From a8aed5e3340d9576814c5c929583b48b192ca719 Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Tue, 12 Aug 2025 11:25:33 -0400
Subject: [PATCH 01/12] updating nsd-conda-wrap for pixi, ironically

---
 src/nsd-conda-wrap.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/nsd-conda-wrap.sh b/src/nsd-conda-wrap.sh
index 37ced1c..ee47dad 100755
--- a/src/nsd-conda-wrap.sh
+++ b/src/nsd-conda-wrap.sh
@@ -13,7 +13,7 @@ if [ -n "$1" ]; then
         _usage
         exit 0
     fi
-    CONDA_ENVIRON="$1"
+    PIXI_ENVIRON="$1"
     shift # drop this argument
 else
     echo "Must specify a conda environment to activate"
@@ -33,8 +33,8 @@ fi
 . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
     . /bin/nsd-app-wrap.sh
 
-# activate the environment - will be deactivated on exit
-activate_conda_environment "${CONDA_ENVIRON}"
-
-# start the application
-"$STARTUP" "$@"
+# launch pixi
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "$STARTUP" "$@") 
+# launch the tool
+pixi_launch "${args[@]}"
-- 
GitLab


From d568f73fabf68e763b44e464e86b39d8b141cc0d Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Tue, 12 Aug 2025 11:26:13 -0400
Subject: [PATCH 02/12] updating nsd-conda-wrap for pixi, ironically

---
 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 01201ac..dd41068 100644
--- a/rpm/nsd-app-wrap.spec
+++ b/rpm/nsd-app-wrap.spec
@@ -1,5 +1,5 @@
 Name:           nsd-app-wrap
-Version:        2.02
+Version:        2.03
 Release:        1%{?dist}
 Summary:        Wrapper scripts to launch python applications installed via anaconda
 Vendor:         Peter F. Peterson
-- 
GitLab


From a8a8630ac82196fff7cf80e3d64f833e98edc738 Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Wed, 20 Aug 2025 11:29:34 -0400
Subject: [PATCH 03/12] a bunch of new launchers

---
 src/addie     | 12 ++++++------
 src/drtsans   | 13 +++++++------
 src/gsas2     | 13 +++++++------
 src/hyspecppt | 11 ++++++-----
 src/inspired  | 25 +++++++++++--------------
 src/licorne   | 22 +++++++++-------------
 6 files changed, 46 insertions(+), 50 deletions(-)

diff --git a/src/addie b/src/addie
index 496a9c2..ba8b459 100644
--- a/src/addie
+++ b/src/addie
@@ -5,18 +5,18 @@
 unset SESSION_MANAGER
 
 # select the environment to use
-CONDA_ENVIRON=addie
+PIXI_ENVIRON=addie
 # If `dev` or `qa` version requested, default to `--mode=mantid`.
 mode_arg=""
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=addie-dev
+    PIXI_ENVIRON=addie_dev
     shift # drop this argument
     if [ -z "$1" ]; then
       mode_arg="--mode=mantid"
     fi
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=addie-qa
+    PIXI_ENVIRON=addie_qa
     shift # drop this argument
     if [ -z "$1" ]; then
       mode_arg="--mode=mantid"
@@ -31,9 +31,9 @@ fi
 
 # put together arguments - conda_env, application, argv
 if [ -n "${mode_arg}" ]; then
-  args=("${CONDA_ENVIRON}" "addie" "${mode_arg}" "${@}")
+  args=("${PIXI_ENVIRON}" "start_gui" "${mode_arg}" "${@}")
 else
-  args=("${CONDA_ENVIRON}" "addie" "${@}")
+  args=("${PIXI_ENVIRON}" "start_gui" "${@}")
 fi
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/drtsans b/src/drtsans
index 63000e4..d3a0acf 100644
--- a/src/drtsans
+++ b/src/drtsans
@@ -1,13 +1,13 @@
 #!/bin/bash
 
 # select the environment to use
-CONDA_ENVIRON=sans
+PIXI_ENVIRON=sans
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=sans-dev
+    PIXI_ENVIRON=sans_dev
     shift  # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=sans-qa
+    PIXI_ENVIRON=sans_qa
     shift  # drop this argument
   fi
 fi
@@ -20,9 +20,10 @@ if [ -n "$1" ] && [ "$1" == "--classic" ]; then
 fi
 
 # import library to do the real work
-. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh"
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
+  || . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${CONDA_ENVIRON}" "${STARTUP}" "$@")
+args=("${PIXI_ENVIRON}" "${STARTUP}" "$@")
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/gsas2 b/src/gsas2
index 5c76908..729d7e5 100644
--- a/src/gsas2
+++ b/src/gsas2
@@ -1,13 +1,14 @@
 #!/bin/sh
 
 # select the environment to use
-CONDA_ENVIRON=gsas2
+PIXI_ENVIRON=gsas2
 
 # import library to do the real work
-. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh"
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
+  || . /bin/nsd-app-wrap.sh
 
-# activate the environment - will be deactivated on exit
-activate_conda_environment "${CONDA_ENVIRON}"
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
 
-# start the application
-python "${CONDA_PREFIX}/GSASII/GSASII.py"
diff --git a/src/hyspecppt b/src/hyspecppt
index ed2574e..25d7181 100644
--- a/src/hyspecppt
+++ b/src/hyspecppt
@@ -2,13 +2,13 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=hyspecppt
+PIXI_ENVIRON=hyspecppt
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=hyspecppt-dev
+    PIXI_ENVIRON=hyspecppt_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=hyspecppt-qa
+    PIXI_ENVIRON=hyspecppt_qa
     shift # drop this argument
   fi
 fi
@@ -17,7 +17,8 @@ fi
 # shellcheck disable=SC1091
 . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
   || . /bin/nsd-app-wrap.sh
+
 # put together arguments - conda_env, application, argv
-args=("${CONDA_ENVIRON}" "hyspecppt" "$@")
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/inspired b/src/inspired
index 705935c..6fc7660 100644
--- a/src/inspired
+++ b/src/inspired
@@ -2,26 +2,23 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=inspired
+PIXI_ENVIRON=inspired
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=inspired-dev
+    PIXI_ENVIRON=inspired_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=inspired-qa
+    PIXI_ENVIRON=inspired_qa
     shift # drop this argument
   fi
 fi
 
-if [ -v CONDA_ENVIRON ]; then
-  # import library to do the real work
-  # shellcheck disable=SC1091
-  . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-    . /bin/nsd-app-wrap.sh
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+  . /bin/nsd-app-wrap.sh
 
-  # activate the environment - will be deactivated on exit
-  activate_conda_environment "${CONDA_ENVIRON}"
-fi
-
-# start the application
-inspired
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
diff --git a/src/licorne b/src/licorne
index 67a465f..1a1e9a3 100644
--- a/src/licorne
+++ b/src/licorne
@@ -2,18 +2,14 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=licorne
+PIXI_ENVIRON=licorne
 
-if [ -v CONDA_ENVIRON ]; then
-    # import library to do the real work
-    # shellcheck disable=SC1091
-    . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-        . /bin/nsd-app-wrap.sh
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+    . /bin/nsd-app-wrap.sh
 
-    # put together arguments - conda_env, application, argv
-    #args=("${CONDA_ENVIRON}" "pyrsplot" "$@")
-    args=("${CONDA_ENVIRON}" "licorne" "$@")
-
-    # start the application
-    activate_and_launch "${args[@]}"
-fi
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
-- 
GitLab


From 17d3e0034fdcc3318bd5865e5b40130e32378233 Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Wed, 20 Aug 2025 16:53:20 -0400
Subject: [PATCH 04/12] a bunch more new launchers

---
 src/ibeatles               | 16 +++++++++++++++-
 src/mantidpythonnightly    |  2 +-
 src/mantidpythonqa         |  2 +-
 src/mantidtotalscattering  | 16 +++++++---------
 src/mantidworkbench        | 17 ++++++++++-------
 src/mantidworkbenchnightly |  6 +++---
 src/mantidworkbenchqa      |  6 +++---
 src/nsd-app-wrap.sh        |  2 +-
 src/paraview               | 18 ++++++++----------
 src/pdfgui2                | 20 +++++++++-----------
 src/pyrs                   | 24 +++++++++++-------------
 11 files changed, 69 insertions(+), 60 deletions(-)

diff --git a/src/ibeatles b/src/ibeatles
index bbceb52..3f07b20 100644
--- a/src/ibeatles
+++ b/src/ibeatles
@@ -1,2 +1,16 @@
 #!/bin/bash
-/opt/anaconda/envs/ibeatles/bin/python -m ibeatles "$@"
+
+# select the environment to use
+# current default is system version
+PIXI_ENVIRON=ibeatles
+
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
+  || . /bin/nsd-app-wrap.sh
+
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
+
diff --git a/src/mantidpythonnightly b/src/mantidpythonnightly
index ab7ebe2..d00210e 100644
--- a/src/mantidpythonnightly
+++ b/src/mantidpythonnightly
@@ -1,2 +1,2 @@
 #!/bin/bash
-"$(dirname "$(realpath "$0")")/nsd-conda-wrap.sh" mantid-dev "$@"
+"$(dirname "$(realpath "$0")")/nsd-conda-wrap.sh" mantid_dev "$@"
diff --git a/src/mantidpythonqa b/src/mantidpythonqa
index 153c18f..8905631 100644
--- a/src/mantidpythonqa
+++ b/src/mantidpythonqa
@@ -1,2 +1,2 @@
 #!/bin/bash
-"$(dirname "$(realpath "$0")")/nsd-conda-wrap.sh" mantid-qa "$@"
+"$(dirname "$(realpath "$0")")/nsd-conda-wrap.sh" mantid_qa "$@"
diff --git a/src/mantidtotalscattering b/src/mantidtotalscattering
index 295536d..4509946 100644
--- a/src/mantidtotalscattering
+++ b/src/mantidtotalscattering
@@ -1,13 +1,13 @@
 #!/bin/bash
 
 # select the environment to use
-CONDA_ENVIRON=mantidtotalscattering
+PIXI_ENVIRON=mantidtotalscattering
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=mantidtotalscattering-dev
+    PIXI_ENVIRON=mantidtotalscattering_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=mantidtotalscattering-qa
+    PIXI_ENVIRON=mantidtotalscattering_qa
     shift
   fi
 fi
@@ -17,9 +17,7 @@ fi
 . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
   . /bin/nsd-app-wrap.sh
 
-# activate the environment - will be deactivated on exit
-activate_conda_environment "${CONDA_ENVIRON}"
-
-# start the application
-echo "$@"
-mantidtotalscattering "$@"
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
diff --git a/src/mantidworkbench b/src/mantidworkbench
index 217a034..aa719f6 100644
--- a/src/mantidworkbench
+++ b/src/mantidworkbench
@@ -8,21 +8,24 @@
 for var in "$@"; do
 	case "$var" in
 	--env=*)
-		CONDA_ENV=$(echo "${var}" | awk -F"=" '{print $2}')
+		PIXI_ENV=$(echo "${var}" | awk -F"=" '{print $2}')
+		PIXI_TASK="start_mantid"
 		shift 1 # remove this argument
 		;;
 	--env)
-		CONDA_ENV="$2" # look ahead by one
-		shift 2        # remove the flag and value
+		PIXI_ENV="$2" # look ahead by one
+		PIXI_TASK="start_mantid"
+                shift 2        # remove the flag and value
 		;;
 	esac
 done
 # default conda environment if it was not specified
-if [ -z "${CONDA_ENV}" ]; then
-	CONDA_ENV="mantid"
+if [ -z "${PIXI_ENV}" ]; then
+	PIXI_ENV="mantid"
+	PIXI_TASK="start_gui"
 fi
 
 # put together arguments - conda_env, application, argv
-args=("${CONDA_ENV}" "/opt/anaconda/envs/${CONDA_ENV}/bin/mantidworkbench" "$@")
+args=("${PIXI_ENV}" "${PIXI_TASK}" "$@")
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/mantidworkbenchnightly b/src/mantidworkbenchnightly
index 3e261d2..6eb4827 100644
--- a/src/mantidworkbenchnightly
+++ b/src/mantidworkbenchnightly
@@ -5,7 +5,7 @@
     . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-CONDA_ENV="mantid-dev"
-args=("${CONDA_ENV}" "/opt/anaconda/envs/${CONDA_ENV}/bin/mantidworkbench" "$@")
+PIXI_ENV="mantid_dev"
+args=("${PIXI_ENV}" "start_gui" "$@")
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/mantidworkbenchqa b/src/mantidworkbenchqa
index e6d2a99..c51b591 100644
--- a/src/mantidworkbenchqa
+++ b/src/mantidworkbenchqa
@@ -5,7 +5,7 @@
     . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-CONDA_ENV="mantid-qa"
-args=("${CONDA_ENV}" "/opt/anaconda/envs/${CONDA_ENV}/bin/mantidworkbench" "$@")
+PIXI_ENV="mantid_qa"
+args=("${PIXI_ENV}" "start_gui" "$@")
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/nsd-app-wrap.sh b/src/nsd-app-wrap.sh
index ee3ef12..6f4154b 100755
--- a/src/nsd-app-wrap.sh
+++ b/src/nsd-app-wrap.sh
@@ -114,7 +114,7 @@ pixi_launch() {
 
         pixi_run="pixi run --frozen --manifest-path $path_to_manifest $PIXI_TASK"
 
-        #echo "pixi command: $pixi_run"
+        echo "pixi command: $pixi_run"
 
         $pixi_run
 
diff --git a/src/paraview b/src/paraview
index eaacc4b..40ae384 100644
--- a/src/paraview
+++ b/src/paraview
@@ -2,15 +2,13 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=paraview
-if [ -v CONDA_ENVIRON ]; then
-    # import library to do the real work
-    . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
-      || . /bin/nsd-app-wrap.sh
+PIXI_ENVIRON=paraview
+# import library to do the real work
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
+   || . /bin/nsd-app-wrap.sh
 
-    # put together arguments - conda_env, application, argv
-    args=("${CONDA_ENVIRON}" "paraview" "$@")
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "paraview" "$@")
 
-    # start the application
-    activate_and_launch "${args[@]}"
-fi
+# start the application
+pixi_launch "${args[@]}"
diff --git a/src/pdfgui2 b/src/pdfgui2
index 1788bfb..a9c248d 100644
--- a/src/pdfgui2
+++ b/src/pdfgui2
@@ -2,16 +2,14 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=pdfgui2
-if [ -v CONDA_ENVIRON ]; then
-    # import library to do the real work
-    # shellcheck disable=SC1091
-    . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-        . /bin/nsd-app-wrap.sh
+PIXI_ENVIRON=pdfgui
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+    . /bin/nsd-app-wrap.sh
 
-    # put together arguments - conda_env, application, argv
-    args=("${CONDA_ENVIRON}" "pdfgui" "$@")
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
 
-    # start the application
-    activate_and_launch "${args[@]}"
-fi
+# start the application
+pixi_launch "${args[@]}"
diff --git a/src/pyrs b/src/pyrs
index 9fa8e32..56f116e 100644
--- a/src/pyrs
+++ b/src/pyrs
@@ -2,26 +2,24 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=pyrs
+PIXI_ENVIRON=pyrs
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=pyrs-dev
+    PIXI_ENVIRON=pyrsi_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=pyrs-qa
+    PIXI_ENVIRON=pyrs_qa
     shift # drop this argument
   fi
 fi
 
-if [ -v CONDA_ENVIRON ]; then
-  # import library to do the real work
-  # shellcheck disable=SC1091
-  . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-    . /bin/nsd-app-wrap.sh
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+  . /bin/nsd-app-wrap.sh
 
-  # put together arguments - conda_env, application, argv
-  args=("${CONDA_ENVIRON}" "pyrsplot" "$@")
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "pyrsplot" "$@")
 
-  # start the application
-  activate_and_launch "${args[@]}"
-fi
+# start the application
+pixi_launch "${args[@]}"
-- 
GitLab


From ef2894a99ada5f3a892484ccd2b8e2e60b5e8476 Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Fri, 22 Aug 2025 11:52:26 -0400
Subject: [PATCH 05/12] adding refred and refl1d updates

---
 src/refl1d | 30 +++++++++++-------------------
 src/refred | 11 +++++------
 2 files changed, 16 insertions(+), 25 deletions(-)

diff --git a/src/refl1d b/src/refl1d
index 0ab392e..4631900 100644
--- a/src/refl1d
+++ b/src/refl1d
@@ -7,31 +7,23 @@ unset SESSION_MANAGER
 COMMAND="refl1d" # --port XXXX
 
 # select the environment to use
-CONDA_ENVIRON=refl1d-qa
+PIXI_ENVIRON=refl1d_qa
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=refl1d-dev
+    PIXI_ENVIRON=refl1d_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=refl1d-qa
+    PIXI_ENVIRON=refl1d_qa
     shift # drop this argument
   fi
 fi
 
-if [ -v CONDA_ENVIRON ]; then
-  # import library to do the real work
-  # shellcheck disable=SC1091
-  . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-    . /bin/nsd-app-wrap.sh # Resolves to /bin/nsd-app-wrap.sh ?
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+  . /bin/nsd-app-wrap.sh # Resolves to /bin/nsd-app-wrap.sh ?
 
-  # override the normal call to activate_and_launch() function
-  activate_conda_environment "${CONDA_ENVIRON}"
-
-  # remove and rebuild the font cache
-  _remove_font_cache
-  fc-cache -r
-
-  # start the application
-  echo "Execute: ${COMMAND} $*"
-  "${COMMAND}" "$@"
-fi
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
diff --git a/src/refred b/src/refred
index f822902..f188dce 100644
--- a/src/refred
+++ b/src/refred
@@ -1,13 +1,13 @@
 #!/bin/bash
 
 # select the environment to use
-CONDA_ENVIRON=refred
+PIXI_ENVIRON=refred
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=refred-dev
+    PIXI_ENVIRON=refred_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=refred-qa
+    PIXI_ENVIRON=refred_qa
     shift # drop this argument
   fi
 fi
@@ -18,7 +18,6 @@ fi
   . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${CONDA_ENVIRON}" "refred-gui" "$@")
-
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
-- 
GitLab


From 3757f639b0342fd4cf7e58a84f5dd2ef8844edcf Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Fri, 22 Aug 2025 15:39:29 -0400
Subject: [PATCH 06/12] adding sasview, shiver, snapwrap, usansred, nseplot and
 mpdf

---
 src/mpdf     |  6 +++---
 src/nseplot  | 20 +++++++++-----------
 src/sasview  | 20 +++++++++-----------
 src/shiver   | 10 +++++-----
 src/snapwrap | 25 +++++++++++--------------
 src/usansred | 24 ++++++++++++------------
 6 files changed, 49 insertions(+), 56 deletions(-)

diff --git a/src/mpdf b/src/mpdf
index 7e5f738..3b57701 100755
--- a/src/mpdf
+++ b/src/mpdf
@@ -2,7 +2,7 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=mpdf
-if [ -v CONDA_ENVIRON ]; then
-    "$(dirname "$(realpath "$0")")/nsd-conda-wrap.sh" "$CONDA_ENVIRON" "$@"
+PIXI_ENVIRON=mpdf
+if [ -v PIXI_ENVIRON ]; then
+    "$(dirname "$(realpath "$0")")/nsd-conda-wrap.sh" "$PIXI_ENVIRON" "$@"
 fi
diff --git a/src/nseplot b/src/nseplot
index 7bd83af..e29dbb1 100755
--- a/src/nseplot
+++ b/src/nseplot
@@ -2,16 +2,14 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=pysen
-if [ -v CONDA_ENVIRON ]; then
-    # import library to do the real work
-    # shellcheck disable=SC1091
-    . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-        . /bin/nsd-app-wrap.sh
+PIXI_ENVIRON=pysen
 
-    # put together arguments - conda_env, application, argv
-    args=("${CONDA_ENVIRON}" "nseplot" "$@")
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+    . /bin/nsd-app-wrap.sh
 
-    # start the application
-    activate_and_launch "${args[@]}"
-fi
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "nseplot" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
diff --git a/src/sasview b/src/sasview
index ae12414..9d85dca 100644
--- a/src/sasview
+++ b/src/sasview
@@ -2,16 +2,14 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=sasview
-if [ -v CONDA_ENVIRON ]; then
-    # import library to do the real work
-    # shellcheck disable=SC1091
-    . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-        . /bin/nsd-app-wrap.sh
+PIXI_ENVIRON=sasview
 
-    # put together arguments - conda_env, application, argv
-    args=("${CONDA_ENVIRON}" "sasview" "$@")
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
+    . /bin/nsd-app-wrap.sh
 
-    # start the application
-    activate_and_launch "${args[@]}"
-fi
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
diff --git a/src/shiver b/src/shiver
index 1fef813..3177800 100644
--- a/src/shiver
+++ b/src/shiver
@@ -1,13 +1,13 @@
 #!/bin/bash
 
 # select the environment to use
-CONDA_ENVIRON=shiver
+PIXI_ENVIRON=shiver
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=shiver-dev
+    PIXI_ENVIRON=shiver_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=shiver-qa
+    PIXI_ENVIRON=shiver_qa
     shift # drop this argument
   fi
 fi
@@ -18,6 +18,6 @@ fi
   . /bin/nsd-app-wrap.sh
 
 # put together arguments - conda_env, application, argv
-args=("${CONDA_ENVIRON}" "shiver" "$@")
+args=("${PIXI_ENVIRON}" "start_gui" "$@")
 # launch the tool
-activate_and_launch "${args[@]}"
+pixi_launch "${args[@]}"
diff --git a/src/snapwrap b/src/snapwrap
index 02eebcc..1f1a55e 100644
--- a/src/snapwrap
+++ b/src/snapwrap
@@ -2,26 +2,23 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=snapwrap
+PIXI_ENVIRON=snapwrap
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=snapwrap-dev
+    PIXI_ENVIRON=snapwrap_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=snapwrap-qa
+    PIXI_ENVIRON=snapwrap_qa
     shift # drop this argument
   fi
 fi
 
-if [ -v CONDA_ENVIRON ]; then
-  # import library to do the real work
-  # shellcheck disable=SC1091
-  . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-    . /bin/nsd-app-wrap.sh
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
+  || . /bin/nsd-app-wrap.sh
 
-  # activate the environment - will be deactivated on exit
-  activate_conda_environment "${CONDA_ENVIRON}"
-fi
-
-# start the application
-python -m workbench
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "python -m workbench" "$@")
+# launch the tool
+pixi_launch "${args[@]}"
diff --git a/src/usansred b/src/usansred
index 920f576..4ff7476 100644
--- a/src/usansred
+++ b/src/usansred
@@ -2,24 +2,24 @@
 
 # select the environment to use
 # current default is system version
-CONDA_ENVIRON=usansred
+PIXI_ENVIRON=usansred
 if [ -n "$1" ]; then
   if [ "$1" == "--dev" ]; then
-    CONDA_ENVIRON=usansred-dev
+    PIXI_ENVIRON=usansred_dev
     shift # drop this argument
   elif [ "$1" == "--qa" ]; then
-    CONDA_ENVIRON=usansred-qa
+    PIXI_ENVIRON=usansred_qa
     shift # drop this argument
   fi
 fi
 
-if [ -v CONDA_ENVIRON ]; then
-  # import library to do the real work
-  # shellcheck disable=SC1091
-  . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-    . /bin/nsd-app-wrap.sh
-  # activate the environment - will be deactivated on exit
-  activate_conda_environment "${CONDA_ENVIRON}"
-fi
+# import library to do the real work
+# shellcheck disable=SC1091
+. "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" \
+  || . /bin/nsd-app-wrap.sh
+
+# put together arguments - conda_env, application, argv
+args=("${PIXI_ENVIRON}" "python" "$@")
 
-# (there is no default appliation to launch)
+# launch the tool
+pixi_launch "${args[@]}"
-- 
GitLab


From f3fda65b79d90cd2ed97447d80a729174ba55cb5 Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Fri, 22 Aug 2025 15:43:47 -0400
Subject: [PATCH 07/12] updating 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 dd41068..12dc08b 100644
--- a/rpm/nsd-app-wrap.spec
+++ b/rpm/nsd-app-wrap.spec
@@ -1,5 +1,5 @@
 Name:           nsd-app-wrap
-Version:        2.03
+Version:        2.04
 Release:        1%{?dist}
 Summary:        Wrapper scripts to launch python applications installed via anaconda
 Vendor:         Peter F. Peterson
-- 
GitLab


From 0ae101810b445683f61eaeee386913e04ef9e11d Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Fri, 22 Aug 2025 15:49:08 -0400
Subject: [PATCH 08/12] somehow messed up the PIXI_TASK variable in
 nsd-app-wrap.sh,   all fixed now

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

diff --git a/src/nsd-app-wrap.sh b/src/nsd-app-wrap.sh
index 6f4154b..1f18fcb 100755
--- a/src/nsd-app-wrap.sh
+++ b/src/nsd-app-wrap.sh
@@ -104,7 +104,7 @@ pixi_launch() {
         shift
 
 	# This grabs everything past the first argument
-        PIXI_TASK="${@}"
+        PIXI_TASK="${*}"
 
         path_to_manifest="${PIXI_PREFIX%/}/${PIXI_ENV}"
 
-- 
GitLab


From a7e605499c5be48ed4414fc13c44468247427bdb Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Tue, 26 Aug 2025 13:41:31 -0400
Subject: [PATCH 09/12] adding nr_launcher

---
 src/nr_launcher | 22 +---------------------
 1 file changed, 1 insertion(+), 21 deletions(-)

diff --git a/src/nr_launcher b/src/nr_launcher
index a21a2e4..a5fabf3 100644
--- a/src/nr_launcher
+++ b/src/nr_launcher
@@ -1,22 +1,2 @@
 #!/bin/bash
-
-# select the environment to use
-CONDA_ENVIRON=refl1d
-
-# check if the conda environment exists
-if ! conda env list | \grep -q "^${CONDA_ENVIRON}[[:space:]]"; then
-    CONDA_ENVIRON=refl1d-qa
-fi
-
-if [ -v CONDA_ENVIRON ]; then
-    # import library to do the real work
-    # shellcheck disable=SC1091
-    . "$(dirname "$(realpath "$0")")/nsd-app-wrap.sh" ||
-        . /bin/nsd-app-wrap.sh
-
-    # put together arguments - conda_env, application, location, arguments passed to this script
-    args=("${CONDA_ENVIRON}" "source" "/SNS/REF_L/shared/launcher/nsd_app_wrap_nr_launcher.sh" "$@")
-
-    # start the application
-    activate_and_launch "${args[@]}"
-fi
+cd /SNS/REF_L/shared/launcher; python launcher.py
-- 
GitLab


From 1798f23d42c1cc21777ecaa032c643ee5b0ca2d6 Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Thu, 28 Aug 2025 10:28:14 -0400
Subject: [PATCH 10/12] commenting out echo

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

diff --git a/src/nsd-app-wrap.sh b/src/nsd-app-wrap.sh
index 1f18fcb..9b61cf4 100755
--- a/src/nsd-app-wrap.sh
+++ b/src/nsd-app-wrap.sh
@@ -114,7 +114,7 @@ pixi_launch() {
 
         pixi_run="pixi run --frozen --manifest-path $path_to_manifest $PIXI_TASK"
 
-        echo "pixi command: $pixi_run"
+        #echo "pixi command: $pixi_run"
 
         $pixi_run
 
-- 
GitLab


From 494250cc565b24b03e12f22cee263cc08eccc5fe Mon Sep 17 00:00:00 2001
From: Randall Petras <petrasrjornl@gmail.com>
Date: Thu, 28 Aug 2025 10:32:09 -0400
Subject: [PATCH 11/12] version number to 2.6

---
 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 12dc08b..b8095c9 100644
--- a/rpm/nsd-app-wrap.spec
+++ b/rpm/nsd-app-wrap.spec
@@ -1,5 +1,5 @@
 Name:           nsd-app-wrap
-Version:        2.04
+Version:        2.6
 Release:        1%{?dist}
 Summary:        Wrapper scripts to launch python applications installed via anaconda
 Vendor:         Peter F. Peterson
-- 
GitLab


From d29437b8be1b0fe1e744e5f5975b7ad61f3878b4 Mon Sep 17 00:00:00 2001
From: "Petras, Randy" <petrasrj@ornl.gov>
Date: Thu, 28 Aug 2025 14:45:49 +0000
Subject: [PATCH 12/12] Edit nsd-app-wrap.spec version 2.7

---
 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 7b731fa..40219da 100644
--- a/rpm/nsd-app-wrap.spec
+++ b/rpm/nsd-app-wrap.spec
@@ -1,5 +1,5 @@
 Name:           nsd-app-wrap
-Version:        2.6
+Version:        2.7
 Release:        1%{?dist}
 Summary:        Wrapper scripts to launch python applications installed via anaconda
 Vendor:         Peter F. Peterson
-- 
GitLab