Feature/update install

.readthedocs.yml

@@ -1,4 +1,4 @@
-# Read the Docs configuration file for IMAS-Matlab
+# Read the Docs configuration file for IMAS-MATLAB
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
@@ -10,21 +10,6 @@ build:
   tools:
     python: "3.11"
 
-  jobs:
-    post_checkout:
-      # Clone IMAS-Core (only if not already present)
-      - |
-        if [ ! -d "IMAS-Core" ]; then
-          git clone --depth 1 --branch develop \
-            https://github.com/iterorganization/IMAS-Core.git \
-            IMAS-Core
-        fi
-      - ls -la
-      - ln -sfn $PWD/IMAS-Core/common/doc_common $PWD/doc/doc_common
-      - ls -la doc/
-      - ls -la doc/doc_common/
-      - echo "Created symlink doc/doc_common -> IMAS-Core/common/doc_common"
-
 # Build documentation in the "doc" directory with Sphinx
 sphinx:
   configuration: doc/conf.py
@@ -35,11 +20,11 @@ formats:
   - pdf
   - epub
 
-# Optional but recommended, declare the Python requirements required
+# Optional but Python requirements required recommended, declare the
 # to build your documentation
 python:
   install:
-    - requirements: IMAS-Core/common/doc_common/requirements.txt
+    - requirements: doc/doc_common/requirements.txt
 
 # Submodules configuration (optional)
 submodules:

CMakeLists.txt

@@ -20,76 +20,70 @@ if(WIN32)
   endif()
 endif()
 
-# Configuration options for common assets
+# Local paths for IMAS-MATLAB
 ################################################################################
+# Include local paths to eliminate AL_COMMON_PATH dependency
+# Use full path since CMAKE_MODULE_PATH hasn't been configured yet
+include(${CMAKE_CURRENT_SOURCE_DIR}/common/cmake/ALLocalPaths.cmake)
 option( AL_DOWNLOAD_DEPENDENCIES "Automatically download assets from the AL git repository" ON )
 set( AL_CORE_GIT_REPOSITORY "https://github.com/iterorganization/IMAS-Core.git" CACHE STRING "Git repository of AL-core" )
 set( AL_CORE_VERSION "main" CACHE STRING "Git commit/tag/branch of AL-core" )
+
 include(FetchContent)
-# Load common assets
+# Load AL-core library (used for the shared library)
 ################################################################################
-if( DEFINED ENV{AL_COMMON_PATH} )
-  # Take common assets from the path in this environment variable instead of al-core
-  set( AL_COMMON_PATH $ENV{AL_COMMON_PATH} )
-else()
-  if(WIN32)
-    if( ${AL_DOWNLOAD_DEPENDENCIES} )
-      # FetchContent_Declare causing reursive call wrapped by vcpkg to _find_package
-      # So manually clone al-core here. Need fix in later release
-      set( al-core_SOURCE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_deps/al-core-src" )
-      if( NOT EXISTS "${al-core_SOURCE_DIR}/.git" )
-        message( STATUS "Cloning al-core from ${AL_CORE_GIT_REPOSITORY}" )
-        execute_process(
-          COMMAND git clone "${AL_CORE_GIT_REPOSITORY}" "${al-core_SOURCE_DIR}"
-          RESULT_VARIABLE _GIT_CLONE_RESULT
-          ERROR_VARIABLE _GIT_CLONE_ERROR
-        )
-        if( _GIT_CLONE_RESULT )
-          message( FATAL_ERROR "Failed to clone al-core: ${_GIT_CLONE_ERROR}" )
-        endif()
-      endif()
-      # Checkout the specified version
-      execute_process(
-        COMMAND git fetch origin
-        WORKING_DIRECTORY "${al-core_SOURCE_DIR}"
-        RESULT_VARIABLE _GIT_FETCH_RESULT
-      )
+if(WIN32)
+  if( ${AL_DOWNLOAD_DEPENDENCIES} )
+    # FetchContent_Declare causing reursive call wrapped by vcpkg to _find_package
+    # So manually clone al-core here. Need fix in later release
+    set( al-core_SOURCE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_deps/al-core-src" )
+    if( NOT EXISTS "${al-core_SOURCE_DIR}/.git" )
+      message( STATUS "Cloning al-core from ${AL_CORE_GIT_REPOSITORY}" )
       execute_process(
-        COMMAND git checkout "${AL_CORE_VERSION}"
-        WORKING_DIRECTORY "${al-core_SOURCE_DIR}"
-        RESULT_VARIABLE _GIT_CHECKOUT_RESULT
-        ERROR_VARIABLE _GIT_CHECKOUT_ERROR
+        COMMAND git clone "${AL_CORE_GIT_REPOSITORY}" "${al-core_SOURCE_DIR}"
+        RESULT_VARIABLE _GIT_CLONE_RESULT
+        ERROR_VARIABLE _GIT_CLONE_ERROR
       )
-      if( _GIT_CHECKOUT_RESULT )
-        message( FATAL_ERROR "Failed to checkout ${AL_CORE_VERSION}: ${_GIT_CHECKOUT_ERROR}" )
-      endif()
-    else()
-      set( al-core_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/../al-core" )
-      if( NOT IS_DIRECTORY "${al-core_SOURCE_DIR}" )
-        message( FATAL_ERROR "${al-core_SOURCE_DIR} does not exist. Set AL_DOWNLOAD_DEPENDENCIES=ON to download." )
+      if( _GIT_CLONE_RESULT )
+        message( FATAL_ERROR "Failed to clone al-core: ${_GIT_CLONE_ERROR}" )
       endif()
     endif()
-    set( AL_COMMON_PATH "${al-core_SOURCE_DIR}/common" )
-  else()
-    if( ${AL_DOWNLOAD_DEPENDENCIES} )
-      # Download common assets from the ITER git:
-      FetchContent_Declare(
-        al-core
-        GIT_REPOSITORY "${AL_CORE_GIT_REPOSITORY}"
-        GIT_TAG "${AL_CORE_VERSION}"
-      )
-    else()
-      FetchContent_Declare(
-        al-core
-        SOURCE_DIR      "${CMAKE_CURRENT_SOURCE_DIR}/../al-core"
-      )
+    # Checkout the specified version
+    execute_process(
+      COMMAND git fetch origin
+      WORKING_DIRECTORY "${al-core_SOURCE_DIR}"
+      RESULT_VARIABLE _GIT_FETCH_RESULT
+    )
+    execute_process(
+      COMMAND git checkout "${AL_CORE_VERSION}"
+      WORKING_DIRECTORY "${al-core_SOURCE_DIR}"
+      RESULT_VARIABLE _GIT_CHECKOUT_RESULT
+      ERROR_VARIABLE _GIT_CHECKOUT_ERROR
+    )
+    if( _GIT_CHECKOUT_RESULT )
+      message( FATAL_ERROR "Failed to checkout ${AL_CORE_VERSION}: ${_GIT_CHECKOUT_ERROR}" )
     endif()
+  elseif ( ${AL_DEVELOPMENT_LAYOUT} )
+    set( al-core_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/../al-core" )
+  endif()
+else()
+  if( ${AL_DOWNLOAD_DEPENDENCIES} )
+    # Download common assets from the ITER git:
+    FetchContent_Declare(
+      al-core
+      GIT_REPOSITORY "${AL_CORE_GIT_REPOSITORY}"
+      GIT_TAG "${AL_CORE_VERSION}"
+    )
+    FetchContent_MakeAvailable( al-core )
+  elseif ( ${AL_DEVELOPMENT_LAYOUT} )
+    FetchContent_Declare(
+      al-core
+      SOURCE_DIR      "${CMAKE_CURRENT_SOURCE_DIR}/../al-core"
+    )
     FetchContent_MakeAvailable( al-core )
-    set( AL_COMMON_PATH "${al-core_SOURCE_DIR}/common" )
- endif()
+  endif()
+  
 endif()
-add_subdirectory( ${AL_COMMON_PATH} _common )
-
 
 # Define project
 ################################################################################
@@ -120,8 +114,6 @@ include( ALCore )
 if( AL_DOCS_ONLY )
   return()
 endif()
-
-
 # Dependencies
 ################################################################################
 find_package( Python3 REQUIRED COMPONENTS Interpreter )
@@ -130,8 +122,6 @@ if(WIN32)
 else()
  find_package( Matlab REQUIRED )
 endif()
-
-
 # Utility sources and target
 ################################################################################
 
@@ -149,7 +139,6 @@ if(WIN32)
   target_link_libraries( al-mex PUBLIC al Matlab::mex Matlab::mx )
   target_include_directories( al-mex PRIVATE src )
   target_include_directories( al-mex PUBLIC ${Matlab_INCLUDE_DIRS} )
-  target_include_directories( al-mex PUBLIC ${AL_COMMON_PATH}/../include )
 
   # Use separate (non-interleaved) complex API for compatibility
   target_compile_definitions( al-mex PUBLIC)
@@ -238,7 +227,7 @@ macro( GENERATE GENERATOR IS_C_GENERATOR OUTPUT_FILES )
   add_custom_command(
     OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${GENERATOR}_dummy.txt
     COMMAND
-      ${_SAXONCHE_VENV_PYTHON} "${AL_COMMON_PATH}/xsltproc.py"
+      ${_SAXONCHE_VENV_PYTHON} "${AL_LOCAL_XSLTPROC_SCRIPT}"
         -xsl ${CMAKE_CURRENT_SOURCE_DIR}/${GENERATOR}.xsl
         -s ${IDSDEF}
         -o ${CMAKE_CURRENT_BINARY_DIR}/${GENERATOR}_output.xml
@@ -273,6 +262,8 @@ if(WIN32)
     target_include_directories( "mex-${NAME}" PRIVATE src )
     # Use separate (non-interleaved) complex API for compatibility
     target_compile_definitions( "mex-${NAME}" PUBLIC)
+    # Add /bigobj flag for large generated code files
+    target_compile_options( "mex-${NAME}" PRIVATE /bigobj )
     list( APPEND MEX_TARGETS "mex-${NAME}" )
   endmacro()
 else()
@@ -283,8 +274,6 @@ else()
     list( APPEND MEX_TARGETS "mex-${NAME}" )
   endmacro()
 endif()
-
-
 # These XSLs generate files in triplets, which are then compiled into one mex target
 foreach( METHOD_NAME allocate delete gen get get_sample get_slice init put put_slice rand validate )
   FILES_FROM_METHOD_NAME( OUTPUT_FILES ${METHOD_NAME} )

CONTRIBUTING.md

@@ -1,23 +1,23 @@
 # Contributing guidelines
 
-We welcome any kind of contribution to `IMAS-Matlab`, 
+We welcome any kind of contribution to `IMAS-MATLAB`, 
 from a simple comment, a question or even a full fledged pull 
 request. 
 Please first make sure you read and follow the 
 [Code of Conduct](CODE_OF_CONDUCT.md).
 
 ## You think you found a bug in the code, or have a question in its use
-1. use the [issue search](https://github.com/iterorganization/IMAS-Matlab/issues)
+1. use the [issue search](https://github.com/iterorganization/IMAS-MATLAB/issues)
 to check if someone already created a similar issue;
 2. if not, make a **new issue** to describe your problem or question. 
 In the case of a bug suspiscion, please try to give all the relevant 
 information to allow reproducing the error or identifying 
-its root cause (version of the IMAS-Matlab, OS and relevant 
+its root cause (version of the IMAS-MATLAB, OS and relevant 
 dependencies, snippet of code);
 3. apply relevant labels to the issue.
 
 ## You want to make or ask some change to the code
-1. use the [issue search](https://github.com/iterorganization/IMAS-Matlab/issues)
+1. use the [issue search](https://github.com/iterorganization/IMAS-MATLAB/issues)
 to check if someone already proposed a similar idea/change;
 2. if not, create a **new issue** to describe what change you would like to see 
 implemented and specify it if you intend to work on it yourself or if some help 

ci/build_docs.sh

@@ -51,7 +51,7 @@ CMAKE_ARGS=(
     -D AL_PLUGINS_VERSION=${AL_PLUGINS_VERSION:-main}
     -D AL_CORE_VERSION=${AL_CORE_VERSION:-main}
     -D DD_VERSION=${DD_VERSION:-main}
-    # Build only documentation
+    # Build only documentationv 
     -D AL_HLI_DOCS=${AL_HLI_DOCS:-ON}
     -D AL_DOCS_ONLY=${AL_DOCS_ONLY:-ON}
 )

common/CMakeLists.txt

@@ -0,0 +1,27 @@
+# CMake configuration for AL common assets
+# Intended for inclusion (using FetchContent_MakeAvailable) in other AL components
+
+# Add ./cmake to the module path in the parent scope:
+set( CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake PARENT_SCOPE )
+
+if ( ${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR} )
+    message( FATAL_ERROR "In-source builds not supported. Please use a separate build directory, for example `cmake -B build [...]`" )
+endif()
+
+if( AL_PYTHON_BINDINGS )
+    find_package( Python3 )
+    set( PYVER "${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}" )
+endif()
+configure_file( al_env.sh.in ${CMAKE_CURRENT_BINARY_DIR}/al_env.sh )
+
+# Don't generate the environment file when building modules:
+if( AL_DOWNLOAD_DEPENDENCIES OR AL_DEVELOPMENT_LAYOUT )
+    install(
+      FILES ${CMAKE_CURRENT_BINARY_DIR}/al_env.sh
+      TYPE BIN
+    )
+endif()
+
+# al-common_SOURCE_DIR is used in some scripts in the cmake/ folder to refer to the
+# current source directory:
+set( al-common_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR} PARENT_SCOPE )

common/al_env.sh.in

@@ -0,0 +1,7 @@
+export PATH="${CMAKE_INSTALL_PREFIX}/bin:$PATH"
+export LD_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$LD_LIBRARY_PATH"
+export PKG_CONFIG_PATH="${CMAKE_INSTALL_PREFIX}/lib/pkgconfig:$PKG_CONFIG_PATH"
+
+if [ -d "${CMAKE_INSTALL_PREFIX}/mex" ]; then
+    export MATLABPATH="${CMAKE_INSTALL_PREFIX}/mex:$MATLABPATH"
+fi