Change from using repr to str for printing the values in input files (#…

…61)

… because repr causes issues with numpy v2

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+        types: [file, python]
+    -   id: end-of-file-fixer
+        types: [file, python]
+    -   id: check-yaml
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.961
+    hooks:
+      - id: mypy
+        files: src/koopmans/
+        args: [--ignore-missing-imports]
+
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v1.6.0
+    hooks:
+    - id: autopep8
+      args: [--max-line-length=120, -i]
+

ase/__init__.py

@@ -19,7 +19,7 @@
 
 __all__ = ['Atoms', 'Atom']
 
-__version__ = '0.1.4'
+__version__ = '0.1.5'
 
 from ase.atom import Atom
 from ase.atoms import Atoms

ase/io/espresso/_koopmans_ham.py

@@ -10,7 +10,7 @@
 from ase.dft.kpoints import BandPath
 from ase.utils import basestring
 from ._utils import construct_kpoints_card, generic_construct_namelist, safe_string_to_list_of_floats, time_to_float, \
-    read_fortran_namelist
+    read_fortran_namelist, dict_to_input_lines
 from ._wann2kc import KEYS as W2KCW_KEYS
 
 from ase.calculators.espresso import KoopmansHam
@@ -38,14 +38,7 @@ def write_koopmans_ham_in(fd, atoms, input_data=None, pseudopotentials=None,
             continue
 
         lines.append('&{0}\n'.format(section.upper()))
-        for key, value in input_parameters[section].items():
-            if value is True:
-                lines.append('   {0:16} = .true.\n'.format(key))
-            elif value is False:
-                lines.append('   {0:16} = .false.\n'.format(key))
-            elif value is not None:
-                # repr format to get quotes around strings
-                lines.append('   {0:16} = {1!r:}\n'.format(key, value))
+        lines += dict_to_input_lines(input_parameters[section])
         lines.append('/\n')  # terminate section
 
     if input_parameters['HAM'].get('do_bands', True):

ase/io/espresso/_koopmans_screen.py

@@ -8,7 +8,7 @@
 from ase import Atoms
 from ase.calculators.singlepoint import SinglePointDFTCalculator
 from ase.utils import basestring
-from ._utils import read_fortran_namelist, generic_construct_namelist, time_to_float, units
+from ._utils import read_fortran_namelist, generic_construct_namelist, time_to_float, units, dict_to_input_lines
 from ._wann2kc import KEYS as W2KCW_KEYS
 from ase.calculators.espresso import KoopmansScreen
 
@@ -34,14 +34,7 @@ def write_koopmans_screen_in(fd, atoms, input_data=None, **kwargs):
             continue
 
         lines.append('&{0}\n'.format(section.upper()))
-        for key, value in input_parameters[section].items():
-            if value is True:
-                lines.append('   {0:16} = .true.\n'.format(key))
-            elif value is False:
-                lines.append('   {0:16} = .false.\n'.format(key))
-            elif value is not None:
-                # repr format to get quotes around strings
-                lines.append('   {0:16} = {1!r:}\n'.format(key, value))
+        lines += dict_to_input_lines(input_parameters[section])
         lines.append('/\n')  # terminate section
 
     fd.writelines(lines)

ase/io/espresso/_ph.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 from ase.utils import basestring
 from ase.atoms import Atoms
-from ._utils import read_fortran_namelist, time_to_float
+from ._utils import read_fortran_namelist, time_to_float, dict_to_input_lines
 from ase.calculators.espresso import EspressoPh
 
 
@@ -70,16 +70,7 @@ def write_ph_in(fd, atoms, **kwargs):
     all_parameters = dict(**atoms.calc.parameters, **masses)
     all_parameters.pop('pseudopotentials', None)
 
-    for key, value in all_parameters.items():
-        if value is True:
-            ph.append('   {0:16} = .true.\n'.format(key))
-        elif value is False:
-            ph.append('   {0:16} = .false.\n'.format(key))
-        elif value is not None:
-            if isinstance(value, Path):
-                value = str(value)
-            # repr format to get quotes around strings
-            ph.append('   {0:16} = {1!r:}\n'.format(key, value))
+    ph += dict_to_input_lines(all_parameters)
     ph.append('/\n')
     ph.append('0.0 0.0 0.0')
 

ase/io/espresso/_projwfc.py

@@ -1,6 +1,6 @@
 from ase.atoms import Atoms
 from ase.calculators.espresso import Projwfc
-from ._utils import read_fortran_namelist, time_to_float
+from ._utils import read_fortran_namelist, time_to_float, dict_to_input_lines
 from pathlib import Path
 
 
@@ -56,16 +56,7 @@ def write_projwfc_in(fd, atoms, **kwargs):
     """
 
     projwf = ['&projwfc\n']
-    for key, value in atoms.calc.parameters.items():
-        if value is True:
-            projwf.append(f'   {key:16} = .true.\n')
-        elif value is False:
-            projwf.append(f'   {key:16} = .false.\n')
-        elif value is not None:
-            if isinstance(value, Path):
-                value = str(value)
-            # repr format to get quotes around strings
-            projwf.append(f'   {key:16} = {value!r:}\n')
+    projwf += dict_to_input_lines(atoms.calc.parameters)
     projwf.append('/\n')
 
     fd.write(''.join(projwf))

ase/io/espresso/_utils.py

@@ -1384,14 +1384,7 @@ def write_espresso_in(fd, atoms, input_data=None, pseudopotentials=None,
     # and that repr converts to a QE readable representation (except bools)
     for section in input_parameters:
         flines.append('&{0}\n'.format(section.upper()))
-        for key, value in input_parameters[section].items():
-            if value is True:
-                flines.append('   {0:16} = .true.\n'.format(key))
-            elif value is False:
-                flines.append('   {0:16} = .false.\n'.format(key))
-            elif value is not None:
-                # repr format to get quotes around strings
-                flines.append('   {0:16} = {1!r:}\n'.format(key, value))
+        flines += dict_to_input_lines(input_parameters[section])
         flines.append('/\n')  # terminate section
     flines.append('\n')
 
@@ -1425,3 +1418,20 @@ def write_espresso_in(fd, atoms, input_data=None, pseudopotentials=None,
 
     # DONE!
     fd.write(''.join(flines))
+
+
+def dict_to_input_lines(dct):
+    out = []
+    for key, value in dct.items():
+        if value is not None:
+            if isinstance(value, Path):
+                value = str(value)
+            if isinstance(value, str):
+                # add quotes around strings
+                value = f"'{value}'"
+            if value is True:
+                value = '.true.'
+            if value is False:
+                value = '.false.'
+            out.append(f'   {key:16} = {value}\n')
+    return out

ase/io/espresso/_wann2kc.py

@@ -8,13 +8,14 @@
 from ase.atoms import Atoms
 from ase.calculators.singlepoint import SinglePointDFTCalculator
 from ase.utils import basestring
-from ._utils import Namelist, read_fortran_namelist, generic_construct_namelist, time_to_float
+from ._utils import Namelist, read_fortran_namelist, generic_construct_namelist, time_to_float, dict_to_input_lines
 from ase.calculators.espresso import Wann2KC
 
 
 KEYS = Namelist((
     ('control', ['prefix', 'outdir', 'kcw_iverbosity', 'kcw_at_ks', 'calculation', 'lrpa',
-                 'mp1', 'mp2', 'mp3', 'homo_only', 'read_unitary_matrix', 'l_vcut', 'assume_isolated', 'spin_component']),
+                 'mp1', 'mp2', 'mp3', 'homo_only', 'read_unitary_matrix', 'l_vcut', 'assume_isolated',
+                 'spin_component']),
     ('wannier', ['seedname', 'check_ks', 'num_wann_occ', 'num_wann_emp', 'have_empty', 'has_disentangle'])))
 
 
@@ -32,14 +33,7 @@ def write_wann2kc_in(fd, atoms, input_data=None, pseudopotentials=None,
     for section in input_parameters:
         assert section in KEYS.keys()
         lines.append('&{0}\n'.format(section.upper()))
-        for key, value in input_parameters[section].items():
-            if value is True:
-                lines.append('   {0:16} = .true.\n'.format(key))
-            elif value is False:
-                lines.append('   {0:16} = .false.\n'.format(key))
-            elif value is not None:
-                # repr format to get quotes around strings
-                lines.append('   {0:16} = {1!r:}\n'.format(key, value))
+        lines += dict_to_input_lines(input_parameters[section])
         lines.append('/\n')  # terminate section
 
     fd.writelines(lines)

ase/io/espresso/_x2y.py

@@ -5,7 +5,7 @@
 from pathlib import Path
 from ase.utils import basestring
 from ase.atoms import Atoms
-from ._utils import read_fortran_namelist, time_to_float
+from ._utils import read_fortran_namelist, time_to_float, dict_to_input_lines
 
 
 def read_x2y_in(fileobj, calc_class):
@@ -60,16 +60,7 @@ def write_x2y_in(fd, atoms, **kwargs):
     """
 
     x2y = ['&inputpp\n']
-    for key, value in atoms.calc.parameters.items():
-        if value is True:
-            x2y.append(f'   {key:16} = .true.\n')
-        elif value is False:
-            x2y.append(f'   {key:16} = .false.\n')
-        elif value is not None:
-            if isinstance(value, Path):
-                value = str(value)
-            # repr format to get quotes around strings
-            x2y.append(f'   {key:16} = {value!r:}\n')
+    x2y += dict_to_input_lines(atoms.calc.parameters)
     x2y.append('/\n')
 
     fd.write(''.join(x2y))

ase/spacegroup/xtal.py

@@ -11,9 +11,9 @@
 from scipy import spatial
 
 import ase
-from ase.symbols import string2symbols
-from ase.spacegroup import Spacegroup
 from ase.geometry import cellpar_to_cell
+from ase.spacegroup import Spacegroup
+from ase.symbols import string2symbols
 
 __all__ = ['crystal']
 
@@ -103,9 +103,9 @@ def crystal(symbols=None, basis=None, occupancies=None, spacegroup=1, setting=1,
     """
     sg = Spacegroup(spacegroup, setting)
     if (not isinstance(symbols, str) and
-        hasattr(symbols, '__getitem__') and
-        len(symbols) > 0 and
-        isinstance(symbols[0], ase.Atom)):
+            hasattr(symbols, '__getitem__') and
+            len(symbols) > 0 and
+            isinstance(symbols[0], ase.Atom)):
         symbols = ase.Atoms(symbols)
     if isinstance(symbols, ase.Atoms):
         basis = symbols
@@ -117,25 +117,25 @@ def crystal(symbols=None, basis=None, occupancies=None, spacegroup=1, setting=1,
         if symbols is None:
             symbols = basis.get_chemical_symbols()
     else:
-        basis_coords = np.array(basis, dtype=float, copy=False, ndmin=2)
+        basis_coords = np.array(basis, dtype=float, ndmin=2)
 
     if occupancies is not None:
         occupancies_dict = {}
-    
+
         for index, coord in enumerate(basis_coords):
             # Compute all distances and get indices of nearest atoms
             dist = spatial.distance.cdist(coord.reshape(1, 3), basis_coords)
             indices_dist = np.flatnonzero(dist < symprec)
-            
+
             occ = {symbols[index]: occupancies[index]}
-            
+
             # Check nearest and update occupancy
             for index_dist in indices_dist:
                 if index == index_dist:
                     continue
                 else:
                     occ.update({symbols[index_dist]: occupancies[index_dist]})
-            
+
             occupancies_dict[index] = occ.copy()
 
     sites, kinds = sg.equivalent_sites(basis_coords,
@@ -154,7 +154,7 @@ def crystal(symbols=None, basis=None, occupancies=None, spacegroup=1, setting=1,
         symbols = [symbols[i] for i in kinds]
     else:
         # make sure that we put the dominant species there
-        symbols = [sorted(occupancies_dict[i].items(), key=lambda x : x[1])[-1][0] for i in kinds]
+        symbols = [sorted(occupancies_dict[i].items(), key=lambda x: x[1])[-1][0] for i in kinds]
 
     if cell is None:
         cell = cellpar_to_cell(cellpar, ab_normal, a_direction)
@@ -164,7 +164,7 @@ def crystal(symbols=None, basis=None, occupancies=None, spacegroup=1, setting=1,
         info['unit_cell'] = 'primitive'
     else:
         info['unit_cell'] = 'conventional'
-        
+
     if 'info' in kwargs:
         info.update(kwargs['info'])
 
@@ -186,7 +186,7 @@ def crystal(symbols=None, basis=None, occupancies=None, spacegroup=1, setting=1,
                 array = basis.get_array(name)
                 atoms.new_array(name, [array[i] for i in kinds],
                                 dtype=array.dtype, shape=array.shape[1:])
-                
+
     if kinds:
         atoms.new_array('spacegroup_kinds', np.asarray(kinds, dtype=int))