Merge pull request #107 from TREX-CoE/trexio_cp

Added trexio_cp

.github/workflows/actions.yml

@@ -57,6 +57,13 @@ jobs:
       - name: check TREXIO
         run: make -j2 check
 
+      - name: Archive test log file
+        if: failure()
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        with:
+          name: test-report-ubuntu
+          path: test-suite.log
+
       - name: create virtual environment
         run: |
           python3 -m venv --clear pytrexio-venv
@@ -96,6 +103,13 @@ jobs:
       - name: recheck TREXIO for memory leaks
         run: make -j2 check
 
+      - name: Archive test log file
+        if: failure()
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        with:
+          name: test-report-ubuntu-2
+          path: test-suite.log
+
       - name: maintainer clean
         run: make maintainer-clean
 
@@ -124,5 +138,12 @@ jobs:
       - name: check TREXIO
         run: make check
 
+      - name: Archive test log file
+        if: failure()
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
+        with:
+          name: test-report-macos
+          path: test-suite.log
+
       - name: clean
         run: make clean

configure.ac

@@ -104,7 +104,7 @@ esac
 ## ---------
 
 # Checks for basic header files.
-AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd.h])
+AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd.h sys/types.h sys/wait.h ])
 
 
 ### HDF5
@@ -130,11 +130,12 @@ if test "x${with_hdf5}" = xno; then
     recommended to build efficient TREXIO.
     ------------------------------------------])
 else
-    AC_HAVE_LIBRARY([hdf5_hl], [], AC_MSG_ERROR([
+    AC_CHECK_LIB([hdf5_hl],[main],[],[AC_MSG_ERROR(
 -----------------------------------
 Error: hdf5_hl library is required
 -----------------------------------
-]), [])
+)],[])ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
+
 fi
 
 CFLAGS="${HDF5_CFLAGS} ${CFLAGS}"

src/templates_front/templator_front.org

@@ -44,6 +44,9 @@ typedef int32_t trexio_exit_code;
 #include <stdbool.h>
 #include <string.h>
 #include <err.h>
+#include <sys/types.h>
+#include <sys/wait.h>
+
 
 #include "trexio.h"
 #include "trexio_private.h"
@@ -1585,6 +1588,139 @@ def _inquire(file_name: str) -> bool:
         raise Error(rc)
    #+end_src
 
+** File copy
+
+ ~trexio_cp~ copies a TREXIO file using =/bin/cp=.
+
+   **Input parameters:**
+     1) ~source_file_name~       - string containing the name of the source file
+     2) ~destination_file_name~  - string containing the name of the new file
+
+   **Output:**
+     - ~trexio_exit_code~
+
+*** C
+
+   #+begin_src c :tangle prefix_front.h :exports none
+trexio_exit_code trexio_cp(const char* source_file_name, const char* dest_file_name);
+   #+end_src
+
+   #+begin_src c :tangle prefix_front.c
+
+trexio_exit_code
+trexio_cp(const char* source, const char* dest)
+{
+
+  if (source == NULL || source[0] == '\0') {
+    return TREXIO_INVALID_ARG_1;
+  }
+
+  if (dest == NULL || dest[0] == '\0') {
+    return TREXIO_INVALID_ARG_2;
+  }
+
+
+  back_end_t back_end_local = TREXIO_AUTO;
+ /* Try to determine the applicable backend if the back_end argument is TREXIO_AUTO */
+#ifdef HAVE_HDF5
+ /* Check if the TREXIO file exists and if it is a directory */
+  trexio_exit_code rc_text = trexio_text_inquire(source);
+  if (rc_text == TREXIO_SUCCESS) {
+    back_end_local = TREXIO_TEXT;
+  } else {
+ /* If not, check if it is an HDF5 file */
+    trexio_exit_code rc_hdf5 = trexio_hdf5_inquire(source);
+    if (rc_hdf5 == TREXIO_SUCCESS) {
+      back_end_local = TREXIO_HDF5;
+    } else {
+ /* File is neither a directory nor an HDF5 file -> return an error */
+      return TREXIO_FILE_ERROR;
+    }
+#else
+ /* In the current implementation if HDF5 back end is not available - then there is only back end left */
+    back_end_local = TREXIO_TEXT;
+#endif
+  }
+  assert (back_end_local != TREXIO_AUTO);
+
+  if (trexio_inquire(dest) == TREXIO_SUCCESS) {
+ /* Destination file already exists */
+    return TREXIO_FILE_ERROR;
+  }
+
+ /* Call cp */
+
+  pid_t pid = fork();
+  if (pid == 0) {
+    switch (back_end_local) {
+    case TREXIO_TEXT:
+      execl("/bin/cp", "/bin/cp", "-r", "-n", source, dest, (char *)0);
+    case TREXIO_HDF5:
+#ifdef HAVE_HDF5
+      execl("/bin/cp", "/bin/cp", "-n", source, dest, (char *)0);
+#else
+      return TREXIO_FILE_ERROR;
+#endif
+/*
+    case TREXIO_JSON:
+      execl("/bin/cp", "/bin/cp", source, dest, (char *)0);
+,*/
+    default:
+      return TREXIO_FILE_ERROR;
+    }
+  } else if (pid < 0) {
+    return TREXIO_FILE_ERROR;
+  } else {
+    int wstatus;
+    pid_t ws = waitpid( pid, &wstatus, 0);
+    if (ws != pid || !WIFEXITED(wstatus) )
+      return TREXIO_FILE_ERROR;
+  }
+
+  return TREXIO_SUCCESS;
+}
+   #+end_src
+
+*** Fortran
+
+   #+begin_src f90 :tangle prefix_fortran.f90
+interface
+   integer(trexio_exit_code) function trexio_cp_c (source, destination) bind(C, name="trexio_cp")
+     use, intrinsic :: iso_c_binding
+     import
+     character(kind=c_char), dimension(*)          :: source, destination
+   end function trexio_cp_c
+end interface
+   #+end_src
+
+*** Python
+
+   #+begin_src python :tangle basic_python.py
+def _cp(source: str, destination: str):
+    """Copies a TREXIO file
+
+    Parameters:
+
+    source: str
+        Name of the source file
+
+    destination: str
+        Name of the destination file
+
+    Examples:
+    >>> from trexio import cp as tr_cp
+    >>> tr_cp("example.h5", "new.h5")
+    """
+
+    from shutil import copytree, copyfile
+
+    f = File(filename=source, mode='r', back_end=TREXIO_AUTO)
+    if f.back_end == TREXIO_TEXT:
+      copytree(source, destination)
+    elif f.back_end == TREXIO_HDF5:
+      copyfile(source, destination)
+   #+end_src
+
 ** File state
 
     **Note:** the use of the functions below is discouraged as of version 2.3.0.
@@ -5871,6 +6007,23 @@ contains
    end function trexio_inquire
   #+end_src
 
+  Similarly, the following function adapts ~trexio_cp~.
+
+  #+begin_src f90 :tangle helper_fortran.f90
+  integer(trexio_exit_code) function trexio_cp (source, destination)
+    use, intrinsic :: iso_c_binding
+    implicit none
+    character(len=*), intent(in)           :: source
+    character(len=*), intent(in)           :: destination
+    character(len=len_trim(source)+1)      :: source_c
+    character(len=len_trim(destination)+1) :: destination_c
+
+    source_c = trim(source) // c_null_char
+    destination_c = trim(destination) // c_null_char
+    trexio_cp = trexio_cp_c(source_c, destination_c)
+  end function trexio_cp
+   #+end_src
+
   The subroutines below wrap the ~to_orbital_list~ functions to shift the MO indices
   by 1 since in Fortran arrays are 1-based and C/Python they are 0-based.
 

tests/io_all.c

@@ -18,19 +18,25 @@ int main() {
 
   bool have_hdf5 = trexio_has_backend(TREXIO_HDF5);
   if(have_hdf5) {
-    rc = system("rm -f -- test_all.h5");
+    rc = system("rm -f -- test_all.h5 test_all2.h5");
     assert (rc == 0);
-    test_write("test_all.h5", TREXIO_HDF5);
+    test_write("test_all.h5" , TREXIO_HDF5);
-    test_read ("test_all.h5", TREXIO_HDF5);
+    rc = trexio_cp ("test_all.h5", "test_all2.h5");
-    rc = system("rm -f -- test_all.h5");
+    assert (rc == TREXIO_SUCCESS);
+    test_read ("test_all2.h5", TREXIO_HDF5);
+    rc = system("rm -f -- test_all.h5 test_all2.h5");
     assert (rc == 0);
   }
 
-  rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir");
+  rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir && \
+               rm -f -- test_all2.dir/*.txt test_all2.dir/*.txt.size test_all2.dir/.lock && rm -fd -- test_all2.dir");
   assert (rc == 0);
-  test_write("test_all.dir", TREXIO_TEXT);
+  test_write("test_all.dir" , TREXIO_TEXT);
-  test_read ("test_all.dir", TREXIO_TEXT);
+  rc = trexio_cp ("test_all.dir" , "test_all2.dir");
-  rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir");
+  assert (rc == TREXIO_SUCCESS);
+  test_read ("test_all2.dir", TREXIO_TEXT);
+  rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir && \
+               rm -f -- test_all2.dir/*.txt test_all2.dir/*.txt.size test_all2.dir/.lock && rm -fd -- test_all2.dir");
   assert (rc == 0);
 
   return 0;
@@ -138,6 +144,7 @@ int test_write(const char* file_name, const back_end_t backend) {
   // open file again in 'write' mode
   file = trexio_open(file_name, 'w', backend, &rc);
   assert (file != NULL);
+  assert (rc == TREXIO_SUCCESS);
 
   // write some missing blocks (e.g. if forgot last time)
   rc = trexio_write_nucleus_charge(file,charge);
@@ -169,6 +176,7 @@ int test_read(const char* file_name, const back_end_t backend) {
   // open existing file on 'read' mode [created by test_write]
   file = trexio_open(file_name, 'r', TREXIO_AUTO, &rc);
   assert (file != NULL);
+  assert (rc == TREXIO_SUCCESS);
 
   // read nucleus_num
   rc = trexio_read_nucleus_num(file,&num);

tests/test_f.f90

@@ -14,12 +14,18 @@ program test_trexio
 
   rc = trexio_info()
 
-  call system('rm -f -- test_write_f.dir/*.txt test_write_f.dir/*.txt.size test_write_f.dir/.lock && rm -fd -- test_write_f.dir')
+  call system('rm -f -- test_write_f.dir/*.txt test_write_f.dir/*.txt.size test_write_f.dir/.lock ' &
+      // 'test_write_f2.dir/*.txt test_write_f2.dir/*.txt.size test_write_f2.dir/.lock && ' &
+      // 'rm -fd -- test_write_f.dir test_write_f2.dir')
   print *, 'call test_write(''test_write_f.dir'', TREXIO_TEXT)'
   call test_write('test_write_f.dir', TREXIO_TEXT)
-  print *, 'call test_read(''test_write_f.dir'', TREXIO_TEXT)'
+  rc = trexio_cp('test_write_f.dir', 'test_write_f2.dir')
-  call test_read('test_write_f.dir', TREXIO_TEXT)
+  call trexio_assert(rc, TREXIO_SUCCESS)
-  call system('rm -f -- test_write_f.dir/*.txt test_write_f.dir/*.txt.size test_write_f.dir/.lock && rm -fd -- test_write_f.dir')
+  print *, 'call test_read(''test_write_f2.dir'', TREXIO_TEXT)'
+  call test_read('test_write_f2.dir', TREXIO_TEXT)
+  call system('rm -f -- test_write_f.dir/*.txt test_write_f.dir/*.txt.size test_write_f.dir/.lock ' &
+      // 'test_write_f2.dir/*.txt test_write_f2.dir/*.txt.size test_write_f2.dir/.lock && ' &
+      // 'rm -fd -- test_write_f.dir test_write_f2.dir')
 
   call test_read_void('test_write_f.dir', TREXIO_TEXT)
 
@@ -27,12 +33,14 @@ program test_trexio
   ! So temporarily disable the test for HDF5 back end at the moment
   have_hdf5 = trexio_has_backend(TREXIO_HDF5)
   if (have_hdf5) then
-    call system('rm -f -- test_write_f.h5')
+    call system('rm -f -- test_write_f.h5 test_write_f2.h5')
     print *, 'call test_write(''test_write_f.h5'', TREXIO_HDF5)'
     call test_write('test_write_f.h5', TREXIO_HDF5)
-    print *, 'call test_read(''test_write_f.h5'', TREXIO_HDF5)'
+    rc = trexio_cp('test_write_f.h5', 'test_write_f2.h5')
-    call test_read('test_write_f.h5', TREXIO_HDF5)
+    call trexio_assert(rc, TREXIO_SUCCESS)
-    call system('rm -f -- test_write_f.h5')
+    print *, 'call test_read(''test_write_f2.h5'', TREXIO_HDF5)'
+    call test_read('test_write_f2.h5', TREXIO_HDF5)
+    call system('rm -f -- test_write_f.h5 test_write_f2.h5')
 
     call test_read_void('test_write_f.h5', TREXIO_HDF5)
   endif