Merge branch 'master' into add-unsafe-open-mode

CMakeLists.txt

@@ -32,8 +32,25 @@ if(EXISTS "${CMAKE_SOURCE_DIR}/.git/config")
   else()
     message(FATAL_ERROR "EMACS not found. It is required to produce TREXIO source code from org-mode files.")
   endif()
+  # in case Git is not available, we default to "unknown"
+  set(GIT_HASH "unknown")
+  # find Git and if available set GIT_HASH variable
+  find_package(Git QUIET)
+  if(GIT_FOUND)
+    execute_process(
+	    COMMAND ${GIT_EXECUTABLE} --no-pager show -s --pretty=format:%H -n 1
+	    OUTPUT_VARIABLE GIT_HASH
+	    OUTPUT_STRIP_TRAILING_WHITESPACE
+	    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+	    ERROR_QUIET)
+  endif()
+  # get the user name from the ${USER} env variable
+  set(TREXIO_USER_NAME $ENV{USER})
+  # replace placeholders in the templace config.h.in file to produce config.h
+  # config.h is needed to insert TREXIO_PACKAGE_VERSION and TREXIO_GIT_HASH into trexio.h
   configure_file(${CMAKE_SOURCE_DIR}/include/cmake_config.h.in
-                 ${CMAKE_SOURCE_DIR}/include/config.h)
+                 ${CMAKE_SOURCE_DIR}/include/config.h
+		 @ONLY)
 endif()
 
 # Set directories to be included at build time.

include/cmake_config.h.in

@@ -3,3 +3,5 @@
 #define VERSION_MAJOR @PROJECT_VERSION_MAJOR@
 #define VERSION_MINOR @PROJECT_VERSION_MINOR@
 #define VERSION_PATCH @PROJECT_VERSION_PATCH@
+#define GIT_HASH "@GIT_HASH@"
+#define TREXIO_USER_NAME "@TREXIO_USER_NAME@"

python/test/test_api.py

@@ -38,6 +38,8 @@ except:
 #============ WRITE THE DATA IN THE TEST FILE ============#
 #=========================================================#
 
+trexio.info()
+
 # create TREXIO file and open it for writing
 test_file = trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
 assert test_file.exists

src/CMakeLists.txt

@@ -1,4 +1,17 @@
 
+# ============= THREADS SUPPORT ==============
+
+# the two options below add preference for the pthread library over other system-wide threads implementations
+set(CMAKE_THREAD_PREFER_PTHREAD TRUE)
+set(THREADS_PREFER_PTHREAD_FLAG TRUE)
+# find thread library
+find_package(Threads REQUIRED)
+
+# ============= STDINT SUPPORT ===============
+
+include(CheckIncludeFile)
+check_include_file(stdint.h HAVE_STDINT_H)
+
 # ========= DEFINE TREXIO C LIBRARY =========
 
 # Set a list of TREXIO source and header files that are always compiled.

src/templates_front/build.sh

@@ -4,18 +4,22 @@
 cat prefix_front.c   > trexio.c
 cat prefix_front.h   > trexio.h
 
-# parse the config-defined version attributes to pass them to Fortran module file
+# parse the config-defined version attributes to pass them to the header files
 VERSION_VAL=`grep "PACKAGE_VERSION" ../../include/config.h | cut -d " " -f 3`
 VERSION_MAJOR_VAL=`grep "VERSION_MAJOR" ../../include/config.h | cut -d " " -f 3`
 VERSION_MINOR_VAL=`grep "VERSION_MINOR" ../../include/config.h | cut -d " " -f 3`
 VERSION_PATCH_VAL=`grep "VERSION_PATCH" ../../include/config.h | cut -d " " -f 3`
 
+# parse the config-defined GIT_HASH to pass them to the header files
+GIT_HASH_STR=`grep "GIT_HASH" ../../include/config.h | cut -d " " -f 3`
+
 # grep some usefull constants from the config.h
 echo "" >> trexio.h
 echo "#define TREXIO_PACKAGE_VERSION ${VERSION_VAL:='0.0.0'}" >> trexio.h
 echo "#define TREXIO_VERSION_MAJOR ${VERSION_MAJOR_VAL:=0}" >> trexio.h
 echo "#define TREXIO_VERSION_MINOR ${VERSION_MINOR_VAL:=0}" >> trexio.h
 echo "#define TREXIO_VERSION_PATCH ${VERSION_PATCH_VAL:=0}" >> trexio.h
+echo "#define TREXIO_GIT_HASH ${GIT_HASH_STR:='0000'}" >> trexio.h
 echo "" >> trexio.h
 
 cat prefix_s_front.h > trexio_s.h
@@ -24,10 +28,11 @@ cat prefix_python.py   > trexio.py
 
 # append version string and attributes to the Fortran module file
 echo "" >> trexio_f.f90
-echo "character(len = 12) :: TREXIO_PACKAGE_VERSION = ${VERSION_VAL}" >> trexio_f.f90
+echo "character(len = 12) :: TREXIO_PACKAGE_VERSION = ${VERSION_VAL:='0.0.0'}" >> trexio_f.f90
 echo "integer :: TREXIO_VERSION_MAJOR = ${VERSION_MAJOR_VAL}" >> trexio_f.f90
 echo "integer :: TREXIO_VERSION_MINOR = ${VERSION_MINOR_VAL}" >> trexio_f.f90
 echo "integer :: TREXIO_VERSION_PATCH = ${VERSION_PATCH_VAL}" >> trexio_f.f90
+echo "character(len = 64) :: TREXIO_GIT_HASH = ${GIT_HASH_STR:='0000'}" >> trexio_f.f90
 echo "" >> trexio_f.f90
 
 # c front end

src/templates_front/templator_front.org

@@ -1211,6 +1211,18 @@ def _close(trexio_file):
     output:
  ~trexio_exit_code~ exit code.
 
+    It returns:
+
+    - ~TREXIO_SUCCESS~ if the ~file_name~ exists and if it correspond to a valid TREXIO file (i.e. a directory OR an HDF5 file)
+    - ~TREXIO_FILE_ERROR~ if ~file_name~ exists but it is not a TREXIO file
+    - ~TREXIO_FAILURE~ otherwise
+
+Also, there is an implicit way to have the aforementioned functionality.
+Attempt to open a non-existing file with ~trexio_open~ function will result in a ~TREXIO_OPEN_ERROR~ exit code
+(see the modified value that has been passed as a 4-th argument to ~trexio_open~).
+
+You can see examples of both functionalities in =test_f.f90=  (search for calls with ~_void~ suffix).
+
 *** C
 
     #+begin_src c :tangle prefix_front.h :exports none
@@ -1397,6 +1409,7 @@ trexio_exit_code
 trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* const num)
 {
   if (file == NULL) return TREXIO_INVALID_ARG_1;
+  if (num  == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
 
   switch (file->back_end) {
@@ -1456,6 +1469,7 @@ trexio_exit_code
 trexio_read_$group_num$_32 (trexio_t* const file, $group_num_dtype_single$* const num)
 {
   if (file == NULL) return TREXIO_INVALID_ARG_1;
+  if (num  == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
 
   $group_num_dtype_double$ num_64 = 0;
@@ -2680,6 +2694,7 @@ trexio_exit_code
 trexio_read_$group_dset$_size(trexio_t* const file, int64_t* const size_max)
 {
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
+  if (size_max == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
 
   switch (file->back_end) {
@@ -3904,6 +3919,7 @@ def has_$group_str$(trexio_file) -> bool:
         return False
      #+end_src
 
+<<<<<<< HEAD
 ** Templates for front end delete an entire group (UNSAFE MODE)
 *** Introduction
 
@@ -3985,6 +4001,69 @@ def delete_$group$(trexio_file) -> None:
     if rc != TREXIO_SUCCESS:
         raise Error(rc)
      #+end_src
+* General helper functions
+
+  This section contains general helper functions like ~trexio_info~.
+
+ ~trexio_info~ prints information about the TREXIO configuration (see =config.h= file).
+  In particular:
+
+  1) ~TREXIO_PACKAGE_VERSION~ [string]
+  2) ~HAVE_HDF5~ [bool]
+  3) ~HDF5_VERSION~ [string] (optional, only if ~HAVE_HDF5~ is ~true~)
+  4) ~TREXIO_GIT_HASH~ [string]
+
+** C
+
+     #+begin_src c :tangle prefix_front.h :exports none
+ trexio_exit_code trexio_info(void);
+     #+end_src
+
+     #+begin_src c :tangle prefix_front.c
+ trexio_exit_code
+ trexio_info (void)
+ {
+   printf("TREXIO_PACKAGE_VERSION : %s\n", TREXIO_PACKAGE_VERSION);
+
+ #ifdef TREXIO_GIT_HASH
+   printf("TREXIO_GIT_HASH        : %s\n", TREXIO_GIT_HASH);
+ #else
+   printf("GIT_HASH is stored in the config.h file, which is missing.");
+ #endif
+
+ #ifdef HAVE_HDF5
+   printf("HAVE_HDF5              : true\n");
+   printf("%s\n", H5_VERS_INFO);
+ #else
+   printf("HAVE_HDF5              : false\n");
+   printf("TREXIO configured without the HDF5 library\n");
+ #endif
+
+   return TREXIO_SUCCESS;
+ }
+     #+end_src
+
+** Fortran
+
+   #+begin_src f90 :tangle prefix_fortran.f90
+interface
+   integer function trexio_info () bind(C)
+     use, intrinsic :: iso_c_binding
+   end function trexio_info
+end interface
+   #+end_src
+
+** Python
+
+   #+begin_src python :tangle basic_python.py
+def info():
+    """Print the info about the installed TREXIO library.
+    """
+
+    rc = pytr.trexio_info()
+    if rc != TREXIO_SUCCESS:
+        raise Error(rc)
+   #+end_src
 
 * Fortran helper/wrapper functions
 

tests/io_all.c

@@ -14,6 +14,8 @@ int main() {
 
   int rc;
 
+  trexio_info();
+
   bool have_hdf5 = trexio_has_backend(TREXIO_HDF5);
   if(have_hdf5) {
     rc = system("rm -f -- test_all.h5");
@@ -223,5 +225,3 @@ int test_read(const char* file_name, const back_end_t backend) {
 
   return 0;
 }
-
-

tests/test_f.f90

@@ -3,6 +3,7 @@ program test_trexio
   use, intrinsic :: iso_c_binding
   implicit none
 
+  integer :: rc
   logical :: have_hdf5
 
   print *      , "============================================"
@@ -11,6 +12,8 @@ program test_trexio
   print'(a,i3)', "         TREXIO MINOR VERSION  : ", TREXIO_VERSION_MINOR
   print *      , "============================================"
 
+  rc = trexio_info()
+
   call system('rm -rf -- test_write_f.dir')
   print *, 'call test_write(''test_write_f.dir'', TREXIO_TEXT)'
   call test_write('test_write_f.dir', TREXIO_TEXT)