Merge remote-tracking branch 'origin'

Author: jtwhite79

.github/workflows/ci-devenv.yml

@@ -1,4 +1,4 @@
-name: pestpp development environment continuous integration
+name: development environment continuous integration
 
 on: 
   schedule:
@@ -10,31 +10,32 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-       
   pestpp-devenv:
-    name: pest++ developer environment
+    name: developer environment
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         include:
           #- {os: macos-latest, shell: bash}
-          - {os: macos-13, shell: bash}
+          - {os: macos-14, shell: bash}
           - {os: ubuntu-latest, shell: bash}
           - {os: ubuntu-22.04, shell: bash}
-          - {os: windows-latest, shell: bash}
+          - {os: windows-2022, shell: bash}
     defaults:
       run:
         shell: ${{ matrix.shell }}
 
     steps:
-      - name: Checkout repo
-        uses: actions/checkout@v5
+      - uses: actions/checkout@v5
 
-      - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.9.1
+      - name: Set Windows ENV
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
+
+      - uses: prefix-dev/setup-pixi@v0.9.2
         with:
-          pixi-version: v0.42.1
+          pixi-version: v0.58.0
           manifest-path: "pixi.toml"
 
       # - name: Install modflow
@@ -43,22 +44,21 @@ jobs:
       #   run: |
       #     pixi run install-modflow
 
-      - name: Build pestpp
-        run: |
-          pixi run build-release 
+      - name: Build release
+        run: pixi run build-release 
 
       # - name: Test pestpp
       #   run: |
       #     pixi run test
 
       - name: Upload binaries
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: binaries-${{ matrix.os }}
           path: bin
 
       - name: Upload test results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: test-results-${{ matrix.os }}
-          path: benchmarks/large_fake_test/master
+          path: benchmarks/large_fake_test/master

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: pestpp continuous integration
+name: continuous integration
 
 on: 
   schedule:
@@ -16,8 +16,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, ubuntu-latest] 
-        python-version: [3.10] # , 3.7, 3.6]
+        os: [windows-latest, ubuntu-latest]
+        # python-version: ["3.10"] # , 3.7, 3.6]
         run-type: [std]
         # test_repo: [""]
         # test_dir: [""]
@@ -48,26 +48,20 @@ jobs:
     env: ${{ matrix.env }}
 
     steps:
+      - uses:  actions/checkout@v5
 
-    - uses:  actions/checkout@v5
-    # - name: Setup Ninja
-      # if: ${{ runner.os == 'Windows' }} 
-    - uses: seanmiddleditch/gha-setup-ninja@master
-  
     # - name: Cache Miniconda
     #   uses: actions/cache@v2.1.0
     #   env:
     #     # Increase this value to reset cache if environment.yml has changed
     #     CACHE_NUMBER: 0
     #   with:
     #     path: ~/conda_pkgs_dir
-    #     key: ${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.run-type }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('etc/environment.yml') }}
-    
-    - name: Set Windows ENV
-      if: runner.os == 'Windows'
-      uses: ilammy/msvc-dev-cmd@v1
+    #     key: ${{ runner.os }}-${{ matrix.run-type }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('etc/environment.yml') }}
 
-    
+      - name: Set Windows ENV
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
 
     # Standard python fails on windows without GDAL installation
     # Using custom bash shell ("shell: bash -l {0}") with Miniconda
@@ -92,12 +86,11 @@ jobs:
     #     # environment-file: etc/environment.yml
     #     # use-only-tar-bz2: true
 
-    - name: setup micromamba
-      uses: mamba-org/setup-micromamba@v2
-      with:
-        environment-file: etc/environment.yml
-        cache-environment: false
-        post-cleanup: 'all'
+      - uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: etc/environment.yml
+          cache-environment: false
+          post-cleanup: 'all'
 
     # - name: Add packages to pyemu environment using mamba or conda
     #   shell: bash -l {0}
@@ -139,52 +132,49 @@ jobs:
     #   if: ${{ runner.os == 'Windows' }} 
     #   uses: lukka/get-cmake@latest
 
-    - name: clone test repo ${{ env.test_repo }}
-      shell: bash -l {0}
-      run: |
-        git clone ${{ env.test_repo }}
+      - name: clone test repo ${{ env.test_repo }}
+        shell: bash -l {0}
+        run: |
+          git clone ${{ env.test_repo }}
 
-    - name: PESTPP exe install
-      shell: bash -l {0}
-      run: |
-        mkdir build && cd build
-        if [[ "$RUNNER_OS" == "Windows" ]]; then
-            cmake -GNinja -DCMAKE_CXX_COMPILER=cl -DCMAKE_C_COMPILER=cl -DCMAKE_BUILD_TYPE=Release ..
-            ninja
-        else
-            cmake -DCMAKE_BUILD_TYPE=Release ..
-            make -j2
-        fi
-        cd ..
+      - name: PESTPP exe install
+        shell: bash -l {0}
+        run: |
+          mkdir build && cd build
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+              cmake -GNinja -DCMAKE_CXX_COMPILER=cl -DCMAKE_C_COMPILER=cl -DCMAKE_BUILD_TYPE=Release ..
+              ninja
+          else
+              cmake -DCMAKE_BUILD_TYPE=Release ..
+              make -j2
+          fi
+          cd ..
 
-    
-    - name: aux bin path hackery
-      shell: bash -l {0}
-      run: |
-        cp -r benchmarks/test_bin/win $HOME/bin
-        echo "../../test_bin/win" >> $GITHUB_PATH
-        if [[ "$RUNNER_OS" == "Windows" ]]; then
-            cp -r benchmarks/test_bin/win $HOME/bin
-            echo "../../test_bin/win" >> $GITHUB_PATH  
-        else
-            echo "../../test_bin/linux" >> $GITHUB_PATH
-            cp -r benchmarks/test_bin/win $HOME/bin
-        fi
-        echo "$HOME/.local/bin" >> $GITHUB_PATH
+      - name: aux bin path hackery
+        shell: bash -l {0}
+        run: |
+          cp -r benchmarks/test_bin/win $HOME/bin
+          echo "../../test_bin/win" >> $GITHUB_PATH
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+              cp -r benchmarks/test_bin/win $HOME/bin
+              echo "../../test_bin/win" >> $GITHUB_PATH
+          else
+              echo "../../test_bin/linux" >> $GITHUB_PATH
+              cp -r benchmarks/test_bin/win $HOME/bin
+          fi
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
 
-    - name: run test script ${{ env.test_script }} in ${{ env.test_dir }}
-      shell: bash -l {0}
-      run: |
-        
-        ls -l
-        cd ${{ env.test_dir }}
-        nosetests -v ${{ env.test_script }}
-        status=$?
-        echo $status
+      - name: run test script ${{ env.test_script }} in ${{ env.test_dir }}
+        shell: bash -l {0}
+        run: |
+          ls -l
+          cd ${{ env.test_dir }}
+          nosetests -v ${{ env.test_script }}
+          status=$?
+          echo $status
 
-        if [ $status -eq 0 ]; then
-            exit 0
-        else
-            exit 127
-        fi
-        
+          if [ $status -eq 0 ]; then
+              exit 0
+          else
+              exit 127
+          fi

.github/workflows/release.yml

@@ -19,19 +19,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-13, macos-14, windows-2022]
+        os: [ubuntu-22.04, macos-14, windows-2022]
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - name: Checkout pest++
-        uses: actions/checkout@v5
+      - uses: actions/checkout@v5
         with:
           repository: usgs/pestpp
           ref: ${{ inputs.branch }}
 
-      - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.9.1
+      - uses: prefix-dev/setup-pixi@v0.9.2
         with:
           pixi-version: v0.41.4
 
@@ -45,11 +43,7 @@ jobs:
           if [[ $RUNNER_OS == "Linux" ]]; then
             ostag="linux"
           elif [[ $RUNNER_OS == "macOS" ]]; then
-            if [[ ${{ matrix.os }} == "macos-13" ]]; then
-              ostag="macintel"
-            elif [[ ${{ matrix.os }} == "macos-14" ]]; then
-              ostag="mac"
-            fi
+            ostag="mac"
           elif [[ $RUNNER_OS == "Windows" ]]; then
             ostag="win"
           fi
@@ -67,7 +61,7 @@ jobs:
           rm -r $path/*/ || true
 
       - name: Upload distribution
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: pestpp-${{ inputs.version }}-${{ steps.ostag.outputs.ostag }}
           path: pestpp-${{ inputs.version }}-${{ steps.ostag.outputs.ostag }}

CMakeLists.txt

@@ -1,5 +1,9 @@
 # This is the top-level CMake file for PEST++
-cmake_minimum_required(VERSION 3.9)
+cmake_minimum_required(VERSION 3.15)
+
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+  add_compile_definitions(_DEBUG)
+endif()
 
 # Get PESTPP_VERSION from common source header
 file(READ "${CMAKE_SOURCE_DIR}/src/libs/common/config_os.h" _file)
@@ -13,43 +17,22 @@ endif()
 message(STATUS
   "Configuring CMake ${CMAKE_VERSION} to build PESTPP ${PESTPP_VERSION}")
 
-# This logic needs to be considered before project()
-set(_change_MSVC_flags FALSE)
 if(WIN32)
-  if(CMAKE_VERSION VERSION_LESS 3.15.0)
-    set(_change_MSVC_flags TRUE)
-  else()
-    # Set MSVC runtime to MultiThreaded (/MT)
-    cmake_policy(SET CMP0091 NEW)
-    set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
-  endif()
+  # Set MSVC runtime to MultiThreaded (/MT)
+  cmake_policy(SET CMP0091 NEW)
+  set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
 endif()
 
 project(PESTPP
   VERSION ${PESTPP_VERSION}
+  HOMEPAGE_URL "https://github.com/usgs/pestpp/"
   LANGUAGES CXX)
 
 # Prevent running cmake in source dir
 if("${PESTPP_SOURCE_DIR}" STREQUAL "${PESTPP_BINARY_DIR}")
    message(SEND_ERROR "In-source builds are not allowed")
 endif()
 
-if(_change_MSVC_flags)
-  # Modify compile flags to change MSVC runtime from /MD to /MT
-  set(_re_match "([\\/\\-]M)D")
-  set(_re_replace "\\1T")
-  string(REGEX REPLACE ${_re_match} ${_re_replace}
-    CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-  string(REGEX REPLACE ${_re_match} ${_re_replace}
-    CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG}")
-  string(REGEX REPLACE ${_re_match} ${_re_replace}
-    CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
-  string(REGEX REPLACE ${_re_match} ${_re_replace}
-    CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL}")
-  string(REGEX REPLACE ${_re_match} ${_re_replace}
-    CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO}")
-endif()
-
 # Fortran is not required (anymore), but can be enabled using either:
 #  1. ENABLE_Fortran=ON and use whatever default compiler is available
 #  2. CMAKE_Fortran_COMPILER=ifort (or other compiler)
@@ -84,6 +67,7 @@ message(STATUS "CMAKE_THREAD_LIBS_INIT=${CMAKE_THREAD_LIBS_INIT}")
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_TRY_COMPILE_TARGET_TYPE)
 
 add_compile_definitions(_HAS_STD_BYTE=0)
 

benchmarks/basic_tests.py

@@ -2124,6 +2124,7 @@ def parse_pst_test():
     pyemu.os_utils.run("{0} control.pst".format(exe_path),cwd=t_d)
 
 
+
 if __name__ == "__main__":
     #parse_pst_test()
     #basic_test()

benchmarks/glm_test_base.py

@@ -945,16 +945,16 @@ def tenpar_xsec_stress_test_5super():
     #tenpar_superpar_restart_test()
     #freyberg_basic_restart_test()
     # jac_diff_invest()
-    #new_fmt_load_test()
+    new_fmt_load_test()
     #tenpar_hotstart_test()
     #tenpar_normalform_test()
     #freyberg_stress_test()
     #shutil.copy2(os.path.join("..","exe","windows","x64","Debug","pestpp-glm.exe"),os.path.join("..","bin","win","pestpp-glm.exe"))
     #tenpar_xsec_stress_test_2()
     #tenpar_xsec_stress_test_3()
-    tenpar_xsec_stress_test_5super()
+    #tenpar_xsec_stress_test_5super()
 
-    tenpar_xsec_stress_test_5()
+    #tenpar_xsec_stress_test_5()