Merge pull request #165 from JuDFTteam/update_tests

Update tests

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,14 @@
+# Next release
+
+## Description of important changes
+
+... Add here ...
+
+## Checklist for next release
+
+- [ ] finish your development and merge it into the `develop` branch
+- [ ] update documentation
+- [ ] update / fix tests
+- [ ] bump version numbers (in files `aiida_kkr/__init__.py`, `pyproject.toml`, `.bumpversion.cfg`)
+
+If everything is done, you can merge your changes from `develop` back into `master` and create a tag for the new version number. Creating a new tag always  triggers publication to pypi (see `.github/workflows/cd.yml` for the definition of this github action).

.github/workflows/cd.yml

@@ -94,7 +94,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
-        aiida: [{version: 'aiida-core==2.6.3', name: '2.6.3'}]
+        aiida: [{version: 'aiida-core==2.5.2', name: '2.5.2'}]
         masci-tools: [{version: 'git+https://github.com/JuDFTteam/masci-tools.git@develop', name: '-masci-develop'}]
         allowed-to-fail: [false]
 
@@ -143,7 +143,6 @@ jobs:
     - name: Install aiida-kkr
       run: |
         pip install ${{ matrix.aiida.version }} ${{ matrix.masci-tools.version }}
-        pip install git+https://github.com/JuDFTteam/aiida-testing.git@4ddb0e48a8a720e8fca5f8d09576c5aff8c36dbf
         pip install .[testing]
         pip install reentry
         reentry scan

.github/workflows/ci.yml

@@ -88,7 +88,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
-        aiida: [{version: 'aiida-core==2.6.3', name: '2.6.3'}]
+        aiida: [{version: 'aiida-core==2.5.2', name: '2.5.2'}]
         masci-tools: [{version: 'git+https://github.com/JuDFTteam/masci-tools.git@develop', name: '-masci-develop'}]
         allowed-to-fail: [false]
 
@@ -137,7 +137,6 @@ jobs:
     - name: Install aiida-kkr
       run: |
         pip install ${{ matrix.aiida.version }} ${{ matrix.masci-tools.version }}
-        pip install git+https://github.com/JuDFTteam/aiida-testing.git@4ddb0e48a8a720e8fca5f8d09576c5aff8c36dbf
         pip install .[testing]
         pip install reentry
         reentry scan

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

README.md

@@ -63,10 +63,19 @@ $ reentry scan -r aiida
 
 # Usage and Documentation
 
-* see http://aiida-kkr.readthedocs.io for user's guide and API reference.
+* see http://aiida-kkr.readthedocs.io for user's and developer's guides and API reference
 * check out http://judft.de and https://jukkr.fz-juelich.de for information of the KKR codes used by the plugin
 
 # Contributing
 
 Thank you for your interest in contributing to aiida-kkr.
 Check out our [contributing guide](CONTRIBUTING.md) for some information.
+
+# Releasing new versions
+
+To create a new release follow these steps:
+- finish your development and merge it into the `develop` branch
+- update documentation
+- update / fix tests
+- bump version numbers (in files `aiida_kkr/__init__.py`, `pyproject.toml`, `.bumpversion.cfg`)
+- merge changes from `develop` back into `master` and create a tag for the new version number (this triggers publication to pypi)

aiida_kkr/calculations/kkrimp.py

@@ -316,6 +316,7 @@ def _get_and_verify_hostfiles(self, tempfolder):
             parent_calc = parent_calcs.first().node
         # extract impurity_info
         found_impurity_inputnode = False
+        found_host_parent = False
         if 'impurity_info' in self.inputs:
             imp_info_inputnode = self.inputs.impurity_info
             if not isinstance(imp_info_inputnode, Dict):

aiida_kkr/calculations/kkrnano.py

@@ -212,7 +212,7 @@ def prepare_for_submission(self, tempfolder):
 
         else:
             raise InputValidationError(
-                'Either `strucwithpot` or a `parent_folder` has to be provided.\          If necessary remove one of the inputs.'
+                'Either `strucwithpot` or a `parent_folder` has to be provided. If necessary remove one of the inputs.'
             )
 
         print('passed lattice constant=', passed_lattice_const)
@@ -278,7 +278,7 @@ def prepare_for_submission(self, tempfolder):
 
         if noco:
             with tempfolder.open(self._DEFAULT_NOCO_INPUT_FILE, u'w') as nonco_angles_handle:
-                self._write_nonco_angles(nonco_angles_handle, nonco_angles, structure)
+                self._write_nonco_angles(nonco_angles_handle, nonco_angles, structure)  # pylint: disable=possibly-used-before-assignment
 
         # Prepare rbasis.xyz and input.conf from Structure and input parameter data unless convert mode
         if not convert:
@@ -288,7 +288,7 @@ def prepare_for_submission(self, tempfolder):
                 self._write_rbasis(rbasis_handle, structure, passed_lattice_const)
         if write_efermi:
             with tempfolder.open(self._DEFAULT_EFERMI_FILE, u'w') as efermi_file_handle:
-                self._write_efermi_file(efermi_file_handle, fermi)
+                self._write_efermi_file(efermi_file_handle, fermi)  # pylint: disable=used-before-assignment
 
         # Prepare potential and shapefun file from strucwithpot, if necessary
         if use_strucwithpot:

aiida_kkr/calculations/voro.py

@@ -107,7 +107,7 @@ def prepare_for_submission(self, tempfolder):
         vca_structure = False
         if found_structure:
             # for VCA: check if input structure and parameter node define VCA structure
-            vca_structure = vca_check(structure, parameters)
+            vca_structure = vca_check(structure, parameters)  # pylint: disable=used-before-assignment
 
         code = self.inputs.code
 
@@ -120,7 +120,7 @@ def prepare_for_submission(self, tempfolder):
 
         if found_parent:
             # check if parent is either Voronoi or previous KKR calculation
-            overwrite_potential, parent_calc = self._check_valid_parent(parent_calc_folder)
+            overwrite_potential, parent_calc = self._check_valid_parent(parent_calc_folder)  # pylint: disable=possibly-used-before-assignment
 
             #cross check if no structure was given and extract structure from parent
             if found_structure and not vca_structure:
@@ -188,7 +188,7 @@ def prepare_for_submission(self, tempfolder):
                 outfolder = parent_calc.outputs.retrieved  # copy from remote folder
                 copylist = [parent_calc.process_class._OUT_POTENTIAL]
             elif has_potfile_overwrite:
-                outfolder = potfile_overwrite  # copy from potential sfd
+                outfolder = potfile_overwrite  # copy from potential sfd  # pylint: disable=possibly-used-before-assignment
                 copylist = [potfile_overwrite.filename]
             else:
                 copylist = []
@@ -197,7 +197,7 @@ def prepare_for_submission(self, tempfolder):
                 filename = file1
                 if (found_parent or has_potfile_overwrite) and file1 == copylist[0]:
                     filename = self._POTENTIAL_IN_OVERWRITE
-                local_copy_list.append((outfolder.uuid, file1, filename))
+                local_copy_list.append((outfolder.uuid, file1, filename))  # pylint: disable=possibly-used-before-assignment
 
             # add shapefun to overwrite
             if 'shapefun_overwrite' in self.inputs:

aiida_kkr/parsers/kkrnano.py

@@ -81,7 +81,7 @@ def _findSimpleEntries(self, string2find, retrieved_folder, output_file_name, li
                     array = np.genfromtxt(StringIO(keyvalue.replace('D', 'e')), delimiter=' ', dtype=None)  #[0]
 
                 try:
-                    returnlist.append(array.item()[0])
+                    returnlist.append(array.item()[0])  # pylint: disable=possibly-used-before-assignment
                 except TypeError:
                     returnlist.append(array.item())
 

aiida_kkr/tools/imp_cluster_tools.py

@@ -183,7 +183,7 @@ def create_combined_imp_info(
 
     # set zimp in scoef file (not used by the code but makes it easier to read the files / debug)
     if single_single:
-        clust1[0][4] = zimp1
+        clust1[0][4] = zimp1  # pylint: disable=possibly-used-before-assignment
     clust2[0][4] = zimp2
     #if debug:
     #    print('cls1:', clust1)

aiida_kkr/tools/ldau.py

@@ -119,9 +119,9 @@ def get_ldaumatrices(retrieved):
                         iphi = ii
                     ii += 1
                 # save matrices to output dict
-                txt_dict_ldaumats['wldau'] = txt[iwldau + 1:iuldau]
-                txt_dict_ldaumats['uldau'] = txt[iuldau + 1:iphi]
-                txt_dict_ldaumats['phi'] = txt[iphi + 1:]
+                txt_dict_ldaumats['wldau'] = txt[iwldau + 1:iuldau]  # pylint: disable=possibly-used-before-assignment
+                txt_dict_ldaumats['uldau'] = txt[iuldau + 1:iphi]  # pylint: disable=possibly-used-before-assignment
+                txt_dict_ldaumats['phi'] = txt[iphi + 1:]  # pylint: disable=possibly-used-before-assignment
 
     return has_ldaupot_file, txt_dict_ldaumats
 
@@ -164,8 +164,8 @@ def get_LDAU_initmatrices_dict(txts_ldaumat1, offset=0):
     # Fill the dictionary with atom-wise information
     for iatom in range(len(iatoms)):
         LDAU_initmatrices_dict[f'iatom={int(iatoms[iatom])-1+offset}'] = {}
-        LDAU_initmatrices_dict[f'iatom={int(iatoms[iatom])-1+offset}']['wldau'] = wldaumat[iatom]
-        LDAU_initmatrices_dict[f'iatom={int(iatoms[iatom])-1+offset}']['uldau'] = uldaumat[iatom]
-        LDAU_initmatrices_dict[f'iatom={int(iatoms[iatom])-1+offset}']['phi'] = phimat[iatom]
+        LDAU_initmatrices_dict[f'iatom={int(iatoms[iatom])-1+offset}']['wldau'] = wldaumat[iatom]  # pylint: disable=possibly-used-before-assignment
+        LDAU_initmatrices_dict[f'iatom={int(iatoms[iatom])-1+offset}']['uldau'] = uldaumat[iatom]  # pylint: disable=used-before-assignment
+        LDAU_initmatrices_dict[f'iatom={int(iatoms[iatom])-1+offset}']['phi'] = phimat[iatom]  # pylint: disable=used-before-assignment
 
     return LDAU_initmatrices_dict

aiida_kkr/tools/plot_kkr.py

@@ -1307,7 +1307,7 @@ def plot_kkrimp_dos_wc(self, node, **kwargs):
                 from aiida_kkr.tools import find_parent_structure
                 natoms = get_natyp(find_parent_structure(calcnode))
                 self.dosplot(
-                    d,
+                    d,  # pylint: disable=possibly-used-before-assignment
                     natoms,
                     nofig,
                     all_atoms,
@@ -1536,7 +1536,7 @@ def plot_kkr_startpot(self, node, **kwargs):
             tit_add = ''
             if emin is not None:
                 axvline(emin, color='r', ls='--', label='emin')
-            if ef_Ry is not None and len(ecore_max) > 0:
+            if ef_Ry is not None and len(ecore_max) > 0:  # pylint: disable=possibly-used-before-assignment
                 if abs((ecore_max[0] - ef_Ry) * get_Ry2eV() - emin) < 20:
                     axvline((ecore_max[0] - ef_Ry) * get_Ry2eV(), color='b', ls='--', label='ecore_max')
                 else:

aiida_kkr/tools/tools_kkrimp.py

@@ -418,10 +418,12 @@ def find_neighbors(structure, structure_array, i, radius, clust_shape='spherical
         box_1 = int(maxval / structure.cell_lengths[0] + 3)
         box_2 = int(maxval / structure.cell_lengths[1] + 3)
         box_3 = int(maxval / sl3 + 3)
+    else:
+        raise ValueError("clust_shape needs to be either 'sperical' or 'cylindrical'")
     #================================================================================================================
 
     #create array of all the atoms in an expanded system
-    box = max(box_1, box_2, box_3)
+    box = max(box_1, box_2, box_3)  #pylint: disable=possibly-used-before-assignment
     cell = np.array(structure.cell)
     cell[2] = c3
     for j in range(len(x)):

aiida_kkr/workflows/_combine_imps.py

@@ -365,7 +365,7 @@ def extract_imps_info_exact_cluster(self):
             imp2_impurity_info = self.ctx.imp2.inputs.impurity_info
 
             try:
-                imps_info_in_exact_cluster = out_workflow_info.get_dict()['imps_info_in_exact_cluster']
+                imps_info_in_exact_cluster = out_workflow_info.get_dict()['imps_info_in_exact_cluster']  # pylint: disable=possibly-used-before-assignment
             except KeyError:
                 parent_input_imp1 = parent_combine_wc.inputs.impurity1_output_node  # TODO: rename combine_wc to the parent_combine_wc
                 parent_input_imp2 = parent_combine_wc.inputs.impurity2_output_node
@@ -654,7 +654,7 @@ def run_gf_writeout(self):
                 print('DEBUG:', self.ctx.imp1, list(self.ctx.imp1.inputs))
             imp1_sub = self.ctx.imp1.get_outgoing(node_class=kkr_imp_sub_wc).first().node
         if gf_writeout_calc is None:
-            gf_writeout_calc = imp1_sub.inputs.remote_data.get_incoming(node_class=KkrCalculation).first().node
+            gf_writeout_calc = imp1_sub.inputs.remote_data.get_incoming(node_class=KkrCalculation).first().node  # pylint: disable=possibly-used-before-assignment
         builder.remote_data = gf_writeout_calc.inputs.parent_folder
 
         # set label and description of the calc
@@ -888,10 +888,10 @@ def get_ldau_combined(self):
         if imp1_has_ldau and imp2_has_ldau:
             # combine LDA+U settings of the two imps
             settings_LDAU_combined = combine_settings_ldau(
-                settings_LDAU1=settings_LDAU1,
-                retrieved1=retrieved1,
-                settings_LDAU2=settings_LDAU2,
-                retrieved2=retrieved2,
+                settings_LDAU1=settings_LDAU1,  # pylint: disable=used-before-assignment
+                retrieved1=retrieved1,  # pylint: disable=used-before-assignment
+                settings_LDAU2=settings_LDAU2,  # pylint: disable=used-before-assignment
+                retrieved2=retrieved2,  # pylint: disable=used-before-assignment
                 kickout_info=self.ctx.kickout_info
             )
         elif imp1_has_ldau:

aiida_kkr/workflows/bs.py

@@ -617,9 +617,8 @@ def parse_BS_data(retrieved_folder, fermi_level, kpoints):
     qdos_file_list = [i for i in retrieved_list if 'qdos.' in i]
     q_vec_file = 'qvec.dat'
 
-    if q_vec_file in retrieved_list:
-        with retrieved_folder.open(q_vec_file) as file_opened:
-            q_vec = np.loadtxt(file_opened, skiprows=1)
+    with retrieved_folder.open(q_vec_file) as file_opened:
+        q_vec = np.loadtxt(file_opened, skiprows=1)
 
     for icount, fname in enumerate(qdos_file_list):
         with retrieved_folder.open(fname) as _f:

aiida_kkr/workflows/kkr_imp_dos.py

@@ -495,7 +495,8 @@ def run_imp_dos(self):
         })
         kkrimp_params = self.ctx.kkrimp_params_dict
         label_imp = 'KKRimp DOS (GF: {}, imp_pot: {}, Zimp: {}, ilayer_cent: {})'.format(
-            gf_writeout_calc.pk, impurity_pot_or_remote.pk,
+            gf_writeout_calc.pk,
+            impurity_pot_or_remote.pk,  # pylint: disable=possibly-used-before-assignment
             imps.get_dict().get('Zimp'),
             imps.get_dict().get('ilayer_center')
         )

aiida_kkr/workflows/kkr_imp_sub.py

@@ -851,7 +851,7 @@ def run_kkrimp(self):
 
         # add LDA+U input node if it was set in parent calculation of last kkrimp_remote or from input port
         if self.ctx.settings_LDAU is not None:
-            inputs['settings_LDAU'] = self.ctx.settings_LDAU
+            inputs['settings_LDAU'] = self.ctx.settings_LDAU  # pylint: disable=possibly-used-before-assignment
 
         # set nonco angles if given
         if 'initial_noco_angles' in self.inputs:
@@ -990,7 +990,7 @@ def inspect_kkrimp(self):
         for name, val in {
             'isteps': isteps,
             'imix': self.ctx.last_mixing_scheme,
-            'mixfac': mixfac,
+            'mixfac': mixfac,  # pylint: disable=possibly-used-before-assignment
             'qbound': qbound,
             'high_sett': self.ctx.kkr_higher_accuracy,
             'first_rms': first_rms,

aiida_kkr/workflows/kkr_scf.py

@@ -1898,14 +1898,14 @@ def create_scf_result_node(**kwargs):
     outdict = {}
 
     if has_last_outpara:
-        outputnode = outpara
+        outputnode = outpara  # pylint: disable=possibly-used-before-assignment
         outputnode.label = 'workflow_Results'
         outputnode.description = ('Contains self-consistency results and '
                                   'information of an kkr_scf_wc run.')
         outdict['output_kkr_scf_wc_ParameterResults'] = outputnode
 
     if has_last_calc_out_dict:
-        outputnode = last_calc_out_dict
+        outputnode = last_calc_out_dict  # pylint: disable=used-before-assignment
         outputnode.label = 'last_calc_out'
         outputnode.description = (
             'Contains the Results Parameter node from the output '
@@ -1914,7 +1914,7 @@ def create_scf_result_node(**kwargs):
         outdict['last_calc_out'] = outputnode
 
     if has_last_RemoteData:
-        outputnode = last_RemoteData_dict
+        outputnode = last_RemoteData_dict  # pylint: disable=used-before-assignment
         outputnode.label = 'last_RemoteData'
         outputnode.description = (
             'Contains a link to the latest remote data node '
@@ -1923,7 +1923,7 @@ def create_scf_result_node(**kwargs):
         outdict['last_RemoteData'] = outputnode
 
     if has_last_InputParameters:
-        outputnode = last_InputParameters_dict
+        outputnode = last_InputParameters_dict  # pylint: disable=used-before-assignment
         outputnode.label = 'last_InputParameters'
         outputnode.description = (
             'Contains the latest parameter data node '
@@ -1932,7 +1932,7 @@ def create_scf_result_node(**kwargs):
         outdict['last_InputParameters'] = outputnode
 
     if has_vorostart_output:
-        outputnode = vorostart_output_dict
+        outputnode = vorostart_output_dict  # pylint: disable=used-before-assignment
         outputnode.label = 'results_vorostart'
         outputnode.description = (
             'Contains the results parameter data node '
@@ -1941,14 +1941,14 @@ def create_scf_result_node(**kwargs):
         outdict['results_vorostart'] = outputnode
 
     if has_starting_dos:
-        outputnode = start_dosdata_interpol_dict
+        outputnode = start_dosdata_interpol_dict  # pylint: disable=used-before-assignment
         outputnode.label = 'starting_dosdata_interpol'
         outputnode.description = ('Contains the interpolated DOS data note, computed '
                                   'from the starting portential.')
         outdict['starting_dosdata_interpol'] = outputnode
 
     if has_final_dos:
-        outputnode = final_dosdata_interpol_dict
+        outputnode = final_dosdata_interpol_dict  # pylint: disable=used-before-assignment
         outputnode.label = 'final_dosdata_interpol'
         outputnode.description = ('Contains the interpolated DOS data note, computed '
                                   'from the converged potential.')

aiida_kkr/workflows/voro_start.py

@@ -547,10 +547,10 @@ def run_voronoi(self):
                 kkr_para.set_value('RCLUSTZ', self.ctx.r_cls)
                 self.report(f'INFO: setting RCLUSTZ to {self.ctx.r_cls}')
             if 'RMAX' in update_list:
-                kkr_para.set_value('RMAX', rmax_input)
+                kkr_para.set_value('RMAX', rmax_input)  # pylint: disable=possibly-used-before-assignment
                 self.report(f'INFO: setting RMAX to {rmax_input} (needed for DOS check with KKRcode)')
             if 'GMAX' in update_list:
-                kkr_para.set_value('GMAX', gmax_input)
+                kkr_para.set_value('GMAX', gmax_input)  # pylint: disable=possibly-used-before-assignment
                 self.report(f'INFO: setting GMAX to {gmax_input} (needed for DOS check with KKRcode)')
             if 'EMIN' in update_list:
                 kkr_para.set_value('EMIN', emin_new)