Merge branch 'master' of github.com:fabm-model/fabm into neccton

.github/workflows/fabm.yml

@@ -9,7 +9,7 @@ jobs:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
     strategy:
       matrix:
-        version: [9, 10, 11, 12, 13]
+        version: [9, 10, 11, 12]
         os: [ubuntu-latest]
         include:
           #- version: 4.8
@@ -24,6 +24,10 @@ jobs:
           - version: 8
             os: ubuntu-20.04
             cmake_args: -DFABM_USE_CONTIGUOUS=OFF
+          - version: 13
+            os: ubuntu-24.04
+          - version: 14
+            os: ubuntu-24.04
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -234,12 +238,22 @@ jobs:
       - name: Build distribution
         run: python -m build
       - name: Install
-        run: python -m pip install .
+        run: python -m pip install -v .
       - name: Test
         run: |
           python -c "import pyfabm;print('pyfabm version =', getattr(pyfabm, '__version__', None))"
           for f in testcases/*.yaml; do fabm_describe_model $f; done
           for f in testcases/*.yaml; do fabm_complete_yaml --add_missing $f; done
+      - name: Install with customization via command line arguments
+        run: |
+          rm -rf build
+          python -m pip install -v -C--build-option=build_ext -C--build-option="--cmake-opts=-DFABM_INSTITUTES=examples" .
+      - name: Install with customization via setup.cfg
+        run: |
+          rm -rf build
+          echo "[build_ext]" > setup.cfg
+          echo "cmake_opts=-DFABM_INSTITUTES=examples" >> setup.cfg
+          python -m pip install -v .
   fabm0d:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
     runs-on: ubuntu-latest
@@ -283,3 +297,19 @@ jobs:
         run: |
           cmake-${{ matrix.cmake-version }}.0-Linux-x86_64/bin/cmake -S . -B build
           cmake-${{ matrix.cmake-version }}.0-Linux-x86_64/bin/cmake --build build --target install
+  ninja:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone FABM
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Install Ninja
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build
+      - name: Build
+        run: |
+          cmake -S . -B build -G Ninja
+          cmake --build build --target install

CMakeLists.txt

@@ -5,7 +5,7 @@
 cmake_minimum_required(VERSION 3.13)
 
 project(fabm
-  VERSION 2.0.1
+  VERSION 2.0.2
   DESCRIPTION "Framework for Aquatic Biogeochemical Models"
   HOMEPAGE_URL https://fabm.net
   LANGUAGES Fortran
@@ -55,13 +55,13 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
 endif()
 
 # Customize compiler flags
-if(${CMAKE_Fortran_COMPILER_ID} STREQUAL "GNU")
+if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "GNU")
   add_compile_options(-ffree-line-length-none)
-elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel")
+elseif("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Intel")
   if(WIN32)
     add_compile_options("$<$<CONFIG:DEBUG>:/Od>")
   endif()
-elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL "Cray")
+elseif("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Cray")
   add_compile_options(-N 1023)
 endif()
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyfabm"
-version = "2.0.1"
+version = "2.0.2"
 authors = [
   {name = "Jorn Bruggeman", email = "[email protected]"},
   {name = "Karsten Bolding", email = "[email protected]"}

src/CMakeLists.txt

@@ -16,6 +16,7 @@ set(DEFAULT_INSTITUTES
     msi          # Marine Systems Institute, Tallinn University of Technology, Estonia
     nersc        # Nansen Environmental and Remote Sensing Center
     niva         # Norwegian Institute for Water Research, Norway
+    ogs          # National Institute of Oceanography and Applied Geophysics - OGS, Italy
     pclake       # The PCLake model - reference implementation
     pisces       # Pelagic Interactions Scheme for Carbon and Ecosystem Studies, https://doi.org/10.5194/gmd-8-2465-2015
     pml          # Plymouth Marine Laboratory, United Kingdom
@@ -24,7 +25,7 @@ set(DEFAULT_INSTITUTES
     uhh          # University of Hamburg, Germany
 )
 
-set(OPTIONAL_INSTITUTES ersem mops pclake pisces ihamocc)
+set(OPTIONAL_INSTITUTES ersem mops pclake pisces ihamocc ogs)
 
 if(CMAKE_CURRENT_LIST_DIR STREQUAL CMAKE_SOURCE_DIR)
   message(FATAL_ERROR "Please point cmake to the top-level directory with FABM source code, not to its src subdirectory.")
@@ -86,19 +87,23 @@ endforeach(institute)
 configure_file(${CMAKE_CURRENT_LIST_DIR}/fabm_library.F90.in
                ${CMAKE_CURRENT_BINARY_DIR}/fabm_library.F90)
 
-set(GIT_COMMIT_ID unknown)
-set(GIT_BRANCH_NAME unknown)
-configure_file(${CMAKE_CURRENT_LIST_DIR}/fabm_version.F90.in ${CMAKE_CURRENT_BINARY_DIR}/fabm_version.F90)
 if(FABM_EMBED_VERSION)
+  # Use git to get description of current FABM tag/commit id and branch
   set(GET_GIT_INFO_SCRIPT "${CMAKE_CURRENT_LIST_DIR}/cmake/Modules/GetGitInfo.cmake")
   add_custom_target(fabm_version
      ${CMAKE_COMMAND} -DINFILE=${CMAKE_CURRENT_LIST_DIR}/fabm_version.F90.in -DOUTFILE=${CMAKE_CURRENT_BINARY_DIR}/fabm_version.F90 -P ${GET_GIT_INFO_SCRIPT}
+     BYPRODUCTS ${CMAKE_CURRENT_BINARY_DIR}/fabm_version.F90
      WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
      COMMENT "Retrieving description of last FABM commit..."
      SOURCES ${CMAKE_CURRENT_LIST_DIR}/fabm_version.F90.in ${GET_GIT_INFO_SCRIPT}
      VERBATIM
   )
   set_property(TARGET fabm_version PROPERTY FOLDER fabm)
+else()
+  # Insert dummy current FABM tag/commit id and branch
+  set(GIT_COMMIT_ID unknown)
+  set(GIT_BRANCH_NAME unknown)
+  configure_file(${CMAKE_CURRENT_LIST_DIR}/fabm_version.F90.in ${CMAKE_CURRENT_BINARY_DIR}/fabm_version.F90)
 endif()
 
 configure_file(${CMAKE_CURRENT_LIST_DIR}/fabm_parameters.F90.in ${CMAKE_CURRENT_BINARY_DIR}/fabm_parameters.F90)

src/drivers/0d/CMakeLists.txt

@@ -19,9 +19,9 @@ find_path(GOTM_BASE
 option(FABM_USE_NetCDF "Enable NetCDF output" ON)
 
 # Specify additional compiler flags
-if(${CMAKE_Fortran_COMPILER_ID} STREQUAL "GNU")
+if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "GNU")
   set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ffree-line-length-none")
-elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel")
+elseif("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Intel")
   if(WIN32)
     set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} /Od")
   endif()

src/drivers/python/CMakeLists.txt

@@ -9,7 +9,7 @@ set(BUILD_SHARED_LIBS ON)
 project(python_fabm Fortran)
 
 # Customize compiler flags
-if(${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel")
+if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Intel")
   if(WIN32)
     set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} /Od")
   else()

src/drivers/python/build_cmake.py

@@ -33,7 +33,7 @@ def __init__(self, name, *cmake_args):
 
 class CMakeBuild(build_ext):
     user_options = build_ext.user_options + [
-        ("cmake_opts=", None, "additional options to pass to cmake"),
+        ("cmake-opts=", None, "additional options to pass to cmake"),
     ]
 
     def run(self):

src/models/nersc/CMakeLists.txt

@@ -3,7 +3,7 @@ add_library(fabm_models_nersc OBJECT
             ecosmo/ecosmo_operational.F90
            )
 
-add_dependencies(fabm_models_nersc fabm_base)
+target_link_libraries(fabm_models_nersc PRIVATE fabm_base)
 
 #-----------------------------------------------------------------------
 # Copyright (C) 2014 - Karsten Bolding and Jorn Bruggeman (BB)         !

src/pyfabm/__init__.py

@@ -854,7 +854,8 @@ def value(self):
             shape = self.model.interior_domain_shape
         else:
             shape = self.model.horizontal_domain.shape
-        return np.ctypeslib.as_array(pdata, shape).newbyteorder("=")
+        arr = np.ctypeslib.as_array(pdata, shape)
+        return arr.view(dtype=self.model.fabm.numpy_dtype)
 
 
 class NamedObjectList(Sequence):
@@ -1575,22 +1576,18 @@ def process_dependencies(dependencies):
             return False
         for i, variable in enumerate(self.interior_diagnostic_variables):
             pdata = self.fabm.get_interior_diagnostic_data(self.pmodel, i + 1)
-            variable.data = (
-                None
-                if not pdata
-                else np.ctypeslib.as_array(
-                    pdata, self.interior_domain_shape
-                ).newbyteorder("=")
-            )
+            if pdata:
+                arr = np.ctypeslib.as_array(pdata, self.interior_domain_shape)
+                variable.data = arr.view(dtype=self.fabm.numpy_dtype)
+            else:
+                variable.data = None
         for i, variable in enumerate(self.horizontal_diagnostic_variables):
             pdata = self.fabm.get_horizontal_diagnostic_data(self.pmodel, i + 1)
-            variable.data = (
-                None
-                if not pdata
-                else np.ctypeslib.as_array(
-                    pdata, self.horizontal_domain_shape
-                ).newbyteorder("=")
-            )
+            if pdata:
+                arr = np.ctypeslib.as_array(pdata, self.horizontal_domain_shape)
+                variable.data = arr.view(dtype=self.fabm.numpy_dtype)
+            else:
+                variable.data = None
         return ready
 
     checkReady = start