Merge branch 'walkers' of github.com:TREX-CoE/trexio into walkers

.github/workflows/actions.yml

@@ -2,12 +2,14 @@ name: TREXIO CI
 
 on:
   push:
-    branches: [ master ]
+    branches:
+      - master
+    tags:
+      # After vMajor.Minor.Patch _anything_ is allowed (without "/") !
+      - v[0-9]+.[0-9]+.[0-9]+*
   pull_request:
     branches: [ master ]
-  release:
-    types:
-      - published
+
 
 jobs:
 

.github/workflows/build-wheels.yml

@@ -38,7 +38,7 @@ jobs:
     needs: get_commit_message
     if: >-
       contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
-      github.event_name == 'release'
+      (github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -99,7 +99,7 @@ jobs:
     needs: get_commit_message
     if: >-
       contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
-      github.event_name == 'release'
+      (github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

ChangeLog

@@ -4,6 +4,7 @@ CHANGES
 2.2
 ---
 
+- Added support for Python-ic `with` statements
 - Merged local and non-local pseudopotential integrals  in #86
 - Fixed backwards incompatibility of the `TREXIO_TEXT` back end in #82
 - Added `TREXIO_AUTO` back end for read-only mode (`r`) in PR #80

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "1.1.0"
+__version__ = "1.2.0"

python/test/test_api.py

@@ -32,7 +32,7 @@ try:
     elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
         shutil.rmtree(output_filename)
 except:
-    print ('Nothing to remove.')
+    print('Nothing to remove.')
 
 #=========================================================#
 #============ WRITE THE DATA IN THE TEST FILE ============#
@@ -40,6 +40,17 @@ except:
 
 trexio.info()
 
+
+# test with ... as ... block
+with trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND) as tfile:
+    trexio.write_metadata_description(tfile, "Test file produced by the Python API")
+    assert trexio.has_metadata_description(tfile)
+    assert tfile.isOpen
+
+# the file handle can remain existing but the file itself is closed upon exit from the `with` block
+assert not tfile.isOpen
+
+
 # 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
@@ -281,7 +292,7 @@ assert rpoint_group==point_group
 
 # another way to read only if the variable exists
 if trexio.has_ao_num(test_file2):
-    rmo_num = trexio.read_ao_num(test_file2)
+    rao_num = trexio.read_ao_num(test_file2)
 else:
     print("Pass on reading the non-existing variable ao_num: checked")
 
@@ -290,12 +301,12 @@ else:
 
 # cleaning (remove the TREXIO file)
 try:
-    if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
-        os.remove(output_filename)
-    elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
-        shutil.rmtree(output_filename)
+   if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
+       os.remove(output_filename)
+   elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
+       shutil.rmtree(output_filename)
 except:
-    print (f'No output file {output_filename} has been produced')
+    print(f'No output file {output_filename} has been produced')
 
 #==========================================================#
 

src/templates_front/templator_front.org

@@ -720,8 +720,7 @@ class File:
 
     def __init__(self, filename, mode='r', back_end=TREXIO_HDF5,
                  pytrexio_s=None, info=None):
-        """This is a TREXIO File constructor."""
-
+        """TREXIO File class constructor."""
         self.filename = filename
         self.mode = mode
         self.back_end = back_end
@@ -740,9 +739,19 @@ class File:
         self.info = info
 
 
+    def __enter__(self):
+        """Enter statement for with ... as ... handling."""
+        return self
+
+
+    def __exit__(self, *args):
+        """Exit statement for with ... as ... handling."""
+        if self.isOpen:
+           self.close()
+
+
     def close(self):
         """Close a TREXIO File."""
-
         if self.isOpen:
             _close(self.pytrexio_s)
             self.isOpen = False
@@ -752,13 +761,11 @@ class File:
 
     def inquire(self):
         """Inquire whether a TREXIO file exists."""
-
         self.exists = _inquire(self.filename)
 
 
     def __del__(self):
-        """This is a TREXIO File destructor."""
-
+        """TREXIO File class destructor."""
         if self.isOpen:
             _close(self.pytrexio_s)
         elif self.isOpen is None:
@@ -1204,6 +1211,12 @@ trexio_close (trexio_t* file)
 
   assert(file->back_end < TREXIO_INVALID_BACK_END);
 
+  /* Things to be done before the closing the file in the back-end */
+  rc = trexio_pre_close(file);
+  if (rc != TREXIO_SUCCESS) {
+    return rc;
+  }
+  
   /* Terminate the back end */
   switch (file->back_end) {
 
@@ -1381,6 +1394,80 @@ def _inquire(file_name: str) -> bool:
         raise Error(rc)
    #+end_src
 
+** Tasks to be done before closing
+   
+    #+begin_src c :tangle trexio_private.h :exports none
+trexio_exit_code trexio_pre_close(trexio_t* file);
+    #+end_src
+
+    #+begin_src c :tangle prefix_front.c
+trexio_exit_code
+trexio_pre_close (trexio_t* file)
+{
+
+  if (file == NULL) return TREXIO_FILE_ERROR;
+
+  { /* Up-spin and down-spin electrons */
+    trexio_exit_code rc;
+    
+    int32_t nup, ndn, nelec;
+    bool has_up   = (trexio_has_electron_up_num(file) == TREXIO_SUCCESS);
+    bool has_dn   = (trexio_has_electron_dn_num(file) == TREXIO_SUCCESS);
+    bool has_updn = (trexio_has_electron_num(file) == TREXIO_SUCCESS);
+    
+    if (has_updn && has_up && has_dn) {
+      rc = trexio_read_electron_up_num(file, &nup);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      rc = trexio_read_electron_dn_num(file, &ndn);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      rc = trexio_read_electron_elec_num(file, &nelec);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      if (nelec != nup + ndn) {
+        return TREXIO_INVALID_NUM;
+      }
+    } else if (has_up && has_dn) {
+      rc = trexio_read_electron_up_num(file, &nup);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      rc = trexio_read_electron_dn_num(file, &ndn);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      nelec = nup + ndn;
+      rc = trexio_write_electron_num(file, nelec);
+      if (rc != TREXIO_SUCCESS) return rc;
+    } else if (has_up) {
+      rc = trexio_read_electron_up_num(file, &nup);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      ndn = 0;
+      rc = trexio_write_electron_dn_num(file, ndn);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      nelec = nup;
+      rc = trexio_write_electron_num(file, nelec);
+      if (rc != TREXIO_SUCCESS) return rc;
+    } else if (has_dn) {
+      rc = trexio_read_electron_dn_num(file, &ndn);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      nup = 0;
+      rc = trexio_write_electron_up_num(file, nup);
+      if (rc != TREXIO_SUCCESS) return rc;
+      
+      nelec = ndn;
+      rc = trexio_write_electron_num(file, nelec);
+      if (rc != TREXIO_SUCCESS) return rc;
+    }
+
+  }
+  
+  return TREXIO_SUCCESS;
+}
+    #+end_src
+   
 * Templates for front end
 ** Description
 

tests/test_f.f90

@@ -51,9 +51,9 @@ subroutine test_write(file_name, back_end)
   character*(*), intent(in) :: file_name
   integer, intent(in) :: back_end
 
-  integer(8) :: trex_file
+  integer(trexio_t) :: trex_file
 
-  integer :: rc = 1
+  integer(trexio_exit_code) :: rc = 1
 
   integer :: num, basis_shell_num
 
@@ -186,10 +186,10 @@ subroutine test_read(file_name, back_end)
   character*(*), intent(in) :: file_name
   integer, intent(in) :: back_end
 
-  integer(8) :: trex_file
+  integer(trexio_t) :: trex_file
 
   integer :: i, j, k, ind, offset, flag
-  integer :: rc = 1
+  integer(trexio_exit_code) :: rc = 1
   integer :: num, num_read, basis_shell_num
 
   integer :: basis_nucleus_index(24)

trex.org

@@ -86,6 +86,7 @@ the [[./examples.html][examples]].
   #+NAME:electron
   | Variable | Type  | Dimensions | Description                         |
   |----------+-------+------------+-------------------------------------|
+  | ~num~    | ~dim~ |            | Number of electrons                 |
   | ~up_num~ | ~int~ |            | Number of \uparrow-spin electrons   |
   | ~dn_num~ | ~int~ |            | Number of \downarrow-spin electrons |
 
@@ -94,7 +95,8 @@ the [[./examples.html][examples]].
   :results:
   #+begin_src python :tangle trex.json
       "electron": {
-          "up_num" : [ "int", []  ]
+             "num" : [ "dim", []  ]
+        , "up_num" : [ "int", []  ]
         , "dn_num" : [ "int", []  ]
       } ,
   #+end_src
@@ -179,7 +181,11 @@ ECP that replaces the core electrons.
 *Note for developers*: avoid having variables with similar prefix in their name.
 HDF5 back end might cause issues due to the way ~find_dataset~ function works.
 For example, in the ECP group we use ~max_ang_mom~ and not ~ang_mom_max~.
-The latter causes issues when written before ~ang_mom~ in the TREXIO file.
+The latter causes issues when written before the ~ang_mom~ array in the TREXIO file.
+*Update*: in fact, the aforementioned issue has only been observed when using HDF5 version 1.10.4
+installed via ~apt-get~. Installing the same version from the ~conda-forge~ channel and running it in
+an isolated ~conda~ environment works just fine. Thus, it seems to be a bug in the ~apt~-provided package.
+If you encounter the aforementioned issue, please report it to our [[https://github.com/TREX-CoE/trexio/issues][issue tracker on GitHub]].
 
 
   #+CALL: json(data=ecp, title="ecp")
@@ -712,23 +718,23 @@ prim_factor =
    of $\uparrow$-spin and then all the $\downarrow$-spin.
 
    #+name: qmc
-  | Variable | Type    | Dimensions               | Description                           |
-  |----------+---------+--------------------------+---------------------------------------|
-  | ~num~    | ~dim~   |                          | Number of 3N-dimensional points       |
-  | ~point~  | ~float~ | ~(3, elec.num, qmc.num)~ | 3N-dimensional points                 |
-  | ~psi~    | ~float~ | ~(qmc.num)~              | Wave function evaluated at the points |
-  | ~e_loc~  | ~float~ | ~(qmc.num)~              | Local energy evaluated at the points  |
+  | Variable | Type    | Dimensions                   | Description                           |
+  |----------+---------+------------------------------+---------------------------------------|
+  | ~num~    | ~dim~   |                              | Number of 3N-dimensional points       |
+  | ~point~  | ~float~ | ~(3, electron.num, qmc.num)~ | 3N-dimensional points                 |
+  | ~psi~    | ~float~ | ~(qmc.num)~                  | Wave function evaluated at the points |
+  | ~e_loc~  | ~float~ | ~(qmc.num)~                  | Local energy evaluated at the points  |
    
    #+CALL: json(data=qmc, title="qmc", last=1)
-
+   
    #+RESULTS:
    :results:
    #+begin_src python :tangle trex.json
        "qmc": {
-             "num" : [ "dim"  , []                             ]
-         , "point" : [ "float", [ "qmc.num", "elec.num", "3" ] ]
-         ,   "psi" : [ "float", [ "qmc.num" ]                  ]
-         , "e_loc" : [ "float", [ "qmc.num" ]                  ]
+             "num" : [ "dim"  , []                                 ]
+         , "point" : [ "float", [ "qmc.num", "electron.num", "3" ] ]
+         ,   "psi" : [ "float", [ "qmc.num" ]                      ]
+         , "e_loc" : [ "float", [ "qmc.num" ]                      ]
        }
    #+end_src
    :end: