From 3ca9a04717fd61357fbfb87764fa970271aa24c5 Mon Sep 17 00:00:00 2001
From: Pete Peterson <petersonpf@ornl.gov>
Date: Thu, 11 Dec 2025 13:29:11 -0500
Subject: [PATCH 1/7] Do not use pre-defined tasks to allow for working on
 read-only filesystems

---
 src/mantidworkbench   |  13 ++--
 src/nsd-app-wrap.sh   | 147 +++++++++++++-----------------------------
 src/nsd-conda-wrap.sh |   7 +-
 src/paraview          |   2 +-
 4 files changed, 54 insertions(+), 115 deletions(-)
 mode change 100644 => 100755 src/mantidworkbench
 mode change 100644 => 100755 src/paraview

diff --git a/src/mantidworkbench b/src/mantidworkbench
old mode 100644
new mode 100755
index aa719f6..51350f2
--- a/src/mantidworkbench
+++ b/src/mantidworkbench
@@ -4,28 +4,25 @@
 . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
 	. /bin/nsd-app-wrap.sh
 
+# default conda environment if it was not specified
+PIXI_ENV="mantid"
+
 # look for a supplied argument
 for var in "$@"; do
 	case "$var" in
 	--env=*)
 		PIXI_ENV=$(echo "${var}" | awk -F"=" '{print $2}')
-		PIXI_TASK="start_mantid"
 		shift 1 # remove this argument
 		;;
 	--env)
 		PIXI_ENV="$2" # look ahead by one
-		PIXI_TASK="start_mantid"
                 shift 2        # remove the flag and value
 		;;
 	esac
 done
-# default conda environment if it was not specified
-if [ -z "${PIXI_ENV}" ]; then
-	PIXI_ENV="mantid"
-	PIXI_TASK="start_gui"
-fi
+PIXI_TASK="mantidworkbench"
 
 # put together arguments - conda_env, application, argv
 args=("${PIXI_ENV}" "${PIXI_TASK}" "$@")
 # launch the tool
-pixi_launch "${args[@]}"
+activate_pixi_and_launch "${args[@]}"
diff --git a/src/nsd-app-wrap.sh b/src/nsd-app-wrap.sh
index cbcd315..bd5cd89 100755
--- a/src/nsd-app-wrap.sh
+++ b/src/nsd-app-wrap.sh
@@ -1,9 +1,8 @@
 #!/bin/bash
 
-CONDA_PREFIX_CENTRAL="/opt/anaconda"
-CONDA_ACTIVATE_SCRIPT="${CONDA_PREFIX_CENTRAL}/bin/activate"
-# several places have conda installed in /usr/local and link it over
-CONDA_PREFIX_ALT="/usr/local/anaconda"
+# overwrite this value with environment injection e.g.
+# PIXI_PREFIX=/path/to/pixitoml/parent/dir nsd-app-wrap.sh
+PIXI_PREFIX="${PIXI_PREFIX:=/usr/local/pixi}"
 
 ########## Utility functions
 _remove_font_cache() {
@@ -14,114 +13,58 @@ _remove_font_cache() {
   fi
 }
 
-########## Connect to central conda command
-_activate_conda_cmd() {
-  if [ -f "${CONDA_ACTIVATE_SCRIPT}" ]; then
-    # shellcheck disable=SC1090,SC1091,SC2039
-    . "${CONDA_ACTIVATE_SCRIPT}" ""  # don't let command line arguments in
-  else
-    echo "\"${CONDA_ACTIVATE_SCRIPT}\" not found"
-    exit 255
-  fi
-}
-
-_activate_central_anaconda() {
-  if [ "$(command -v conda)" ]; then
-    if [ "${CONDA_ACTIVATE_SCRIPT}" != "$(which conda)" ]; then
-      echo "Switching to central anaconda install in \"${CONDA_PREFIX_CENTRAL}\""
-      _activate_conda_cmd
-    fi
-  else
-    echo "Activating central anaconda install in \"${CONDA_PREFIX_CENTRAL}\""
-    _activate_conda_cmd
-  fi
-
-  # make sure that conda is found in the correct place
-  if [ "${CONDA_PREFIX}" != "${CONDA_PREFIX_CENTRAL}" ] && [ "${CONDA_PREFIX}" != "${CONDA_PREFIX_ALT}" ]; then
-    echo "Found conda at \"${CONDA_PREFIX}\" rather than \"${CONDA_PREFIX_CENTRAL}\""
-    exit 255
-  fi
-}
+########## Generate the path to the manifest directory
+# if the
+_get_pixi_manifest_path() {
+  # pixi environment
+  PIXI_ENV="${1}"
 
-# this should be included in scripts after activate_conda_environment
-# but before the actual command to be activated using a trap
-#
-# trap deactivate_conda_environment EXIT
-#
-# this will preserve the exit code from the main command
-_deactivate_conda_environment() {
-    echo "Deactivate conda environment"
-    conda deactivate
+  echo "${PIXI_PREFIX%/}/${PIXI_ENV}"
 }
 
-########## Activate the environment in the central conda install
-activate_conda_environment () {
-  CONDA_EXP_ENV="${1}"
-
-  # verify that central conda install is the one being used
-  _activate_central_anaconda
-
-  # activate the environment
-  conda activate "${CONDA_EXP_ENV}"
-
-  # verify that the correct one was activated
-  if [ ! "$CONDA_DEFAULT_ENV" == "$CONDA_EXP_ENV" ]; then
-    echo "Failed to activate \"${CONDA_EXP_ENV}\" conda environment"
-    exit 255
-  else
-    echo "Activated \"$CONDA_EXP_ENV\" conda environment"
+########## Activate the environment in the central pixi install
+# this assumes that "pixi" is in the user's path
+activate_pixi_environment () {
+  # pixi environment
+  PIXI_ENV="${1}"
+
+  _path_to_manifest=$(_get_pixi_manifest_path "${PIXI_ENV}")
+  # check the directory exists
+  if [ ! -d "${_path_to_manifest}" ]; then
+    echo "Manfest path does not exist: ${_path_to_manifest}"
+    exit 1 # error ends the script
   fi
 
-  # unload the environment on exit
-  trap _deactivate_conda_environment EXIT
+  # activate the environment
+  pixi shell --frozen --manifest-path "${_path_to_manifest}"
 }
 
 ########## Activate the environment and start the application
-# The arguments are (conda_env, command, argv) and can be put
+# The arguments are (pixi_env, command, argv) and can be put
 # together and supplied like
 #
 # args=("mantid-dev" "mantidworkbench" "$@")
-# activate_and_launch "${args[@]}"
-activate_and_launch() {
-    # first argument is conda environment
-    CONDA_EXP_ENV="${1}"
-    shift
-    # second argument is startup command
-    COMMAND="${1}"
-    shift
-    # the rest is passed to the command being started
-
-    _remove_font_cache
-    activate_conda_environment "${CONDA_EXP_ENV}"
-
-    echo "Execute: ${COMMAND} $*"
-    "${COMMAND}" "$@"
-}
-
-pixi_launch() {
-        PIXI_PREFIX="/usr/local/pixi"
-        PIXI_ENV="${1}"
-        shift
-      	# This grabs everything past the first argument
-        PIXI_TASK="${*}"
-
-        path_to_manifest="${PIXI_PREFIX%/}/${PIXI_ENV}"
-
-        # Verify path_to_manifest directory exists
-      	if [ ! -d "${path_to_manifest}" ]; then
-	          echo "No pixi environment found at ${path_to_manifest}"
-	          exit 1
-	      fi
-
-        #echo "P: $PIXI_PREFIX, E: $PIXI_ENV, T: $PIXI_TASK - ptm: $path_to_manifest."
-
-        _remove_font_cache
-
-        pixi_run="pixi run --frozen --manifest-path $path_to_manifest $PIXI_TASK"
-
-        #echo "pixi command: $pixi_run"
-
-        $pixi_run
+# activate_pixi_and_launch "${args[@]}"
+#
+# This assumes that "pixi" is in the user's path
+activate_pixi_and_launch() {
+  # first argument is pixi environment
+  PIXI_ENV="${1}"
+  shift
+  # second argument is startup command
+  COMMAND="${1}"
+  shift
+  # the rest is passed to the command being started
+
+  _path_to_manifest=$(_get_pixi_manifest_path "${PIXI_ENV}")
+  # check the directory exists
+  if [ ! -d "${_path_to_manifest}" ]; then
+    echo "Manfest path does not exist: ${_path_to_manifest}"
+    exit 1 # error ends the script
+  fi
 
+  _remove_font_cache
+  # activate the environment and run the command
+  echo "run \"${COMMAND} $*\" in the \"${PIXI_ENV}\" pixi environment"
+  pixi run --frozen --manifest-path "${_path_to_manifest}" "${COMMAND}" "$@"
 }
-
diff --git a/src/nsd-conda-wrap.sh b/src/nsd-conda-wrap.sh
index ee47dad..6897db1 100755
--- a/src/nsd-conda-wrap.sh
+++ b/src/nsd-conda-wrap.sh
@@ -33,8 +33,7 @@ fi
 . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
     . /bin/nsd-app-wrap.sh
 
-# launch pixi
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "$STARTUP" "$@") 
-# launch the tool
-pixi_launch "${args[@]}"
+args=("${PIXI_ENVIRON}" "$STARTUP" "$@")
+# launch pixi
+activate_pixi_and_launch "${args[@]}"
diff --git a/src/paraview b/src/paraview
old mode 100644
new mode 100755
index 40ae384..d60db56
--- a/src/paraview
+++ b/src/paraview
@@ -11,4 +11,4 @@ PIXI_ENVIRON=paraview
 args=("${PIXI_ENVIRON}" "paraview" "$@")
 
 # start the application
-pixi_launch "${args[@]}"
+activate_pixi_and_launch "${args[@]}"
-- 
GitLab


From af630e84383fef38532c4345cbd6e9b0250acba6 Mon Sep 17 00:00:00 2001
From: Pete Peterson <petersonpf@ornl.gov>
Date: Thu, 11 Dec 2025 14:06:22 -0500
Subject: [PATCH 2/7] Stop installing the neutron-imaging launcher

Currently, the imaging users are using a different approach for using
the appropriate software.
---
 rpm/nsd-app-wrap.spec |  3 ++-
 src/neutron-imaging   | 61 +++++++++++++++++++++++++------------------
 2 files changed, 37 insertions(+), 27 deletions(-)

diff --git a/rpm/nsd-app-wrap.spec b/rpm/nsd-app-wrap.spec
index 3cf8a52..6122206 100644
--- a/rpm/nsd-app-wrap.spec
+++ b/rpm/nsd-app-wrap.spec
@@ -41,7 +41,8 @@ install -m 755 mantidpython                           %{buildroot}%{_bindir}/
 install -m 755 mantidworkbench                        %{buildroot}%{_bindir}/
 install -m 755 mantidtotalscattering                  %{buildroot}%{_bindir}/
 install -m 755 mcstas                                 %{buildroot}%{_bindir}/
-install -m 755 neutron-imaging                        %{buildroot}%{_bindir}/
+# not used right now - things that look like scriptlets cannot be in comments
+#install -m 755 neutron-imaging                        {buildroot}{_bindir}/
 install -m 755 nr_launcher                            %{buildroot}%{_bindir}/
 install -m 755 nsd-app-wrap.sh                        %{buildroot}%{_bindir}/
 install -m 755 nsd-conda-wrap.sh                      %{buildroot}%{_bindir}/
diff --git a/src/neutron-imaging b/src/neutron-imaging
index d1f4793..a09e712 100644
--- a/src/neutron-imaging
+++ b/src/neutron-imaging
@@ -1,29 +1,38 @@
 #!/bin/sh
 
-# select the environment to use
-CONDA_ENVIRON=neutron-imaging
-NOTEBOOK_DIR=~/notebooks/IPTS_notebooks
-if [ -n "$1" ]; then
-  if [ "--dev" = "$1" ]; then
-    CONDA_ENVIRON=neutron-imaging-dev
-    NOTEBOOK_DIR=~/notebooks/IPTS_notebooks_testing
-    shift  # drop this argument
-  fi
-fi
+######################################################################
+# Currently this scipt is not used
+######################################################################
+echo "Contact Jean Bilheux <bilheuxjm@ornl.gov> for alternate method of running the notebooks"
+exit 1
 
-# import library to do the real work
-. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh"
-
-# activate the environment - will be deactivated on exit
-activate_conda_environment "${CONDA_ENVIRON}"
-
-# start the application
-echo "Update the notebooks..."
-rsync --exclude '.git*' -a /SNS/software/share/jupyter/notebooks/ ~/notebooks/
-echo "Done!"
-
-cd $NOTEBOOK_DIR || exit 1
-
-echo "Starting Jupyter... (be patient please while we set up your system!)"
-# assumes the correct jupyter is in the path
-jupyter notebook notebooks
+######################################################################
+# remove a single # from each of the following lines
+######################################################################
+## select the environment to use
+#CONDA_ENVIRON=neutron-imaging
+#NOTEBOOK_DIR=~/notebooks/IPTS_notebooks
+#if [ -n "$1" ]; then
+#  if [ "--dev" = "$1" ]; then
+#    CONDA_ENVIRON=neutron-imaging-dev
+#    NOTEBOOK_DIR=~/notebooks/IPTS_notebooks_testing
+#    shift  # drop this argument
+#  fi
+#fi
+#
+## import library to do the real work
+#. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh"
+#
+## activate the environment - will be deactivated on exit
+#activate_conda_environment "${CONDA_ENVIRON}"
+#
+## start the application
+#echo "Update the notebooks..."
+#rsync --exclude '.git*' -a /SNS/software/share/jupyter/notebooks/ ~/notebooks/
+#echo "Done!"
+#
+#cd $NOTEBOOK_DIR || exit 1
+#
+#echo "Starting Jupyter... (be patient please while we set up your system!)"
+## assumes the correct jupyter is in the path
+#jupyter notebook notebooks
-- 
GitLab


From 9f63d7a9b8b3a5e456621b4eae231b431d91b712 Mon Sep 17 00:00:00 2001
From: Pete Peterson <petersonpf@ornl.gov>
Date: Thu, 11 Dec 2025 14:44:19 -0500
Subject: [PATCH 3/7] gsas2 doesn't have a pixi deploy environment

---
 rpm/nsd-app-wrap.spec |  3 ++-
 src/gsas2             | 21 +++++++++------------
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/rpm/nsd-app-wrap.spec b/rpm/nsd-app-wrap.spec
index 6122206..a8e928d 100644
--- a/rpm/nsd-app-wrap.spec
+++ b/rpm/nsd-app-wrap.spec
@@ -27,7 +27,8 @@ mkdir -p %{buildroot}%{_bindir}/
 install -m 755 addie                                  %{buildroot}%{_bindir}/
 install -m 755 data2config                            %{buildroot}%{_bindir}/
 install -m 755 drtsans                                %{buildroot}%{_bindir}/
-install -m 755 gsas2                                  %{buildroot}%{_bindir}/
+# no pixi environment exists yet
+#install -m 755 gsas2                                  {buildroot}{_bindir}/
 install -m 755 hyspecppt                              %{buildroot}%{_bindir}/
 install -m 755 ibeatles                               %{buildroot}%{_bindir}/
 install -m 755 inspired                               %{buildroot}%{_bindir}/
diff --git a/src/gsas2 b/src/gsas2
index 729d7e5..65168c9 100644
--- a/src/gsas2
+++ b/src/gsas2
@@ -1,14 +1,11 @@
 #!/bin/sh
 
-# select the environment to use
-PIXI_ENVIRON=gsas2
-
-# import library to do the real work
-. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
-  || . /bin/nsd-app-wrap.sh
-
-# put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
-# launch the tool
-pixi_launch "${args[@]}"
-
+######################################################################
+# Currently this scipt is not used
+######################################################################
+exit 1
+
+######################################################################
+# remove a single # from each of the following lines
+######################################################################
+#"$(dirname "$(realpath "$0")")/nsd-conda-wrap.sh" gsas2 --classic /path/to/GSASII.py
-- 
GitLab


From 2c370e34c615d2d1d932ca2c7f19f4f50252b356 Mon Sep 17 00:00:00 2001
From: Pete Peterson <petersonpf@ornl.gov>
Date: Thu, 11 Dec 2025 14:53:57 -0500
Subject: [PATCH 4/7] Copy start_gui command from the toml files

---
 src/addie                  | 4 ++--
 src/hyspecppt              | 2 +-
 src/ibeatles               | 3 +--
 src/inspired               | 2 +-
 src/licorne                | 2 +-
 src/mantidtotalscattering  | 2 +-
 src/mantidworkbench        | 2 +-
 src/mantidworkbenchnightly | 2 +-
 src/mantidworkbenchqa      | 2 +-
 src/mcstas                 | 2 +-
 src/nsd-app-wrap.sh        | 4 ++--
 src/nsd-conda-wrap.sh      | 2 +-
 src/paraview               | 2 +-
 src/pdfgui2                | 2 +-
 src/quicknxs               | 3 +--
 src/refl1d                 | 2 +-
 src/refred                 | 2 +-
 src/sasview                | 2 +-
 src/shiver                 | 2 +-
 19 files changed, 21 insertions(+), 23 deletions(-)

diff --git a/src/addie b/src/addie
index ba8b459..0010035 100644
--- a/src/addie
+++ b/src/addie
@@ -31,9 +31,9 @@ fi
 
 # put together arguments - conda_env, application, argv
 if [ -n "${mode_arg}" ]; then
-  args=("${PIXI_ENVIRON}" "start_gui" "${mode_arg}" "${@}")
+  args=("${PIXI_ENVIRON}" "addie" "${mode_arg}" "${@}")
 else
-  args=("${PIXI_ENVIRON}" "start_gui" "${@}")
+  args=("${PIXI_ENVIRON}" "addie" "${@}")
 fi
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/hyspecppt b/src/hyspecppt
index 25d7181..10d02d3 100644
--- a/src/hyspecppt
+++ b/src/hyspecppt
@@ -19,6 +19,6 @@ fi
   || . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "hyspecppt" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/ibeatles b/src/ibeatles
index 3f07b20..567f899 100644
--- a/src/ibeatles
+++ b/src/ibeatles
@@ -10,7 +10,6 @@ PIXI_ENVIRON=ibeatles
   || . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "start" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
-
diff --git a/src/inspired b/src/inspired
index 6fc7660..c50ccae 100644
--- a/src/inspired
+++ b/src/inspired
@@ -19,6 +19,6 @@ fi
   . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "inspired" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/licorne b/src/licorne
index 1a1e9a3..756a3a7 100644
--- a/src/licorne
+++ b/src/licorne
@@ -10,6 +10,6 @@ PIXI_ENVIRON=licorne
     . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "licorne" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/mantidtotalscattering b/src/mantidtotalscattering
index 4509946..fadeffa 100644
--- a/src/mantidtotalscattering
+++ b/src/mantidtotalscattering
@@ -18,6 +18,6 @@ fi
   . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "mantidtotalscattering" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/mantidworkbench b/src/mantidworkbench
index 51350f2..5489bc8 100755
--- a/src/mantidworkbench
+++ b/src/mantidworkbench
@@ -25,4 +25,4 @@ PIXI_TASK="mantidworkbench"
 # put together arguments - conda_env, application, argv
 args=("${PIXI_ENV}" "${PIXI_TASK}" "$@")
 # launch the tool
-activate_pixi_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/mantidworkbenchnightly b/src/mantidworkbenchnightly
index 6eb4827..82dc02e 100644
--- a/src/mantidworkbenchnightly
+++ b/src/mantidworkbenchnightly
@@ -6,6 +6,6 @@
 
 # put together arguments - conda_env, application, argv
 PIXI_ENV="mantid_dev"
-args=("${PIXI_ENV}" "start_gui" "$@")
+args=("${PIXI_ENV}" "mantidworkbench" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/mantidworkbenchqa b/src/mantidworkbenchqa
index c51b591..765422f 100644
--- a/src/mantidworkbenchqa
+++ b/src/mantidworkbenchqa
@@ -6,6 +6,6 @@
 
 # put together arguments - conda_env, application, argv
 PIXI_ENV="mantid_qa"
-args=("${PIXI_ENV}" "start_gui" "$@")
+args=("${PIXI_ENV}" "mantidworkbench" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/mcstas b/src/mcstas
index 08387a6..a2c2e2d 100644
--- a/src/mcstas
+++ b/src/mcstas
@@ -10,6 +10,6 @@ PIXI_ENVIRON=mctsas
   || . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "mcgui" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/nsd-app-wrap.sh b/src/nsd-app-wrap.sh
index bd5cd89..c75a94e 100755
--- a/src/nsd-app-wrap.sh
+++ b/src/nsd-app-wrap.sh
@@ -44,10 +44,10 @@ activate_pixi_environment () {
 # together and supplied like
 #
 # args=("mantid-dev" "mantidworkbench" "$@")
-# activate_pixi_and_launch "${args[@]}"
+# pixi_launch "${args[@]}"
 #
 # This assumes that "pixi" is in the user's path
-activate_pixi_and_launch() {
+pixi_launch() {
   # first argument is pixi environment
   PIXI_ENV="${1}"
   shift
diff --git a/src/nsd-conda-wrap.sh b/src/nsd-conda-wrap.sh
index 6897db1..f6e7c63 100755
--- a/src/nsd-conda-wrap.sh
+++ b/src/nsd-conda-wrap.sh
@@ -36,4 +36,4 @@ fi
 # put together arguments - conda_env, application, argv
 args=("${PIXI_ENVIRON}" "$STARTUP" "$@")
 # launch pixi
-activate_pixi_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/paraview b/src/paraview
index d60db56..40ae384 100755
--- a/src/paraview
+++ b/src/paraview
@@ -11,4 +11,4 @@ PIXI_ENVIRON=paraview
 args=("${PIXI_ENVIRON}" "paraview" "$@")
 
 # start the application
-activate_pixi_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/pdfgui2 b/src/pdfgui2
index a9c248d..af8209f 100644
--- a/src/pdfgui2
+++ b/src/pdfgui2
@@ -9,7 +9,7 @@ PIXI_ENVIRON=pdfgui
     . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "pdfgui" "$@")
 
 # start the application
 pixi_launch "${args[@]}"
diff --git a/src/quicknxs b/src/quicknxs
index c01d79c..0559990 100644
--- a/src/quicknxs
+++ b/src/quicknxs
@@ -18,7 +18,6 @@ fi
 . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
   || . /bin/nsd-app-wrap.sh
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "quicknxs-gui" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
-
diff --git a/src/refl1d b/src/refl1d
index 97b2d46..728c657 100644
--- a/src/refl1d
+++ b/src/refl1d
@@ -24,6 +24,6 @@ fi
   . /bin/nsd-app-wrap.sh # Resolves to /bin/nsd-app-wrap.sh ?
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "refl1d" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/refred b/src/refred
index f188dce..2987cb9 100644
--- a/src/refred
+++ b/src/refred
@@ -18,6 +18,6 @@ fi
   . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "refred-gui" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/sasview b/src/sasview
index 9d85dca..7114989 100644
--- a/src/sasview
+++ b/src/sasview
@@ -10,6 +10,6 @@ PIXI_ENVIRON=sasview
     . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "sasview" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
diff --git a/src/shiver b/src/shiver
index 3177800..dec673f 100644
--- a/src/shiver
+++ b/src/shiver
@@ -18,6 +18,6 @@ fi
   . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${PIXI_ENVIRON}" "start_gui" "$@")
+args=("${PIXI_ENVIRON}" "shiver" "$@")
 # launch the tool
 pixi_launch "${args[@]}"
-- 
GitLab


From 802d5740b99942005dd925c6f8309b180f447612 Mon Sep 17 00:00:00 2001
From: Pete Peterson <petersonpf@ornl.gov>
Date: Thu, 11 Dec 2025 14:57:53 -0500
Subject: [PATCH 5/7] Call main mantidworkbench with a named environment

---
 src/mantidworkbenchnightly | 11 ++---------
 src/mantidworkbenchqa      | 11 ++---------
 2 files changed, 4 insertions(+), 18 deletions(-)

diff --git a/src/mantidworkbenchnightly b/src/mantidworkbenchnightly
index 82dc02e..02cb331 100644
--- a/src/mantidworkbenchnightly
+++ b/src/mantidworkbenchnightly
@@ -1,11 +1,4 @@
 #!/bin/bash
-# import library to do the real work
-# shellcheck disable=SC1091
-. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-    . /bin/nsd-app-wrap.sh
-
-# put together arguments - conda_env, application, argv
+# call the main mantidworkbench with an environment
 PIXI_ENV="mantid_dev"
-args=("${PIXI_ENV}" "mantidworkbench" "$@")
-# launch the tool
-pixi_launch "${args[@]}"
+"$(dirname "$(realpath "$0")")/mantidworkbench" --env "${PIXI_ENV}"
diff --git a/src/mantidworkbenchqa b/src/mantidworkbenchqa
index 765422f..9c0acee 100644
--- a/src/mantidworkbenchqa
+++ b/src/mantidworkbenchqa
@@ -1,11 +1,4 @@
 #!/bin/bash
-# import library to do the real work
-# shellcheck disable=SC1091
-. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-    . /bin/nsd-app-wrap.sh
-
-# put together arguments - conda_env, application, argv
+# call the main mantidworkbench with an environment
 PIXI_ENV="mantid_qa"
-args=("${PIXI_ENV}" "mantidworkbench" "$@")
-# launch the tool
-pixi_launch "${args[@]}"
+"$(dirname "$(realpath "$0")")/mantidworkbench" --env "${PIXI_ENV}"
-- 
GitLab


From 2bc104d4c344e33c0222b15a64cca6aae900812e Mon Sep 17 00:00:00 2001
From: Pete Peterson <petersonpf@ornl.gov>
Date: Thu, 11 Dec 2025 15:08:48 -0500
Subject: [PATCH 6/7] Fix shellcheck issue

---
 src/paraview | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/paraview b/src/paraview
index 40ae384..8da3521 100755
--- a/src/paraview
+++ b/src/paraview
@@ -4,8 +4,9 @@
 # current default is system version
 PIXI_ENVIRON=paraview
 # import library to do the real work
-. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
-   || . /bin/nsd-app-wrap.sh
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+    . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
 args=("${PIXI_ENVIRON}" "paraview" "$@")
-- 
GitLab


From 35ff57b06ee06ea1b5ea96040266356bde36de46 Mon Sep 17 00:00:00 2001
From: Pete Peterson <petersonpf@ornl.gov>
Date: Thu, 11 Dec 2025 15:39:02 -0500
Subject: [PATCH 7/7] Bump version number

---
 rpm/nsd-app-wrap.spec | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rpm/nsd-app-wrap.spec b/rpm/nsd-app-wrap.spec
index a8e928d..d6a7bf2 100644
--- a/rpm/nsd-app-wrap.spec
+++ b/rpm/nsd-app-wrap.spec
@@ -1,5 +1,5 @@
 Name:           nsd-app-wrap
-Version:        2.11
+Version:        2.12
 Release:        1%{?dist}
 Summary:        Wrapper scripts to launch python applications installed via anaconda
 Vendor:         Peter F. Peterson
-- 
GitLab