Update develop

.github/workflows/build_all.yml

@@ -14,7 +14,7 @@ jobs:
     name: Build All
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-13, windows-2019]
+        os: [ubuntu-22.04, macos-13, windows-2022]
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -69,6 +69,19 @@ jobs:
           echo 'C:\ProgramData\Chocolatey\lib\mingw\tools\install\mingw64\bin\' >> $GITHUB_PATH
           echo 'C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin\' >> $GITHUB_PATH
           echo 'MW_MINGW64_LOC=/c/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/' >> $GITHUB_ENV
+      - name: Install Visual Studio 2019 Build Tools (for cuda 10)
+        if: ${{ matrix.os == 'windows-2022' }}
+        run: |
+          choco install visualstudio2019community --package-parameters "--add Microsoft.VisualStudio.Workload.MSBuildTools --add Microsoft.VisualStudio.Workload.VCTools --add Microsoft.VisualStudio.Component.VC.Tools.x86.x64 --add Microsoft.VisualStudio.Component.Windows10SDK"
+      - name: Setup MSVC environment (Windows only)
+        shell: cmd
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvars64.bat"
+          echo PATH=%PATH% >> %GITHUB_ENV%
+          echo INCLUDE=%INCLUDE% >> %GITHUB_ENV%
+          echo LIB=%LIB% >> %GITHUB_ENV%
+          echo VCINSTALLDIR=%VCINSTALLDIR% >> %GITHUB_ENV%
       - name: Install CUDA (Linux only)
         if: ${{ runner.os == 'Linux' }}
         run: |
@@ -100,7 +113,7 @@ jobs:
         uses: Jimver/cuda-toolkit@v0.2.10
         id: cuda-toolkit
         with:
-          cuda: '9.2.148'
+          cuda: '10.2.89'
           method: 'network'
           sub-packages: '["nvcc"]'
       - name: Link libgomp.a (MacOS only)
@@ -132,7 +145,7 @@ jobs:
             make oct CC=gcc-10 CXX=g++-10 USEROCTOPT="CXXFLAGS='-pipe -Os -arch x86_64' DL_LD=g++-10 DL_LDFLAGS='-fopenmp -static-libgcc -static-libstdc++'"
             otool -L ../mcxlab/mcx.mex
           else
-            ln -s "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2" cuda
+            ln -s "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.2" cuda
             make oct INCLUDEDIRS="-I./cuda/include" CUDA_PATH="./cuda" XTRA_CFLAGS='-openmp' XTRA_CXXFLAGS='-openmp' INCLUDEDIR=' '
             objdump -p ../mcxlab/mcx.mex | grep "DLL Name:"
           fi
@@ -198,7 +211,7 @@ jobs:
             zip -FSr --symlink packages/mcxlab-${{ env.RELEASE_TAG }}.zip mcxlab
           fi
       - name: Upload mcxlab package
-        if: ${{ matrix.os == 'ubuntu-22.04' || matrix.os == 'macos-13' || matrix.os == 'windows-2019' }}
+        if: ${{ matrix.os == 'ubuntu-22.04' || matrix.os == 'macos-13' || matrix.os == 'windows-2022' }}
         uses: actions/upload-artifact@v4
         with:
           name: all-mcxlab-packages-${{ env.RELEASE_TAG }}
@@ -230,7 +243,7 @@ jobs:
             zip -FSr --symlink mcx/packages/mcx-${{ env.RELEASE_TAG }}.zip mcx -x 'mcx/packages*'
           fi
       - name: Upload mcx package
-        if: ${{ matrix.os == 'ubuntu-22.04' || matrix.os == 'macos-13' || matrix.os == 'windows-2019' }}
+        if: ${{ matrix.os == 'ubuntu-22.04' || matrix.os == 'macos-13' || matrix.os == 'windows-2022' }}
         uses: actions/upload-artifact@v4
         with:
           name: all-mcx-packages-${{ env.RELEASE_TAG }}
@@ -245,7 +258,7 @@ jobs:
       - name: Download mcx
         uses: actions/download-artifact@v4
         with:
-          pattern: all-mcxlab-packages-*
+          pattern: all-mcx*
           merge-multiple: true
           path: packages
       - name: Create all-in-one octave mcxlab

.github/workflows/build_macos_arm64_wheel.yml

@@ -0,0 +1,74 @@
+name: Build+Upload MacOS Apple Silicon Python Wheels
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - master
+
+
+jobs:
+  build_macos_wheels:
+    if: false
+    name: Build macOS wheels
+    runs-on: macos-14
+    strategy:
+      matrix:
+        python_version: [ '3.12' ]
+    outputs:
+      perform_pypi_upload: ${{ steps.perform_pypi_upload_check.outputs.perform_pypi_upload }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+      - name: Update RCS keywords
+        shell: bash
+        run: |
+          printf '\n[filter "rcs-keywords"]\n\tclean  = .git_filters/rcs-keywords.clean\n\tsmudge = .git_filters/rcs-keywords.smudge %f\n' >> .git/config
+          rm -rf src/*.c
+          git checkout src/*.c
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python_version }}
+      - name: Build Wheels
+        run: |
+          cd pmcx/
+          perl -pi -e 's/^\s+(ext_modules|cmdclass)/#$1/g' setup.py
+          python -m pip install --upgrade pip
+          pip install wheel setuptools
+          pip wheel . -w ../dist/ --verbose
+          ls ../dist/
+          cd ../
+      - name: Check If the Build Version Exists on PyPI
+        id: perform_pypi_upload_check
+        run: |
+          bash $GITHUB_WORKSPACE/.github/check-pypi-upload.sh
+      - name: Prepare Wheels for Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: macos-wheels-${{ matrix.os }}-${{ matrix.python_version }}
+          path: dist/
+
+  upload_macos_wheels:
+    needs: build_macos_wheels
+    runs-on: ubuntu-latest
+    if: ${{ github.repository_owner == 'fangq' && needs.build_macos_wheels.outputs.perform_pypi_upload == 1 && github.event_name != 'pull_request'}}
+    steps:
+      - name: Download Wheels from Build Job
+        uses: actions/download-artifact@v4
+        with:
+          pattern: macos-wheels-*
+          merge-multiple: true
+          path: dist/
+      - name: Upload packages to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          verify_metadata: false
+          verbose: true
+          skip_existing: true

.github/workflows/build_windows_wheel.yml

@@ -13,10 +13,10 @@ on:
 jobs:
   build_windows_wheels:
     name: Build Windows wheels
-    runs-on: windows-2019
+    runs-on: windows-2022
     strategy:
       matrix:
-        python_version: [ '3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12', 'pypy3.7', 'pypy3.8', 'pypy3.9', 'pypy3.10']
+        python_version: [ '3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12', '3.13', 'pypy3.7', 'pypy3.8', 'pypy3.9', 'pypy3.10']
     outputs:
       perform_pypi_upload: ${{ steps.perform_pypi_upload_check.outputs.perform_pypi_upload }}
     steps:
@@ -34,6 +34,18 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python_version }}
+      - name: Install Visual Studio 2019 Build Tools (for cuda 10)
+        run: |
+          choco install visualstudio2019buildtools --package-parameters "--add Microsoft.VisualStudio.Workload.VCTools --add Microsoft.VisualStudio.Component.VC.Tools.x86.x64" -y
+      - name: Setup MSVC environment (Windows only)
+        shell: cmd
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          call "C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Auxiliary\Build\vcvars64.bat"
+          echo PATH=%PATH% >> %GITHUB_ENV%
+          echo INCLUDE=%INCLUDE% >> %GITHUB_ENV%
+          echo LIB=%LIB% >> %GITHUB_ENV%
+          echo VCINSTALLDIR=%VCINSTALLDIR% >> %GITHUB_ENV%
       - name: Install CUDA
         uses: Jimver/cuda-toolkit@v0.2.10
         id: cuda-toolkit
@@ -54,6 +66,9 @@ jobs:
           echo "CMAKE_LIBRARY_PATH=$PWD\zlib\lib" >> $env:GITHUB_ENV
           rm zlib.zip
       - name: Build Wheels
+        env:
+          CMAKE_GENERATOR: "Visual Studio 16 2019"
+          CMAKE_GENERATOR_PLATFORM: "x64"
         run: |
           cd pmcx/
           pip install wheel setuptools

.github/workflows/release_test.yml

@@ -9,7 +9,7 @@ jobs:
     name: Release package tests
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04, macos-13, macos-14, windows-2019, windows-2022]
+        os: [ubuntu-22.04, ubuntu-24.04, macos-13, macos-14, windows-2022, windows-2022]
     runs-on: ${{ matrix.os }}
     defaults:
       run:

ChangeLog.txt

@@ -2,7 +2,53 @@
 
 Major updates are marked with a "*"
 
-== MCX v2025.6.pre (Kilo-Kelvin - 2.8), FangQ <q.fang (a) neu.edu> ==
+== MCX v2025.9 (Kilo-Kelvin - 2.8), FangQ <q.fang (a) neu.edu> ==
+ 2025-09-25 [e230514] [bug] when srctype is unknown, the program can run successfully
+ 2025-08-26 [84adbfc] [pmcx] bump version to 0.5.1, some fixes after new unit tests
+ 2025-08-26 [e12bbef]*[pmcx] add additional unit tests
+ 2025-08-25 [521fcf0] [pmcx] pmcx v0.5.0
+ 2025-08-25 [501d6b3] [pmcx] bump version 0.4.6 to update macos apple silicon src
+ 2025-08-24 [37c1205]*[pmcx] initial port of all remaining utils matlab functions to python
+ 2025-08-24 [101f3c7] [doc] fix inaccurate descrption of the 'energy' output type
+ 2025-08-24 [196d1de] [pmcx] bump pmcx version to 0.4.3
+ 2025-07-20 [fbf5942]*[ci] build none-any pmcx package for Apple silicon macos
+ 2025-06-01 [6752c76] [i18n] updated es_MX translations verified by Edgar Guevara
+ 2025-06-01 [bdc9a79] [lang] fix some octave warnings, improve translations
+ 2025-06-01 [3ebff5b] [bug] use consistent message
+ 2025-06-01 [8097604] [feat] read env variable MCX_LANG to set language
+ 2025-06-01 [a2c8ef5] [bug] fix typos in translations, there could be more
+ 2025-06-01 [fc7c1cf] [pmcx] bump version to 0.4.2 to support cfg['lang'], print lang name
+ 2025-06-01 [8ece5d6] [pmcx] fix ci error for windows, support locale in pmcx, pass test
+ 2025-06-01 [70958b9] [ci] fix windows vs error, make mcx_lang const visible in c++
+ 2025-06-01 [b99a33f] [ci] fix macos build error, add missing new unit in cmake
+ 2025-06-01 [729fc37]*[feat] initial i18n support for international languages
+ 2025-05-12 [8663b80] Fix photontof index in WPTOF calculation
+ 2025-04-21 [174e35c]*[feat] further polish rf replay for mus Jacobian, close #241
+ 2025-04-21 [346a638] [feat] dynamically detect the lowest supported gpu arch by nvcc
+ 2025-04-18 [0b3c364] Create demo script for computing any or all of the available Jacobian types in replay mode
+ 2025-04-16 [512ea26] [pmcx] fix ci build errors
+ 2025-04-16 [9ec9be1] Fix typo in pmcx.cpp
+ 2025-04-15 [3e8b730] fix typo cfg.issaveexit to cfg["issaveexit"]
+ 2025-04-12 [0bf148c]*[bug] ensure tshift can not exceed gcfg->maxgate, fix #242
+ 2025-03-18 [98c92ea] Fix undefined variable cfg, should be mcx_config.
+ 2025-03-18 [c1bc350] Format updated code and simplify example
+ 2025-03-18 [d94e4f4] Add terminal output types for new features.
+ 2025-03-17 [0d4c892] Fix typo in cfg struct name.
+ 2025-03-17 [ded9aba]*Implement computation of the total time-of-flight (TOF) and final detected weight
+ 2025-03-17 [eb4b171] Implement computation of total time-of-flight (TOF)- and final detected weight
+ 2025-03-14 [aa7bbdd] [doc] fix typo in mcxlab, fix mcxpreview format
+ 2025-03-12 [6d60f81]*[feat] accelerate mcxpreview using isosurface, must transpose
+ 2025-03-10 [2eacfb8] [example] fix rf replay script to use .jdat output, fix #239
+ 2025-03-06 [4e02a5b] Add object files to gitignore
+ 2025-03-06 [c7df8d9] Fix memory error by unifying handling of otRF and otRFmus
+ 2025-03-06 [7e7d88b] Fix function name
+ 2025-03-06 [5f7d9c6] Fix compliation errors
+ 2025-02-27 [7f05c3b] Remove redundant ifdef
+ 2025-02-27 [c1b7c3c] Implement RFmus calculation
+ 2025-02-27 [40882be] Add RFmus output type and start implementing calculation
+ 2025-02-27 [7f09134] rename new example
+ 2025-02-27 [6599a1c] Added new example functions for RF scattering Jacobians.
+ 2025-02-23 [986ec46] [doc] post v2025 release action, close #238
 
 
 == MCX v2025 (Jumbo Jolt - 2.6), FangQ <q.fang (a) neu.edu> ==
@@ -44,7 +90,6 @@ Major updates are marked with a "*"
  2024-11-08 [ee5be15] [feat] make onecube benchmark maskdet work, fix --dumpmask
  2024-11-08 [f2d3bc4] [feat] support 1x1x1 volume, add onecube/twocube benchmarks, det not working
  2024-11-06 [eaafb0b] [feat] disabling issaveref if issave2pt is false
- 2024-10-14 [6dbcc0f] Merge pull request #234 from epini/epini-patch-1
  2024-10-09 [0411ec6] Fix data ordering in traj.iquv
  2024-09-25 [8c0cfec] [pmcx] bump up pmcx version to 0.3.5 after fixing #233
  2024-09-25 [58dec12] [bug] angleinvcdf and invcdf are not read in full in pmcx, fix #233
@@ -78,7 +123,7 @@ Major updates are marked with a "*"
  2024-03-18 [94961f3] [bug] return source ID in multi-source simulation, fix #217
  2024-03-17 [3c3d755] [release] post v2024.2 release action, close #216
  2024-03-17 [7902a4e] [mcxcloud] update docker image to v2024.2
- 2024-03-15 [08bfe11] [feat] support _ArrayData_ in Shapes volume input
+ 2024-03-15 [08bfe11]*[feat] support _ArrayData_ in Shapes volume input
 
 == MCX v2024.2 (Interstellar Ion - 2.2), FangQ <q.fang (a) neu.edu> ==