mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-24 22:21:43 +02:00
commit
f829036f0e
21
.github/workflows/actions.yml
vendored
21
.github/workflows/actions.yml
vendored
@ -57,6 +57,13 @@ jobs:
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- name: check TREXIO
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run: make -j2 check
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- name: Archive test log file
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if: failure()
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uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
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with:
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name: test-report-ubuntu
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path: test-suite.log
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- name: create virtual environment
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run: |
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python3 -m venv --clear pytrexio-venv
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@ -96,6 +103,13 @@ jobs:
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- name: recheck TREXIO for memory leaks
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run: make -j2 check
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- name: Archive test log file
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if: failure()
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uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
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with:
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name: test-report-ubuntu-2
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path: test-suite.log
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- name: maintainer clean
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run: make maintainer-clean
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@ -124,5 +138,12 @@ jobs:
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- name: check TREXIO
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run: make check
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- name: Archive test log file
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if: failure()
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uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
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with:
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name: test-report-macos
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path: test-suite.log
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- name: clean
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run: make clean
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@ -104,7 +104,7 @@ esac
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## ---------
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# Checks for basic header files.
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AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd.h])
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AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd.h sys/types.h sys/wait.h ])
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### HDF5
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@ -130,11 +130,12 @@ if test "x${with_hdf5}" = xno; then
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recommended to build efficient TREXIO.
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------------------------------------------])
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else
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AC_HAVE_LIBRARY([hdf5_hl], [], AC_MSG_ERROR([
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AC_CHECK_LIB([hdf5_hl],[main],[],[AC_MSG_ERROR(
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-----------------------------------
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Error: hdf5_hl library is required
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-----------------------------------
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]), [])
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)],[])ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
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fi
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CFLAGS="${HDF5_CFLAGS} ${CFLAGS}"
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@ -44,6 +44,9 @@ typedef int32_t trexio_exit_code;
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#include <stdbool.h>
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#include <string.h>
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#include <err.h>
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#include <sys/types.h>
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#include <sys/wait.h>
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#include "trexio.h"
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#include "trexio_private.h"
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@ -1585,6 +1588,139 @@ def _inquire(file_name: str) -> bool:
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raise Error(rc)
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#+end_src
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** File copy
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~trexio_cp~ copies a TREXIO file using =/bin/cp=.
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**Input parameters:**
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1) ~source_file_name~ - string containing the name of the source file
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2) ~destination_file_name~ - string containing the name of the new file
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**Output:**
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- ~trexio_exit_code~
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*** C
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#+begin_src c :tangle prefix_front.h :exports none
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trexio_exit_code trexio_cp(const char* source_file_name, const char* dest_file_name);
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_cp(const char* source, const char* dest)
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{
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if (source == NULL || source[0] == '\0') {
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return TREXIO_INVALID_ARG_1;
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}
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if (dest == NULL || dest[0] == '\0') {
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return TREXIO_INVALID_ARG_2;
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}
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back_end_t back_end_local = TREXIO_AUTO;
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/* Try to determine the applicable backend if the back_end argument is TREXIO_AUTO */
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#ifdef HAVE_HDF5
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/* Check if the TREXIO file exists and if it is a directory */
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trexio_exit_code rc_text = trexio_text_inquire(source);
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if (rc_text == TREXIO_SUCCESS) {
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back_end_local = TREXIO_TEXT;
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} else {
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/* If not, check if it is an HDF5 file */
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trexio_exit_code rc_hdf5 = trexio_hdf5_inquire(source);
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if (rc_hdf5 == TREXIO_SUCCESS) {
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back_end_local = TREXIO_HDF5;
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} else {
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/* File is neither a directory nor an HDF5 file -> return an error */
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return TREXIO_FILE_ERROR;
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}
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#else
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/* In the current implementation if HDF5 back end is not available - then there is only back end left */
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back_end_local = TREXIO_TEXT;
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#endif
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}
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assert (back_end_local != TREXIO_AUTO);
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if (trexio_inquire(dest) == TREXIO_SUCCESS) {
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/* Destination file already exists */
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return TREXIO_FILE_ERROR;
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}
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/* Call cp */
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pid_t pid = fork();
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if (pid == 0) {
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switch (back_end_local) {
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case TREXIO_TEXT:
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execl("/bin/cp", "/bin/cp", "-r", "-n", source, dest, (char *)0);
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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execl("/bin/cp", "/bin/cp", "-n", source, dest, (char *)0);
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#else
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return TREXIO_FILE_ERROR;
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#endif
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/*
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case TREXIO_JSON:
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execl("/bin/cp", "/bin/cp", source, dest, (char *)0);
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,*/
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default:
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return TREXIO_FILE_ERROR;
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}
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} else if (pid < 0) {
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return TREXIO_FILE_ERROR;
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} else {
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int wstatus;
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pid_t ws = waitpid( pid, &wstatus, 0);
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if (ws != pid || !WIFEXITED(wstatus) )
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return TREXIO_FILE_ERROR;
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}
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return TREXIO_SUCCESS;
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}
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#+end_src
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*** Fortran
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#+begin_src f90 :tangle prefix_fortran.f90
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interface
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integer(trexio_exit_code) function trexio_cp_c (source, destination) bind(C, name="trexio_cp")
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use, intrinsic :: iso_c_binding
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import
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character(kind=c_char), dimension(*) :: source, destination
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end function trexio_cp_c
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end interface
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#+end_src
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*** Python
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#+begin_src python :tangle basic_python.py
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def _cp(source: str, destination: str):
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"""Copies a TREXIO file
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Parameters:
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source: str
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Name of the source file
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destination: str
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Name of the destination file
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Examples:
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>>> from trexio import cp as tr_cp
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>>> tr_cp("example.h5", "new.h5")
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"""
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from shutil import copytree, copyfile
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f = File(filename=source, mode='r', back_end=TREXIO_AUTO)
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if f.back_end == TREXIO_TEXT:
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copytree(source, destination)
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elif f.back_end == TREXIO_HDF5:
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copyfile(source, destination)
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#+end_src
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** File state
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**Note:** the use of the functions below is discouraged as of version 2.3.0.
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@ -5871,6 +6007,23 @@ contains
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end function trexio_inquire
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#+end_src
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Similarly, the following function adapts ~trexio_cp~.
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#+begin_src f90 :tangle helper_fortran.f90
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integer(trexio_exit_code) function trexio_cp (source, destination)
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use, intrinsic :: iso_c_binding
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implicit none
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character(len=*), intent(in) :: source
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character(len=*), intent(in) :: destination
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character(len=len_trim(source)+1) :: source_c
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character(len=len_trim(destination)+1) :: destination_c
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source_c = trim(source) // c_null_char
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destination_c = trim(destination) // c_null_char
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trexio_cp = trexio_cp_c(source_c, destination_c)
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end function trexio_cp
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#+end_src
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The subroutines below wrap the ~to_orbital_list~ functions to shift the MO indices
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by 1 since in Fortran arrays are 1-based and C/Python they are 0-based.
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@ -18,19 +18,25 @@ int main() {
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bool have_hdf5 = trexio_has_backend(TREXIO_HDF5);
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if(have_hdf5) {
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rc = system("rm -f -- test_all.h5");
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rc = system("rm -f -- test_all.h5 test_all2.h5");
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assert (rc == 0);
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test_write("test_all.h5", TREXIO_HDF5);
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test_read ("test_all.h5", TREXIO_HDF5);
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rc = system("rm -f -- test_all.h5");
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test_write("test_all.h5" , TREXIO_HDF5);
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rc = trexio_cp ("test_all.h5", "test_all2.h5");
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assert (rc == TREXIO_SUCCESS);
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test_read ("test_all2.h5", TREXIO_HDF5);
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rc = system("rm -f -- test_all.h5 test_all2.h5");
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assert (rc == 0);
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}
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rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir");
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rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir && \
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rm -f -- test_all2.dir/*.txt test_all2.dir/*.txt.size test_all2.dir/.lock && rm -fd -- test_all2.dir");
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assert (rc == 0);
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test_write("test_all.dir", TREXIO_TEXT);
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test_read ("test_all.dir", TREXIO_TEXT);
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rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir");
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test_write("test_all.dir" , TREXIO_TEXT);
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rc = trexio_cp ("test_all.dir" , "test_all2.dir");
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assert (rc == TREXIO_SUCCESS);
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test_read ("test_all2.dir", TREXIO_TEXT);
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rc = system("rm -f -- test_all.dir/*.txt test_all.dir/*.txt.size test_all.dir/.lock && rm -fd -- test_all.dir && \
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rm -f -- test_all2.dir/*.txt test_all2.dir/*.txt.size test_all2.dir/.lock && rm -fd -- test_all2.dir");
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assert (rc == 0);
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return 0;
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@ -138,6 +144,7 @@ int test_write(const char* file_name, const back_end_t backend) {
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// open file again in 'write' mode
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file = trexio_open(file_name, 'w', backend, &rc);
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assert (file != NULL);
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assert (rc == TREXIO_SUCCESS);
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// write some missing blocks (e.g. if forgot last time)
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rc = trexio_write_nucleus_charge(file,charge);
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@ -169,6 +176,7 @@ int test_read(const char* file_name, const back_end_t backend) {
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// open existing file on 'read' mode [created by test_write]
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file = trexio_open(file_name, 'r', TREXIO_AUTO, &rc);
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assert (file != NULL);
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assert (rc == TREXIO_SUCCESS);
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// read nucleus_num
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rc = trexio_read_nucleus_num(file,&num);
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@ -14,12 +14,18 @@ program test_trexio
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rc = trexio_info()
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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')
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call system('rm -f -- test_write_f.dir/*.txt test_write_f.dir/*.txt.size test_write_f.dir/.lock ' &
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// 'test_write_f2.dir/*.txt test_write_f2.dir/*.txt.size test_write_f2.dir/.lock && ' &
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// 'rm -fd -- test_write_f.dir test_write_f2.dir')
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print *, 'call test_write(''test_write_f.dir'', TREXIO_TEXT)'
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call test_write('test_write_f.dir', TREXIO_TEXT)
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print *, 'call test_read(''test_write_f.dir'', TREXIO_TEXT)'
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call test_read('test_write_f.dir', TREXIO_TEXT)
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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')
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rc = trexio_cp('test_write_f.dir', 'test_write_f2.dir')
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call trexio_assert(rc, TREXIO_SUCCESS)
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print *, 'call test_read(''test_write_f2.dir'', TREXIO_TEXT)'
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call test_read('test_write_f2.dir', TREXIO_TEXT)
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call system('rm -f -- test_write_f.dir/*.txt test_write_f.dir/*.txt.size test_write_f.dir/.lock ' &
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// 'test_write_f2.dir/*.txt test_write_f2.dir/*.txt.size test_write_f2.dir/.lock && ' &
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// 'rm -fd -- test_write_f.dir test_write_f2.dir')
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call test_read_void('test_write_f.dir', TREXIO_TEXT)
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@ -27,12 +33,14 @@ program test_trexio
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! So temporarily disable the test for HDF5 back end at the moment
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have_hdf5 = trexio_has_backend(TREXIO_HDF5)
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if (have_hdf5) then
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call system('rm -f -- test_write_f.h5')
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call system('rm -f -- test_write_f.h5 test_write_f2.h5')
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print *, 'call test_write(''test_write_f.h5'', TREXIO_HDF5)'
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call test_write('test_write_f.h5', TREXIO_HDF5)
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print *, 'call test_read(''test_write_f.h5'', TREXIO_HDF5)'
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call test_read('test_write_f.h5', TREXIO_HDF5)
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call system('rm -f -- test_write_f.h5')
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rc = trexio_cp('test_write_f.h5', 'test_write_f2.h5')
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call trexio_assert(rc, TREXIO_SUCCESS)
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print *, 'call test_read(''test_write_f2.h5'', TREXIO_HDF5)'
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call test_read('test_write_f2.h5', TREXIO_HDF5)
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call system('rm -f -- test_write_f.h5 test_write_f2.h5')
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call test_read_void('test_write_f.h5', TREXIO_HDF5)
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endif
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