Sync with main

cmake/support/run-scripts/labenv.bat.in

@@ -13,8 +13,9 @@ SET EXT=%%~xi
 
 @IF "%EXT%"==".instr" (
   @FLAVOR@-pygen %INSTRUMENT%
-  SET INSTRUMENT="%BASE%_generated.py"
-  goto :JupyText 
+  sed s/INSTRUMENT/%BASE%/g %BINDIR%\@MCCODE_RELPATH_BINDIR2TOOLDIR@\Python\@MCCODE_PREFIX@run\template.ipynb.in > %BASE%_generated.ipynb
+  SET INSTRUMENT="%BASE%_generated.ipynb"
+  goto :JupyLaunch 
 ) ELSE IF "%EXT%"==".py" (
   goto :JupyLaunch
 ) ELSE IF "%EXT%"==".ipynb" (

mcstas-comps/optics/Elliptic_guide_gravity.comp

@@ -140,7 +140,7 @@ SETTING PARAMETERS (xwidth = 0,yheight = 0,l,
 	string verbose = "on",
 	enableGravity = 1.0,
 	curvature=0,
-	nSegments=-1,
+	int nSegments=-1,
 	vector mvaluesright=NULL, vector mvaluesleft=NULL, vector mvaluestop=NULL, vector mvaluesbottom=NULL,
 		    vector seglength=NULL)
 

mcstas-comps/optics/Pol_mirror.comp

@@ -111,7 +111,7 @@ INITIALIZE
   if (strlen(rUpData) && strcmp(rUpData,"NULL")){
     if (Table_Read(&rUpTable, rUpData, 1) <= 0) {
       fprintf(stderr,"Pol_mirror: %s: can not read file %s\n",
-          NAME_CURRENT_COMP, rUpPar);
+          NAME_CURRENT_COMP, rUpData);
       exit(1);
     }
     rUpTableFlag=1;
@@ -121,7 +121,7 @@ INITIALIZE
   if (strlen(rUpData) && strcmp(rUpData,"NULL")){
     if (Table_Read(&rDownTable, rDownData, 1) <= 0) {
       fprintf(stderr,"Pol_mirror: %s: can not read file %s\n",
-          NAME_CURRENT_COMP, rDownPar);
+          NAME_CURRENT_COMP, rDownData);
       exit(1);
     }
     rDownTableFlag=1;

meta-pkgs/windows/McStas-metapackage64.iss

@@ -53,7 +53,6 @@ Source: "dist\mcstas-tools-python-mcdisplay-pyqtgraph-NSIS64-@[email protected]
 Source: "dist\mcstas-tools-python-mcdisplay-matplotlib-NSIS64-@[email protected]"; DestDir: "{tmp}"
 Source: "dist\mcstas-tools-python-mcdisplay-mantid-NSIS64-@[email protected]"; DestDir: "{tmp}"
 Source: "dist\mcstas-tools-python-mcdoc-NSIS64-@[email protected]"; DestDir: "{tmp}"
-Source: "dist\mcstas-mcpl-NSIS64-@[email protected]"; DestDir: "{tmp}"
 Source: "Support\Miniforge3-Windows-x86_64.exe"; DestDir: "{tmp}"
 
 [Run]
@@ -76,7 +75,6 @@ Filename: "{tmp}\mcstas-tools-python-mcdisplay-pyqtgraph-NSIS64-@VERSION@-mingw6
 Filename: "{tmp}\mcstas-tools-python-mcdisplay-matplotlib-NSIS64-@[email protected]"; Parameters: "/S"
 Filename: "{tmp}\mcstas-tools-python-mcdisplay-mantid-NSIS64-@[email protected]"; Parameters: "/S"
 Filename: "{tmp}\mcstas-tools-python-mcdoc-NSIS64-@[email protected]"; Parameters: "/S"
-Filename: "{tmp}\mcstas-mcpl-NSIS64-@[email protected]"; Parameters: "/S"
 Filename: "{tmp}\docupdate.bat";
 
 ; NOTE: Don't use "Flags: ignoreversion" on any shared system files

meta-pkgs/windows/McXtrace-metapackage64.iss

@@ -48,7 +48,6 @@ Source: "dist\mcxtrace-tools-python-mxdisplay-webgl-NSIS64-@[email protected]
 Source: "dist\mcxtrace-tools-python-mxdisplay-pyqtgraph-NSIS64-@[email protected]"; DestDir: "{tmp}"
 Source: "dist\mcxtrace-tools-python-mxdisplay-matplotlib-NSIS64-@[email protected]"; DestDir: "{tmp}"
 Source: "dist\mcxtrace-tools-python-mxdoc-NSIS64-@[email protected]"; DestDir: "{tmp}"
-Source: "dist\mcxtrace-mcpl-NSIS64-@[email protected]"; DestDir: "{tmp}"
 Source: "Support\Miniforge3-Windows-x86_64.exe"; DestDir: "{tmp}"
 
 [Run]
@@ -66,7 +65,6 @@ Filename: "{tmp}\mcxtrace-tools-python-mxdisplay-webgl-NSIS64-@VERSION@-mingw64.
 Filename: "{tmp}\mcxtrace-tools-python-mxdisplay-pyqtgraph-NSIS64-@[email protected]"; Parameters: "/S"
 Filename: "{tmp}\mcxtrace-tools-python-mxdisplay-matplotlib-NSIS64-@[email protected]"; Parameters: "/S"
 Filename: "{tmp}\mcxtrace-tools-python-mxdoc-NSIS64-@[email protected]"; Parameters: "/S"
-Filename: "{tmp}\mcxtrace-mcpl-NSIS64-@[email protected]"; Parameters: "/S"
 Filename: "{tmp}\docupdate.bat";
 
 ; NOTE: Don't use "Flags: ignoreversion" on any shared system files

meta-pkgs/windows/environment.yml

@@ -6,6 +6,8 @@ channels:
 
 dependencies:
   - m2-msys2-runtime
+  - m2-which
+  - m2-sed
   - m2w64-gcc
   - m2w64-gsl
   - msmpi

tools/Python/mcrun/CMakeLists.txt

@@ -51,7 +51,7 @@ set(CPACK_NSIS_DISPLAY_NAME "${NSIS_NAME}")
 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "${NSIS_NAME}")
 
 # Debian
-set(CPACK_DEBIAN_PACKAGE_DEPENDS "${FLAVOR}, python3-yaml")
+set(CPACK_DEBIAN_PACKAGE_DEPENDS "${FLAVOR}, python3-yaml, python3-numpy")
 set(CPACK_DEBIAN_PACKAGE_REPLACES "${FLAVOR}-tools-python-${P}run-3.5.1")
 
 # RPM
@@ -90,8 +90,8 @@ install(
   RENAME "${P}run.py"
   )
 
-# Other .py infrastructure
-foreach(NAME "__init__.py" "log.py" "mccode.py" "optimisation.py" "mcsplit.py")
+# Copy in place .py and other infrastructure
+foreach(NAME "__init__.py" "log.py" "mccode.py" "optimisation.py" "mcsplit.py" "template.ipynb.in")
   install(
     FILES "${PROJECT_SOURCE_DIR}/${NAME}"
     DESTINATION "${DEST_TOOLDIR}/${TOOLS_NAME}"

tools/Python/mcrun/jupylab.in

@@ -33,10 +33,9 @@ canrun() {
 if ( canrun ); then
     INSTR=$1 # We can actually assume a single input here
     BASE=`basename ${INSTR} .instr`
-    PYINSTR="${BASE}_generated.py"
     JUPYBK="${BASE}_generated.ipynb"
     @FLAVOR@-pygen ${INSTR}
-    jupytext --to ipynb ${PYINSTR}
+    sed s/INSTRUMENT/${BASE}/g ${UTILDIR}/template.ipynb.in > ${JUPYBK}
     jupyter lab ${JUPYBK}
 else
     @FLAVOR@_errmsg Failed to run Python ${TOOL} - permissions or missing dependencies\?

tools/Python/mcrun/template.ipynb.in

@@ -0,0 +1,159 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import mcstasscript as ms\n",
+    "from INSTRUMENT_generated import make"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "instr=make()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Use instr.settings() to add e.g. seed=1000, ncount=1e7, mpi=8, openacc=True, force_compile=False etc.)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Show diagram\n",
+    "instr.show_diagram()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Visualise with default parameters (defaults to 'window'/pyqtgraph visualisation)\n",
+    "instr.show_instrument(format='window')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Generate a dataset with default parameters.\n",
+    "data = instr.backengine()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Overview plot:\n",
+    "ms.make_sub_plot(data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Other useful commands follow...\n",
+    "# One plot pr. window\n",
+    "#ms.make_plot(data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load another dataset\n",
+    "#data2 = ms.load_data('some_other_folder')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Adjusting a specific plot\n",
+    "#ms.name_plot_options(\\\"PSD_4PI\\\", data, log=1, colormap=\\\"hot\\\", orders_of_mag=5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Bring up the 'interface' - only relevant in Jupyter\n",
+    "#%matplotlib widget\n",
+    "#import mcstasscript.jb_interface as ms_widget\n",
+    "#ms_widget.show(data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Bring up the simulation 'interface' - only relevant in Jupyter\n",
+    "#%matplotlib widget\n",
+    "#import mcstasscript.jb_interface as ms_widget\n",
+    "#sim_widget = ms_widget.SimInterface(instr)\n",
+    "#sim_widget.show_interface()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Acessing data from the interface\n",
+    "#data = sim_widget.get_data()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}