Merge pull request #168 from JuDFTteam/develop

Update to latest released version

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.1.0
+current_version = 2.2.1
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?

.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

@@ -16,16 +16,16 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.12
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: pip-docs-${{ hashFiles('**/setup.json') }}
@@ -53,21 +53,21 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
         restore-keys: |
           pip-pre-commit-
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.12
 
     - name: Install python dependencies
       run: |
@@ -93,8 +93,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        aiida: [{version: 'aiida-core==2.3.0', name: '2.3.0'}]
+        python-version: ["3.10", "3.11", "3.12"]
+        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]
 
@@ -122,10 +122,10 @@ jobs:
           - 5001:22
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -143,7 +143,7 @@ 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 git+https://github.com/PhilippRue/aiida-test-cache.git@change_aiida-core_version
         pip install .[testing]
         pip install reentry
         reentry scan
@@ -176,14 +176,14 @@ jobs:
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: 3.12
       - name: Install flit
         run: |
-          pip install flit~=3.4
+          pip install flit~=3.10
       - name: Build and publish to PyPi
         run: |
           flit publish

.github/workflows/ci.yml

@@ -10,16 +10,16 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.12
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: pip-docs-${{ hashFiles('**/setup.json') }}
@@ -47,21 +47,21 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
         restore-keys: |
           pip-pre-commit-
 
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.12
 
     - name: Install python dependencies
       run: |
@@ -87,8 +87,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        aiida: [{version: 'aiida-core==2.3.0', name: '2.3.0'}]
+        python-version: ["3.10", "3.11", "3.12"]
+        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]
 
@@ -116,10 +116,10 @@ jobs:
           - 5001:22
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -137,7 +137,7 @@ 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 git+https://github.com/PhilippRue/aiida-test-cache.git@change_aiida-core_version
         pip install .[testing]
         pip install reentry
         reentry scan
@@ -174,14 +174,14 @@ jobs:
         GITHUB_SUITE=True ./run_all.sh || exit 0
 
     - name: Archive test output artifacts
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: test-results-AIIDA__${{ matrix.aiida.name }}__MASCI__${{ matrix.masci-tools.name }}
         path: tests
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./tests/coverage.xml

.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/__init__.py

@@ -2,4 +2,4 @@
 AiiDA KKR
 """
 
-__version__ = '2.1.0'
+__version__ = '2.2.1'

aiida_kkr/calculations/kkrimp.py

@@ -318,6 +318,7 @@ 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 +197,13 @@ 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:
+                shapefun_overwrite = self.inputs.shapefun_overwrite
+                filename = shapefun_overwrite.filename
+                local_copy_list.append((shapefun_overwrite.uuid, filename, 'shapefun_overwrite'))
 
             # 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

@@ -190,7 +190,7 @@ 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: