_prefix}" ]] || [[ "${force}" == 'yes' ]]; then
-		$DRY mkdir -p "${target_prefix}/${rel_module_prefix}" || return $?
-		$DRY rsync --links --perms --recursive --delete \
+		$DRY ${mkdir} -p "${target_prefix}/${rel_module_prefix}" || return $?
+		$DRY ${rsync} --links --perms --recursive --delete \
 		      "${src_prefix}/${rel_module_prefix}/" \
 		      "${target_prefix}/${rel_module_prefix}/" || exit $?
 	fi
@@ -246,8 +266,8 @@ sync_module() {
 
 	# create target directory for module- and release-file
 	if [[ -e "${src_modulefile}" ]] || [[ -e "${src_releasefile}" ]]; then
-	        local dir=$( dirname "${target_modulefile}" )
-		$DRY mkdir -p "${dir}" || return $?
+	        local dir=$( ${dirname} "${target_modulefile}" )
+		$DRY ${mkdir} -p "${dir}" || return $?
 	fi
 
 	# copy modulefile template
@@ -260,20 +280,20 @@ sync_module() {
 	local -r src_template="${src_prefix}/${template}"
 	local -r target_template="${target_prefix}/${template}"
 	if [[ -e "${src_template}" ]]; then
-		$DRY mkdir -p "${target_template}"
-		$DRY rsync --links --perms --recursive \
+		$DRY ${mkdir} -p "${target_template}"
+		$DRY ${rsync} --links --perms --recursive \
 		     "${src_template}" "${target_template}" || exit $?
 	fi
 
 	# copy modulefile
 	if [[ -e "${src_modulefile}" ]]; then
-	        $DRY rsync --links --perms --recursive \
+	        $DRY ${rsync} --links --perms --recursive \
 		     "${src_modulefile}" "${target_modulefile}" || exit $?
 	fi
 
 	# copy release-file
 	if [[ -e "${src_releasefile}" ]]; then
-	        $DRY rsync --links --perms --recursive \
+	        $DRY ${rsync} --links --perms --recursive \
 		     "${src_releasefile}" "${target_releasefile}" || exit $?
 	fi
 
@@ -290,9 +310,8 @@ sync_module() {
 sync_config() {
 	src="$1/${PMODULES_CONFIG_DIR}/"
 	dst="$2/${PMODULES_CONFIG_DIR}/"
-	$DRY rsync --recursive --links --perms --delete \
+	$DRY ${rsync} --recursive --links --perms --delete \
 		"${src}" "${dst}" 2>/dev/null || return $?
-	sed -i.bak "s/PMODULES_VERSION=\(.*\)/PMODULES_VERSION=${PMODULES_VERSION}/" "${dst}/environment.bash"
 	echo
 }
 
@@ -416,7 +435,7 @@ environment at '${PMODULES_ROOT}'
 		fi
 		force='yes'
 		echo "Creating target directory '${target_prefix}'..."
-		$DRY mkdir -p "${target_prefix}" || \
+		$DRY ${mkdir} -p "${target_prefix}" || \
 		        std::die 1 "Error: make directory failed!"
 		echo
 
@@ -430,13 +449,12 @@ environment at '${PMODULES_ROOT}'
 			    "${src_prefix}" \
 			    "${target_prefix}" || \
 		        std::die 1 "Error: sync Pmodules failed!"
-		mkdir -p "${target_prefix}/Tools/${PMODULES_MODULEFILES_DIR}"
-		echo
 
 		dst="${target_prefix}/${PMODULES_CONFIG_DIR}/environment.bash"
 		echo "Adding installation source '${src_prefix}' to '${dst}'..."
 		sed -i.bak '/PMODULES_INSTALL_SOURCE/d' "${dst}"
 		echo "declare -x PMODULES_INSTALL_SOURCE=\"${src_prefix}\"" >> "${dst}"
+		${mkdir} -p "${target_prefix}/Tools/${PMODULES_MODULEFILES_DIR}"
 		echo
 
 		if [[ -n "${user}" ]]; then
@@ -505,7 +523,7 @@ get_group_depths () {
 		cd "${root}"
 		local group
 		for group in "${Groups[@]}"; do
-			local  fname=$(find "${group}/${modulefiles_dir}" \
+			local  fname=$(${find} "${group}/${modulefiles_dir}" \
 					    -depth \( -type f -o -type l \) -print -quit)
 			[[ -n ${fname} ]] || continue
 			local -a tmp
@@ -591,7 +609,7 @@ subcommand_install() {
 			[[ -z ${dep} ]] && continue
 
 			# search for module with current modulepath and remember
-			local modulename=$(find "${modulepath[@]}" -path "*/${dep}" \
+			local modulename=$(${find} "${modulepath[@]}" -path "*/${dep}" \
                                                 2>/dev/null | head -n 1 )
 			[[ -n ${modulename} ]] || \
 			        std::die 3 "Oops: required module '${dep}' not found!"
@@ -606,7 +624,7 @@ subcommand_install() {
 				modulepath+=( "${path}" )
 			fi
 		done < "${tmpfile}"
-                rm "${tmpfile}"
+                ${rm} "${tmpfile}"
 	}
 
 	#......................................................................
@@ -729,7 +747,7 @@ subcommand_install() {
 			map_to_family[$_key]=${_family}
 		fi
 	done < <({ cd "${src_prefix}" && \
-				 find */"${PMODULES_MODULEFILES_DIR}" \
+				 ${find} */"${PMODULES_MODULEFILES_DIR}" \
 				      \( -type l -o -type f \) \! -name ".*"; } 2>/dev/null )
 
 	#

From 47bccd5fa8f8062eaea33ea7d7b80b0720e1eee6 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 30 Apr 2021 15:30:17 +0200
Subject: [PATCH 40/94] modmange: functions from libpmodules.bash added

---
 Pmodules/modmanage.bash.in | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/Pmodules/modmanage.bash.in b/Pmodules/modmanage.bash.in
index 62727e3..6e11be2 100755
--- a/Pmodules/modmanage.bash.in
+++ b/Pmodules/modmanage.bash.in
@@ -345,11 +345,26 @@ delete_module() {
 #		Initialize a new module environment in this directory-
 # 		
 subcommand_init() {
+	check_env() {
+		[[ -n "${PMODULES_ROOT}" ]] &&
+			[[ -d "${PMODULES_ROOT}" ]] &&
+			[[ -n "${PMODULES_HOME}" ]] &&
+			[[ -n "${PMODULES_VERSION}" ]] || \
+				std::die 1 "
+Error: the module environment you are going to use as so  urce has not been
+initialized properly!"
+
+		[[ -d "${src_prefix}/${PMODULES_CONFIG_DIR}" ]] &&
+			[[ -d "${src_prefix}/Tools/Pmodules/${PMODULES_VERSION}" ]] || \
+				std::die 1 "
+Error: the module environment '${src_prefix}' has not been initialized properly!"
+	}
+	
 	local src=''
 	local target_prefixes=()
 	local user=''
 	local opts=''
-	opts=$(pmodules::get_options -o h -l src: -l user: -l help -l version: -- "$@")
+	opts=$(${getopt} -o h -l src: -l user: -l help -l version: -- "$@")
 	if [[ $? != 0 ]]; then
 		subcommand_help_init
 		exit 1
@@ -407,7 +422,7 @@ subcommand_init() {
 		    std::die 1 "Error: --user option is only allowed if running as root!"
 	fi
 
-	pmodules::check_env || \
+	check_env || \
 		std::die 1 "Giving up..."
 
 	echo "
@@ -449,11 +464,6 @@ environment at '${PMODULES_ROOT}'
 			    "${src_prefix}" \
 			    "${target_prefix}" || \
 		        std::die 1 "Error: sync Pmodules failed!"
-
-		dst="${target_prefix}/${PMODULES_CONFIG_DIR}/environment.bash"
-		echo "Adding installation source '${src_prefix}' to '${dst}'..."
-		sed -i.bak '/PMODULES_INSTALL_SOURCE/d' "${dst}"
-		echo "declare -x PMODULES_INSTALL_SOURCE=\"${src_prefix}\"" >> "${dst}"
 		${mkdir} -p "${target_prefix}/Tools/${PMODULES_MODULEFILES_DIR}"
 		echo
 
@@ -667,7 +677,7 @@ subcommand_install() {
 		std::info ""
 	}
 	
-	opts=$(pmodules::get_options -o hf -l dry-run -l force -l with: -l release: -l help -l src: -- "$@")
+	opts=$(${getopt} -o hf -l dry-run -l force -l with: -l release: -l help -l src: -- "$@")
 	if [[ $? != 0 ]]; then
 		subcommand_help_install
 		exit 1

From 415a94293121a35a066d717d4143242aea71bb27 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 09:11:44 +0200
Subject: [PATCH 41/94] libmodules.tcl: bugfixes in module-addgroup() handling
 overlays

replacing(global) overlays were not handle properly
---
 Pmodules/libmodules.tcl | 46 ++++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/Pmodules/libmodules.tcl b/Pmodules/libmodules.tcl
index d886a90..756f5c1 100644
--- a/Pmodules/libmodules.tcl
+++ b/Pmodules/libmodules.tcl
@@ -26,6 +26,7 @@ debug "loading libmodules"
 package require base64
 
 set ::MODULEFILES_DIR "modulefiles"
+set ::ol_replacing "r"
 
 proc _pmodules_parse_pmodules_env { } {
         debug "enter"
@@ -65,33 +66,29 @@ proc module-addgroup { group } {
 	set	::${group}		$name
 	set	::${group}_version	$version
 
-        debug "mode=[module-info mode]"
 	if { [module-info mode load] } {
-		array set overlayed_groups {}
-		foreach overlay [lreverse_n $::OverlayList 1] {
+	        set overlays_to_add {}
+		foreach overlay $::OverlayList {
+			lappend overlays_to_add $overlay
+			debug $overlay
+			if { [string compare $::OverlayDict($overlay) $ol_replacing=] == 0 } {
+				break
+			}
+		}
+		foreach overlay [lreverse_n $overlays_to_add 1] {
 			debug "overlay=$overlay"
-			if {![info exists overlayed_groups($group)]}	{
-				debug "group=$group"
-				debug "::variant=$::variant"
-				set dir [file join \
-					     $overlay \
-					     $group \
-					     $::MODULEFILES_DIR \
-					     {*}$::variant]
-				if { [file isdirectory $dir] } {
-					debug "prepend $dir to MODULEPATH "
-					prepend-path MODULEPATH $dir
-				}
+			debug "group=$group"
+			debug "::variant=$::variant"
+			set dir [file join \
+				     $overlay \
+				     $group \
+				     $::MODULEFILES_DIR \
+				     {*}$::variant]
+			if { [file isdirectory $dir] } {
+				debug "prepend $dir to MODULEPATH "
+				prepend-path MODULEPATH $dir
 			}
-			# don't add if overlayed
-			if { [string compare $::OverlayDict($overlay) "g"] == 0 } {
-				# get groups in this overlay
-				set dirs [glob -directory $overlay -type d {[A-Z]*}]
-				foreach dir $dirs {
-					set overlayed_groups([lindex [file split $dir] end]) 1
-				}
-			}
-                }
+		}
 		debug "end foreach"
 		prepend-path UsedGroups $group
 	} elseif { [module-info mode remove] } {
@@ -120,6 +117,7 @@ proc module-addgroup { group } {
                                      $group \
                                      $::MODULEFILES_DIR \
                                      {*}$::variant]
+		        debug "remove $dir"
                         remove-path MODULEPATH $dir
                 }
 		remove-path UsedGroups $group

From 325551eecdfc691c59bbb16bd4d9267b86b57343 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 09:19:46 +0200
Subject: [PATCH 42/94] modulecmd: fixes in adding/removing overlays

bugfix in the code to prevent adding an overlay if modules are already
loaded, same for removing

more clear error message if an overlay cannot be added/removed

use constants for overlay modifiers
---
 Pmodules/modulecmd.bash.in | 45 ++++++++++++++++++++++++--------------
 1 file changed, 29 insertions(+), 16 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 5d98ad6..5502845 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -49,6 +49,9 @@ else
 	declare -r  modulecmd="${libexecdir}/modulecmd.bin"
 fi
 
+declare -r ol_hiding='h'
+declare -r ol_replacing='r'
+
 declare verbosity_lvl=${PMODULES_VERBOSITY:-'verbose'}
 
 # use default IFS
@@ -878,7 +881,7 @@ get_available_modules() {
 					# - new version and not hidden by overlay
 					local name="${mod%/*}"
 					if [[ -z "${modulenames[${name}]}" ]]; then
-						if [[ "${OverlayDict[$overlay]}" == 'h' ]]; then
+						if [[ "${OverlayDict[$overlay]}" == "${ol_hiding}" ]]; then
 							modulenames[${name}]="${overlay}"
 						else
 							modulenames[${name}]='0'
@@ -1353,11 +1356,16 @@ subcommand_use() {
 
 	use () {
                 use_overlay() {
-			if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
-				std::die 3 "%s %s: %s -- %s" \
-					 "${CMD}" "${subcommand}" \
-					 "overlays can be added as long as no modules are loaded!" \
-					 "${overlay}"
+			if [[ -n ${LOADEDMODULES} ]]; then
+				if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
+					std::error "%s %s: %s" \
+						   "${CMD}" "${subcommand}" \
+						   "overlay cannot be added since some modules are already loaded!"
+					std::die 3 "%s %s: %s -- %s" \
+						 "${CMD}" "${subcommand}" \
+						 "overlay failed" \
+						 "${overlay}"
+				fi
 			fi
 			local overlay=''
 			local modifier='0'
@@ -1365,7 +1373,7 @@ subcommand_use() {
 				modifier=${1##*:}
 				overlay=${1%:*}
 				case ${modifier} in
-					g | h )
+					${ol_replacing} | ${ol_hiding} )
 						:
 						;;
 					* )
@@ -1392,9 +1400,9 @@ subcommand_use() {
 				return 0
 			fi  
 				
-			if [[ "${modifier}" == "g" ]]; then
-				# if this overlay hides groups, we have to remove
-				# the modules made available by other overlays
+			if [[ "${modifier}" == "${ol_replacing}" ]]; then
+				# if this overlay replaces groups, we have to remove
+				# the modules made available by other overlays in these groups
 				for group in ${UsedGroups//:/ }; do
 					# first test whether this group is in the to be added overlay
                                         local dir="${overlay}/"
@@ -1558,11 +1566,16 @@ subcommand_unuse() {
 	unset IFS
         unuse() {
                 unuse_overlay() {
-			if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
-				std::die 3 "%s %s: %s -- %s" \
-					 "${CMD}" "${subcommand}" \
-					 "overlays can NOT be removed as long as modules are loaded!" \
-					 "${overlay}"
+			if [[ -n ${LOADEDMODULES} ]]; then
+				if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
+					std::error "%s %s: %s" \
+						   "${CMD}" "${subcommand}" \
+						   "overlay cannot be removed since some modules are still loaded!"
+					std::die 3 "%s %s: %s -- %s" \
+						 "${CMD}" "${subcommand}" \
+						 "overlay failed" \
+						 "${overlay}"
+				fi
 			fi
 			overlay=${overlay%:*}  # ignore any modifier
 			overlay=${overlay%/} # remove trailing '/' if there is one
@@ -1582,7 +1595,7 @@ subcommand_unuse() {
                                          "not an used overlay" \
                                          "${overlay}"
 				
-			if [[ "${modifier}" == 'g' ]]; then
+			if [[ "${modifier}" == "${ol_replacing}" ]]; then
 				# if this overlay hides groups, we have to re-add
 				# the modules made available by other overlays
 				for group in ${UsedGroups//:/ }; do

From 9a0d55ed85b3ce769eef0315dc82dd74d63a8fa0 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 09:25:26 +0200
Subject: [PATCH 43/94] modulecmd: save environment after unloading a module

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

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 5502845..d593fc0 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -729,6 +729,7 @@ subcommand_unload() {
 		PMODULES_HOME=${saved_home}
 		export_env 'PMODULES_HOME'
 	fi
+	g_env_must_be_saved='yes'
 }
 
 ##############################################################################

From d25663a32e7d9f3453be59fb94bd971d72ea2b61 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 09:27:28 +0200
Subject: [PATCH 44/94] modulefile: bugfix in modifying PATH

---
 Pmodules/modulefile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Pmodules/modulefile b/Pmodules/modulefile
index 2a9311d..1893fdb 100644
--- a/Pmodules/modulefile
+++ b/Pmodules/modulefile
@@ -17,6 +17,8 @@ Pmodules are a hierarchical module environment based on Environment Modules.
 if { [module-info mode load] } {
     set PATH ":$::env(PATH):"
     if { [regexp -- {.*:(.*/Pmodules/[^:]*):} $PATH -> str] } {
-    	remove-path PATH $str
+        if { [string compare $str $PREFIX/bin] != 0 } {
+    	    remove-path PATH $str
+        }
     }
 }

From fcf37f8b44a0ca964b07a091749cd698d6e71569 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 28 Apr 2021 16:52:58 +0000
Subject: [PATCH 45/94] Pmodule modulefile: remove Pmodules bin dir from PATH

in some cases it might happen that we have a Pmodules bin directory
in PATH. This has to be removed if we load a Pmodule module.


(cherry picked from commit d23fdf930a523796de8562dfb91a76cccd9b6ef1)
---
 Pmodules/modulefile | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/Pmodules/modulefile b/Pmodules/modulefile
index 65aa4c1..2a9311d 100644
--- a/Pmodules/modulefile
+++ b/Pmodules/modulefile
@@ -8,3 +8,15 @@ module-maintainer	"Achim Gsell <achim.gsell@psi.ch>"
 module-help	"
 Pmodules are a hierarchical module environment based on Environment Modules.
 "
+
+#
+# It might be that '${PMODULES_ROOT}/Tools/Pmodules/VERSION' is in PATH.
+# Why? With older version the PATH might have been set without loading
+# a module.
+#
+if { [module-info mode load] } {
+    set PATH ":$::env(PATH):"
+    if { [regexp -- {.*:(.*/Pmodules/[^:]*):} $PATH -> str] } {
+    	remove-path PATH $str
+    }
+}

From 2faf42a4e046250b936f9ac2dcd9f664b5df5a17 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 07:27:28 +0000
Subject: [PATCH 46/94] modulefile: bugfix in modifying PATH

(cherry picked from commit d25663a32e7d9f3453be59fb94bd971d72ea2b61)
---
 Pmodules/modulefile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Pmodules/modulefile b/Pmodules/modulefile
index 2a9311d..1893fdb 100644
--- a/Pmodules/modulefile
+++ b/Pmodules/modulefile
@@ -17,6 +17,8 @@ Pmodules are a hierarchical module environment based on Environment Modules.
 if { [module-info mode load] } {
     set PATH ":$::env(PATH):"
     if { [regexp -- {.*:(.*/Pmodules/[^:]*):} $PATH -> str] } {
-    	remove-path PATH $str
+        if { [string compare $str $PREFIX/bin] != 0 } {
+    	    remove-path PATH $str
+        }
     }
 }

From daead01197aec7ef060b076edd75af765abfbbfd Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 07:25:26 +0000
Subject: [PATCH 47/94] modulecmd: save environment after unloading a module

(cherry picked from commit 9a0d55ed85b3ce769eef0315dc82dd74d63a8fa0)
---
 Pmodules/modulecmd.bash.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 124c95d..f630ddf 100755
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -642,6 +642,7 @@ subcommand_unload() {
 		PMODULES_HOME=${saved_home}
 		export_env 'PMODULES_HOME'
 	fi
+	g_env_must_be_saved='yes'
 }
 
 ##############################################################################

From dc1ad90c70a16a6e2c4bebf0564140359ed100e6 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 11:28:10 +0200
Subject: [PATCH 48/94] modulecmd: align columns in sub-cmd avail

---
 Pmodules/modulecmd.bash.in | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)
 mode change 100755 => 100644 Pmodules/modulecmd.bash.in

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
old mode 100755
new mode 100644
index f630ddf..a49cdb9
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -875,14 +875,15 @@ subcommand_avail() {
 	human_readable_output() {
 		output_header
 
-		local -i column=$cols
-		local -i colsize=16
-		for ((i=0; i<${#mods[@]}; i+=3 )); do
+		local -a available_modules=()
+		local mod=''
+		local -i max_length=1
+		for ((i=0; i<${#mods[@]}; i+=3)); do
 			if [[ ${verbosity_lvl} == 'verbose' ]]; then
 			        local  release=${mods[i+1]}
 			        case ${mods[i+1]} in
 					stable )
-						mod=${mods[i]}
+						mod="${mods[i]}"
 						;;
 					* )
 						mod="${mods[i]}(${release:0:1})"
@@ -891,9 +892,17 @@ subcommand_avail() {
 			else
 				mod=${mods[i]}
 			fi
+			local -i n=${#mod}
+			(( n > max_length )) && (( max_length=n ))
+			available_modules+=("${mod}")
+		done
+		IFS=$'\n' available_modules=($(sort <<<"${available_modules[*]}"))
+		unset IFS
+		local -i span=$(( max_length / 16 + 1 ))	# compute column size
+		local -i colsize=$(( span * 16 ))		# as multiple of 16
+		local -i column=$cols				# force a line-break
+		for mod in "${available_modules[@]}"; do
 			local -i len=${#mod}
-			local -i span=$(( len / 16 + 1 ))
-			local -i colsize=$(( span * 16 ))
 			if (( column+len >= cols )); then
 			        printf -- "\n" 1>&2
 				column=0

From e3299a1afa236804bb57352710a4c09270fce8d4 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 14:22:30 +0200
Subject: [PATCH 49/94] modulecmd: sub-cmd avail: pass group as argument to
 output function

---
 Pmodules/modulecmd.bash.in | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index a49cdb9..2534bab 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -818,9 +818,7 @@ subcommand_avail() {
 	cols=$(tput cols)
 
 	output_header() {
-		local caption=${dir/${PMODULES_ROOT}\/}
-		local caption=${caption/\/${PMODULES_MODULEFILES_DIR}/: }
-		local caption=${caption/: \//: }
+		local caption="$1"
 		let i=($cols-${#caption})/2-2
 		printf -- "%0.s-" $(seq 1 $i) 1>&2
 		printf -- " %s " "${caption}" 1>&2
@@ -829,7 +827,7 @@ subcommand_avail() {
 	}
 
 	terse_output() {
-		output_header
+		output_header "$1"
 		for (( i=0; i<${#mods[@]}; i+=3 )); do
 			local mod=${mods[i]}
 			local release=${mods[i+1]}
@@ -855,7 +853,7 @@ subcommand_avail() {
 	#
 	# :FIXME: for the time being, this is the same as terse_output!
 	long_output() {
-		output_header
+		output_header "$1"
 		for (( i=0; i<${#mods[@]}; i+=3 )); do
 			local mod=${mods[i]}
 			local release=${mods[i+1]}
@@ -873,7 +871,7 @@ subcommand_avail() {
 	}
 
 	human_readable_output() {
-		output_header
+		output_header "$1"
 
 		local -a available_modules=()
 		local mod=''
@@ -968,7 +966,7 @@ subcommand_avail() {
                                 "${opt_use_releases}" \
 				"${dir}"
 			[[ ${#mods[@]} == 0 ]] && continue
-			${output_function}
+			${output_function} "${group}"
 		done
 	done
 }

From 6318a0a59186c3a7e0a9f69a9caa66ab3fb0161b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 14:23:55 +0200
Subject: [PATCH 50/94] modulecmd: sub-cmd avail: group argument added

It's now possible to list available modules in certain groups only.
---
 Pmodules/modulecmd.bash.in | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 2534bab..fa4cf9b 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -917,18 +917,15 @@ subcommand_avail() {
 	}
 	local pattern=()
 	local output_function='human_readable_output'
-	local opt_all_groups='no'
 	local opt_use_releases="${UsedReleases}"
+	local -A opt_groups=()
+	local val=''
 	while (($# > 0)); do
 		case $1 in
-                        -H | --help )
+                        -H | --help | -\? )
                                 print_help "${subcommand}"
                                 ;;
-			-a | --all )
-				opt_all_groups='yes'
-				opt_use_releases="${PMODULES_DEFINED_RELEASES}"
-				;;
-			--all-releases )
+			-a | --all | --all-releases )
 				opt_use_releases="${PMODULES_DEFINED_RELEASES}"
 				;;
 			-h | --human )
@@ -943,6 +940,15 @@ subcommand_avail() {
 			-m | --machine )
 				output_function='machine_output'
 				;;
+			-g | --group | --group=* )
+				if [[ $1 == --group=* ]]; then
+					val="${1/--group=}"
+				else
+					val="$2"
+					shift
+				fi
+				opt_groups[${val}]=1
+				;;
 			-- | '' )
 				;;
 			* )
@@ -960,6 +966,11 @@ subcommand_avail() {
         local string
 	for string in "${pattern[@]}"; do
 		for dir in "${modulepath[@]}"; do
+			local group="${dir/${PMODULES_ROOT}\/}"
+			group="${group%%/*}"
+			if (( ${#opt_groups[@]} > 0 )) && [[ ! -v opt_groups[${group}] ]]; then
+				continue
+			fi
 			get_available_modules \
 				mods \
 				"${string}" \

From f5351f025edcb7cc4f06d8aa1bd107a4918b796a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 14:40:12 +0200
Subject: [PATCH 51/94] modulecmd: use default IFS

---
 Pmodules/modulecmd.bash.in | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index fa4cf9b..ddf0701 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -51,9 +51,8 @@ fi
 
 declare verbosity_lvl=${PMODULES_VERBOSITY:-'verbose'}
 
-# we use newline as internal field separator
-IFS=$' \t\n'
-declare -r __IFS=${IFS}	# used to restore IFS
+# use default IFS
+unset IFS
 
 shopt -s nullglob
 
@@ -290,7 +289,7 @@ subcommand_load() {
 
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${__IFS}
+	unset IFS
 
 	#
 	# Test whether a given module is available.
@@ -433,7 +432,7 @@ subcommand_load() {
 
 			IFS=':'
 			local -a toks=($m)
-			IFS=${__IFS}
+			unset IFS
 			local group=''
 			local release=''
 			if is_group "${toks[0]}"; then
@@ -962,7 +961,7 @@ subcommand_avail() {
 	fi
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${__IFS}
+	unset IFS
         local string
 	for string in "${pattern[@]}"; do
 		for dir in "${modulepath[@]}"; do
@@ -1052,7 +1051,7 @@ subcommand_use() {
         local -r subcommand='use'
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
-	IFS=${__IFS}
+	unset IFS
         local add2path_func='std::append_path'
 
         group_is_used() {
@@ -1843,7 +1842,7 @@ subcommand_search() {
 					for ((j = -depth-2; j < -2; j += 2)); do
 						deps+=( "${toks[*]: $j:2}" );
 					done
-					IFS=${__IFS}
+					unset IFS
 				fi
 				
 				echo ${name} ${release} ${group} ${modulefile} \

From a3835d3f0b6bda05418bcc1fbe34dcd85a2fea90 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 18:12:44 +0200
Subject: [PATCH 52/94] libmodules.tcl: bugfix in module-addgroup{}

---
 Pmodules/libmodules.tcl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/libmodules.tcl b/Pmodules/libmodules.tcl
index 756f5c1..58e266d 100644
--- a/Pmodules/libmodules.tcl
+++ b/Pmodules/libmodules.tcl
@@ -71,7 +71,7 @@ proc module-addgroup { group } {
 		foreach overlay $::OverlayList {
 			lappend overlays_to_add $overlay
 			debug $overlay
-			if { [string compare $::OverlayDict($overlay) $ol_replacing=] == 0 } {
+			if { [string compare $::OverlayDict($overlay) $::ol_replacing] == 0 } {
 				break
 			}
 		}

From ab1f6c263dade381017f486c19aa97eea3117eaa Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 18:14:07 +0200
Subject: [PATCH 53/94] modulecmd: fixed in sub-cmd avail

- bugfix in loop collecting per group directories in MODULEPATH
- use UsedGroups to loop over the groups, this defines a clear oder
- in pmodules_init(): prepend groups to UseGroups instead of
  appending. This fixes an issue in the order the groups were listed.
---
 Pmodules/modulecmd.bash.in | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index ef24187..ba2e66b 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1185,27 +1185,26 @@ subcommand_avail() {
 	IFS=':'
 	local -a modulepath=(${MODULEPATH})
 	unset IFS
-        local overlay=''
+	local dir
         local group=''
-        local -a groups=()
+        local overlay=''
         for dir in "${modulepath[@]}"; do
                 group='other'
                 find_overlay overlay group "${dir}"
-		if [[ -v modulepath_${group} ]]; then
-			path+=("${dir}")
-		else
-			typeset -a modulepath_${group}="${dir}"
-			typeset -n path=modulepath_${group}
-			groups+=("${group}")
+		if [[ ! -v modulepath_${group} ]]; then
+			typeset -a modulepath_${group}
 		fi
+		typeset -n path=modulepath_${group}
+		path+=("${dir}")
         done
         local p
 	for p in  "${pattern[@]}"; do
-                for group in "${groups[@]}"; do
+                for group in ${UsedGroups//:/ } other; do
 			if (( ${#opt_groups[@]} > 0 )) && [[ ! -v opt_groups[${group}] ]]; then
 				continue
 			fi
-			declare -n path=modulepath_${group}
+			[[ -v modulepath_${group} ]] || continue
+			typeset -n path=modulepath_${group}
 			get_available_modules \
 				mods \
                                 "${p}" \
@@ -1807,7 +1806,7 @@ pmodules_init() {
 		UsedGroups=''
 		local group
 		for group in ${PMODULES_DEFAULT_GROUPS}; do
-			std::append_path UsedGroups "${group}"
+			std::prepend_path UsedGroups "${group}"
 		done
 		g_env_must_be_saved='yes'
 	}

From 0ea9e54cc47bf128cf66dd88d6ea0061182976b0 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 6 May 2021 19:04:27 +0200
Subject: [PATCH 54/94] modulecmd: reinitialize Pmodules if Pmodules version
 changed

---
 Pmodules/modulecmd.bash.in | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index ddf0701..84b586e 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -102,7 +102,7 @@ declare g_env_must_be_saved='no'
 
 save_env() {
         [[ $1 == 'no' ]] && return 0
-        local vars=( GroupDepths UsedReleases UseFlags UsedGroups )
+        local vars=( Version GroupDepths UsedReleases UseFlags UsedGroups )
         vars+=( PMODULES_DEFAULT_GROUPS PMODULES_DEFINED_RELEASES )
         vars+=( PMODULES_DEFAULT_RELEASES )
 
@@ -1345,6 +1345,7 @@ reset_modulepath() {
                 local dir="${root}/${group}/${PMODULES_MODULEFILES_DIR}"
                 [[ -d "${dir}" ]] && std::prepend_path MODULEPATH "${dir}"
         done
+        g_env_must_be_saved='yes'
 }
 
 reset_used_groups() {
@@ -1364,7 +1365,6 @@ reset_used_releases() {
         g_env_must_be_saved='yes'
 }
 
-
 init_manpath() {
         std::replace_path MANPATH "${PMODULES_HOME%/*}/.*"
 
@@ -1391,7 +1391,9 @@ pmodules_init() {
 	declare -gx MODULEPATH=''
 
 	declare -Ag GroupDepths='()'
+	unset UseFlags
 	declare -Ag  UseFlags=()
+	declare -g Version="${PMODULES_VERSION}"
         reset_modulepath
         reset_used_groups
         reset_used_releases
@@ -2259,6 +2261,9 @@ fi
 
 if [[ -n ${PMODULES_ENV} ]]; then
 	eval "$("${base64}" -d <<< "${PMODULES_ENV}" 2>/dev/null)"
+	if [[ -z ${Version} ]] || [[ ${Version} != ${PMODULES_VERSION} ]]; then
+		pmodules_init
+	fi
 else
 	pmodules_init
 fi

From 183e7f40a260ef6e09745183ce768986bab29daf Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 7 May 2021 15:51:28 +0200
Subject: [PATCH 55/94] libstd.bash: function to check Bash variable type added

---
 Pmodules/libstd.bash | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/Pmodules/libstd.bash b/Pmodules/libstd.bash
index eb8525d..e5a2f46 100644
--- a/Pmodules/libstd.bash
+++ b/Pmodules/libstd.bash
@@ -244,6 +244,33 @@ std::get_os_release() {
 	${func_map[${OS}]}
 }
 
+std::get_type() {
+	local -a signature=$(typeset -p "$1")
+	case ${signature[1]} in
+		-Ai* )
+			echo 'int dict'
+			;;
+		-A* )
+			echo 'dict'
+			;;
+		-ai* )
+			echo 'int array'
+			;;
+		-a* )
+			echo 'array'
+			;;
+		-i* )
+			echo 'integer'
+			;;
+		-- )
+			echo 'string'
+			;;
+		* )
+			echo 'none'
+			return 1
+	esac
+}
+
 # Local Variables:
 # mode: sh
 # sh-basic-offset: 8

From bff9055b20cb0fa2cd4eb5b111218e57e4ce4aeb Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 7 May 2021 16:40:08 +0200
Subject: [PATCH 56/94] modulecmd: bugfix in tmp file setup/cleanup

---
 Pmodules/modulecmd.bash.in | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 84b586e..6937055 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1465,7 +1465,6 @@ subcommand_purge() {
 	local output=$("${modulecmd}" 'bash' 'purge' 2> "${tmpfile}")
 
 	local error=$( < "${tmpfile}")
-	${rm} "${tmpfile}"
 	if [[ "${error}" =~ ":ERROR:" ]]; then
                 local s=${error%%$'\n'*}
                 local error_txt='failed'
@@ -1755,8 +1754,6 @@ subcommand_search() {
                         func_print_line='print_line_csv'
                 }
 
-                local -r tmpfile=$1
-
                 if [[ "${opt_print_modulefiles}" == 'yes' ]]; then
                         print_modulefiles
                 elif [[ "${opt_print_csv}" == 'yes' ]]; then
@@ -1852,7 +1849,6 @@ subcommand_search() {
 			done
 		done
 		print_result "${tmpfile}"
-		${rm} -f "${tmpfile}"
 	}
 
 	while (( $# > 0 )); do
@@ -2277,6 +2273,9 @@ case ${subcommand} in
 		declare -r tmpfile=$( ${mktemp} /tmp/Pmodules.XXXXXX ) \
 			|| std::die 1 "Oops: unable to create tmp file!"
 		;;
+	* )
+		declare -r tmpfile=''
+		;;
 esac
 
 declare options

From d32f04ea832c5043435e8aacad0d2ec9c31f7193 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Fri, 7 May 2021 16:41:00 +0200
Subject: [PATCH 57/94] modulecmd: bugfix in basic initialization

---
 Pmodules/modulecmd.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 6937055..e497fb2 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1394,8 +1394,8 @@ pmodules_init() {
 	unset UseFlags
 	declare -Ag  UseFlags=()
 	declare -g Version="${PMODULES_VERSION}"
-        reset_modulepath
         reset_used_groups
+        reset_modulepath
         reset_used_releases
         init_manpath
         export_env \

From ca4c530a5e27af157d4dd2bb21fb6a51fb520d59 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 10 May 2021 15:53:06 +0200
Subject: [PATCH 58/94] modulecmd: prevent loading Pmodules module if other
 modules are loaded

---
 Pmodules/modulecmd.bash.in | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index e497fb2..5599f5e 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -508,8 +508,20 @@ subcommand_load() {
 		fi
                 if [[ ${current_modulefile} =~ ${PMODULES_ROOT} ]] \
                            && [[ ! ${m} =~ / ]]; then
+			# the module is in our hierarchy but no version
+			# has been specified. We take the version from
+			# current_modulefile and append it
                         m+="/${current_modulefile##*/}"
                 fi
+		if [[ ${m} == Pmodules/*  ]] && [[ -n ${LOADEDMODULES} ]]; then
+			std::error "%s %s: %s" \
+				   "${CMD}" "${subcommand}" \
+				   "cannot load a Pmodules module because other modules are already load!"
+			std::die 3 "%s %s: %s -- %s\n" \
+                                 "${CMD}" "${subcommand}" \
+                                 "failed" \
+                                 "${m}"
+		fi
 		if [[ ":${LOADEDMODULES}:" =~ ":${m}:" ]]; then
                         continue
 		fi

From fcec9f77c205095bdfc94e3a1252fda30985c3fa Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 10 May 2021 15:55:19 +0200
Subject: [PATCH 59/94] modulecmd: restore some env.vars after loading Pmodules
 module

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

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 5599f5e..871caf0 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2270,7 +2270,16 @@ fi
 if [[ -n ${PMODULES_ENV} ]]; then
 	eval "$("${base64}" -d <<< "${PMODULES_ENV}" 2>/dev/null)"
 	if [[ -z ${Version} ]] || [[ ${Version} != ${PMODULES_VERSION} ]]; then
+		# the Pmodules version changed!
+		# we save _LMFILES_ and LOADEDMODULES and restore them
+		# later. Otherwise the Pmodules module would not be listed
+		# by module list
+		declare saved_LMFILES_="${_LMFILES_}"
+		declare saved_LOADEDMODULES="${LOADEDMODULES}"
 		pmodules_init
+		_LMFILES_="${saved_LMFILES_}"
+		LOADEDMODULES="${saved_LOADEDMODULES}"
+		export_env _LMFILES_ LOADEDMODULES
 	fi
 else
 	pmodules_init

From e0950bcd250d68946821041cf218a5fce1b2f004 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 11 May 2021 12:05:00 +0200
Subject: [PATCH 60/94] modulecmd: fix initialisation after loading a Pmodule
 module

---
 Pmodules/modulecmd.bash.in | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 871caf0..e449b61 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2271,15 +2271,8 @@ if [[ -n ${PMODULES_ENV} ]]; then
 	eval "$("${base64}" -d <<< "${PMODULES_ENV}" 2>/dev/null)"
 	if [[ -z ${Version} ]] || [[ ${Version} != ${PMODULES_VERSION} ]]; then
 		# the Pmodules version changed!
-		# we save _LMFILES_ and LOADEDMODULES and restore them
-		# later. Otherwise the Pmodules module would not be listed
-		# by module list
-		declare saved_LMFILES_="${_LMFILES_}"
-		declare saved_LOADEDMODULES="${LOADEDMODULES}"
-		pmodules_init
-		_LMFILES_="${saved_LMFILES_}"
-		LOADEDMODULES="${saved_LOADEDMODULES}"
-		export_env _LMFILES_ LOADEDMODULES
+		declare -g Version="${PMODULES_VERSION}"
+		g_env_must_be_saved='yes'
 	fi
 else
 	pmodules_init

From 69bcb98a07c38706c5057f7b370d6c093459b203 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 11 May 2021 14:05:19 +0200
Subject: [PATCH 61/94] modulecmd: create a tmpdile for sub-cmd switch

---
 Pmodules/modulecmd.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index e449b61..799ee94 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2283,7 +2283,7 @@ if (( ${#GroupDepths[@]} == 0 )); then
 fi
 
 case ${subcommand} in
-	load|purge|search )
+	load|purge|search|switch )
 		declare -r tmpfile=$( ${mktemp} /tmp/Pmodules.XXXXXX ) \
 			|| std::die 1 "Oops: unable to create tmp file!"
 		;;

From fd21f982542835a93843f8ba120dc5f3c4584dc3 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 11 May 2021 15:09:20 +0200
Subject: [PATCH 62/94] modulecmd: optional overlay configuration in config
 file added

---
 Pmodules/modulecmd.bash.in | 47 +++++++++++++++++++++++---------------
 1 file changed, 29 insertions(+), 18 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index f3400a0..f29f89f 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -49,6 +49,7 @@ else
 	declare -r  modulecmd="${libexecdir}/modulecmd.bin"
 fi
 
+declare -r ol_normal='n'
 declare -r ol_hiding='h'
 declare -r ol_replacing='r'
 
@@ -1374,7 +1375,8 @@ subcommand_use() {
 	use () {
                 use_overlay() {
 			if [[ -n ${LOADEDMODULES} ]]; then
-				if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
+				if [[  $LOADEDMODULES == *:*  ]] \
+					   || [[ $LOADEDMODULES != Pmodules/* ]]; then
 					std::error "%s %s: %s" \
 						   "${CMD}" "${subcommand}" \
 						   "overlay cannot be added since some modules are already loaded!"
@@ -1385,24 +1387,29 @@ subcommand_use() {
 				fi
 			fi
 			local overlay=''
-			local modifier='0'
+			local type="${ol_normal}"
 			if [[ $1 == *:* ]]; then
-				modifier=${1##*:}
+				type=${1##*:}
 				overlay=${1%:*}
-				case ${modifier} in
-					${ol_replacing} | ${ol_hiding} )
-						:
-						;;
-					* )
-						std::die 3 "%s %s: %s -- %s" \
-							 "${CMD}" "${subcommand}" \
-							 "invalid modifier '${modifier}!" \
-							 "${overlay}"
-						;;
-				esac
+			elif [[ -d $1 ]] && [[ -r $1/config/overlay.conf ]]; then
+				overlay=$1
+				source "${overlay}/config/overlay.conf"
 			else
 				overlay=$1
 			fi
+			
+			case ${type} in
+				${ol_normal} | ${ol_replacing} | ${ol_hiding} )
+					:
+					;;
+				* )
+					std::die 3 "%s %s: %s -- %s" \
+						 "${CMD}" "${subcommand}" \
+						 "invalid type '${type}!" \
+						 "${overlay}"
+					;;
+			esac
+			
                         overlay=${overlay%/} # remove trailing '/' if there is one
                         [[ -d "${overlay}" ]] || \
                                 std::die 3 "%s %s: %s -- %s" \
@@ -1417,7 +1424,7 @@ subcommand_use() {
 				return 0
 			fi  
 				
-			if [[ "${modifier}" == "${ol_replacing}" ]]; then
+			if [[ "${type}" == "${ol_replacing}" ]]; then
 				# if this overlay replaces groups, we have to remove
 				# the modules made available by other overlays in these groups
 				for group in ${UsedGroups//:/ }; do
@@ -1442,7 +1449,7 @@ subcommand_use() {
                                 fi
                         done
 
-                        OverlayDict[${overlay}]=${modifier}
+                        OverlayDict[${overlay}]=${type}
                         OverlayList=( "${overlay}" "${OverlayList[@]}" )
                         export_env OverlayList
                         g_env_must_be_saved='yes'
@@ -1517,6 +1524,10 @@ subcommand_use() {
                 fi
 
                 local dir="$(cd "${arg}" && pwd)"
+		if [[ -r ${dir}/config/overlay.conf ]]; then
+			use_overlay "${dir}"
+			return
+		fi
                 local overlay
                 for overlay in "${OverlayList[@]}"; do
                         if [[ ${dir}/ =~ ^${overlay}/ ]]; then
@@ -1594,7 +1605,7 @@ subcommand_unuse() {
 						 "${overlay}"
 				fi
 			fi
-			overlay=${overlay%:*}  # ignore any modifier
+			overlay=${overlay%:*}  # ignore any type
 			overlay=${overlay%/} # remove trailing '/' if there is one
                         [[ -d "${overlay}" ]] || \
                                 std::die 3 "%s %s: %s -- %s" \
@@ -1612,7 +1623,7 @@ subcommand_unuse() {
                                          "not an used overlay" \
                                          "${overlay}"
 				
-			if [[ "${modifier}" == "${ol_replacing}" ]]; then
+			if [[ "${OverlayDict[${overlay}]}" == "${ol_replacing}" ]]; then
 				# if this overlay hides groups, we have to re-add
 				# the modules made available by other overlays
 				for group in ${UsedGroups//:/ }; do

From f31dc385133cf45ae52cf17a59ed7ed180eae72a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 20 May 2021 14:41:19 +0200
Subject: [PATCH 63/94] modulecmd: some unnecessary return statements removed
 after std::die

---
 Pmodules/modulecmd.bash.in | 20 +++++---------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index f29f89f..43b0633 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1512,7 +1512,6 @@ subcommand_use() {
                                  "${CMD}" "${subcommand}" \
                                  "illegal group" \
                                  "${arg}"
-                        return
                 fi
                 # arg must be a directory!
 		if [[ ! -d ${arg} ]]; then
@@ -1520,7 +1519,6 @@ subcommand_use() {
                                  "${CMD}" "${subcommand}" \
                                  "illegal argument" \
                                  "${arg}"
-                        return
                 fi
 
                 local dir="$(cd "${arg}" && pwd)"
@@ -1700,7 +1698,6 @@ subcommand_unuse() {
                                  "${CMD}" "${subcommand}" \
                                  "illegal group" \
                                  "${arg}"
-                        return
                 fi
                 # user wants to append a directory to MODULEPATH
 		if [[ ! -d ${arg} ]]; then
@@ -1708,21 +1705,14 @@ subcommand_unuse() {
                                  "${CMD}" "${subcommand}" \
                                  "illegal argument" \
                                  "${arg}"
-                        return
                 fi
 
                 local dir="$(cd "${arg}" && pwd)"
-                local overlay
-                for overlay in "${OverlayList[@]}"; do
-                        if [[ ${dir}/ =~ ^${overlay}/ ]]; then
-                                # dir is in one of our used overlays
-			        std::die 3 "%s %s: %s -- %s" \
-                                         "${CMD}" "${subcommand}" \
-                                         "illegal argument" \
-                                         "${arg}"
-                                return
-                        fi
-                done
+		if [[ -r ${dir}/config/overlay.conf ]] || [[ -v OverlayDict[${dir}] ]]; then
+			unuse_overlay "${dir}"
+			return
+		fi
+
                 # argument is a modulepath
                 std::remove_path MODULEPATH "${dir}"
 

From 5941ded0d4828c9464271cad6711ff6b9208e19f Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 20 May 2021 14:52:46 +0200
Subject: [PATCH 64/94] modulecmd: more descriptive error message in sub-cmd
 use

---
 Pmodules/modulecmd.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 43b0633..3898101 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1517,7 +1517,7 @@ subcommand_use() {
 		if [[ ! -d ${arg} ]]; then
 			std::die 3 "%s %s: %s -- %s" \
                                  "${CMD}" "${subcommand}" \
-                                 "illegal argument" \
+                                 "illegal argument: is neither a valid keyword, group nor directory" \
                                  "${arg}"
                 fi
 

From 5c393560dfa495dec8f0a82b18658c2755a1f857 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 20 May 2021 14:54:03 +0200
Subject: [PATCH 65/94] modulecmd: re-using overlay check improved/simplified

---
 Pmodules/modulecmd.bash.in | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 3898101..2d79e3f 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1526,17 +1526,16 @@ subcommand_use() {
 			use_overlay "${dir}"
 			return
 		fi
-                local overlay
-                for overlay in "${OverlayList[@]}"; do
-                        if [[ ${dir}/ =~ ^${overlay}/ ]]; then
-                                # dir is in one of our used overlays
-			        std::die 3 "%s %s: %s -- %s" \
-                                         "${CMD}" "${subcommand}" \
-                                         "illegal argument" \
-                                         "${arg}"
-                                return
-                        fi
-                done
+		# Is ${dir} a used overlay?
+		# Note: the config.file 'overlay.conf is *not* required
+		#       in an overlay!'
+		if [[ -v OverlayDict[${dir}] ]]; then
+			std::die 3 "%s %s: %s -- %s" \
+                                 "${CMD}" "${subcommand}" \
+                                 "illegal argument: is already loaded as overlay" \
+                                 "${dir}"
+		fi
+
                 # argument is a modulepath
                 ${add2path_func} MODULEPATH "${dir}"
 	}

From 0b87dc8ac4e92a3911b1a29b43a6d06b5ba4b3ad Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 20 May 2021 14:57:37 +0200
Subject: [PATCH 66/94] modulecmd: bugfix in unuse an overlay

- local declaration of overlay was missing
---
 Pmodules/modulecmd.bash.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 2d79e3f..d6b5d56 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1591,6 +1591,7 @@ subcommand_unuse() {
 	unset IFS
         unuse() {
                 unuse_overlay() {
+			local overlay="$1"
 			if [[ -n ${LOADEDMODULES} ]]; then
 				if [[  $LOADEDMODULES == *:*  ]] || [[ $LOADEDMODULES != Pmodules/* ]]; then
 					std::error "%s %s: %s" \

From 4f6b8c89b5684713977bd6ae335de0adbbb69347 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 20 May 2021 16:40:43 +0200
Subject: [PATCH 67/94] set version to 1.0.0rc10

---
 config/versions.conf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/versions.conf b/config/versions.conf
index 442193e..66ce460 100644
--- a/config/versions.conf
+++ b/config/versions.conf
@@ -4,5 +4,5 @@ findutils	4.7.0
 getopt		1.1.6
 gettext		0.21
 modules		3.2.10.1
-Pmodules	1.0.0rc9
+Pmodules	1.0.0rc10
 Tcl		8.6.10

From 4e2572211807d9a9def02df854976d58024aa03e Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 20 May 2021 16:41:30 +0200
Subject: [PATCH 68/94] set version to 1.1.2

---
 config/versions.conf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/versions.conf b/config/versions.conf
index f106cbc..15a3cf2 100644
--- a/config/versions.conf
+++ b/config/versions.conf
@@ -4,6 +4,6 @@ findutils	4.7.0
 getopt		1.1.6
 gettext		0.21
 modules		3.2.10.1
-Pmodules	1.1.1
+Pmodules	1.1.2
 Tcl		8.6.10
 tcllib		1.20

From 8ba396930a7eb66dfd6d9ad1e21f56e9b089b4ee Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 25 May 2021 13:59:30 +0200
Subject: [PATCH 69/94] refactor variable PMODULES_DEFINED_RELEASES

- new name is ReleaseStages

- new name is ReleaseStages
---
 Pmodules/libpbuild.bash    |  2 +-
 Pmodules/modulecmd.bash.in | 12 ++++++------
 Pmodules/profile.bash.in   |  2 +-
 Pmodules/profile.csh.in    |  2 +-
 Pmodules/profile.zsh.in    |  2 +-
 Pmodules/zsh               |  4 ++--
 config/modbuild.conf.in    |  2 +-
 7 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/Pmodules/libpbuild.bash b/Pmodules/libpbuild.bash
index 3404b63..50f5687 100644
--- a/Pmodules/libpbuild.bash
+++ b/Pmodules/libpbuild.bash
@@ -1302,7 +1302,7 @@ pbuild.build_module() {
 	build_dependency() {
 		local -r m=$1
 		std::debug "${m}: module not available"
-		local rels=( ${PMODULES_DEFINED_RELEASES//:/ } )
+		local rels=( ${ReleaseStages//:/ } )
 		[[ ${dry_run} == yes ]] && \
 			std::die 1 \
 				 "%s " \
diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 799ee94..71031c0 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -38,7 +38,7 @@ fi
 
 source "${libdir}/libstd.bash"
 
-: ${PMODULES_DEFINED_RELEASES:=':unstable:stable:deprecated:'}
+: ${ReleaseStages:=':unstable:stable:deprecated:'}
 
 declare -r  version='@PMODULES_VERSION@'
 
@@ -103,7 +103,7 @@ declare g_env_must_be_saved='no'
 save_env() {
         [[ $1 == 'no' ]] && return 0
         local vars=( Version GroupDepths UsedReleases UseFlags UsedGroups )
-        vars+=( PMODULES_DEFAULT_GROUPS PMODULES_DEFINED_RELEASES )
+        vars+=( PMODULES_DEFAULT_GROUPS ReleaseStages )
         vars+=( PMODULES_DEFAULT_RELEASES )
 
 	local s=$(typeset -p ${vars[@]})
@@ -151,7 +151,7 @@ get_release() {
 }
 
 is_release() {
-	[[ ${PMODULES_DEFINED_RELEASES} =~ :$1: ]]
+	[[ ${ReleaseStages} =~ :$1: ]]
 }
 
 #
@@ -937,7 +937,7 @@ subcommand_avail() {
                                 print_help "${subcommand}"
                                 ;;
 			-a | --all | --all-releases )
-				opt_use_releases="${PMODULES_DEFINED_RELEASES}"
+				opt_use_releases="${ReleaseStages}"
 				;;
 			-h | --human )
 				output_function='human_readable_output'
@@ -1095,7 +1095,7 @@ subcommand_use() {
 			std::info "\t${r}"
 		done
 		std::info "\nUnused releases:"
-		for r in ${PMODULES_DEFINED_RELEASES//:/ }; do
+		for r in ${ReleaseStages//:/ }; do
 			if ! release_is_used $r; then
 				std::info "\t${r}"
 			fi
@@ -1916,7 +1916,7 @@ subcommand_search() {
                                 done
 				;;
 			-a | --all-releases )
-				opt_use_releases="${PMODULES_DEFINED_RELEASES}"
+				opt_use_releases="${ReleaseStages}"
 				;;
 			--src )
 				# :FIXME: do we have to add some sanity checks here?
diff --git a/Pmodules/profile.bash.in b/Pmodules/profile.bash.in
index 3cc380c..aec73c1 100644
--- a/Pmodules/profile.bash.in
+++ b/Pmodules/profile.bash.in
@@ -27,7 +27,7 @@ export	PMODULES_DEFAULT_RELEASES
 export	PMODULES_VERSION
 
 declare -x PMODULES_MODULEFILES_DIR='modulefiles'
-declare -x PMODULES_DEFINED_RELEASES=':unstable:stable:deprecated:'
+declare -x ReleaseStages=':unstable:stable:deprecated:'
 
 declare -x PMODULES_ROOT=$(cd $(dirname "${BASH_SOURCE}")/.. && pwd)
 declare -x PMODULES_CONFIG_DIR=$(basename $(cd $(dirname "${BASH_SOURCE}") && pwd))
diff --git a/Pmodules/profile.csh.in b/Pmodules/profile.csh.in
index 0047bdb..b5b5843 100755
--- a/Pmodules/profile.csh.in
+++ b/Pmodules/profile.csh.in
@@ -14,7 +14,7 @@ endif
 #############################################################################
 
 setenv PMODULES_MODULEFILES_DIR 'modulefiles'
-setenv PMODULES_DEFINED_RELEASES ':unstable:stable:deprecated:'
+setenv ReleaseStages ':unstable:stable:deprecated:'
 
 setenv PMODULES_ROOT "@PMODULES_ROOT@"
 setenv PMODULES_CONFIG_DIR 'config'
diff --git a/Pmodules/profile.zsh.in b/Pmodules/profile.zsh.in
index 83a2ac9..04b184e 100644
--- a/Pmodules/profile.zsh.in
+++ b/Pmodules/profile.zsh.in
@@ -20,7 +20,7 @@ declare -x  PMODULES_VERSION
 #############################################################################
 
 declare -x PMODULES_MODULEFILES_DIR='modulefiles'
-declare -x PMODULES_DEFINED_RELEASES=':unstable:stable:deprecated:'
+declare -x ReleaseStages=':unstable:stable:deprecated:'
 
 declare -x PMODULES_ROOT=$(cd $(dirname "${(%):-%N}")/.. && pwd)
 declare -x PMODULES_CONFIG_DIR=$(basename $(cd $(dirname "${(%):-%N}") && pwd))
diff --git a/Pmodules/zsh b/Pmodules/zsh
index 80dc338..1ef378c 100644
--- a/Pmodules/zsh
+++ b/Pmodules/zsh
@@ -82,12 +82,12 @@ for r in ${PMODULES_DEFAULT_RELEASES[@]}; do
 	usedreleases=( "${r}" ${(m)usedreleases:#${r}} )
 done
 
-eval $(save_env UsedReleases PMODULES_DEFAULT_RELEASES PMODULES_DEFAULT_GROUPS PMODULES_DEFINED_RELEASES)
+eval $(save_env UsedReleases PMODULES_DEFAULT_RELEASES PMODULES_DEFAULT_GROUPS ReleaseStages)
 
 unset UsedReleases
 unset PMODULES_DEFAULT_RELEASES
 unset PMODULES_DEFAULT_GROUPS
-unset PMODULES_DEFINED_RELEASES
+unset ReleaseStages
 
 # initialize MANPATH with output of `man --path` if not set
 [[ -z "${MANPATH}" ]] && manpath=$( man --path )
diff --git a/config/modbuild.conf.in b/config/modbuild.conf.in
index 60d33c3..e943e79 100644
--- a/config/modbuild.conf.in
+++ b/config/modbuild.conf.in
@@ -13,6 +13,6 @@ declare -x PMODULES_MODULEFILES_DIR='modulefiles'
 declare -x PMODULES_HOME="${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}"
 
 declare -x PMODULES_DEFAULT_GROUPS='Tools Programming'
-declare -x PMODULES_DEFINED_RELEASES=':unstable:stable:deprecated:'
+declare    ReleaseStages=':unstable:stable:deprecated:'
 declare -x PMODULES_DEFAULT_RELEASES='stable'
 

From edd3fc40098c3a98a443da7d4dac03713b9ed0b8 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 25 May 2021 14:35:59 +0200
Subject: [PATCH 70/94] refactor variable PMODULES_DEFAULT_RELEASES

- new name is DefaultUsedReleaseStages
---
 Pmodules/modulecmd.bash.in | 4 ++--
 Pmodules/profile.bash.in   | 4 ++--
 Pmodules/profile.csh.in    | 2 +-
 Pmodules/profile.zsh.in    | 4 ++--
 Pmodules/zsh               | 6 +++---
 config/modbuild.conf.in    | 2 +-
 6 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 71031c0..37dc83e 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -104,7 +104,7 @@ save_env() {
         [[ $1 == 'no' ]] && return 0
         local vars=( Version GroupDepths UsedReleases UseFlags UsedGroups )
         vars+=( PMODULES_DEFAULT_GROUPS ReleaseStages )
-        vars+=( PMODULES_DEFAULT_RELEASES )
+        vars+=( DefaultUsedReleaseStages )
 
 	local s=$(typeset -p ${vars[@]})
 	declare -g PMODULES_ENV=$( "${base64}" --wrap=0 <<< "$s" )
@@ -1371,7 +1371,7 @@ reset_used_groups() {
 
 reset_used_releases() {
 	declare -g  UsedReleases=''
-	for r in ${PMODULES_DEFAULT_RELEASES//:/ }; do
+	for r in ${DefaultUsedReleaseStages//:/ }; do
 		std::append_path UsedReleases "${r}"
 	done
         g_env_must_be_saved='yes'
diff --git a/Pmodules/profile.bash.in b/Pmodules/profile.bash.in
index aec73c1..851d5b8 100644
--- a/Pmodules/profile.bash.in
+++ b/Pmodules/profile.bash.in
@@ -7,7 +7,7 @@
 : ${PMODULES_DEFAULT_GROUPS:='Tools Programming'}
 
 # set releases which should be available after initialization
-: ${PMODULES_DEFAULT_RELEASES:='stable'}
+: ${DefaultUsedReleaseStages:='stable'}
 
 # set default version
 : ${PMODULES_VERSION:=@PMODULES_VERSION@}
@@ -23,7 +23,7 @@
 #
 
 export	PMODULES_DEFAULT_GROUPS
-export	PMODULES_DEFAULT_RELEASES
+export	DefaultUsedReleaseStages
 export	PMODULES_VERSION
 
 declare -x PMODULES_MODULEFILES_DIR='modulefiles'
diff --git a/Pmodules/profile.csh.in b/Pmodules/profile.csh.in
index b5b5843..5baa5c4 100755
--- a/Pmodules/profile.csh.in
+++ b/Pmodules/profile.csh.in
@@ -1,7 +1,7 @@
 #!/bin/tcsh
 
 setenv PMODULES_DEFAULT_GROUPS 'Tools Programming'
-setenv PMODULES_DEFAULT_RELEASES 'stable'
+setenv DefaultUsedReleaseStages 'stable'
 if ( ! $?PMODULES_VERSION ) then
 	setenv PMODULES_VERSION "@PMODULES_VERSION@"
 endif
diff --git a/Pmodules/profile.zsh.in b/Pmodules/profile.zsh.in
index 04b184e..b8bb938 100644
--- a/Pmodules/profile.zsh.in
+++ b/Pmodules/profile.zsh.in
@@ -8,11 +8,11 @@
 #
 
 declare -xa PMODULES_DEFAULT_GROUPS
-declare -xa PMODULES_DEFAULT_RELEASES
+declare -xa DefaultUsedReleaseStages
 declare -x  PMODULES_VERSION
 
 : ${PMODULES_DEFAULT_GROUPS:=(Tools Programming)}
-: ${PMODULES_DEFAULT_RELEASES:=(stable)}
+: ${DefaultUsedReleaseStages:=(stable)}
 : ${PMODULES_VERSION:=@PMODULES_VERSION@}
 
 #############################################################################
diff --git a/Pmodules/zsh b/Pmodules/zsh
index 1ef378c..2fda058 100644
--- a/Pmodules/zsh
+++ b/Pmodules/zsh
@@ -78,14 +78,14 @@ done
 # build initial list of used releases
 declare -x UsedReleases=''
 typeset -T UsedReleases usedreleases
-for r in ${PMODULES_DEFAULT_RELEASES[@]}; do
+for r in ${DefaultUsedReleaseStages[@]}; do
 	usedreleases=( "${r}" ${(m)usedreleases:#${r}} )
 done
 
-eval $(save_env UsedReleases PMODULES_DEFAULT_RELEASES PMODULES_DEFAULT_GROUPS ReleaseStages)
+eval $(save_env UsedReleases DefaultUsedReleaseStages PMODULES_DEFAULT_GROUPS ReleaseStages)
 
 unset UsedReleases
-unset PMODULES_DEFAULT_RELEASES
+unset DefaultUsedReleaseStages
 unset PMODULES_DEFAULT_GROUPS
 unset ReleaseStages
 
diff --git a/config/modbuild.conf.in b/config/modbuild.conf.in
index e943e79..5c28cd9 100644
--- a/config/modbuild.conf.in
+++ b/config/modbuild.conf.in
@@ -14,5 +14,5 @@ declare -x PMODULES_HOME="${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}"
 
 declare -x PMODULES_DEFAULT_GROUPS='Tools Programming'
 declare    ReleaseStages=':unstable:stable:deprecated:'
-declare -x PMODULES_DEFAULT_RELEASES='stable'
+declare    DefaultUsedReleaseStages='stable'
 

From 25129b57f776942fd18d6b5551f85c5a61fb25cf Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 25 May 2021 15:37:09 +0200
Subject: [PATCH 71/94] refactored PMODULES_DEFAULT_GROUPS to DefaultGroups

---
 Pmodules/csh               | 2 +-
 Pmodules/modulecmd.bash.in | 4 ++--
 Pmodules/profile.bash.in   | 4 ++--
 Pmodules/profile.csh.in    | 2 +-
 Pmodules/profile.zsh.in    | 4 ++--
 Pmodules/zsh               | 6 +++---
 config/modbuild.conf.in    | 2 +-
 7 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/Pmodules/csh b/Pmodules/csh
index 854152a..5fb9926 100644
--- a/Pmodules/csh
+++ b/Pmodules/csh
@@ -35,7 +35,7 @@ unset prefix
 unset postfix
 
 setenv MODULEPATH
-foreach group ( ${PMODULES_DEFAULT_GROUPS} )
+foreach group ( ${DefaultGroups} )
 	if ( "${MODULEPATH}" == "" ) then
 		setenv MODULEPATH "${PMODULES_ROOT}/${group}/${PMODULES_MODULEFILES_DIR}"
 	else
diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 37dc83e..8ab7be5 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -103,7 +103,7 @@ declare g_env_must_be_saved='no'
 save_env() {
         [[ $1 == 'no' ]] && return 0
         local vars=( Version GroupDepths UsedReleases UseFlags UsedGroups )
-        vars+=( PMODULES_DEFAULT_GROUPS ReleaseStages )
+        vars+=( DefaultGroups ReleaseStages )
         vars+=( DefaultUsedReleaseStages )
 
 	local s=$(typeset -p ${vars[@]})
@@ -1363,7 +1363,7 @@ reset_modulepath() {
 reset_used_groups() {
 	UsedGroups=''
         local group
-        for group in ${PMODULES_DEFAULT_GROUPS}; do
+        for group in ${DefaultGroups}; do
                 std::append_path UsedGroups "${group}"
         done
         g_env_must_be_saved='yes'
diff --git a/Pmodules/profile.bash.in b/Pmodules/profile.bash.in
index 851d5b8..959c245 100644
--- a/Pmodules/profile.bash.in
+++ b/Pmodules/profile.bash.in
@@ -4,7 +4,7 @@
 # in a system wide profile or in a user's profile.
 
 # set groups which should be available after initialization
-: ${PMODULES_DEFAULT_GROUPS:='Tools Programming'}
+: ${DefaultGroups:='Tools Programming'}
 
 # set releases which should be available after initialization
 : ${DefaultUsedReleaseStages:='stable'}
@@ -22,7 +22,7 @@
 #	  ${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}
 #
 
-export	PMODULES_DEFAULT_GROUPS
+export	DefaultGroups
 export	DefaultUsedReleaseStages
 export	PMODULES_VERSION
 
diff --git a/Pmodules/profile.csh.in b/Pmodules/profile.csh.in
index 5baa5c4..79f20e7 100755
--- a/Pmodules/profile.csh.in
+++ b/Pmodules/profile.csh.in
@@ -1,6 +1,6 @@
 #!/bin/tcsh
 
-setenv PMODULES_DEFAULT_GROUPS 'Tools Programming'
+setenv DefaultGroups 'Tools Programming'
 setenv DefaultUsedReleaseStages 'stable'
 if ( ! $?PMODULES_VERSION ) then
 	setenv PMODULES_VERSION "@PMODULES_VERSION@"
diff --git a/Pmodules/profile.zsh.in b/Pmodules/profile.zsh.in
index b8bb938..4d36775 100644
--- a/Pmodules/profile.zsh.in
+++ b/Pmodules/profile.zsh.in
@@ -7,11 +7,11 @@
 #	  ${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}
 #
 
-declare -xa PMODULES_DEFAULT_GROUPS
+declare -xa DefaultGroups
 declare -xa DefaultUsedReleaseStages
 declare -x  PMODULES_VERSION
 
-: ${PMODULES_DEFAULT_GROUPS:=(Tools Programming)}
+: ${DefaultGroups:=(Tools Programming)}
 : ${DefaultUsedReleaseStages:=(stable)}
 : ${PMODULES_VERSION:=@PMODULES_VERSION@}
 
diff --git a/Pmodules/zsh b/Pmodules/zsh
index 2fda058..e59c6f8 100644
--- a/Pmodules/zsh
+++ b/Pmodules/zsh
@@ -70,7 +70,7 @@ declare -x _LMFILES_=''
 # build initial MODULEPATH
 declare -x MODULEPATH=''
 typeset -T MODULEPATH modulepath
-for group in ${PMODULES_DEFAULT_GROUPS[@]}; do
+for group in ${DefaultGroups[@]}; do
 	dir="${PMODULES_ROOT}/${group}/${PMODULES_MODULEFILES_DIR}"
 	modulepath=( "${dir}" ${(m)modulepath:#${dir}} )
 done
@@ -82,11 +82,11 @@ for r in ${DefaultUsedReleaseStages[@]}; do
 	usedreleases=( "${r}" ${(m)usedreleases:#${r}} )
 done
 
-eval $(save_env UsedReleases DefaultUsedReleaseStages PMODULES_DEFAULT_GROUPS ReleaseStages)
+eval $(save_env UsedReleases DefaultUsedReleaseStages DefaultGroups ReleaseStages)
 
 unset UsedReleases
 unset DefaultUsedReleaseStages
-unset PMODULES_DEFAULT_GROUPS
+unset DefaultGroups
 unset ReleaseStages
 
 # initialize MANPATH with output of `man --path` if not set
diff --git a/config/modbuild.conf.in b/config/modbuild.conf.in
index 5c28cd9..bbf1032 100644
--- a/config/modbuild.conf.in
+++ b/config/modbuild.conf.in
@@ -12,7 +12,7 @@ declare -x PMODULES_MODULEFILES_DIR='modulefiles'
 
 declare -x PMODULES_HOME="${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}"
 
-declare -x PMODULES_DEFAULT_GROUPS='Tools Programming'
+declare -x DefaultGroups='Tools Programming'
 declare    ReleaseStages=':unstable:stable:deprecated:'
 declare    DefaultUsedReleaseStages='stable'
 

From 9b33e1723aff5aa0ed8eecd763f5423dc304228e Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 26 May 2021 16:42:50 +0200
Subject: [PATCH 72/94] build: tcllib added

---
 build                | 7 +++++++
 config/versions.conf | 1 +
 2 files changed, 8 insertions(+)

diff --git a/build b/build
index 5e7febf..481d566 100755
--- a/build
+++ b/build
@@ -358,6 +358,10 @@ pmodules::compile() {
 		build Tcl
 	fi
 
+	if [[ ! -e "${PMODULES_HOME}/lib/tcllib1.20" ]] || [[ ${opt_force} == 'yes' ]]; then
+		build tcllib
+	fi
+
 	if [[ ! -e "${PMODULES_HOME}/libexec/modulecmd.bin" ]] || [[ ${opt_force} == 'yes' ]]; then
 		build modules
 	fi
@@ -493,6 +497,9 @@ pmodules::install() {
 	sed "${sed_cmd}" "${SRC_DIR}/modmanage.bash.in"   > "${PMODULES_HOME}/libexec/modmanage.bash"
 	chmod 0755 "${PMODULES_HOME}/libexec/modmanage.bash"
 
+	test -e "${PMODULES_ROOT}/${CONFIG_DIR}/Pmodules.conf" || \
+	    install -m 0644 "${SRC_DIR}/Pmodules.conf"	"${PMODULES_ROOT}/${CONFIG_DIR}"
+	
 	install -m 0644 "${SRC_DIR}/bash"		"${PMODULES_HOME}/init"
 	install -m 0644 "${SRC_DIR}/bash_completion"	"${PMODULES_HOME}/init"
 	install -m 0644 "${SRC_DIR}/csh"		"${PMODULES_HOME}/init"
diff --git a/config/versions.conf b/config/versions.conf
index 66ce460..670deb3 100644
--- a/config/versions.conf
+++ b/config/versions.conf
@@ -6,3 +6,4 @@ gettext		0.21
 modules		3.2.10.1
 Pmodules	1.0.0rc10
 Tcl		8.6.10
+tcllib		1.20

From 85c89df9f5ddd12ccfc68eeeb061db2741b65f1b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 26 May 2021 16:43:38 +0200
Subject: [PATCH 73/94] initialization of Pmodules environment reviewed

- introduce new configuration file ${PMODULES_ROOT}/config/Pmodules.conf
- move as much as possible from profile.bash and init/bash to
  modulecmd
- expose less environment variables to the user
---
 Pmodules/bash              |   5 ++
 Pmodules/libmodules.tcl    |  16 ++++++
 Pmodules/modulecmd.bash.in | 104 ++++++++++++++++++++++---------------
 Pmodules/profile.bash.in   |  25 ---------
 4 files changed, 83 insertions(+), 67 deletions(-)

diff --git a/Pmodules/bash b/Pmodules/bash
index c7e9bf5..5afa1be 100644
--- a/Pmodules/bash
+++ b/Pmodules/bash
@@ -35,6 +35,11 @@ unset MODULE_VERSION_STACK
 unset MODULESHOME
 unset PMODULES_ENV
 
+declare -x PMODULES_MODULEFILES_DIR='modulefiles'
+declare -x PMODULES_CONFIG_DIR='config'
+declare -x PMODULES_DIR="${PMODULES_HOME}"
+
+
 #############################################################################
 # implement module comand as shell function
 #
diff --git a/Pmodules/libmodules.tcl b/Pmodules/libmodules.tcl
index e94b022..e8776a3 100644
--- a/Pmodules/libmodules.tcl
+++ b/Pmodules/libmodules.tcl
@@ -22,6 +22,22 @@ if {[info exists env(PMODULES_DEBUG)] && $env(PMODULES_DEBUG)} {
 
 debug "loading libmodules"
 
+package require base64
+
+proc _pmodules_parse_pmodules_env { } {
+        debug "enter"
+	foreach line [split [base64::decode $::env(PMODULES_ENV)] "\n"] {
+		if { ![regexp -- {.* -[aAx]* (.*)=\((.*)\)} $line -> name value] } {
+			continue
+		}
+		switch $name {
+			UsedGroups {
+				set ::UsedGroups $value
+			}
+		}
+	}
+}
+
 proc module-addgroup { group } {
 	global env
 	global name
diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 8ab7be5..446da1d 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -38,10 +38,6 @@ fi
 
 source "${libdir}/libstd.bash"
 
-: ${ReleaseStages:=':unstable:stable:deprecated:'}
-
-declare -r  version='@PMODULES_VERSION@'
-
 if [[ ${PMODULES_PURETCL} == yes ]]; then
 	declare -r  modulecmd="${libexecdir}/modulecmd.tcl"
 else
@@ -62,8 +58,10 @@ declare -A Subcommands
 declare -A Options
 declare -A Help
 
+declare -r pmodules_config_file="${PMODULES_ROOT}/${PMODULES_CONFIG_DIR}/Pmodules.conf"
+
 Help['version']="
-Pmodules ${version} using Tcl Environment Modules @MODULES_VERSION@
+Pmodules @PMODULES_VERSION@ using Tcl Environment Modules @MODULES_VERSION@
 Copyright GNU GPL v2
 "
 
@@ -89,6 +87,18 @@ export_env() {
 		printf "${fmt}" "$1" "${!1}"
 		shift
 	done
+	# :FIXME: UsedGroups can be modified in libmodule.tcl using
+	# append-path/remove-path! But we keep the state in PMODULES_ENV
+	# so we don't have to export it.
+	# 
+	case "${Shell}" in
+	sh | bash | zsh )
+		echo "unset UsedGroups; "
+		;;
+	csh | tcsh )
+		echo "unsetenv UsedGroups; "
+		;;
+	esac
 }
 
 #
@@ -154,6 +164,42 @@ is_release() {
 	[[ ${ReleaseStages} =~ :$1: ]]
 }
 
+#
+# compute depth of modulefile directory.
+#
+# Args:
+#       $1: absolute path of a modulefile directory
+#
+compute_group_depth () {
+        local -r dir=$1
+	test -d "${dir}" || return 1
+        local group=${dir%/*}
+        local group=${group##*/}
+        [[ -n "${GroupDepths[${group}]}" ]] && return 0
+	local -i depth=$(${find} "${dir}" -depth \( -type f -o -type l \) \
+                          -printf "%d" -quit 2>/dev/null)
+	(( depth-=2 ))
+	# if a group doesn't contain a modulefile, depth is negativ
+	# :FIXME: better solution?
+	(( depth < 0 )) && (( depth = 0 ))
+	GroupDepths[$group]=${depth}
+        g_env_must_be_saved='yes'
+}
+
+#
+# (Re-)Scan available groups in given root and compute group depth's
+#
+# Args:
+#       $1: root of modulefile hierarchy
+#
+scan_groups () {
+	local -r root="$1"
+	local moduledir
+	for moduledir in ${root}/*/${PMODULES_MODULEFILES_DIR}; do
+		compute_group_depth "${moduledir}"
+	done
+}
+
 #
 # Check whether argument is a group
 #
@@ -993,42 +1039,6 @@ subcommand_avail() {
 	done
 }
 
-#
-# compute depth of modulefile directory.
-#
-# Args:
-#       $1: absolute path of a modulefile directory
-#
-compute_group_depth () {
-        local -r dir=$1
-	test -d "${dir}" || return 1
-        local group=${dir%/*}
-        local group=${group##*/}
-        [[ -n "${GroupDepths[${group}]}" ]] && return 0
-	local -i depth=$(${find} "${dir}" -depth \( -type f -o -type l \) \
-                          -printf "%d" -quit 2>/dev/null)
-	(( depth-=2 ))
-	# if a group doesn't contain a modulefile, depth is negativ
-	# :FIXME: better solution?
-	(( depth < 0 )) && (( depth = 0 ))
-	GroupDepths[$group]=${depth}
-        g_env_must_be_saved='yes'
-}
-
-#
-# (Re-)Scan available groups in given root and compute group depth's
-#
-# Args:
-#       $1: root of modulefile hierarchy
-#
-scan_groups () {
-	local -r root="$1"
-	local moduledir
-	for moduledir in ${root}/*/${PMODULES_MODULEFILES_DIR}; do
-		compute_group_depth "${moduledir}"
-	done
-}
-
 ##############################################################################
 #
 # use [-a|--append|-p|--prepend] [directory|group|release...]
@@ -1397,15 +1407,19 @@ init_manpath() {
 }
 
 pmodules_init() {
+	source "${pmodules_config_file}" || \
+		std::die 3 "Oops: cannot parse config file  -- %s\n" \
+                         "${pmodules_config_file}"
+
 	declare -gx LOADEDMODULES=''
 	declare -gx _LMFILES_=''
 	declare -gx UsedGroups=''
 	declare -gx MODULEPATH=''
-
 	declare -Ag GroupDepths='()'
 	unset UseFlags
 	declare -Ag  UseFlags=()
 	declare -g Version="${PMODULES_VERSION}"
+
         reset_used_groups
         reset_modulepath
         reset_used_releases
@@ -2274,6 +2288,12 @@ if [[ -n ${PMODULES_ENV} ]]; then
 		declare -g Version="${PMODULES_VERSION}"
 		g_env_must_be_saved='yes'
 	fi
+	if [[ -v DefaultGroups ]] || [[ -v DefaultUsedReleaseStages ]] || [[ -v ReleaseStages ]]; then
+		source "${pmodules_config_file}" || \
+			std::die 3 "Oops: cannot parse config file  -- %s\n" \
+				 "${pmodules_config_file}"
+
+	fi
 else
 	pmodules_init
 fi
diff --git a/Pmodules/profile.bash.in b/Pmodules/profile.bash.in
index 959c245..f25eee8 100644
--- a/Pmodules/profile.bash.in
+++ b/Pmodules/profile.bash.in
@@ -3,36 +3,11 @@
 # The following settings are system defaults. They can be (re-)defined
 # in a system wide profile or in a user's profile.
 
-# set groups which should be available after initialization
-: ${DefaultGroups:='Tools Programming'}
-
-# set releases which should be available after initialization
-: ${DefaultUsedReleaseStages:='stable'}
-
 # set default version
 : ${PMODULES_VERSION:=@PMODULES_VERSION@}
 
-#############################################################################
-#          N O   C H A N G E S   B E L O W   T H I S   L I N E !            #
-#
-# Notes:
-#	- PMODULES_ROOT is derived from the location of this file.
-#	- Some for PMODULES_CONFIG_DIR.
-#	- The Pmodules software must be installed in
-#	  ${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}
-#
-
-export	DefaultGroups
-export	DefaultUsedReleaseStages
-export	PMODULES_VERSION
-
-declare -x PMODULES_MODULEFILES_DIR='modulefiles'
-declare -x ReleaseStages=':unstable:stable:deprecated:'
-
 declare -x PMODULES_ROOT=$(cd $(dirname "${BASH_SOURCE}")/.. && pwd)
-declare -x PMODULES_CONFIG_DIR=$(basename $(cd $(dirname "${BASH_SOURCE}") && pwd))
 declare -x PMODULES_HOME="${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}"
-declare -x PMODULES_DIR="${PMODULES_HOME}"
 
 test -r "${PMODULES_HOME}/init/bash" && source "$_"
 

From dfb133cae73e60836a4f440a3ecb140fadcc8ecb Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 26 May 2021 16:50:10 +0200
Subject: [PATCH 74/94] config/Pmodules.conf added

---
 Pmodules/Pmodules.conf | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 Pmodules/Pmodules.conf

diff --git a/Pmodules/Pmodules.conf b/Pmodules/Pmodules.conf
new file mode 100644
index 0000000..5f9230c
--- /dev/null
+++ b/Pmodules/Pmodules.conf
@@ -0,0 +1,8 @@
+# set groups which should be available after initialization
+DefaultGroups='Tools Programming'
+
+# define available release stages
+ReleaseStages=':unstable:stable:deprecated:'
+
+# set releases which should be available after initialization
+DefaultUsedReleaseStages='stable'

From fd6708352c3b847b1b4bffb7410095c2d23ec6ae Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 26 May 2021 16:50:41 +0200
Subject: [PATCH 75/94] tcllib added

---
 Tools/tcllib/build | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 Tools/tcllib/build

diff --git a/Tools/tcllib/build b/Tools/tcllib/build
new file mode 100644
index 0000000..ea151ba
--- /dev/null
+++ b/Tools/tcllib/build
@@ -0,0 +1,5 @@
+#!/usr/bin/env modbuild
+
+pbuild::set_download_url "https://core.tcl-lang.org/tcllib/uv/$P-$V.tar.xz"
+
+

From b40297d1a42f38b8669d106ec709e329e748fc2c Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 26 May 2021 17:47:26 +0200
Subject: [PATCH 76/94] variable DefaultUsedReleaseStages renamed to
 DefaultReleaseStages

---
 Pmodules/Pmodules.conf     | 2 +-
 Pmodules/modulecmd.bash.in | 6 +++---
 Pmodules/profile.csh.in    | 2 +-
 Pmodules/profile.zsh.in    | 4 ++--
 Pmodules/zsh               | 6 +++---
 config/modbuild.conf.in    | 2 +-
 6 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/Pmodules/Pmodules.conf b/Pmodules/Pmodules.conf
index 5f9230c..fffe8a3 100644
--- a/Pmodules/Pmodules.conf
+++ b/Pmodules/Pmodules.conf
@@ -5,4 +5,4 @@ DefaultGroups='Tools Programming'
 ReleaseStages=':unstable:stable:deprecated:'
 
 # set releases which should be available after initialization
-DefaultUsedReleaseStages='stable'
+DefaultReleaseStages='stable'
diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 446da1d..713b786 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -114,7 +114,7 @@ save_env() {
         [[ $1 == 'no' ]] && return 0
         local vars=( Version GroupDepths UsedReleases UseFlags UsedGroups )
         vars+=( DefaultGroups ReleaseStages )
-        vars+=( DefaultUsedReleaseStages )
+        vars+=( DefaultReleaseStages )
 
 	local s=$(typeset -p ${vars[@]})
 	declare -g PMODULES_ENV=$( "${base64}" --wrap=0 <<< "$s" )
@@ -1381,7 +1381,7 @@ reset_used_groups() {
 
 reset_used_releases() {
 	declare -g  UsedReleases=''
-	for r in ${DefaultUsedReleaseStages//:/ }; do
+	for r in ${DefaultReleaseStages//:/ }; do
 		std::append_path UsedReleases "${r}"
 	done
         g_env_must_be_saved='yes'
@@ -2288,7 +2288,7 @@ if [[ -n ${PMODULES_ENV} ]]; then
 		declare -g Version="${PMODULES_VERSION}"
 		g_env_must_be_saved='yes'
 	fi
-	if [[ -v DefaultGroups ]] || [[ -v DefaultUsedReleaseStages ]] || [[ -v ReleaseStages ]]; then
+	if [[ -v DefaultGroups ]] || [[ -v DefaultReleaseStages ]] || [[ -v ReleaseStages ]]; then
 		source "${pmodules_config_file}" || \
 			std::die 3 "Oops: cannot parse config file  -- %s\n" \
 				 "${pmodules_config_file}"
diff --git a/Pmodules/profile.csh.in b/Pmodules/profile.csh.in
index 79f20e7..b00013e 100755
--- a/Pmodules/profile.csh.in
+++ b/Pmodules/profile.csh.in
@@ -1,7 +1,7 @@
 #!/bin/tcsh
 
 setenv DefaultGroups 'Tools Programming'
-setenv DefaultUsedReleaseStages 'stable'
+setenv DefaultReleaseStages 'stable'
 if ( ! $?PMODULES_VERSION ) then
 	setenv PMODULES_VERSION "@PMODULES_VERSION@"
 endif
diff --git a/Pmodules/profile.zsh.in b/Pmodules/profile.zsh.in
index 4d36775..8077e79 100644
--- a/Pmodules/profile.zsh.in
+++ b/Pmodules/profile.zsh.in
@@ -8,11 +8,11 @@
 #
 
 declare -xa DefaultGroups
-declare -xa DefaultUsedReleaseStages
+declare -xa DefaultReleaseStages
 declare -x  PMODULES_VERSION
 
 : ${DefaultGroups:=(Tools Programming)}
-: ${DefaultUsedReleaseStages:=(stable)}
+: ${DefaultReleaseStages:=(stable)}
 : ${PMODULES_VERSION:=@PMODULES_VERSION@}
 
 #############################################################################
diff --git a/Pmodules/zsh b/Pmodules/zsh
index e59c6f8..f1a0a4c 100644
--- a/Pmodules/zsh
+++ b/Pmodules/zsh
@@ -78,14 +78,14 @@ done
 # build initial list of used releases
 declare -x UsedReleases=''
 typeset -T UsedReleases usedreleases
-for r in ${DefaultUsedReleaseStages[@]}; do
+for r in ${DefaultReleaseStages[@]}; do
 	usedreleases=( "${r}" ${(m)usedreleases:#${r}} )
 done
 
-eval $(save_env UsedReleases DefaultUsedReleaseStages DefaultGroups ReleaseStages)
+eval $(save_env UsedReleases DefaultReleaseStages DefaultGroups ReleaseStages)
 
 unset UsedReleases
-unset DefaultUsedReleaseStages
+unset DefaultReleaseStages
 unset DefaultGroups
 unset ReleaseStages
 
diff --git a/config/modbuild.conf.in b/config/modbuild.conf.in
index bbf1032..cfce2aa 100644
--- a/config/modbuild.conf.in
+++ b/config/modbuild.conf.in
@@ -14,5 +14,5 @@ declare -x PMODULES_HOME="${PMODULES_ROOT}/Tools/Pmodules/${PMODULES_VERSION}"
 
 declare -x DefaultGroups='Tools Programming'
 declare    ReleaseStages=':unstable:stable:deprecated:'
-declare    DefaultUsedReleaseStages='stable'
+declare    DefaultReleaseStages='stable'
 

From d5925192522dcdeb4761696903fe22384e320a63 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 2 Jun 2021 13:56:28 +0200
Subject: [PATCH 77/94] use term release stage instead of release

- refactor variables and function names
- internal: refactor UseFlags -> UsedFlags and change type to normal array
---
 Pmodules/modulecmd.bash.in | 259 ++++++++++++++++++-------------------
 1 file changed, 129 insertions(+), 130 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 713b786..a7274da 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -112,9 +112,11 @@ declare g_env_must_be_saved='no'
 
 save_env() {
         [[ $1 == 'no' ]] && return 0
-        local vars=( Version GroupDepths UsedReleases UseFlags UsedGroups )
-        vars+=( DefaultGroups ReleaseStages )
-        vars+=( DefaultReleaseStages )
+        local vars=( Version )
+	vars+=( UsedReleaseStages UsedFlags UsedGroups )
+	vars+=( DefaultGroups DefaultReleaseStages )
+        vars+=( ReleaseStages )
+	vars+=( GroupDepths )
 
 	local s=$(typeset -p ${vars[@]})
 	declare -g PMODULES_ENV=$( "${base64}" --wrap=0 <<< "$s" )
@@ -129,16 +131,16 @@ _exit() {
 trap '_exit' EXIT
 
 #
-# get release of module
+# get release stage of module
 # Note:
-# - the release of a modulefile outside ${PMODULES_ROOT} is 'stable'
-# - the release of a modulefile inside ${PMODULES_ROOT} without a
-#   coresponding release file is 'unstable'
+# - the release stage of a modulefile outside ${PMODULES_ROOT} is 'stable'
+# - the release stage of a modulefile inside ${PMODULES_ROOT} without a
+#   coresponding file is 'unstable'
 #
 # Args:
 # 	$1: absolute modulefile name
 #
-get_release() {
+get_release_stage() {
 	local "$1"
 	local -r modulefile="$2"
 
@@ -149,10 +151,10 @@ get_release() {
 	fi
 
 	# we are inside ${PMODULES_ROOT}
-	local -r releasefile="${modulefile%/*}/.release-${modulefile##*/}"
-	if [[ -r ${releasefile} ]]; then
-		# read releasefile, remove empty lines, spaces etc
-		local -r data=$( < "${releasefile}" )
+	local -r rel_stage_file="${modulefile%/*}/.release-${modulefile##*/}"
+	if [[ -r ${rel_stage_file} ]]; then
+		# read file, remove empty lines, spaces etc
+		local -r data=$( < "${rel_stage_file}" )
 		std::upvar $1 "${data}"
 	else
 		std::upvar $1 'unstable'
@@ -160,7 +162,7 @@ get_release() {
 	return 0
 }
 
-is_release() {
+is_release_stage() {
 	[[ ${ReleaseStages} =~ :$1: ]]
 }
 
@@ -328,7 +330,7 @@ USAGE:
 
 subcommand_load() {
         local -r subcommand='load'
-	local release='undef'
+	local rel_stage='undef'
 	local current_modulefile=''
 	local prefix=''
 	local m=''
@@ -361,12 +363,12 @@ subcommand_load() {
 	#
 	# possible return values:
 	# 	0: module is loadable
-	# 	1: either not a modulefile or unsused release
+	# 	1: either not a modulefile or unsused release stage
 	#
 	# The following variables in the enclosing function are set:
         #       current_modulefile
         #       prefix
-	#	release
+	#	rel_stage
 	#
 	is_available() {
 		local  m=$1
@@ -387,7 +389,7 @@ subcommand_load() {
 		current_modulefile="${array[0]}"
 		prefix="${array[1]}"
 		test -n "${current_modulefile}" || return 1
-		get_release release "${current_modulefile}" "${UsedReleases}"
+		get_release_stage rel_stage "${current_modulefile}" "${UsedReleaseStages}"
 	}
 
 	#
@@ -401,11 +403,11 @@ subcommand_load() {
 	#	none
 	output_load_hints() {
 		local output=''
-		local release=''
+		local rel_stage=''
 		while read -a line; do
-			release=${line[1]}
-			if [[ ! ":${UsedReleases}:" =~ "${release}" ]]; then
-				output+="module use ${release}; "
+			rel_stage=${line[1]}
+			if [[ ! ":${UsedReleaseStages}:" =~ "${rel_stage}" ]]; then
+				output+="module use ${rel_stage}; "
 			fi
 			local group=${line[2]}
 	        	if [[ ! ":${UsedGroups}:" =~ ":${group}:" ]] && \
@@ -471,22 +473,22 @@ subcommand_load() {
 
 			# extendet module name is either
 			# - group:name or
-			# - group:name:release or
-			# - release:name or
-			# - release:group:name or
-			# - name:release
+			# - group:name:rel_stage or
+			# - rel_stage:name or
+			# - rel_stage:group:name or
+			# - name:rel_stage
 
 			IFS=':'
 			local -a toks=($m)
 			unset IFS
 			local group=''
-			local release=''
+			local rel_stage=''
 			if is_group "${toks[0]}"; then
 				group=${toks[0]}
 				m=${toks[1]}
-				release=${toks[2]}
-			elif is_release "${toks[0]}"; then
-				release=${toks[0]}
+				rel_stage=${toks[2]}
+			elif is_release_stage "${toks[0]}"; then
+				rel_stage=${toks[0]}
 				if is_group "${toks[1]}"; then
 					group=${toks[1]}
 					m=${toks[2]}
@@ -498,9 +500,9 @@ subcommand_load() {
 				m=${toks[0]}
 				if is_group "${toks[1]}"; then
 					group=${toks[1]}
-					release=${toks[2]}
+					rel_stage=${toks[2]}
 				else
-					release=${toks[1]}
+					rel_stage=${toks[1]}
 					group=${toks[2]}
 				fi
 			fi
@@ -520,32 +522,26 @@ subcommand_load() {
                                 MODULEPATH+="${PMODULES_MODULEFILES_DIR}"
 				modulepath=( ${MODULEPATH} )
 			fi
-			if [[ -n ${release} ]]; then
-			        is_release "${release}" || \
+			if [[ -n ${rel_stage} ]]; then
+			        is_release_stage "${rel_stage}" || \
                                         std::die 3 "%s %s: %s -- %s\n" \
                                                  "${CMD}" "${subcommand}" \
-                                                 "illegal release name"
-                                                 "${release}"
-				std::append_path UsedReleases "${release}"
+                                                 "illegal release stage"
+                                                 "${rel_stage}"
+				std::append_path UsedReleaseStages "${rel_stage}"
                                 g_env_must_be_saved='yes'
 			fi
 		fi
 		local found=''
-		for flag in "${!UseFlags[@]}"; do
+		for flag in "${UsedFlags[@]/#/_}" ''; do
                	        # :FIXME: this doesn't work if ${m} is a
                        	#         modulename without version
-			if is_available "${m}_${flag}"; then
-				m+="_${flag}"
+			if is_available "${m}"; then
+				m+="${flag}"
 				found=':'
 				break
 			fi
 		done
-		if [[ ! "${found}" ]]; then
-			# no use-flags set
-			if is_available "${m}"; then
-				found=':'
-			fi
-		fi
 		if [[ ! "${found}" ]]; then
 			std::info "%s %s: module unavailable -- %s" \
                                   "${CMD}" 'load' "${m}"
@@ -614,10 +610,10 @@ subcommand_load() {
 
 		local msg=$(printf "%s %s: %s -- %s" \
                                   "${CMD}" 'load' \
-                                  "${release} module has been loaded" \
+                                  "${rel_stage} module has been loaded" \
                                   "${m}")
 		if [[ ${verbosity_lvl} != silent ]] && \
-                           [[ ${release} != stable ]]; then
+                           [[ ${rel_stage} != stable ]]; then
 		        std::info "%s" "${msg}"
 		fi
 		${logger} -t Pmodules "${msg}"
@@ -803,27 +799,27 @@ subcommand_show() {
 #
 # get all available modules in given directory.
 # return list like
-#	modulename1 release1 modulename2 release2 ...
+#	modulename_1 rel_stage_1 modulefile_1 modulename_2 rel_stage_2 modulefile_1 ...
 #
 get_available_modules() {
 	local var="$1"
 	local -r module="$2"
-	local -r use_releases="${3:-${UsedReleases}}"
+	local -r used_rel_stages="${3:-${UsedReleaseStages}}"
 	shift 3 # in the for loop below we use $@ to loop over the directories
 
 	local -a mods=()
-	local    release
-	local dir=''
+	local    rel_stage=''
+	local	 dir=''
 	
 	for dir in "$@"; do
 		test -d "${dir}" || continue
 		{
 			cd "${dir}"
 			while read mod; do
-				get_release release "${dir}/${mod}"
+				get_release_stage rel_stage "${dir}/${mod}"
 				
-				if [[ :${use_releases}: =~ :${release}: ]]; then
-					mods+=( "${mod}" ${release} "${dir}/${mod}")
+				if [[ :${used_rel_stages}: =~ :${rel_stage}: ]]; then
+					mods+=( "${mod}" ${rel_stage} "${dir}/${mod}")
 				fi
 			done < <(${find} -L * \( -type f -o -type l \) -not -name ".*" -ipath "${module}*")
 		}
@@ -836,7 +832,7 @@ get_available_modules() {
 # avail [-hlt] [<module-pattern>...]
 #
 Subcommands[avail]='avail'
-Options[avail]='-l help -o Hahlmt -l all -l all-releases -l human -l long -l machine -l terse'
+Options[avail]='-l help -o Hahlmt -l all -l all-release-stages -l human -l long -l machine -l terse'
 Help[avail]="
 USAGE:
         module avail [switches] string
@@ -850,8 +846,8 @@ USAGE:
 		e.g. a compiler, or with the sub-command 'use'.
 
 SWITCHES:
-        -a|--all||--all-releases
-		List all available modules independend of the release.
+        -a|--all||--all-release-stages
+		List all available modules independend of the release stage.
 
 	-t|--terse
 		Output in short format.
@@ -885,15 +881,16 @@ subcommand_avail() {
 
 	terse_output() {
 		output_header "$1"
-		for (( i=0; i<${#mods[@]}; i+=3 )); do
+		local -i i=0
+		for i in ${!mods[@]}; do
 			local mod=${mods[i]}
-			local release=${mods[i+1]}
-			case $release in
+			local rel_stage=${mods[i+1]}
+			case ${rel_stage} in
 				stable )
 					out=''
 					;;
 				* )
-					out="${release}"
+					out="${rel_stage}"
 					;;
 			esac
 			printf "%-20s\t%s\n" "${mod}" "${out}" 1>&2
@@ -913,13 +910,13 @@ subcommand_avail() {
 		output_header "$1"
 		for (( i=0; i<${#mods[@]}; i+=3 )); do
 			local mod=${mods[i]}
-			local release=${mods[i+1]}
-			case $release in
+			local rel_stage=${mods[i+1]}
+			case ${rel_stage} in
 				stable )
 					out=''
 					;;
 				* )
-					out=${release}
+					out=${rel_stage}
 					;;
 			esac
 			printf "%-20s\t%s\n" "${mod}" "${out}" 1>&2
@@ -935,13 +932,13 @@ subcommand_avail() {
 		local -i max_length=1
 		for ((i=0; i<${#mods[@]}; i+=3)); do
 			if [[ ${verbosity_lvl} == 'verbose' ]]; then
-			        local  release=${mods[i+1]}
-			        case ${mods[i+1]} in
+			        local  rel_stage=${mods[i+1]}
+			        case ${rel_stage} in
 					stable )
 						mod="${mods[i]}"
 						;;
 					* )
-						mod="${mods[i]}(${release:0:1})"
+						mod="${mods[i]}(${rel_stage:0:1})"
 						;;
 				esac
 			else
@@ -974,7 +971,7 @@ subcommand_avail() {
 	}
 	local pattern=()
 	local output_function='human_readable_output'
-	local opt_use_releases="${UsedReleases}"
+	local opt_use_rel_stages="${UsedReleaseStages}"
 	local -A opt_groups=()
 	local val=''
 	while (($# > 0)); do
@@ -982,8 +979,8 @@ subcommand_avail() {
                         -H | --help | -\? )
                                 print_help "${subcommand}"
                                 ;;
-			-a | --all | --all-releases )
-				opt_use_releases="${ReleaseStages}"
+			-a | --all | --all-release-stages )
+				opt_use_rel_stages="${ReleaseStages}"
 				;;
 			-h | --human )
 				output_function='human_readable_output'
@@ -1031,7 +1028,7 @@ subcommand_avail() {
 			get_available_modules \
 				mods \
 				"${string}" \
-                                "${opt_use_releases}" \
+                                "${opt_use_rel_stages}" \
 				"${dir}"
 			[[ ${#mods[@]} == 0 ]] && continue
 			${output_function} "${group}"
@@ -1041,17 +1038,17 @@ subcommand_avail() {
 
 ##############################################################################
 #
-# use [-a|--append|-p|--prepend] [directory|group|release...]
+# use [-a|--append|-p|--prepend] [directory|group|release_stage...]
 #
 Subcommands[use]='use'
 Options[use]='-l help -o Hap -l append -l prepend'
 Help[use]="
 USAGE:
-        module use [-a|--append|-p|--prepend] [directory|group|release...]
+        module use [-a|--append|-p|--prepend] [directory|group|release_stage|...]
 		Without arguments this sub-command displays information about
-		the module search path, used families and releases. You can
-		use this sub-command to get a list of available families and
-		releases.
+		the module search path, used groups and release stages. You can
+		use this sub-command to get a list of available groups and
+		releases stages.
 
 		With a directory as argument, this directory will either be
 		prepended or appended to the module search path. The default
@@ -1080,10 +1077,6 @@ subcommand_use() {
 	        [[ :${UsedGroups}: =~ :$1: ]]
         }
 
-        release_is_used() {
-	        [[ ":${UsedReleases}:" =~ :$1: ]]
-        }
-
 	print_info() {
 		local f
 		local r
@@ -1100,19 +1093,17 @@ subcommand_use() {
 			fi
 		done
 
-		std::info "\nUsed releases:"
-		for r in ${UsedReleases//:/ }; do
+		std::info "\nUsed releases stages:"
+		for r in ${UsedReleaseStages//:/ }; do
 			std::info "\t${r}"
 		done
-		std::info "\nUnused releases:"
+		std::info "\nUnused release stages:"
 		for r in ${ReleaseStages//:/ }; do
-			if ! release_is_used $r; then
-				std::info "\t${r}"
-			fi
+			[[ ":${UsedReleaseStages}:" =~ :$r: ]] && std::info "\t${r}"
 		done
 
 		std::info "\nUsed flags:"
-		for flag in "${!UseFlags[@]}"; do
+		for flag in "${UsedFlags[@]}"; do
 			std::info "\t${flag}"
 		done
 
@@ -1133,14 +1124,14 @@ subcommand_use() {
 	use () {
 		local arg=$1
 
-		if is_release "${arg}"; then
-                        # argument is release
-			std::append_path UsedReleases "${arg}"
+		if is_release_stage "${arg}"; then
+                        # argument is release stage
+			std::append_path UsedReleaseStages "${arg}"
                         return
                 fi
 		if [[ "${arg}" =~ "flag=" ]]; then
                         # argument is flag
-			UseFlags["${arg/flag=}"]=1
+			UsedFlags+=( "${arg/flag=}" )
                         return
                 fi
                 if [[ -z ${GroupDepths[${arg}]} ]] && [[ -d "${PMODULES_ROOT}/${arg}" ]]; then
@@ -1221,14 +1212,14 @@ subcommand_use() {
 
 ##############################################################################
 #
-# unuse directory|group|release...
+# unuse directory|group|release_stage|...
 #
 Subcommands[unuse]='unuse'
 Options[unuse]='-o H -l help'
 Help[unuse]='
 unuse directory|group|release...
-		Remove the given directory, group or release from the search
-		path.
+		Remove the given modulefiles directory, group, release stage,
+                flag or overlay from the search path.
 '
 
 subcommand_unuse() {
@@ -1236,14 +1227,18 @@ subcommand_unuse() {
         unuse() {
                 local arg=$1
 
-                if is_release "${arg}"; then
-                        # argument is release
-			std::remove_path UsedReleases "${arg}"
+                if is_release_stage "${arg}"; then
+                        # argument is release stage
+			std::remove_path UsedReleaseStages "${arg}"
                         return
                 fi
 		if [[ "${arg}" =~ "flag=" ]]; then
                         # argument is flag
-			unset UseFlags["${arg/flag=}"]
+			local flag="${arg/flag=}"
+			local i
+			for i in ${!UsedFlags[@]}; do
+				[[ ${UsedFlags[i]} == ${flag} ]] && unset UsedFlags[i]
+			done
                         return
                 fi
                 if [[ -n ${GroupDepths[${arg}]} ]] &&
@@ -1380,9 +1375,9 @@ reset_used_groups() {
 }
 
 reset_used_releases() {
-	declare -g  UsedReleases=''
+	declare -g  UsedReleaseStages=''
 	for r in ${DefaultReleaseStages//:/ }; do
-		std::append_path UsedReleases "${r}"
+		std::append_path UsedReleaseStages "${r}"
 	done
         g_env_must_be_saved='yes'
 }
@@ -1411,14 +1406,13 @@ pmodules_init() {
 		std::die 3 "Oops: cannot parse config file  -- %s\n" \
                          "${pmodules_config_file}"
 
-	declare -gx LOADEDMODULES=''
-	declare -gx _LMFILES_=''
-	declare -gx UsedGroups=''
-	declare -gx MODULEPATH=''
-	declare -Ag GroupDepths='()'
-	unset UseFlags
-	declare -Ag  UseFlags=()
-	declare -g Version="${PMODULES_VERSION}"
+	declare -gx  LOADEDMODULES=''
+	declare -gx  _LMFILES_=''
+	declare -gx  UsedGroups=''
+	declare -gx  MODULEPATH=''
+	declare -Ag  GroupDepths='()'
+	declare -ag  UsedFlags=()
+	declare -g   Version="${PMODULES_VERSION}"
 
         reset_used_groups
         reset_modulepath
@@ -1615,7 +1609,7 @@ subcommand_clear() {
 #
 Subcommands[search]='search'
 Options[search]='-o aH -l help -l no-header -l print-modulefiles '
-Options[search]+='-l release: -l with: -l all-releases -l src: -l print-csv '
+Options[search]+='-l release-stage: -l with: -l all-release-stages -l src: -l print-csv '
 Options[search]+='-l verbose '
 Options[search]+='-l all-deps -l wrap'
 Help[search]='
@@ -1625,7 +1619,7 @@ USAGE:
 		for modules whose name match the argument.
 
 SWITCHES:
-        -a|--all-releases
+        -a|--all-release-stages
 		Search within all releases.
 
 	--all-deps
@@ -1634,10 +1628,10 @@ SWITCHES:
         --no-header
 		Suppress output of a header.
 
-        --release=RELEASE
-		Search for modules within this release. You can specify this
-		switch multiple times.  Without this switch, the used releases
-		will be searched.
+        --release-stage=RELEASE_STAGE
+		Search for modules within this release stage. You can specify
+                this switch multiple times.  Without this switch, the release
+                stages in use will be searched.
 
         --verbose
                 vebose output
@@ -1697,7 +1691,7 @@ subcommand_search() {
 
                 print_header_default() {
 		        std::info ''
-		        std::info "${fmt}" "Module" "Release" "Group" "Requires"
+		        std::info "${fmt}" "Module" "Rel.stage" "Group" "Requires"
 		        std::info '-%.0s' $(seq 1 ${cols})
 	        }
 
@@ -1736,7 +1730,7 @@ subcommand_search() {
                 
                 print_header_verbose() {
 		        std::info ''
-		        std::info "${fmt}" "Module" "Release" "Group" "Dependencies/Modulefile"
+		        std::info "${fmt}" "Module" "Rel.stage" "Group" "Dependencies/Modulefile"
 		        std::info '-%.0s' $(seq 1 ${cols})
 	        }
 
@@ -1830,19 +1824,18 @@ subcommand_search() {
 			local modulepath=( ${src_prefix[@]/%//${group}/modulefiles$s} )
 			
 			# get and print all available modules in $mpath
-			# with respect to the requested releases
-			# tmpfile: module/version release group group-
-                        # dependencies...
+			# with respect to the requested release stage
+			# tmpfile: module/version rel_stage group dependencies...
 			local mods
 			get_available_modules \
 				mods \
 				"${module}" \
-				"${opt_use_releases}" \
+				"${opt_use_rel_stages}" \
 				"${modulepath[@]}" \
 
 			for (( i=0; i<${#mods[@]}; i+=3 )); do
 				local name=${mods[i]}
-				local release=${mods[i+1]}
+				local rel_stage=${mods[i+1]}
 				local modulefile=${mods[i+2]}
 
 				if (( ${#name} > max_len_modulename)); then
@@ -1870,7 +1863,7 @@ subcommand_search() {
 					unset IFS
 				fi
 				
-				echo ${name} ${release} ${group} ${modulefile} \
+				echo ${name} ${rel_stage} ${group} ${modulefile} \
                                      ${deps[@]} >> "${tmpfile}"
 			done
 		done
@@ -1896,19 +1889,19 @@ subcommand_search() {
 				opt_print_csv='yes'
 				opt_print_header='no'
 				;;
-			--release | --release=* )
+			--release-stage | --release-stage=* )
                                 if [[ "$1" == "--release" ]]; then
                                         local arg=$2
                                         shift
                                 else
                                         local arg=${1/--release=}
                                 fi
-				is_release "${arg}" || \
+				is_release_stage "${arg}" || \
 				        std::die 1 "%s %s: %s -- %s" \
                                                  "${CMD}" 'search' \
-                                                 "illegal release name" \
+                                                 "illegal release stage" \
                                                  "${arg}"
-				opt_use_releases+="${arg}:"
+				opt_use_rel_stages+="${arg}:"
 				;;
 			--with | --with=* )
                                 if [[ "$1" == --with ]]; then
@@ -1930,7 +1923,7 @@ subcommand_search() {
                                 done
 				;;
 			-a | --all-releases )
-				opt_use_releases="${ReleaseStages}"
+				opt_use_rel_stages+="${ReleaseStages}"
 				;;
 			--src )
 				# :FIXME: do we have to add some sanity checks here?
@@ -1955,8 +1948,8 @@ subcommand_search() {
 	        src_prefix="${PMODULES_ROOT}"
 	fi
 
-	if [[ "${opt_use_releases}" == ":" ]]; then
-                opt_use_releases=":${UsedReleases}:"
+	if [[ "${opt_use_rel_stages}" == ":" ]]; then
+                opt_use_rel_stages=":${UsedReleaseStages}:"
 	fi
 
 	if [[ ${#modules[@]} == 0 ]]; then
@@ -2042,7 +2035,7 @@ subcommand_help() {
                 	print_help "${arg}"
                 else
 		        # :FIXME: print help of newest *available* module
-		        # (respecting UsedReleases)
+		        # (respecting UsedReleaseStages)
                         "${modulecmd}" "${Shell}" "${subcommand}" "${arg}"
 	        fi
         done
@@ -2286,6 +2279,12 @@ if [[ -n ${PMODULES_ENV} ]]; then
 	if [[ -z ${Version} ]] || [[ ${Version} != ${PMODULES_VERSION} ]]; then
 		# the Pmodules version changed!
 		declare -g Version="${PMODULES_VERSION}"
+		# renamed in version 1.0.0rc10 and type changed from
+		# associative array to normal array
+		if [[ -v UseFlags ]]; then
+			declare -a UsedFlags=( "${!UseFlags[@]}" )
+			unset UseFlags
+		fi
 		g_env_must_be_saved='yes'
 	fi
 	if [[ -v DefaultGroups ]] || [[ -v DefaultReleaseStages ]] || [[ -v ReleaseStages ]]; then

From d908a4041c1329c02b4c46b1b44050f82367a2b8 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 2 Jun 2021 18:21:53 +0200
Subject: [PATCH 78/94] modulecmd: bugfix in listing unused release stages

---
 Pmodules/modulecmd.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index a7274da..cf18a35 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1099,7 +1099,7 @@ subcommand_use() {
 		done
 		std::info "\nUnused release stages:"
 		for r in ${ReleaseStages//:/ }; do
-			[[ ":${UsedReleaseStages}:" =~ :$r: ]] && std::info "\t${r}"
+			[[ ! ":${UsedReleaseStages}:" =~ :$r: ]] && std::info "\t${r}"
 		done
 
 		std::info "\nUsed flags:"

From b3a6adf9f830657776d809ec60f6f18f7b34c93a Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 2 Jun 2021 18:23:04 +0200
Subject: [PATCH 79/94] modulecmd: handle changes in PMODULES_ENV for old
 versions

---
 Pmodules/modulecmd.bash.in | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index cf18a35..4bf884a 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2285,6 +2285,25 @@ if [[ -n ${PMODULES_ENV} ]]; then
 			declare -a UsedFlags=( "${!UseFlags[@]}" )
 			unset UseFlags
 		fi
+		if [[ ! -v UsedFlags ]]; then
+			declare -a UsedFlags=()
+		fi
+		if [[ -v UsedReleases ]]; then
+			declare -- UsedReleaseStages="${UsedReleases}"
+			unset UsedReleases
+		fi
+		if [[ -v PMODULES_DEFAULT_GROUPS ]]; then
+			declare -- DefaultGroups="${PMODULES_DEFAULT_GROUPS}"
+			unset PMODULES_DEFAULT_GROUPS
+		fi
+		if [[ -v PMODULES_DEFINED_RELEASES ]]; then
+			declare -- ReleaseStages="${PMODULES_DEFINED_RELEASES}"
+			unset PMODULES_DEFINED_RELEASES
+		fi
+		if [[ -v PMODULES_DEFAULT_RELEASES ]]; then
+			declare -- DefaultReleaseStages="${PMODULES_DEFAULT_RELEASES}"
+			unset PMODULES_DEFAULT_RELEASES
+		fi
 		g_env_must_be_saved='yes'
 	fi
 	if [[ -v DefaultGroups ]] || [[ -v DefaultReleaseStages ]] || [[ -v ReleaseStages ]]; then

From 129d6ff5400d47d2978068558b5d9a1c22d133b6 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 7 Jun 2021 14:14:57 +0200
Subject: [PATCH 80/94] bugfix in terse output of sub-cmd avail

---
 Pmodules/modulecmd.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 4bf884a..e0a20b3 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -882,7 +882,7 @@ subcommand_avail() {
 	terse_output() {
 		output_header "$1"
 		local -i i=0
-		for i in ${!mods[@]}; do
+		for (( i=0; i<${#mods[@]}; i+=3 )); do
 			local mod=${mods[i]}
 			local rel_stage=${mods[i+1]}
 			case ${rel_stage} in

From 5edcec45446ffd0ea7e905bdffdddd3fab38a2c3 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 7 Jun 2021 15:27:08 +0200
Subject: [PATCH 81/94] modulecmd: sort module names version aware

- call sort with option --version-sort in getting available modules
  and search cmd
---
 Pmodules/modulecmd.bash.in | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index e0a20b3..57bd58e 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -821,7 +821,10 @@ get_available_modules() {
 				if [[ :${used_rel_stages}: =~ :${rel_stage}: ]]; then
 					mods+=( "${mod}" ${rel_stage} "${dir}/${mod}")
 				fi
-			done < <(${find} -L * \( -type f -o -type l \) -not -name ".*" -ipath "${module}*")
+			done < <(${find} -L * \
+					 \( -type f -o -type l \) -not -name ".*" \
+					 -ipath "${module}*" \
+					 | ${sort} --version-sort)
 		}
 	done
 	std::upvar ${var} "${mods[@]}"
@@ -948,8 +951,6 @@ subcommand_avail() {
 			(( n > max_length )) && (( max_length=n ))
 			available_modules+=("${mod}")
 		done
-		IFS=$'\n' available_modules=($(sort <<<"${available_modules[*]}"))
-		unset IFS
 		local -i span=$(( max_length / 16 + 1 ))	# compute column size
 		local -i colsize=$(( span * 16 ))		# as multiple of 16
 		local -i column=$cols				# force a line-break
@@ -1787,7 +1788,7 @@ subcommand_search() {
                 ${func_print_header}
                 while read -a toks; do
                         ${func_print_line} "${toks[@]}"
-                done < <("${sort}" -k 1,1 -k 4,4 -k 5,5 "${tmpfile}" | \
+                done < <("${sort}" --version-sort -k 1,1 -k 4,4 -k 5,5 "${tmpfile}" | \
                                  ${awk} "${with_modules}")
         }
 

From 586493f69fff33a483897784678276f9364353b5 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 8 Jun 2021 10:01:14 +0200
Subject: [PATCH 82/94] libmodules.tcl: missing curly bracket fixed

---
 Pmodules/libmodules.tcl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Pmodules/libmodules.tcl b/Pmodules/libmodules.tcl
index 7bba9db..b287f88 100644
--- a/Pmodules/libmodules.tcl
+++ b/Pmodules/libmodules.tcl
@@ -45,6 +45,7 @@ proc _pmodules_parse_pmodules_env { } {
 			        foreach k $l {
 				        lappend ::OverlayList $tmp($k)
 			        }
+			}
 			UsedGroups {
 				set ::UsedGroups $value
 			}

From 20a2c0376e959ec4e10fd77f488ec2beb1a9adf9 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 8 Jun 2021 10:02:34 +0200
Subject: [PATCH 83/94] modulecmd: fixed refactored function name

---
 Pmodules/modulecmd.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 172c14b..a9dcc15 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1043,7 +1043,7 @@ find_module() {
 		                for flag in "${UseFlags[@]/#/_}" ""; do
                                         [[ ${mod} == ${module}/*${flag} ]] || continue
                                         std::upvar $1 "${dir}/${mod}"
-                                        get_release \
+                                        get_release_stage \
 						rel_stage \
                                                 "${dir}" \
 						"${mod}"

From 49aa32f4dfb5f8ef52b50418d47ab6e4de3f5da3 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 9 Jun 2021 09:58:47 +0200
Subject: [PATCH 84/94] modulecmd: set defaults for DefaultGroups, etc

- defaults are set for DefaultsGroups, DefaultReleaseStages and ReleaseStages
---
 Pmodules/modulecmd.bash.in | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index 57bd58e..e5c9f2e 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -60,11 +60,29 @@ declare -A Help
 
 declare -r pmodules_config_file="${PMODULES_ROOT}/${PMODULES_CONFIG_DIR}/Pmodules.conf"
 
+# the following settings are used if the Pmodules.conf is not available
+
+# set groups which should be available after initialization
+declare -- DefaultGroups='Tools Programming'
+
+# define available release stages
+declare -- ReleaseStages=':unstable:stable:deprecated:'
+
+# set releases which should be available after initialization
+declare -- DefaultReleaseStages='stable'
+
+# In the dictionary Help we store the help text of each single command
+# and for displaying the version.
+
+# initialize help text of 'module --version'
 Help['version']="
 Pmodules @PMODULES_VERSION@ using Tcl Environment Modules @MODULES_VERSION@
 Copyright GNU GPL v2
 "
 
+#
+# display help text for command given in $1
+#
 print_help() {
         echo -e "${Help[$1]}" 1>&2
         std::die 1

From 12a5fcd8728cb457e9ca0f3ec89940aad259125c Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 9 Jun 2021 10:00:34 +0200
Subject: [PATCH 85/94] modulecmd: fix in 'unuse' help text

---
 Pmodules/modulecmd.bash.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index e5c9f2e..fd74b0c 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1238,7 +1238,7 @@ Options[unuse]='-o H -l help'
 Help[unuse]='
 unuse directory|group|release...
 		Remove the given modulefiles directory, group, release stage,
-                flag or overlay from the search path.
+                flag from the search path.
 '
 
 subcommand_unuse() {

From 4ef135c6ab9c626fc9d714e441518de869bd5de7 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 9 Jun 2021 10:01:13 +0200
Subject: [PATCH 86/94] modulecmd: soure Pmodules.conf only if exist and
 readable

---
 Pmodules/modulecmd.bash.in | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index fd74b0c..c6d822b 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -1421,10 +1421,11 @@ init_manpath() {
 }
 
 pmodules_init() {
-	source "${pmodules_config_file}" || \
-		std::die 3 "Oops: cannot parse config file  -- %s\n" \
-                         "${pmodules_config_file}"
-
+	if [[ -r "${pmodules_config_file}" ]]; then
+		source "${pmodules_config_file}" || \
+			std::die 3 "Oops: cannot parse config file  -- %s\n" \
+				 "${pmodules_config_file}"
+	fi
 	declare -gx  LOADEDMODULES=''
 	declare -gx  _LMFILES_=''
 	declare -gx  UsedGroups=''

From d4132018d1175358895f34bae6a9e80186b13418 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 9 Jun 2021 10:01:47 +0200
Subject: [PATCH 87/94] modulecmd: do not source Pmodules.conf if PMODULES_ENV
 exist

- if PMODULES_ENV is set but DefaultGroups, DefaultReleaseStages or
  ReleaseStages is not set in PMODULES_ENV, the the default defined in
  modulecmd is used
---
 Pmodules/modulecmd.bash.in | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index c6d822b..dde1dd8 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -2326,12 +2326,6 @@ if [[ -n ${PMODULES_ENV} ]]; then
 		fi
 		g_env_must_be_saved='yes'
 	fi
-	if [[ -v DefaultGroups ]] || [[ -v DefaultReleaseStages ]] || [[ -v ReleaseStages ]]; then
-		source "${pmodules_config_file}" || \
-			std::die 3 "Oops: cannot parse config file  -- %s\n" \
-				 "${pmodules_config_file}"
-
-	fi
 else
 	pmodules_init
 fi

From 7a721b859bbf61825974ef42aa7871156da9229b Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 23 Jun 2021 09:33:12 +0200
Subject: [PATCH 88/94] libpbuild.bash: bugfix in version cmp

---
 Pmodules/libpbuild.bash | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Pmodules/libpbuild.bash b/Pmodules/libpbuild.bash
index 8272a93..20732b8 100644
--- a/Pmodules/libpbuild.bash
+++ b/Pmodules/libpbuild.bash
@@ -90,7 +90,7 @@ pbuild::version_lt() {
 pbuild::version_le() {
         pbuild::version_compare "$1" "$2"
         local -i exit_code=$?
-        (( exit_code == 0 || exit_code = 2 ))
+        (( exit_code == 0 || exit_code == 2 ))
 }
 
 
@@ -98,7 +98,7 @@ pbuild::version_gt() {
         pbuild::version_compare "$1" "$2"
         (( $? == 1 ))
         local -i exit_code=$?
-        (( exit_code == 0 || exit_code = 1 ))
+        (( exit_code == 0 || exit_code == 1 ))
 }
 
 pbuild::version_eq() {

From 2d12850de0c6af3d547d4c746321ba878fc6f7ec Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 20 Jul 2021 15:44:46 +0200
Subject: [PATCH 89/94] libpbuild.bash: bugfix in version compare functions

---
 Pmodules/libpbuild.bash | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Pmodules/libpbuild.bash b/Pmodules/libpbuild.bash
index 50f5687..35ce306 100644
--- a/Pmodules/libpbuild.bash
+++ b/Pmodules/libpbuild.bash
@@ -90,7 +90,7 @@ pbuild::version_lt() {
 pbuild::version_le() {
         pbuild::version_compare "$1" "$2"
         local -i exit_code=$?
-        (( exit_code == 0 || exit_code = 2 ))
+        (( exit_code == 0 || exit_code == 2 ))
 }
 
 
@@ -98,7 +98,7 @@ pbuild::version_gt() {
         pbuild::version_compare "$1" "$2"
         (( $? == 1 ))
         local -i exit_code=$?
-        (( exit_code == 0 || exit_code = 1 ))
+        (( exit_code == 0 || exit_code == 1 ))
 }
 
 pbuild::version_eq() {

From 4f625ed86b5435eeb942a2367ace9dcd979164e9 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Tue, 20 Jul 2021 15:54:21 +0200
Subject: [PATCH 90/94] libstd.bash: fix in std.get_os_release_linux() for
 current CentOS

---
 Pmodules/libstd.bash | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Pmodules/libstd.bash b/Pmodules/libstd.bash
index e5a2f46..fedd0c4 100644
--- a/Pmodules/libstd.bash
+++ b/Pmodules/libstd.bash
@@ -220,8 +220,8 @@ std.get_os_release_linux() {
         fi
 
 	case "${ID}" in
-		RedHatEnterpriseServer | RedHatEnterprise | Scientific | rhel | centos | fedora )
-			echo "rhel${VERSION_ID%.*}"
+		RedHatEnterpriseServer | RedHatEnterprise | Scientific | rhel | centos | CentOS | fedora )
+			echo "rhel${VERSION_ID%%.*}"
 			;;
 		Ubuntu )
 			echo "Ubuntu${VERSION_ID%.*}"

From 6ceb76e8fb538d0cfa5e7bad02ef35af99d428f6 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 12 Aug 2021 18:12:13 +0200
Subject: [PATCH 91/94] bash_completion: sub-commands dependencies and sync
 removed

---
 Pmodules/bash_completion | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Pmodules/bash_completion b/Pmodules/bash_completion
index 76c789a..ed47153 100644
--- a/Pmodules/bash_completion
+++ b/Pmodules/bash_completion
@@ -39,9 +39,9 @@ _module() {
 
 	COMPREPLY=()
 
-	cmds="add apropos avail clear dependencies display help\
+	cmds="add apropos avail clear display help\
 	      initadd initclear initlist initprepend initrm initswitch\
-	      keyword list load purge refresh rm search show swap switch sync\
+	      keyword list load purge refresh rm search show swap switch \
 	      unload unuse update use whatis"
 
 	opts="-c -f -h -i -l -s -t -u -v -H -V\

From 02d1939c81eb7c4f9236f451b6059569b52d53da Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 12 Aug 2021 18:14:37 +0200
Subject: [PATCH 92/94] modulecmd: module sub-command --help bugs fixed

---
 Pmodules/modulecmd.bash.in | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index dde1dd8..f620f21 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -262,6 +262,7 @@ subcommand_generic0() {
 				args+=( "$1" )
 				;;
 		esac
+		shift 1
 	done
         if (( ${#args[@]} > 0 )); then
 	        std::die 3 "%s %s: %s\n" \
@@ -459,7 +460,7 @@ subcommand_load() {
 	while (($# > 0)); do
 		case $1 in
                         -H | --help )
-                                print_help "${subcommand_load}"
+                                print_help "${subcommand}"
                                 ;;
 			-f | --force )
 				opts+=(' -f')
@@ -2294,6 +2295,24 @@ if [[ -z "${Subcommands[${subcommand}]}" ]]; then
 	std::die 1 "${CMD}: unknown sub-command -- ${subcommand}\n"
 fi
 
+case ${subcommand} in
+	add )
+		subcommand='load'
+		;;
+	display )
+		subcommand='show'
+		;;
+	keyword )
+		subcommand='apropos'
+		;;
+	rm )
+		subcommand='unload'
+		;;
+	switch )
+		subcommand='swap'
+		;;
+esac
+
 if [[ -n ${PMODULES_ENV} ]]; then
 	eval "$("${base64}" -d <<< "${PMODULES_ENV}" 2>/dev/null)"
 	if [[ -z ${Version} ]] || [[ ${Version} != ${PMODULES_VERSION} ]]; then
@@ -2335,7 +2354,7 @@ if (( ${#GroupDepths[@]} == 0 )); then
 fi
 
 case ${subcommand} in
-	load|purge|search|switch )
+	load|purge|search|swap )
 		declare -r tmpfile=$( ${mktemp} /tmp/Pmodules.XXXXXX ) \
 			|| std::die 1 "Oops: unable to create tmp file!"
 		;;

From e3d8ee97809fcdfc66dd461b7add91e9411442ff Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Thu, 12 Aug 2021 18:27:01 +0200
Subject: [PATCH 93/94] modulecmd: bugfix in removing tmp file in _exit

---
 Pmodules/modulecmd.bash.in | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Pmodules/modulecmd.bash.in b/Pmodules/modulecmd.bash.in
index f620f21..fc51ad6 100644
--- a/Pmodules/modulecmd.bash.in
+++ b/Pmodules/modulecmd.bash.in
@@ -143,7 +143,9 @@ save_env() {
 
 _exit() {
 	save_env "${g_env_must_be_saved}"
-	${rm} -f "${tmpfile}"
+	if [[ -n "${tmpfile}" ]] && [[ -e "${tmpfile}" ]]; then
+		${rm} -f "${tmpfile}" || :
+	fi
 }
 
 trap '_exit' EXIT

From 6093d858ef6da8c3b034f68c94aaf72c62d3fb53 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Mon, 23 Aug 2021 14:46:48 +0200
Subject: [PATCH 94/94] modbuild: some comments added/modified

---
 Pmodules/modbuild.in | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/Pmodules/modbuild.in b/Pmodules/modbuild.in
index a992d9a..a9dd620 100755
--- a/Pmodules/modbuild.in
+++ b/Pmodules/modbuild.in
@@ -409,9 +409,13 @@ build_modules() {
 
 declare -r OVERLAY_CONF="${PMODULES_ROOT}/${PMODULES_CONFIG_DIR}/overlays.conf"
 
+#
+# Return overlay name *and* directory for an overlay given
+# by name *or* directory. Search in the config file ${OVERLAY_CONF}.
+#
 get_overlay_name_and_dir() {
-	local "$1"
-	local "$2"
+	local "$1"	# upvar for overlay name
+	local "$2"	# upvar for overlay directory
 	if [[ -r "${OVERLAY_CONF}" ]]; then
 		local toks=()
 		while read -a toks; do
@@ -430,6 +434,8 @@ get_overlay_name_and_dir() {
 
 parse_args "$@"
 
+#
+# set overlay_name, overlay_dir and opt_system
 #
 # --overlay=name
 #    lookup overlay directory, system name equivalent to overlay name
@@ -438,7 +444,7 @@ parse_args "$@"
 # --overlay=dir
 #    use given overlay dir and default system name
 # --system=name
-#    lookup name, set overlay_dir of found confi
+#    lookup name, set overlay_dir of found config
 declare overlay_name=''
 declare overlay_dir=''
 if [[ -n "${opt_overlay_name_or_dir}" ]]; then