Merge pull request #2255 from mccode-dev/doc-preparations-3.6.0

LAST TO MERGE BEFORE RELEASE (Doc preparations 3.6.0)

Author: willend

CHANGES_McStas

@@ -58,11 +58,158 @@
 * Modified by: PW February 2025: version 3.5.24
 * Modified by: PW April 2025: version 3.5.27
 * Modified by: PW June 2025: version 3.5.32
+* Modified by: PW December 2025: version 3.6.0
 *
-* This file is part of McStas 3.5.32, released April 29th 2025.
+* This file is part of McStas 3.6.0, released December 12th 2025.
 * It gives a 'changes' list from the beginning of the project
 *
 *******************************************************************************/
+Changes in McStas/McXtrace 3.6.0, December 12th, 2025
+
+* Code quality improvements
+  * Remove compiler warnings by @willend in https://github.com/mccode-dev/McCode/pull/2088
+  * Implement 'cppcheck' linting support on Unix, can be utilised via mcrun or mctest by @willend in https://github.com/mccode-dev/McCode/pull/2090
+  * Big overhaul of many component docstings, retire obsoleted components and instruments, component fixes by @willend in https://github.com/mccode-dev/McCode/pull/2117,  https://github.com/mccode-dev/McCode/pull/2118, https://github.com/mccode-dev/McCode/pull/2116,  https://github.com/mccode-dev/McCode/pull/2120, https://github.com/mccode-dev/McCode/pull/2119, https://github.com/mccode-dev/McCode/pull/2115, https://github.com/mccode-dev/McCode/pull/2122, https://github.com/mccode-dev/McCode/pull/2125, https://github.com/mccode-dev/McCode/pull/2144, https://github.com/mccode-dev/McCode/pull/2153, https://github.com/mccode-dev/McCode/pull/2154, https://github.com/mccode-dev/McCode/pull/2156
+  * Linter-oritented fixes in various components by @willend in https://github.com/mccode-dev/McCode/pull/2136, https://github.com/mccode-dev/McCode/pull/2248
+  * Clean up various components / libs where linter output was a bit 'noisy' by @willend in https://github.com/mccode-dev/McCode/pull/2218
+  * Suppres warning from MSVC by using %zi in place of %li by @willend in https://github.com/mccode-dev/McCode/pull/2220
+
+* User gui / command line tools:
+  * mcrun:
+    * Run scan steps in parallel - one scan step pr. one cpu core by @Lomholy in https://github.com/mccode-dev/McCode/pull/2081 (similar to now-deprecated, historical feature of mcrun.pl)
+    * Implement env vars to override mpirun setting by @willend in https://github.com/mccode-dev/McCode/pull/2087 (`MCSTAS_MPIRUN_OVERRIDE` / `MCXTRACE_MPIRUN_OVERRIDE` )
+    * Implement 'cppcheck' linting support on Unix, use `mcrun -C` or mcrun `--c-lint`
+    * Improved error-handling in mccode.py by @willend in https://github.com/mccode-dev/McCode/pull/2139 
+    * Fixes for parameter quoting issues by @tkittel in https://github.com/mccode-dev/McCode/pull/2151
+  * mcgui:
+    * Fixes for parameter quoting issues by @tkittel in https://github.com/mccode-dev/McCode/pull/2151
+  * mctest:
+    * Implement 'cppcheck' linting support on Unix, use `mctest  --lint`
+    * Update mctest with log of attained test value if test ran by @willend in https://github.com/mccode-dev/McCode/pull/2161
+    * Add --local=DIR input to mctest, will test instruments from that folder instead of 'system' by @willend in https://github.com/mccode-dev/McCode/pull/2221
+    * Add mctest feature to filter tested instruments by use of given COMP by @willend in https://github.com/mccode-dev/McCode/pull/2236
+  * mcdisplay: 
+    * Let mcdisplay-webgl and -classic honour -d directory by @willend in https://github.com/mccode-dev/McCode/pull/2093
+    * mcdisplay-webgl 1st run notice (wait until node.js install is done) @willend in https://github.com/mccode-dev/McCode/pull/2140
+    * Bring back mcdisplay-matlab/octave by @willend in https://github.com/mccode-dev/McCode/pull/2256
+    * Correct visualisation artefacts in Matlab/multiline mcdisplay by @willend in https://github.com/mccode-dev/McCode/pull/2257
+    * Minor tool improvements: mcdisplay-cad  by @willend in https://github.com/mccode-dev/McCode/pull/2258
+ * mcplot:
+   * Use multiple # Data entries in output files if -USR2 is used for intermediate saves by @willend in https://github.com/mccode-dev/McCode/pull/2181
+   * mcplot plot only last # Data block in files with multiple entries by @willend in https://github.com/mccode-dev/McCode/pull/2182
+   * Bring back mcplot-matlab/octave by @willend in https://github.com/mccode-dev/McCode/pull/2256
+   * Correct visualisation artefacts in Matlab/multiline mcdisplay by @willend in https://github.com/mccode-dev/McCode/pull/2257
+ * mcdoc:
+   * mcdoc is now more tolerant to e.g. missing asterisks in header by @willend in https://github.com/mccode-dev/McCode/pull/2121
+   *  mcdoc fills in "short description" if not found by parsing by @willend in https://github.com/mccode-dev/McCode/pull/2123
+   * Improve clarity  of mcdoc Generate buttion and clipboard by @willend in https://github.com/mccode-dev/McCode/pull/2141
+   * Allow mcdoc to work with --dir .  by @willend in https://github.com/mccode-dev/McCode/pull/2147
+   * Bugfix to filtered search https://github.com/mccode-dev/McCode/pull/2148
+   * Fix mcdoc for single-file search (e.g. BNL_H8.instr)  by @willend in https://github.com/mccode-dev/McCode/pull/2166
+   * Mcdoc patch, tolerate missing ^* in header description / parameters by @willend in https://github.com/mccode-dev/McCode/pull/2179
+* Code generator/Grammar/runtime libs: 
+  * Let `-pygen` generated McStasScript code propose using `mcdisplay-webgl-classic` in Jupyter by @willend in https://github.com/mccode-dev/McCode/pull/2091
+* Common work on McStas / McXtrace components
+  * Include all %{%} section in Arm comp(s) as we propose these as "template" comps by @willend in https://github.com/mccode-dev/McCode/pull/2165
+  * Let random numbers picked in INITIALIZE become controlled by --seed by @willend in https://github.com/mccode-dev/McCode/pull/2227
+
+### McXtrace specific:
+* mcxtrace:Fluorescence: flag enhance low concentrations by @farhi in https://github.com/mccode-dev/McCode/pull/2237
+
+### McStas specific:
+* Sample components, validation-work / alignment with analytical expressions by @Lomholy in:
+  * Phonon_simple by @Lomholy in https://github.com/mccode-dev/McCode/pull/2082 and https://github.com/mccode-dev/McCode/pull/2094,  @willend in https://github.com/mccode-dev/McCode/pull/2195, @mads-bertelsen in https://github.com/mccode-dev/McCode/pull/2215
+  * SANS_Spheres to align with analytical validations. by @Lomholy in https://github.com/mccode-dev/McCode/pull/2083
+  * PowderN, add in order parameter to make it possibly to use no multiple scattering by @Lomholy in https://github.com/mccode-dev/McCode/pull/2098
+  * Single_crystal, added MPI_MASTER to selected printf statements by @aaronfinke in https://github.com/mccode-dev/McCode/pull/2169
+  * KU-SANS-samples, tweak expected values in Test_SANS by @willend in https://github.com/mccode-dev/McCode/pull/2209
+* NCrystal
+  * Fix NCrystal_sample 3D visualisation. by @tkittel in https://github.com/mccode-dev/McCode/pull/2150
+  * Update NCrystal_example.instr to account for, and test, cmdline arg parsing by @tkittel in https://github.com/mccode-dev/McCode/pull/2159
+* Tools/mcdisplay-mantid:
+  * Fix to OFF parsing by @willend in https://github.com/mccode-dev/McCode/pull/2099
+* Optics components
+  * Bugfixes to Monchromator_bent by @Lomholy in https://github.com/mccode-dev/McCode/pull/2103
+  * Make beamstop components SCATTER for nicer visualisation by @tkittel in https://github.com/mccode-dev/McCode/pull/2163
+* Monitor components
+  * Bugfix to NPI_tof_dhkl_detector  after discussion with Jan Saroun by @willend in https://github.com/mccode-dev/McCode/pull/2137 
+ * Union components
+   * Union surface and fix of focus system by @mads-bertelsen in https://github.com/mccode-dev/McCode/pull/2149, https://github.com/mccode-dev/McCode/pull/2203
+   * Add new scattering_process_struct_init function for union processes by @tkittel in https://github.com/mccode-dev/McCode/pull/2177
+   * Followup fix to #2177 with correct order of memset args by @tkittel in https://github.com/mccode-dev/McCode/pull/2196
+   * Off file mesh msvc linter patches by @willend in https://github.com/mccode-dev/McCode/pull/2229
+   * Off file mesh component by @Lomholy in https://github.com/mccode-dev/McCode/pull/2219, https://github.com/mccode-dev/McCode/pull/2249
+   * Support for binary STL also on Windows by @Lomholy in https://github.com/mccode-dev/McCode/pull/2260
+   * Union cleanup before release by @mads-bertelsen in https://github.com/mccode-dev/McCode/pull/2243
+   * Mesh surface compatibility by @mads-bertelsen in https://github.com/mccode-dev/McCode/pull/2251
+   * Fix union lib surface stack by @willend in https://github.com/mccode-dev/McCode/pull/2253
+   * Removing debug prints from Sphere and 3D logger in Union. by @mads-bertelsen in https://github.com/mccode-dev/McCode/pull/2252
+ * New comps and instruments 
+   * Comp updates etc from ISIS by @willend in https://github.com/mccode-dev/McCode/pull/2190
+ 
+* Developer tools / User contribution tools
+  * Script for flexible+convenient creation of .yml files by @tkittel in https://github.com/mccode-dev/McCode/pull/2105
+  * New test/devel tool to build McCode in a conda env by @willend in https://github.com/mccode-dev/McCode/pull/2106, https://github.com/mccode-dev/McCode/pull/2160, @tkittel in https://github.com/mccode-dev/McCode/pull/2155, 
+  * New PR template by @willend in https://github.com/mccode-dev/McCode/pull/2129, https://github.com/mccode-dev/McCode/pull/2130, https://github.com/mccode-dev/McCode/pull/2131, https://github.com/mccode-dev/McCode/pull/2132, https://github.com/mccode-dev/McCode/pull/2133, https://github.com/mccode-dev/McCode/pull/2134, https://github.com/mccode-dev/McCode/pull/2138, @tkittel in https://github.com/mccode-dev/McCode/pull/2176
+
+* Deployment and CI
+  * The 'autobuild' workflows automatically build non-conda packages for McStas and McXtrace on any new release tag by @willend in https://github.com/mccode-dev/McCode/pull/2079
+  * Automated testing of modified instrs/comps by @willend in https://github.com/mccode-dev/McCode/pull/2100, https://github.com/mccode-dev/McCode/pull/2101, https://github.com/mccode-dev/McCode/pull/2102
+  * Nightly tests based on conda by @willend in https://github.com/mccode-dev/McCode/pull/2106
+  * CI: Run "full test" in case 20 or more comps/instrs have been changed. by @willend in https://github.com/mccode-dev/McCode/pull/2126
+  * Transition to conda-based basictests for Windows and macOS by @willend in https://github.com/mccode-dev/McCode/pull/2191
+  * Handle case with single modified comp (and no matching instr) better by @willend in https://github.com/mccode-dev/McCode/pull/2197
+  * Minor ci change: Avoid running duplicate version of same instr by @willend in https://github.com/mccode-dev/McCode/pull/2223
+  * Deploy --comp=COMP filter to test instruments including changed components by @willend in https://github.com/mccode-dev/McCode/pull/2238
+
+
+* Platform support
+  * Windows + Conda, update install-docs (#2245, thanks @LelandWH) by @willend in https://github.com/mccode-dev/McCode/pull/2246
+  * Complex number support on Windows with MSVC  (#2192 complex numbers) by @willend in https://github.com/mccode-dev/McCode/pull/2205,  https://github.com/mccode-dev/McCode/pull/2207, SANSPDB/SAXSPDB only by @willend in https://github.com/mccode-dev/McCode/pull/2208, https://github.com/mccode-dev/McCode/pull/2210 and Update headers in complex-lib by @willend in https://github.com/mccode-dev/McCode/pull/2216
+  * Fix for ppc64 Linux (conda-forge platform for IBM Power systems) by @willend in https://github.com/mccode-dev/McCode/pull/2085
+  * Win32 "define-massage" to ensure proper execution with recent MinGW releases by @willend in https://github.com/mccode-dev/McCode/pull/2135
+  * Remove duplicate rpaths on macOS by @willend in https://github.com/mccode-dev/McCode/pull/2140
+  * Add grep in "monolithic" windows builds by @willend in https://github.com/mccode-dev/McCode/pull/2152
+  * Qt message box for error message by @willend in https://github.com/mccode-dev/McCode/pull/2164
+  * -DUSE_NEXUS defines were missing for Windows / NeXus by @willend in https://github.com/mccode-dev/McCode/pull/2167
+  * Consolidate micromamba bulky installers by @willend in https://github.com/mccode-dev/McCode/pull/2183
+  * Fixes for mctest windows nexus: Should now function with .h5 output by @willend in https://github.com/mccode-dev/McCode/pull/2206
+
+
+* General maintenance
+   * Minor fixes, contributions from Daniel Lomholt by @willend in https://github.com/mccode-dev/McCode/pull/2108 
+   * Fix header typo by @willend in https://github.com/mccode-dev/McCode/pull/2109
+   * GPU-related edits for V Transmission_V_polarisator.comp and Test_StatisticalChopper.instr by @willend in https://github.com/mccode-dev/McCode/pull/2110
+   * If running under conda, add env prefix when saving/loading user mccode_config by @willend in https://github.com/mccode-dev/McCode/pull/2142
+   * Temporarily, avoid deploying xraylib via brew on macOS 15 by @willend in https://github.com/mccode-dev/McCode/pull/2145, https://github.com/mccode-dev/McCode/pull/2146
+   * Fix SDKROOT assignment for macOS configuration by @willend in https://github.com/mccode-dev/McCode/pull/2157
+   * Fix to autobuild scripts, remove v from tag... by @willend in https://github.com/mccode-dev/McCode/pull/2170
+   * Drop xrl-based test on macOS (we should use conda instead) by @willend in https://github.com/mccode-dev/McCode/pull/2180
+   * Remove mcplot-html dep python3-pyqt5.qtsvg to get python3-pyqt6.qtsvg by @willend in https://github.com/mccode-dev/McCode/pull/2184
+   * Suppress superfluous debug string in mctest by @willend in https://github.com/mccode-dev/McCode/pull/2185
+   * Temporarily disable test McXtrace randvec_target_rect by @willend in https://github.com/mccode-dev/McCode/pull/2186
+   * Beef up statistics 20 fold on Test_RNG instruments by @willend in https://github.com/mccode-dev/McCode/pull/2187
+   * Drop macOS 13 which will soon be deprecated by @willend in https://github.com/mccode-dev/McCode/pull/2189
+   * Partial revert on macOS bundle injector  by @willend in https://github.com/mccode-dev/McCode/pull/2193
+   * Adjustment of %Example values that were off for the nightly test scenarios by @willend in https://github.com/mccode-dev/McCode/pull/2194
+   * Use rglob in cleanfiles tool, rmtree in case of out.dsym by @willend in https://github.com/mccode-dev/McCode/pull/2211
+   * Clean simdirs by @willend in https://github.com/mccode-dev/McCode/pull/2212
+   * Update workflows to use same simdir cleanup strategy everywhere by @willend in https://github.com/mccode-dev/McCode/pull/2213
+   * Various work on CI output and platforms by @willend in https://github.com/mccode-dev/McCode/pull/2217
+   * GPU box update by @willend in https://github.com/mccode-dev/McCode/pull/2233
+   * Recent linter patches require corrections for GPU/OpenACC... by @willend in https://github.com/mccode-dev/McCode/pull/2235
+   * Deprecate unused features of 'mctest' by @willend in https://github.com/mccode-dev/McCode/pull/2239
+   * Add timestamp to 'testroot' folder to avoid double-layer file structure by @willend in https://github.com/mccode-dev/McCode/pull/2241
+   * Restore ability to "run version via config file" in mctest by @willend in https://github.com/mccode-dev/McCode/pull/2244
+   * Preparations 3.6 by @willend in https://github.com/mccode-dev/McCode/pull/2254
+
+
+## New Contributors
+* @aaronfinke made their first contribution in https://github.com/mccode-dev/McCode/pull/2169
+
+**Full Changelog**: https://github.com/mccode-dev/McCode/compare/v3.5.32...v3.6.0
+
+
 Changes in McStas/McXtrace 3.5.32, June 17th, 2025
 ## What's Changed
 ### Common changes to McStas and McXtrace