Merge branch 'develop' into feature/ccpp

.github/workflows/docs.yml

@@ -2,9 +2,9 @@ name: Doxygen docs
 
 on:
   push:
-    branches: [feature/catchem_begins]
+    branches: [develop]
   pull_request:
-    branches: [feature/catchem_begins]
+    branches: [develop]
 permissions:
   contents: write
 
@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Install dependencies
-        run: sudo apt-get install -y doxygen graphviz
+        run: sudo apt-get update && sudo apt-get install -y doxygen graphviz
 
       - name: Build
         run: |
@@ -24,7 +24,7 @@ jobs:
           cd -
 
       - name: Deploy
-        if: github.ref == 'refs/heads/feature/catchem_begins'
+        if: github.ref == 'refs/heads/develop'
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages

.pre-commit-config.yaml

@@ -5,18 +5,18 @@ repos:
       - id: check-useless-excludes
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.6.0"
+    rev: "v5.0.0"
     hooks:
       - id: trailing-whitespace
         args: ['--markdown-linebreak-ext=md,markdown']
       - id: end-of-file-fixer
       - id: check-yaml
 
   - repo: https://github.com/zmoon/findent-pre-commit
-    rev: "65627b8"
+    rev: "17b1b07"
     hooks:
-      # NOTE: doesn't work on Windows currently
       - id: findent-pypi
+        additional_dependencies: [findent==4.3.1]
         args: ['-i3']
         exclude: |
             (?x)^(
@@ -29,16 +29,11 @@ repos:
                 src/external/GOCART/.*
             )$
 
-  - repo: https://github.com/cheshirekow/cmake-format-precommit
-    rev: v0.6.13
+  - repo: https://github.com/BlankSpruce/gersemi
+    rev: "0.18.1"
     hooks:
-      - id: cmake-format
-        additional_dependencies: [PyYAML]
-        exclude: (?x)^(
-            cmake/FindNetCDF.cmake
-          )$
-      - id: cmake-lint
-        additional_dependencies: [PyYAML]
+      - id: gersemi
+        args: [--in-place, --indent=2]
         exclude: (?x)^(
             cmake/FindNetCDF.cmake
           )$

CMakeLists.txt

@@ -1,9 +1,6 @@
 cmake_minimum_required(VERSION 3.5)
 
-project(
-  CATChem
-  VERSION 0.1.0
-  LANGUAGES Fortran)
+project(CATChem VERSION 0.1.0 LANGUAGES Fortran)
 
 include(CMakePrintHelpers)
 
@@ -13,9 +10,16 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Debug)
 endif()
-cmake_print_variables(CMAKE_Fortran_COMPILER CMAKE_Fortran_COMPILER_ID CMAKE_BUILD_TYPE)
+cmake_print_variables(
+  CMAKE_Fortran_COMPILER
+  CMAKE_Fortran_COMPILER_ID
+  CMAKE_BUILD_TYPE
+)
 set(_catchem_compiler_options "")
-if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU|G95" AND CMAKE_BUILD_TYPE MATCHES "Debug")
+if(
+  CMAKE_Fortran_COMPILER_ID MATCHES "GNU|G95"
+  AND CMAKE_BUILD_TYPE MATCHES "Debug"
+)
   list(
     APPEND
     _catchem_compiler_options
@@ -26,8 +30,12 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU|G95" AND CMAKE_BUILD_TYPE MATCHES "Deb
     -fcheck=all
     -ffpe-trap=invalid,zero,overflow
     -fbacktrace
-    -fmax-errors=0)
-elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel" AND CMAKE_BUILD_TYPE MATCHES "Debug")
+    -fmax-errors=0
+  )
+elseif(
+  CMAKE_Fortran_COMPILER_ID MATCHES "Intel"
+  AND CMAKE_BUILD_TYPE MATCHES "Debug"
+)
   list(
     APPEND
     _catchem_compiler_options
@@ -42,7 +50,8 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel" AND CMAKE_BUILD_TYPE MATCHES "D
     -error-limit
     0
     -diag-disable
-    6379,10448)
+    6379,10448
+  )
 endif()
 
 add_subdirectory(src)

src/api/CMakeLists.txt

@@ -8,5 +8,8 @@ target_link_libraries(${_lib} PUBLIC CATChem_process_dust)
 target_link_libraries(${_lib} PUBLIC CATChem_process_seasalt)
 target_link_libraries(${_lib} PUBLIC CATChem_process_plumerise)
 target_link_libraries(${_lib} PUBLIC CATChem_process_drydep)
-set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  ${_lib}
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 target_compile_options(${_lib} PRIVATE ${_catchem_compiler_options})

src/core/CMakeLists.txt

@@ -1,21 +1,26 @@
-set(_srcs
-    charpak_mod.F90
-    chemstate_mod.F90
-    cmn_size_mod.F90
-    config_mod.F90
-    config_opt_mod.F90
-    constants.F90
-    diagstate_mod.F90
-    emisstate_mod.F90
-    error_mod.F90
-    gridstate_mod.F90
-    init_mod.F90
-    metstate_mod.F90
-    precision_mod.F90
-    qfyaml_mod.F90
-    species_mod.F90
-    state_mod.F90)
+set(
+  _srcs
+  charpak_mod.F90
+  chemstate_mod.F90
+  cmn_size_mod.F90
+  config_mod.F90
+  config_opt_mod.F90
+  constants.F90
+  diagstate_mod.F90
+  emisstate_mod.F90
+  error_mod.F90
+  gridstate_mod.F90
+  init_mod.F90
+  metstate_mod.F90
+  precision_mod.F90
+  qfyaml_mod.F90
+  species_mod.F90
+  state_mod.F90
+)
 
 add_library(CATChem_core ${_srcs})
-set_target_properties(CATChem_core PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  CATChem_core
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 target_compile_options(CATChem_core PRIVATE ${_catchem_compiler_options})

src/external/CMakeLists.txt

@@ -1,4 +1,8 @@
-set(_srcs GOCART/Process_Library/GOCART2G_Process.F90 GOCART/Process_Library/GOCART2G_MieMod.F90)
+set(
+  _srcs
+  GOCART/Process_Library/GOCART2G_Process.F90
+  GOCART/Process_Library/GOCART2G_MieMod.F90
+)
 set(_lib GOCART2G)
 
 add_library(${_lib} ${_srcs})
@@ -11,4 +15,7 @@ find_package(NetCDF REQUIRED COMPONENTS Fortran)
 target_link_libraries(${_lib} NetCDF::NetCDF_Fortran)
 # target_link_libraries(${_lib} PUBLIC CATChem_core)
 
-set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  ${_lib}
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)

src/process/drydep/CMakeLists.txt

@@ -6,4 +6,7 @@ add_library(${_lib} ${_srcs})
 target_link_libraries(${_lib} PUBLIC CATChem_core)
 target_link_libraries(${_lib} PUBLIC GOCART2G)
 
-set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  ${_lib}
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)

src/process/drydep/ccpr_scheme_GOCART_DryDep_mod.F90

@@ -160,7 +160,7 @@ subroutine CCPr_Scheme_GOCART_DryDep(km,              &
       if (associated(GOCART_LWI)) nullify(GOCART_LWI)
       if (associated(GOCART_HFLUX)) nullify(GOCART_HFLUX)
       if (associated(GOCART_Z0H)) nullify(GOCART_Z0H)
-      
+
 ! End GOCART Code
 
 

src/process/dust/CMakeLists.txt

@@ -1,8 +1,16 @@
-set(_srcs CCPr_Dust_Mod.F90 ccpr_dust_common_mod.F90 ccpr_scheme_fengsha_mod.F90
-          ccpr_scheme_ginoux_mod.F90)
+set(
+  _srcs
+  CCPr_Dust_Mod.F90
+  ccpr_dust_common_mod.F90
+  ccpr_scheme_fengsha_mod.F90
+  ccpr_scheme_ginoux_mod.F90
+)
 
 set(_lib CATChem_process_dust)
 
 add_library(${_lib} ${_srcs})
 target_link_libraries(${_lib} PUBLIC CATChem_core)
-set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  ${_lib}
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)

src/process/plumerise/CMakeLists.txt

@@ -1,7 +1,15 @@
-set(_srcs CCPr_Plumerise_Mod.F90 CCPr_Scheme_Briggs_mod.F90 CCPr_Scheme_Sofiev_mod.F90)
+set(
+  _srcs
+  CCPr_Plumerise_Mod.F90
+  CCPr_Scheme_Briggs_mod.F90
+  CCPr_Scheme_Sofiev_mod.F90
+)
 
 set(_lib CATChem_process_plumerise)
 
 add_library(${_lib} ${_srcs})
 target_link_libraries(${_lib} PUBLIC CATChem_core)
-set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  ${_lib}
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)

src/process/seasalt/CMakeLists.txt

@@ -1,8 +1,17 @@
-set(_srcs CCPr_SeaSalt_Mod.F90 ccpr_seasalt_common_mod.F90 ccpr_scheme_gong03_mod.F90
-          ccpr_scheme_gong97_mod.F90 ccpr_scheme_geos12_mod.F90)
+set(
+  _srcs
+  CCPr_SeaSalt_Mod.F90
+  ccpr_seasalt_common_mod.F90
+  ccpr_scheme_gong03_mod.F90
+  ccpr_scheme_gong97_mod.F90
+  ccpr_scheme_geos12_mod.F90
+)
 
 set(_lib CATChem_process_seasalt)
 
 add_library(${_lib} ${_srcs})
 target_link_libraries(${_lib} PUBLIC CATChem_core)
-set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  ${_lib}
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)

tests/CMakeLists.txt

@@ -1,70 +1,94 @@
+include(CTest)
+
 add_compile_options(${_catchem_compiler_options})
 
 add_library(testing testing_mod.f90)
 target_link_libraries(testing PRIVATE CATChem_core)
-set_target_properties(testing PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
-
-enable_testing()
+set_target_properties(
+  testing
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 
 add_executable(test_main test_main.F90)
 target_link_libraries(test_main PRIVATE CATChem_core)
 target_link_libraries(test_main PRIVATE CATChem)
 target_link_libraries(test_main PRIVATE testing)
-set_target_properties(test_main PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  test_main
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 
 add_test(
   NAME test_main
   COMMAND test_main
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+)
 
 add_test(
   NAME test_main_missing_config
   COMMAND test_main
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
+  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+)
 set_property(TEST test_main_missing_config PROPERTY WILL_FAIL TRUE)
 
 add_executable(test_dust test_dust.f90)
 target_link_libraries(test_dust PRIVATE CATChem_core)
 target_link_libraries(test_dust PRIVATE CATChem)
 target_link_libraries(test_dust PRIVATE CATChem_process_dust)
 target_link_libraries(test_dust PRIVATE testing)
-set_target_properties(test_dust PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  test_dust
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 
 add_test(
   NAME test_ccpr_dust
   COMMAND test_dust
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+)
 
 add_executable(test_seasalt test_seasalt.F90)
 target_link_libraries(test_seasalt PRIVATE CATChem_core)
 target_link_libraries(test_seasalt PRIVATE CATChem)
 target_link_libraries(test_seasalt PRIVATE CATChem_process_seasalt)
 target_link_libraries(test_seasalt PRIVATE testing)
-set_target_properties(test_seasalt PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  test_seasalt
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 
 add_test(
   NAME test_ccpr_seasalt
   COMMAND test_seasalt
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+)
 
 add_executable(test_prise test_plumerise.F90)
 target_link_libraries(test_prise PRIVATE CATChem_core)
 target_link_libraries(test_prise PRIVATE CATChem)
 target_link_libraries(test_prise PRIVATE testing)
-set_target_properties(test_prise PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  test_prise
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 
 add_test(
   NAME test_plumerise
   COMMAND test_prise
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+)
 
 add_executable(test_drydep test_drydep.f90)
 target_link_libraries(test_drydep PRIVATE CATChem_core)
 target_link_libraries(test_drydep PRIVATE CATChem)
 target_link_libraries(test_drydep PRIVATE testing)
-set_target_properties(test_drydep PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
+set_target_properties(
+  test_drydep
+  PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include
+)
 
 add_test(
   NAME test_drydep
   COMMAND test_drydep
-  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+)