Merge pull request #176 from JuDFTteam/release-0.11.2

🚀 Release `0.11.2`

.github/workflows/cd.yml

@@ -97,8 +97,15 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.10','3.9', '3.8', '3.7']
+        experimental: [false]
+        # include:
+        #   - python-version: '3.11-dev'
+        #     experimental: true
       fail-fast: false
 
+    name: tests-python-${{ matrix.python-version }}
+    continue-on-error: ${{ matrix.experimental }}
+
     steps:
     - uses: actions/checkout@v3
 

.github/workflows/ci.yml

@@ -93,6 +93,9 @@ jobs:
       matrix:
         python-version: ['3.10','3.9', '3.8', '3.7']
         experimental: [false]
+#         include:
+#           - python-version: '3.11-dev'
+#             experimental: true
       fail-fast: false
 
     name: tests-python-${{ matrix.python-version }}
@@ -115,6 +118,14 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install Build dependecies (for experimental builds)
+      if: ${{ matrix.experimental }}
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libxml2-dev libxslt-dev libhdf5-serial-dev
+        pip install --upgrade pip setuptools wheel
+        pip install --upgrade cython
+        pip list
 
     - name: Install python dependencies
       run: |

.pre-commit-config.yaml

@@ -108,6 +108,7 @@ repos:
             masci_tools/util/fleur_calculate_expression.py|
             masci_tools/tools/fleur_inpxml_converter.py|
             masci_tools/tools/greensfunction.py|
+            masci_tools/tools/greensf_calculations.py|
             masci_tools/cmdline/parameters/slice.py|
             masci_tools/vis/parameters.py|
             masci_tools/util/ipython.py|

CHANGELOG.md

@@ -1,13 +1,26 @@
 # Changelog
 
+## v.0.11.2
+[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.11.1...v0.11.2)
+
+### Improvements
+- Several changes in KKR IO functions to make them compatible with `aiida-core>=2.0` [[#175]](https://github.com/JuDFTteam/masci-tools/pull/175)
+- Add function to calculate fourier transform of e.g. `J_ij` constants calculated from Green's functions (`masci_tools.tools.greensf_calculations.heisenberg_reciprocal`)
+
+### Bugfixes
+- Fixed nondeterministic order in bokeh regression tests if multiple dictionaries with the same values but differing keys in the same list (e.g. Providing the same data for different columns)
+- Fixed wrong names for columns entered in `decompose_jij_tensor`, i.e. `J_ji` -> `J_ij`
+
+### Deprecations
+- Deprecated the unused modules `util/kkr_rms_tracker.py` and `util/modify_potential.py`
+
 ## v.0.11.1
 
 [full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.11.0...v0.11.1)
 
 ### Bugfixes
 - Bugfix in `reverse_xinclude`. Version `0.11.0` broke this function for versions, where the `relaxation` tag was not allowed.
 
-
 ## v.0.11.0
 [full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.10.1...v0.11.0)
 

masci_tools/__init__.py

@@ -21,7 +21,7 @@
 __copyright__ = ('Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. '
                  'All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file.'
-__version__ = '0.11.1'
+__version__ = '0.11.2'
 __authors__ = 'The JuDFT team. Also see AUTHORS.txt file.'
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

masci_tools/io/common_functions.py

@@ -59,12 +59,27 @@ def open_general(filename_or_handle: FileLike, iomode: str | None = None) -> IO[
             if iomode is None:
                 f = open(f.name, f.mode, encoding='utf8')
             else:
-                f = open(f.name, iomode, encoding='utf8')
+                f = open(f.name, iomode, encoding='utf8')  #pylint: disable=consider-using-with
         else:  # make sure reading the file now starts at the beginning again
             f.seek(0)
+
     return f
 
 
+def get_outfile_txt(outfile):
+    """Get the content of a file
+    In case the outfile is a file handle, we just roll it back and read everything in again.
+    For an ordinary file path we open the file in a context manager and then read it.
+    """
+    if getattr(outfile, 'readlines', None) is not None:
+        outfile.seek(0)
+        tmptxt = outfile.readlines()
+    else:
+        with open_general(outfile) as f:
+            tmptxt = f.readlines()
+    return tmptxt
+
+
 def skipHeader(seq: Iterable[Any], n: int) -> Generator[Any, None, None]:
     """Iterate over a sequence skipping the first n elements
 
@@ -204,8 +219,7 @@ def vec_to_angles(vec: np.ndarray) -> tuple[np.ndarray, np.ndarray, np.ndarray]
 
 
 def get_version_info(outfile: FileLike) -> tuple[str, str, str]:
-    with open_general(outfile) as f:
-        tmptxt = f.readlines()
+    tmptxt = get_outfile_txt(outfile)
     itmp = search_string('Code version:', tmptxt)
     if itmp == -1:  # try to find serial number from header of file
         itmp = search_string('# serial:', tmptxt)
@@ -223,8 +237,7 @@ def get_version_info(outfile: FileLike) -> tuple[str, str, str]:
 
 def get_corestates_from_potential(potfile: FileLike = 'potential') -> tuple[list, list, list]:
     """Read core states from potential file"""
-    with open_general(potfile) as f:
-        txt = f.readlines()
+    txt = get_outfile_txt(potfile)
 
     #get start of each potential part
     istarts = [iline for iline in range(len(txt)) if 'POTENTIAL' in txt[iline]]
@@ -361,9 +374,8 @@ def get_ef_from_potfile(potfile: FileLike) -> float:
     """
     extract fermi energy from potfile
     """
-    with open_general(potfile) as f:
-        txt = f.readlines()
-    ef = float(txt[3].split()[1])
+    tmptxt = get_outfile_txt(potfile)
+    ef = float(tmptxt[3].split()[1])
     return ef
 
 

masci_tools/io/io_nmmpmat.py

@@ -135,25 +135,25 @@ def write_nmmpmat_from_orbitals(orbital: int,
                                 phi: float | None = None,
                                 theta: float | None = None,
                                 inverse: bool = False) -> list[str]:
-    """
+    r"""
     Generate list of str for n_mmp_mat file from orbital occupations
 
     orbital occupations are provided in the following order
     (expressed as the spherical harmonics since it can be used for all orbitals):
 
-        - Y_l^0
-        - 1/sqrt(2) (Y_l^-1 + Y_l^1)
-        - i/sqrt(2) (Y_l^-1 - Y_l^1)
-        - 1/sqrt(2) (Y_l^-2 + Y_l^2)
-        - i/sqrt(2) (Y_l^-2 - Y_l^2)
+        - :math:`Y_l^0`
+        - :math:`\frac{1}{\sqrt{2}} \left(Y_l^{-1} + Y_l^1\right)`
+        - :math:`\frac{i}{\sqrt{2}} \left(Y_l^{-1} - Y_l^1\right)`
+        - :math:`\frac{1}{\sqrt{2}} \left(Y_l^{-2} + Y_l^2\right)`
+        - :math:`\frac{i}{\sqrt{2}} \left(Y_l^{-2} - Y_l^2\right)`
         - and so on ...
 
     :param orbital: int of the orbital for the current block
     :param orbital_occupations: list like with length 2*orbital+1 with the occupations of the orbitals
     :param phi: float, angle (radian), by which to rotate the density matrix
     :param theta: float, angle (radian), by which to rotate the density matrix
 
-    :returns: list of str formatted in lines for the n_mmp_mat file
+    :returns: list of str formatted in lines for the `n_mmp_mat` file
     """
 
     denmat = np.zeros((2 * orbital + 1, 2 * orbital + 1), dtype=complex)

masci_tools/io/modify_potential.py

@@ -12,12 +12,6 @@
 """
 Tools for the impurity caluclation plugin and its workflows
 """
-from sys import version_info
-if version_info[0] >= 3:
-
-    def raw_input(msg):
-        return eval(eval(input(msg)))
-
 
 __copyright__ = ('Copyright (c), 2018, Forschungszentrum Jülich GmbH,'
                  'IAS-1/PGI-1, Germany. All rights reserved.')
@@ -43,7 +37,7 @@ def _check_potstart(self, str1, mode='pot', shape_ver='new'):
 
     def _read_input(self, filepath):
         #print(filepath)
-        with open(filepath) as file:
+        with open(filepath, encoding='utf8') as file:
             data = file.readlines()
 
         if 'shapefun' in filepath:
@@ -56,8 +50,8 @@ def _read_input(self, filepath):
         # read file
         index1 = []
         index2 = []
-        for i in range(len(data)):
-            if self._check_potstart(data[i], mode=mode):
+        for i, d in enumerate(data):
+            if self._check_potstart(d, mode=mode):
                 index1.append(i)
                 if len(index1) > 1:
                     index2.append(i - 1)
@@ -67,8 +61,8 @@ def _read_input(self, filepath):
         if mode == 'shape' and len(index1) < 1:
             index1 = []
             index2 = []
-            for i in range(len(data)):
-                if self._check_potstart(data[i], mode=mode, shape_ver='old'):
+            for i, d in enumerate(data):
+                if self._check_potstart(d, mode=mode, shape_ver='old'):
                     index1.append(i)
                 if len(index1) > 1:
                     index2.append(i - 1)
@@ -97,7 +91,7 @@ def shapefun_from_scoef(self, scoefpath, shapefun_path, atom2shapes, shapefun_ne
 
         order = list(range(len(index1)))
 
-        with open(scoefpath) as f:
+        with open(scoefpath, encoding='utf8') as f:
             lines = f.readlines()
             natomtemp = int(lines[0])
             filedata = lines[1:natomtemp + 1]
@@ -109,8 +103,8 @@ def shapefun_from_scoef(self, scoefpath, shapefun_path, atom2shapes, shapefun_ne
         order = listnew
 
         datanew = []
-        for i in range(len(order)):
-            for ii in range(index1[order[i]], index2[order[i]] + 1):
+        for i in order:
+            for ii in range(index1[i], index2[i] + 1):
                 datanew.append(data[ii])
 
         # add header to shapefun_new
@@ -155,10 +149,10 @@ def neworder_potential(self, potfile_in, potfile_out, neworder, potfile_2=None,
             # check if also replace_from_pot2 is given correctly
             if replace_from_pot2 is None:
                 raise ValueError('replace_from_pot2 not given')
-            else:
-                replace_from_pot2 = array(replace_from_pot2)
-                if shape(replace_from_pot2)[1] != 2:
-                    raise ValueError('replace_from_pot2 needs to be a 2D array!')
+
+            replace_from_pot2 = array(replace_from_pot2)
+            if shape(replace_from_pot2)[1] != 2:
+                raise ValueError('replace_from_pot2 needs to be a 2D array!')
         else:
             if replace_from_pot2 is not None:
                 raise ValueError('replace_from_pot2 given but potfile_2 not given')
@@ -179,5 +173,5 @@ def neworder_potential(self, potfile_in, potfile_out, neworder, potfile_2=None,
                     datanew.append(data[ii])
 
         # write out new potential
-        with open(potfile_out, 'w') as f:
+        with open(potfile_out, 'w', encoding='utf8') as f:
             f.writelines(datanew)