Merge pull request #95 from TREX-CoE/add-has-group

Add trexio_has_group functionality

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files

ChangeLog

@@ -1,6 +1,12 @@
 CHANGES
 =======
 
+2.3
+---
+
+- Added `trexio_has_group` functionality
+- Added OCaml binding
+
 2.2
 ---
 

Makefile.am

@@ -146,7 +146,6 @@ check_PROGRAMS = $(TESTS)
 LDADD = src/libtrexio.la
 
 test_trexio_f = $(srcdir)/tests/trexio_f.f90
-CLEANFILES += $(test_trexio_f)
 
 $(test_trexio_f): $(trexio_f)
 	cp $(trexio_f) $(test_trexio_f)

ocaml/trexio/dune-project

@@ -1,7 +1,7 @@
 (lang dune 3.1)
 
 (name trexio)
-(version 2.2.0)
+(version 2.3.0)
 
 (generate_opam_files true)
 

ocaml/trexio/read_json.py

@@ -34,6 +34,17 @@ CAMLprim value caml_delete_{group}(value file)
     caml_failwith(trexio_string_of_error(rc));
   }
 }
+
+CAMLprim value caml_has_{group}(value file)
+{
+  CAMLparam1(file);
+  trexio_exit_code rc = trexio_has_{group}( File_val(file) );
+  if (rc == TREXIO_SUCCESS) {
+    CAMLreturn ( Val_bool(true) );
+  } else {
+    CAMLreturn ( Val_bool(false) );
+  }
+}
 """
             f.write( t.replace("{group}",group) )
 
@@ -437,7 +448,8 @@ def write_mli(data):
         f.write(content_pre)
 
         for group in data:
-            t = "val delete_{group}: trexio_file -> unit\n"
+            t  = "val delete_{group}: trexio_file -> unit\n"
+            t += "val has_{group}: trexio_file -> bool\n"
             f.write( t.replace("{group}",group) )
 
             for element in data[group]:
@@ -526,7 +538,8 @@ def write_ml(data):
         f.write(content_pre)
 
         for group in data:
-            t = "external delete_{group}: trexio_file -> unit = \"caml_delete_{group}\"\n"
+            t  = "external delete_{group}: trexio_file -> unit = \"caml_delete_{group}\"\n"
+            t += "external has_{group}: trexio_file -> bool = \"caml_has_{group}\"\n"
             f.write( t.replace("{group}",group) )
 
             for element in data[group]:

python/test/test_api.py

@@ -192,11 +192,21 @@ class TestIO:
         self.test_array_1D()
         self.test_array_2D()
 
+        assert trexio.has_nucleus(self.test_file)
+
         trexio.delete_nucleus(self.test_file)
 
         assert not trexio.has_nucleus_num(self.test_file)
         assert not trexio.has_nucleus_charge(self.test_file)
         assert not trexio.has_nucleus_coord(self.test_file)
+        assert not trexio.has_nucleus(self.test_file)
+
+
+    def test_has_group(self):
+        """Check existense of a group."""
+        self.open()
+        assert trexio.has_nucleus(self.test_file)
+        assert not trexio.has_rdm(self.test_file)
 
 
     def test_context_manager(self):

src/templates_front/templator_front.org

@@ -1755,6 +1755,98 @@ trexio_pre_close (trexio_t* file)
    considered dimensioning variables and cannot be negative or 0. An attempt to write negative or 0
    value will result in ~TREXIO_INVALID_ARG_2~ exit code.
 
+** Templates for front end has_group functions
+*** Introduction
+
+   This section concerns API calls related to TREXIO groups
+
+   | Function name        | Description                       |
+   |----------------------+-----------------------------------|
+   | ~trexio_has_$group$~ | Check if a group exists in a file |
+
+*** C templates for front end
+
+   The ~C~ templates that correspond to each of the abovementioned
+   functions can be found below.  First parameter is the ~TREXIO~ file
+   handle.
+
+**** Function declarations
+
+     #+begin_src c :tangle hrw_group_front.h :exports none
+trexio_exit_code trexio_has_$group$(trexio_t* const file);
+     #+end_src
+
+**** Source code
+
+     #+begin_src c :tangle has_group_front.c
+trexio_exit_code
+trexio_has_$group$ (trexio_t* const file)
+{
+
+  if (file == NULL) return TREXIO_INVALID_ARG_1;
+
+  assert(file->back_end < TREXIO_INVALID_BACK_END);
+
+  switch (file->back_end) {
+
+  case TREXIO_TEXT:
+    return trexio_text_has_$group$(file);
+
+  case TREXIO_HDF5:
+#ifdef HAVE_HDF5
+    return trexio_hdf5_has_$group$(file);
+#else
+    return TREXIO_BACK_END_MISSING;
+#endif
+/*
+  case TREXIO_JSON:
+    return trexio_json_has_$group$(file);
+    break;
+,*/
+  }
+
+  return TREXIO_FAILURE;
+}
+     #+end_src
+
+*** Fortran templates for front end
+
+    The ~Fortran~ templates that provide an access to the ~C~ API calls from Fortran.
+    These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
+
+     #+begin_src f90 :tangle has_group_front_fortran.f90
+interface
+   integer(trexio_exit_code) function trexio_has_$group$ (trex_file) bind(C)
+     use, intrinsic :: iso_c_binding
+     import
+     integer(c_int64_t), intent(in), value :: trex_file
+   end function trexio_has_$group$
+end interface
+     #+end_src
+
+*** Python templates for front end
+
+     #+begin_src python :tangle has_group_front.py
+def has_$group$(trexio_file) -> bool:
+    """Check that $group$ group exists in the TREXIO file.
+
+    Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
+
+    Returns:
+          True if the variable exists, False otherwise
+
+    Raises:
+        - trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
+        - Exception from some other error (e.g. RuntimeError).
+    """
+
+    rc = pytr.trexio_has_$group$(trexio_file.pytrexio_s)
+    if rc == TREXIO_FAILURE:
+        raise Error(rc)
+
+    return rc == TREXIO_SUCCESS
+     #+end_src
+
 ** Templates for front end has/read/write a single numerical attribute
 *** Introduction
 

src/templates_hdf5/templator_hdf5.org

@@ -179,6 +179,38 @@ trexio_hdf5_deinit (trexio_t* const file)
 }
   #+end_src
 
+* Template for HDF5 has a group
+
+  #+begin_src c :tangle hrw_group_hdf5.h :exports none
+trexio_exit_code trexio_hdf5_has_$group$ (trexio_t* const file);
+  #+end_src
+
+
+  #+begin_src c :tangle has_group_hdf5.c
+trexio_exit_code
+trexio_hdf5_has_$group$ (trexio_t* const file)
+{
+
+  if (file == NULL) return TREXIO_INVALID_ARG_1;
+
+  const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
+
+  struct H5G_info_t group_info;
+
+ /* H5Gget_info return info about the HDF5 group as a group_info struct */
+  herr_t status = H5Gget_info(f->$group$_group, &group_info);
+  if (status < 0) return TREXIO_FAILURE;
+
+ /* If nlinks==0 --> the group is empty, i.e. non-existent */
+  if (group_info.nlinks == (hsize_t) 0) {
+    return TREXIO_HAS_NOT;
+  } else {
+    return TREXIO_SUCCESS;
+  }
+
+}
+    #+end_src
+
 * Template for HDF5 has/read/write a numerical attribute
 
   #+begin_src c :tangle hrw_attr_num_hdf5.h :exports none

src/templates_text/build.sh

@@ -13,6 +13,9 @@ cat basic_text.h   >> trexio_text.h
 cat hrw_determinant_text.h >> trexio_text.h
 cat *_determinant_text.c >> trexio_text.c
 
+cat populated/pop_has_group_text.c >> trexio_text.c
+cat populated/pop_hrw_group_text.h >> trexio_text.h
+
 cat populated/pop_free_group_text.c >> trexio_text.c
 cat populated/pop_read_group_text.c >> trexio_text.c
 cat populated/pop_flush_group_text.c >> trexio_text.c

src/templates_text/templator_text.org

@@ -112,6 +112,22 @@ trexio_exit_code trexio_text_inquire(const char* file_name);
 trexio_exit_code trexio_text_deinit(trexio_t* const file);
 trexio_exit_code trexio_text_lock(trexio_t* const file);
 trexio_exit_code trexio_text_unlock(trexio_t* const file);
+bool trexio_text_file_exists(const char* file_name);
+    #+end_src
+
+    #+begin_src c :tangle basic_text.c
+bool
+trexio_text_file_exists (const char* file_name)
+{
+ /* Check if the file with "file_name" exists */
+  struct stat st;
+
+  int rc = stat(file_name, &st);
+
+  bool file_exists = rc == 0;
+
+  return file_exists;
+}
     #+end_src
 
     #+begin_src c :tangle basic_text.c
@@ -493,6 +509,47 @@ trexio_text_read_$group$ (trexio_text_t* const file)
 }
    #+end_src
 
+* Template for text has a group
+
+    #+begin_src c :tangle hrw_group_text.h :exports none
+trexio_exit_code trexio_text_has_$group$(trexio_t* const file);
+    #+end_src
+
+    #+begin_src c :tangle has_group_text.c
+trexio_exit_code
+trexio_text_has_$group$ (trexio_t* const file)
+{
+
+  if (file  == NULL) return TREXIO_INVALID_ARG_1;
+
+ /* Flush the group to make sure the group.txt file is created */
+  if (file->mode != 'r') {
+    trexio_exit_code rc = trexio_text_flush_$group$((trexio_text_t*) file);
+    if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
+  }
+
+ /* Build the file name */
+  char $group$_full_path[TREXIO_MAX_FILENAME_LENGTH];
+
+  const char* $group$_file_name = "/$group$.txt";
+
+  strncpy ($group$_full_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
+  strncat ($group$_full_path, $group$_file_name,
+           TREXIO_MAX_FILENAME_LENGTH-strlen($group$_file_name));
+
+  if ($group$_full_path[TREXIO_MAX_FILENAME_LENGTH-1] != '\0') return TREXIO_FAILURE;
+
+  bool file_exists;
+  file_exists = trexio_text_file_exists($group$_full_path);
+
+  if (file_exists) {
+    return TREXIO_SUCCESS;
+  } else {
+    return TREXIO_HAS_NOT;
+  }
+}
+   #+end_src
+
 * Template for text flush a group
 
     #+begin_src c :tangle flush_group_text.h :exports none
@@ -1063,6 +1120,23 @@ trexio_exit_code trexio_text_write_$group_dset$(trexio_t* const file,
   rc = fclose(f_wSize);
   if (rc != 0) return TREXIO_FILE_ERROR;
 
+  const char $group$_file_name[256] = "/$group$.txt";
+
+  memset (file_full_path, 0, TREXIO_MAX_FILENAME_LENGTH);
+ /* Copy directory name in file_full_path */
+  strncpy (file_full_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
+ /* Append name of the file with sparse data */
+  strncat (file_full_path, $group$_file_name,
+           TREXIO_MAX_FILENAME_LENGTH-strlen($group$_file_name));
+
+  bool file_exists = trexio_text_file_exists(file_full_path);
+
+ /* Create an empty file for the trexio_text_has_group to work */
+  if (!file_exists) {
+    FILE *fp = fopen(file_full_path, "ab+");
+    fclose(fp);
+  }
+
  /* Exit upon success */
   return TREXIO_SUCCESS;
 }
@@ -1533,6 +1607,24 @@ trexio_exit_code trexio_text_write_determinant_list(trexio_t* const file,
   rc = fclose(f);
   if (rc != 0) return TREXIO_FILE_ERROR;
 
+ /* Additional part for the trexio_text_has_group to work */
+  const char det_file_name[256] = "/determinant.txt";
+
+  memset (file_full_path, 0, TREXIO_MAX_FILENAME_LENGTH);
+ /* Copy directory name in file_full_path */
+  strncpy (file_full_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
+ /* Append name of the file with sparse data */
+  strncat (file_full_path, det_file_name,
+           TREXIO_MAX_FILENAME_LENGTH-strlen(det_file_name));
+
+  bool file_exists = trexio_text_file_exists(file_full_path);
+
+ /* Create an empty file for the trexio_text_has_group to work */
+  if (!file_exists) {
+    FILE *fp = fopen(file_full_path, "ab+");
+    fclose(fp);
+  }
+
  /* Exit upon success */
   return TREXIO_SUCCESS;
 }
@@ -1602,6 +1694,24 @@ trexio_exit_code trexio_text_write_determinant_coefficient(trexio_t* const file,
   rc = fclose(f_wSize);
   if (rc != 0) return TREXIO_FILE_ERROR;
 
+ /* Additional part for the trexio_text_has_group to work */
+  const char det_file_name[256] = "/determinant.txt";
+
+  memset (file_full_path, 0, TREXIO_MAX_FILENAME_LENGTH);
+ /* Copy directory name in file_full_path */
+  strncpy (file_full_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
+ /* Append name of the file with sparse data */
+  strncat (file_full_path, det_file_name,
+           TREXIO_MAX_FILENAME_LENGTH-strlen(det_file_name));
+
+  bool file_exists = trexio_text_file_exists(file_full_path);
+
+ /* Create an empty file for the trexio_text_has_group to work */
+  if (!file_exists) {
+    FILE *fp = fopen(file_full_path, "ab+");
+    fclose(fp);
+  }
+
  /* Exit upon success */
   return TREXIO_SUCCESS;
 }

tests/io_dset_int_hdf5.c

@@ -55,6 +55,14 @@ static int test_has_dset (const char* file_name, const back_end_t backend) {
   file = trexio_open(file_name, 'r', backend, &rc);
   assert (file != NULL);
 
+  // check that the group exists
+  rc = trexio_has_basis(file);
+  assert(rc==TREXIO_SUCCESS);
+
+  // check that the group does not exist
+  rc = trexio_has_mo(file);
+  assert(rc==TREXIO_HAS_NOT);
+
   // check that the previously written dataset exists
   rc = trexio_has_basis_nucleus_index(file);
   assert (rc == TREXIO_SUCCESS);
@@ -130,5 +138,3 @@ int main(void) {
 
   return 0;
 }
-
-

tests/io_dset_int_text.c

@@ -55,6 +55,14 @@ static int test_has_dset (const char* file_name, const back_end_t backend) {
   file = trexio_open(file_name, 'r', backend, &rc);
   assert (file != NULL);
 
+  // check that the group exists
+  rc = trexio_has_basis(file);
+  assert(rc==TREXIO_SUCCESS);
+
+  // check that the group does not exist
+  rc = trexio_has_mo(file);
+  assert(rc==TREXIO_HAS_NOT);
+
   // check that the previously written dataset exists
   rc = trexio_has_basis_nucleus_index(file);
   assert (rc == TREXIO_SUCCESS);
@@ -130,5 +138,3 @@ int main(void) {
 
   return 0;
 }
-
-

tests/io_dset_sparse_hdf5.c

@@ -86,6 +86,14 @@ static int test_has_dset_sparse (const char* file_name, const back_end_t backend
   assert (file != NULL);
   assert (rc == TREXIO_SUCCESS);
 
+  // check that the group exists
+  rc = trexio_has_mo_2e_int(file);
+  assert(rc==TREXIO_SUCCESS);
+
+  // check that the group does not exist
+  rc = trexio_has_rdm(file);
+  assert(rc==TREXIO_HAS_NOT);
+
   // first check that mo_2e_int_eri_lr (we only write non-lr component in this unit test)
   rc = trexio_has_mo_2e_int_eri_lr(file);
   assert(rc==TREXIO_HAS_NOT);
@@ -147,7 +155,7 @@ static int test_read_dset_sparse (const char* file_name, const back_end_t backen
   assert(index_read[4*offset_data_read] == 4 * (int32_t) (offset_file_read-offset));
 
   // now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
-  offset_file_read = 97;
+  offset_file_read = 97L;
   offset_data_read = 1;
   int64_t eof_read_size_check = SIZE - offset_file_read; // if offset_file_read=97 => only 3 integrals will be read out of total of 100
 
@@ -159,11 +167,6 @@ static int test_read_dset_sparse (const char* file_name, const back_end_t backen
   assert(chunk_read == eof_read_size_check);
   assert(index_read[4*size_r-1] == 0);
   assert(index_read[4*offset_data_read] == 4 * (int32_t) (offset_file_read-offset));
-  /*
-  for(int i=0; i<size_r; ++i){
-    printf("%d %lf\n", index_read[4*i], value_read[i]);
-  }
-  */
 
   // close current session
   rc = trexio_close(file);

tests/io_dset_sparse_text.c

@@ -86,6 +86,14 @@ static int test_has_dset_sparse (const char* file_name, const back_end_t backend
   assert (file != NULL);
   assert (rc == TREXIO_SUCCESS);
 
+  // check that the group exists
+  rc = trexio_has_mo_2e_int(file);
+  assert(rc==TREXIO_SUCCESS);
+
+  // check that the group does not exist
+  rc = trexio_has_rdm(file);
+  assert(rc==TREXIO_HAS_NOT);
+
   // first check that mo_2e_int_eri_lr (we only write non-lr component in this unit test)
   rc = trexio_has_mo_2e_int_eri_lr(file);
   assert(rc==TREXIO_HAS_NOT);

tests/test_f.f90

@@ -143,6 +143,12 @@ subroutine test_write(file_name, back_end)
   rc = trexio_has_determinant_list(trex_file)
   call trexio_assert(rc, TREXIO_HAS_NOT, 'SUCCESS HAS NOT 4')
 
+  rc = trexio_has_nucleus(trex_file)
+  call trexio_assert(rc, TREXIO_HAS_NOT, 'SUCCESS HAS NOT 5')
+
+  rc = trexio_has_ao_2e_int(trex_file)
+  call trexio_assert(rc, TREXIO_HAS_NOT, 'SUCCESS HAS NOT 6')
+
   rc = trexio_write_nucleus_num(trex_file, nucleus_num)
   call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE NUM')
 
@@ -207,6 +213,12 @@ subroutine test_write(file_name, back_end)
   rc = trexio_has_determinant_list(trex_file)
   call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS HAS 4')
 
+  rc = trexio_has_nucleus(trex_file)
+  call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS HAS 5')
+
+  rc = trexio_has_ao_2e_int(trex_file)
+  call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS HAS 6')
+
   rc = trexio_close(trex_file)
   call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS CLOSE')
 

tools/generator.py

@@ -65,7 +65,7 @@ for fname in files_todo['dset_sparse']:
 # populate group-related functions with mixed scheme
 for fname in files_todo['group']:
     # recursive scheme for delete_group functions
-    if 'delete' in fname:
+    if 'delete' in fname or 'has' in fname:
         recursive_populate_file(fname, template_paths, group_dict)
     # mixed (iterative+recursive) scheme [text backend]
     else: