Merge pull request #109 from JuDFTteam/develop

Next release

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.11.post1
+current_version = 1.1.12
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?

.github/workflows/ci.yml

@@ -176,10 +176,17 @@ jobs:
         chmod +x kkr.x voronoi.exe kkrflex.exe
 
     - name: Run pytest
+      if: ${{ ! matrix.allowed-to-fail }}
       run: |
         cd tests/
         GITHUB_SUITE=True ./run_all.sh
 
+    - name: Run pytest allow failure
+      if: ${{ matrix.allowed-to-fail }}
+      run: |
+        cd tests/
+        GITHUB_SUITE=True ./run_all.sh || exit 0
+
     - name: Archive test output artifacts
       uses: actions/upload-artifact@v3
       if: failure()

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.3.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -18,15 +18,16 @@ repos:
       - id: forbid-new-submodules
 
   - repo: https://github.com/pre-commit/mirrors-yapf
-    rev: v0.31.0
+    rev: v0.32.0
     hooks:
       - id: yapf
         name: yapf
         types: [python]
         args: ["-i"]
+        additional_dependencies: [toml]
 
   - repo: https://github.com/ikamensh/flynt/
-    rev: '0.55'
+    rev: '0.76'
     hooks:
     -   id: flynt
         args: [

aiida_kkr/__init__.py

@@ -2,4 +2,4 @@
 AiiDA KKR
 """
 
-__version__ = '1.1.11.post1'
+__version__ = '1.1.12'

aiida_kkr/calculations/kkr.py

@@ -19,13 +19,15 @@
 )
 from masci_tools.io.common_functions import get_alat_from_bravais, get_Ang2aBohr
 from aiida_kkr.tools.tools_kkrimp import make_scoef, write_scoef_full_imp_cls
+from aiida_kkr.tools.find_parent import find_parent_structure
 from masci_tools.io.kkr_params import __kkr_default_params__, kkrparams
 import six
 from six.moves import range
 
-__copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, ' 'IAS-1/PGI-1, Germany. All rights reserved.')
+__copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, '
+                 'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.12.1'
+__version__ = '0.12.2'
 __contributors__ = ('Jens Bröder', 'Philipp Rüßmann')
 
 verbose = False
@@ -442,7 +444,7 @@ def _get_structure_inputs(self, parent_calc, parameters):
         structure = None
         self.logger.info('KkrCalculation: Get structure node from voronoi parent')
         try:
-            structure, voro_parent = VoronoiCalculation.find_parent_structure(parent_calc)
+            structure, voro_parent = find_parent_structure(parent_calc)
         except:
             self.logger.error(f'KkrCalculation: Could not get structure from Voronoi parent ({parent_calc}).')
             raise ValidationError(f'Cound not find structure node from parent {parent_calc}')
@@ -625,7 +627,7 @@ def _get_local_copy_list(self, parent_calc, voro_parent, tempfolder, parameters)
             # add shapefun file from voronoi parent if needed
             if self._SHAPEFUN not in copylist:
                 try:
-                    struc, voro_parent = VoronoiCalculation.find_parent_structure(parent_calc)
+                    struc, voro_parent = find_parent_structure(parent_calc)
                 except ValueError:
                     return self.exit_codes.ERROR_NO_SHAPEFUN_FOUND  # pylint: disable=no-member
                 # copy shapefun from retrieved of voro calc
@@ -738,13 +740,13 @@ def _get_qdos_filelist(self, parameters, natom, nspin, addition=''):
             add_files = [self._QVEC]
             for iatom in range(natom):
                 for ispin in range(nspin):
-                    add_files.append((self._QDOS_ATOM % (iatom + 1, ispin + 1)).replace(' ', '0'))
+                    add_files.append((self._QDOS_ATOM % (iatom + 1, ispin + 1)).replace(' ', '0') + addition)
                     # try to retrieve both old and new version of the files
-                    add_files.append((self._QDOS_ATOM_OLD % (iatom + 1, ispin + 1)).replace(' ', '0'))
+                    add_files.append((self._QDOS_ATOM_OLD % (iatom + 1, ispin + 1)).replace(' ', '0') + addition)
                 # retrieve also qdos_sx,y,z files if written out
-                add_files.append((self._QDOS_SX % (iatom + 1)).replace(' ', '0'))
-                add_files.append((self._QDOS_SY % (iatom + 1)).replace(' ', '0'))
-                add_files.append((self._QDOS_SZ % (iatom + 1)).replace(' ', '0'))
+                add_files.append((self._QDOS_SX % (iatom + 1)).replace(' ', '0') + addition)
+                add_files.append((self._QDOS_SY % (iatom + 1)).replace(' ', '0') + addition)
+                add_files.append((self._QDOS_SZ % (iatom + 1)).replace(' ', '0') + addition)
 
         return add_files
 
@@ -807,7 +809,7 @@ def _get_BdG_filelist(self, parameters, natom, nspin):
 
             #also retrieve BdG DOS files for anomalous density and hole part
             for BdGadd in ['_eh', '_he', '_hole']:
-                add_files += self._get_dos_filelist(natom, nspin, parameters, BdGadd)
+                add_files += self._get_dos_filelist(parameters, natom, nspin, BdGadd)
                 add_files += self._get_qdos_filelist(parameters, natom, nspin, BdGadd)
 
         return add_files
@@ -869,7 +871,7 @@ def _set_ef_value_potential(self, ef_set, local_copy_list, tempfolder):
             self.report(f'set ef {ef_set} in potential starting in line {ipotstart}')
             tmpline = txt[ipotstart + 3]
             tmpline = tmpline.split()
-            newline = '%10.5f%20.14f%20.14f\n' % (float(tmpline[0]), ef_set, float(tmpline[-1]))
+            newline = f'{float(tmpline[0]):10.5f}{ef_set:20.14f}{float(tmpline[-1]):20.14f}\n'
 
             txt[ipotstart + 3] = newline
 
@@ -952,7 +954,7 @@ def _prepare_qdos_calc(self, parameters, kpath, structure, tempfolder, use_alat_
             alat_input = alat
         kpath_array = kpath_array * (alat_input / alat) / get_Ang2aBohr() / (2 * np.pi / alat)
         # now write file
-        qvec = ['%i\n' % len(kpath_array)]
+        qvec = [f'{len(kpath_array)}\n']
         qvec += [f'{kpt[0]:e} {kpt[1]:e} {kpt[2]:e}\n' for kpt in kpath_array]
         with tempfolder.open(self._QVEC, 'w') as qvecfile:
             qvecfile.writelines(qvec)

aiida_kkr/calculations/kkrimp.py

@@ -21,7 +21,8 @@
 import six
 from six.moves import range
 
-__copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, ' 'IAS-1/PGI-1, Germany. All rights reserved.')
+__copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, '
+                 'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
 __version__ = '0.7.0'
 __contributors__ = (u'Philipp Rüßmann', u'Fabian Bertoldo')

aiida_kkr/calculations/kkrimporter.py

@@ -17,7 +17,8 @@
 #from aiida_kkr.tools.common_workfunctions import structure_from_params
 #from six.moves import range
 
-__copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, ' 'IAS-1/PGI-1, Germany. All rights reserved.')
+__copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, '
+                 'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
 __version__ = '0.2'
 __contributors__ = ('Philipp Rüßmann')

aiida_kkr/calculations/kkrnano.py

@@ -2,21 +2,21 @@
 """
 Input plug-in for a KKRnano calculation.
 """
-from aiida.engine import CalcJob
-from aiida.orm import CalcJobNode, Dict, Bool, Float, RemoteData, StructureData
-from aiida_kkr.data.strucwithpot import StrucWithPotData
-from aiida.common.datastructures import (CalcInfo, CodeInfo)
+
+import numpy as np
 from masci_tools.io.common_functions import get_Ang2aBohr
+from aiida.orm import CalcJobNode, Dict, Bool, Float, RemoteData, StructureData
+from aiida.engine import CalcJob
 from aiida.common import NotExistent
+from aiida.common.datastructures import (CalcInfo, CodeInfo)
 from aiida.common.exceptions import InputValidationError, UniquenessError
+from aiida_kkr.tools.find_parent import get_remote, get_parent
+from aiida_kkr.data.strucwithpot import StrucWithPotData
 
-from aiida_kkr.calculations.voro import VoronoiCalculation
-
-import numpy as np
-
-__copyright__ = (u'Copyright (c), 2021, Forschungszentrum Jülich GmbH, ' 'IAS-1/PGI-1, Germany. All rights reserved.')
+__copyright__ = (u'Copyright (c), 2021, Forschungszentrum Jülich GmbH, '
+                 'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.0.1'
+__version__ = '0.0.2'
 __contributors__ = ('Markus Struckmann', 'Philipp Rüßmann')
 
 
@@ -703,9 +703,9 @@ def find_parent_struc_from_voro_or_stwpd(self, parent_folder):
         """
         iiter = 0
         Nmaxiter = 1000
-        parent_folder_tmp = VoronoiCalculation.get_remote(parent_folder)
+        parent_folder_tmp = get_remote(parent_folder)
         while not self._has_struc(parent_folder_tmp) and iiter < Nmaxiter:
-            parent_folder_tmp = VoronoiCalculation.get_remote(VoronoiCalculation.get_parent(parent_folder_tmp))
+            parent_folder_tmp = get_remote(get_parent(parent_folder_tmp))
             iiter += 1
             if iiter % 200 == 0:
                 print(

aiida_kkr/calculations/voro.py

@@ -10,11 +10,12 @@
 from aiida.common.exceptions import (InputValidationError, ValidationError)
 from aiida.common.datastructures import (CalcInfo, CodeInfo)
 from aiida_kkr.tools.common_workfunctions import generate_inputcard_from_structure, check_2Dinput_consistency, vca_check
-from aiida.common.exceptions import UniquenessError, NotExistent
+from aiida.common.exceptions import UniquenessError
 import os
 import six
 
-__copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, ' 'IAS-1/PGI-1, Germany. All rights reserved.')
+__copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, '
+                 'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
 __version__ = '0.5.3'
 __contributors__ = ('Jens Broeder', 'Philipp Rüßmann')
@@ -147,7 +148,8 @@ def prepare_for_submission(self, tempfolder):
         else:
             overwrite_potential = False
             if not found_structure:
-                raise InputValidationError('Neither structure nor parent_KKR specified for this ' 'calculation')
+                raise InputValidationError('Neither structure nor parent_KKR specified for this '
+                                           'calculation')
 
         # check if overwrite potential is given explicitly
         if 'potential_overwrite' in self.inputs:
@@ -273,86 +275,11 @@ def _is_KkrCalc(self, calc):
 
         return is_KKR
 
-    @classmethod
-    def _get_struc(self, parent_calc):
-        """
-        Get structure from a parent_folder (result of a calculation, typically a remote folder)
-        """
-        return parent_calc.inputs.structure
-
-    @classmethod
-    def _has_struc(self, parent_folder):
-        """
-        Check if parent_folder has structure information in its input
-        """
-        success = True
-        if 'structure' not in parent_folder.get_incoming().all_link_labels():
-            success = False
-        return success
-
-    @classmethod
-    def get_remote(self, parent_folder):
-        """
-        get remote_folder from input if parent_folder is not already a remote folder
-        """
-        parent_folder_tmp0 = parent_folder
-        try:
-            parent_folder_tmp = parent_folder_tmp0.get_incoming().get_node_by_label('remote_folder')
-        except NotExistent:
-            parent_folder_tmp = parent_folder_tmp0
-        return parent_folder_tmp
-
-    @classmethod
-    def get_parent(self, input_folder):
-        """
-        get the  parent folder of the calculation. If not parent was found return input folder
-        """
-        input_folder_tmp0 = input_folder
-
-        # first option: parent_calc_folder (KkrimpCalculation)
-        try:
-            parent_folder_tmp = input_folder_tmp0.get_incoming().get_node_by_label('parent_calc_folder')
-            return_input = False
-        except NotExistent:
-            return_input = True
-
-        # second option: parent_folder (KkrCalculation)
-        try:
-            parent_folder_tmp = input_folder_tmp0.get_incoming().get_node_by_label('parent_folder')
-            return_input = False
-        except NotExistent:
-            return_input = return_input & True
-
-        # third option: parent_KKR option (special mode of VoronoiCalculation)
-        try:
-            parent_folder_tmp = input_folder_tmp0.get_incoming().get_node_by_label('parent_KKR')
-            return_input = False
-        except NotExistent:
-            return_input = return_input & True
-
-        if return_input:
-            parent_folder_tmp = input_folder_tmp0
-
-        return parent_folder_tmp
-
     @classmethod
     def find_parent_structure(self, parent_folder):
         """
         Find the Structure node recuresively in chain of parent calculations (structure node is input to voronoi calculation)
+        This is a copy of the find_parent_structure that moved to tools.find_parent to keep backwards compatibility.
         """
-        iiter = 0
-        Nmaxiter = 1000
-        parent_folder_tmp = self.get_remote(parent_folder)
-        while not self._has_struc(parent_folder_tmp) and iiter < Nmaxiter:
-            parent_folder_tmp = self.get_remote(self.get_parent(parent_folder_tmp))
-            iiter += 1
-            if iiter % 200 == 0:
-                print(
-                    'Warning: find_parent_structure takes quite long (already searched {} ancestors). Stop after {}'.
-                    format(iiter, Nmaxiter)
-                )
-        if self._has_struc(parent_folder_tmp):
-            struc = self._get_struc(parent_folder_tmp)
-            return struc, parent_folder_tmp
-        else:
-            raise ValueError('structure not found')
+        from aiida_kkr.tools.find_parent import find_parent_structure
+        return find_parent_structure(parent_folder)