Temp as value (#306)

* update hooks

* fix conversion

* black update

* fix test

* merge fix

* pr suggestion

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: mixed-line-ending
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.1
+    rev: v1.5.1
     hooks:
     - id: mypy
       exclude: "tests/|doc/|examples/"

autode/__init__.py

@@ -1,3 +1,5 @@
+import importlib.metadata
+
 from autode import methods
 from autode import geom
 from autode import pes
@@ -25,14 +27,10 @@
 from autode.utils import temporary_config
 
 """
-Bumping the version number requires following the release proceedure:
-
-- Update changelog (doc/changelog.rst)
+Bumping the version number requires following the release procedure:
 
 - Run tests/benchmark.py with both organic and organometallic sets
 
-- Change __version__ here and in setup.py
-
 - Release on conda-forge
   - Fork https://github.com/conda-forge/autode-feedstock
   - Make a local branch
@@ -41,8 +39,7 @@
   - Merge when tests pass
 """
 
-__version__ = "1.4.1"
-
+__version__ = importlib.metadata.version("autode")
 
 __all__ = [
     "KeywordsSet",

autode/atoms.py

@@ -219,7 +219,6 @@ def group(self) -> int:
         """
 
         for group_idx in range(1, 18):
-
             if self.label in PeriodicTable.group(group_idx):
                 return group_idx
 
@@ -242,7 +241,6 @@ def period(self) -> int:
         """
 
         for period_idx in range(1, 7):
-
             if self.label in PeriodicTable.period(period_idx):
                 return period_idx
 
@@ -692,7 +690,6 @@ def moi(self) -> MomentOfInertia:
         moi = MomentOfInertia(np.zeros(shape=(3, 3)), units="amu Å^2")
 
         for atom in self:
-
             mass, (x, y, z) = atom.mass, atom.coord
 
             moi[0, 0] += mass * (y**2 + z**2)
@@ -887,7 +884,6 @@ def are_planar(self, distance_tol: Distance = Distance(1e-3, "Å")) -> bool:
         normal_vec = np.cross(arr[1, :] - x0, arr[2, :] - x0)
 
         for i in range(3, len(self)):
-
             # Calculate the 0->i atomic vector, which must not have any
             # component in the direction in the normal if the atoms are planar
             if np.dot(normal_vec, arr[i, :] - x0) > distance_tol_float:
@@ -1253,7 +1249,6 @@ def dihedral(self, w: int, x: int, y: int, z: int) -> Angle:
 
 
 class PeriodicTable:
-
     # fmt: off
     table = np.array(
         [['H',    '',   '',   '',   '',  '',    '',   '',   '',   '',   '',   '',   '',   '',   '',   '',   '', 'He'],

autode/bond_rearrangement.py

@@ -246,7 +246,6 @@ def add_bond_rearrangment(bond_rearrangs, reactant, product, fbonds, bbonds):
     bbond_atoms = [atom for bbond in bbonds for atom in bbond]
     for fbond in fbonds:
         for idx in fbond:
-
             if (
                 reactant.graph.degree(idx)
                 == reactant.atoms[idx].maximal_valance
@@ -358,7 +357,6 @@ def get_fbonds_bbonds_2b(
         for bbond1, bbond2 in itertools.product(
             all_possible_bbonds[0], all_possible_bbonds[1]
         ):
-
             possible_brs = add_bond_rearrangment(
                 possible_brs, reac, prod, fbonds=[], bbonds=[bbond1, bbond2]
             )
@@ -672,7 +670,6 @@ def strip_equiv_bond_rearrs(possible_brs, mol, depth=6):
 
         # Compare bond_rearrang to all those already considered to be unique,
         for unique_br in unique_brs:
-
             if unique_br.get_active_atom_neighbour_lists(
                 species=mol, depth=depth
             ) == br.get_active_atom_neighbour_lists(species=mol, depth=depth):
@@ -736,7 +733,6 @@ def prune_small_ring_rearrs(possible_brs, mol):
 
         # Check against all other rearrangements
         for j, other_br in enumerate(possible_brs):
-
             # Only consider brs with the same set of elements
             if elems[i] != elems[j]:
                 continue

autode/calculations/executors.py

@@ -41,7 +41,6 @@ def __init__(
         n_cores: int = 1,
         point_charges: Optional[List[PointCharge]] = None,
     ):
-
         # Calculation names that start with "-" can break EST methods
         self.name = f"{_string_without_leading_hyphen(name)}_{method.name}"
 
@@ -185,7 +184,6 @@ def _no_except_set_hessian(self) -> None:
         self.molecule.hessian = self.method.hessian_from(self)
 
     def clean_up(self, force: bool = False, everything: bool = False) -> None:
-
         if not self.method.uses_external_io:  # Then there are no i/o files
             return None
 
@@ -203,7 +201,6 @@ def clean_up(self, force: bool = False, everything: bool = False) -> None:
         logger.info(f"Deleting: {set(filenames)}")
 
         for filename in [fn for fn in set(filenames) if fn is not None]:
-
             try:
                 os.remove(filename)
             except FileNotFoundError:

autode/calculations/output.py

@@ -8,7 +8,6 @@
 
 class CalculationOutput:
     def __init__(self, filename: Optional[str] = None):
-
         self._filename = filename
 
     @property
@@ -17,7 +16,6 @@ def filename(self) -> Optional[str]:
 
     @filename.setter
     def filename(self, value: str):
-
         self._filename = str(value)
         self.clear()
 

autode/config.py

@@ -403,7 +403,6 @@ def __setattr__(self, key, value):
             value = Allocation(value).to("MB")
 
         if key == "freq_scale_factor":
-
             if value is not None:
                 if not (0.0 < value <= 1.0):
                     raise ValueError(

autode/conformers/conf_gen.py

@@ -148,7 +148,7 @@ def _get_atoms_rotated_stereocentres(species, atoms, rand):
     ]
 
     # Check on every pair of stereocenters
-    for (i, j) in combinations(stereocentres, 2):
+    for i, j in combinations(stereocentres, 2):
         if (i, j) not in species.graph.edges:
             continue
 
@@ -232,8 +232,7 @@ def _add_dist_consts_for_stereocentres(species, dist_consts):
             dist_consts[(atom_i, atom_j)] = species.distance(atom_i, atom_j)
 
     # Check on every pair of stereocenters
-    for (atom_i, atom_j) in combinations(stereocentres, 2):
-
+    for atom_i, atom_j in combinations(stereocentres, 2):
         # If they are not bonded don't alter
         if (atom_i, atom_j) not in species.graph.edges:
             continue
@@ -243,7 +242,6 @@ def _add_dist_consts_for_stereocentres(species, dist_consts):
         for i_neighbour in species.graph.neighbors(atom_i):
             for j_neighbour in species.graph.neighbors(atom_j):
                 if i_neighbour != atom_j and j_neighbour != atom_i:
-
                     # Fix the distance to the current value
                     dist = species.distance(i_neighbour, j_neighbour)
                     dist_consts[(i_neighbour, j_neighbour)] = dist

autode/conformers/conformer.py

@@ -173,7 +173,6 @@ def atoms(self, value: Optional[Atoms]):
             return
 
         for i, atom in enumerate(value):
-
             parent_atom = self._parent_atoms[i]
             if atom.label != parent_atom.label:
                 raise ValueError(

autode/conformers/conformers.py

@@ -133,7 +133,6 @@ def prune_on_energy(
             idxs_with_energy = [j for j in idxs_with_energy if j < len(self)]
 
             if np.abs(conf.energy - avg_e) / std_dev_e > n_sigma:
-
                 logger.warning(
                     f"Conformer {idx} had an energy >{n_sigma}σ "
                     f"from the average - removing"
@@ -150,7 +149,6 @@ def prune_on_energy(
                 for o_idx in idxs_with_energy
                 if o_idx != idx
             ):
-
                 logger.info(f"Conformer {idx} had a non unique energy")
                 del self[idx]
                 continue
@@ -195,15 +193,13 @@ def prune_on_rmsd(
         # Only enumerate up to but not including the final index, as at
         # least one of the conformers must be unique in geometry
         for idx in reversed(range(len(self) - 1)):
-
             conf = self[idx]
 
             if any(
                 calc_heavy_atom_rmsd(conf.atoms, other.atoms) < rmsd_tol
                 for o_idx, other in enumerate(self)
                 if o_idx != idx
             ):
-
                 logger.info(
                     f"Conformer {idx} was close in geometry to at "
                     f"least one other - removing"

autode/constants.py

@@ -1,5 +1,4 @@
 class Constants:
-
     n_a = 6.022140857e23  # molecules mol-1
 
     ha_to_kcalmol = ha2kcalmol = 627.509  # Hartree^-1 kcal mol^-1

autode/geom.py

@@ -161,7 +161,6 @@ def get_neighbour_list(
 
     dists_and_atom_labels = {}
     for atom_j, dist in enumerate(distance_vector):
-
         if index_set is not None and atom_j not in index_set:
             continue
 

autode/hessians.py

@@ -40,7 +40,6 @@
 
 
 class Hessian(ValueArray):
-
     implemented_units = [
         ha_per_ang_sq,
         ha_per_a0_sq,
@@ -220,7 +219,6 @@ def _proj_matrix(self) -> np.ndarray:
         m_half = np.diag(np.sqrt(masses))
 
         for t_i in (t1, t2, t3, t4, t5, t6):
-
             t_i[:] = np.dot(m_half, np.array(t_i))
             t_i /= np.linalg.norm(t_i)
 
@@ -427,7 +425,6 @@ def __init__(
         shift: Distance,
         n_cores: Optional[int] = None,
     ):
-
         self._species = species
         self._method = method
         self._keywords = self._validated(keywords)
@@ -467,7 +464,6 @@ def calculate(self) -> None:
 
         # Although n_rows may be < n_cores there will not be > n_rows processes
         with ProcessPool(max_workers=self._n_total_cores) as pool:
-
             func_name = "_cdiff_row" if self._do_c_diff else "_diff_row"
 
             jobs = [
@@ -541,7 +537,6 @@ def _idxs_to_calculate(self) -> Iterator:
         need to be calculated"""
 
         for row_idx in range(self._n_rows):
-
             if row_idx not in self._calculated_rows:
                 self._calculated_rows.append(row_idx)
 

autode/input_output.py

@@ -34,7 +34,6 @@ def xyz_file_to_atoms(filename: str) -> Atoms:
     n_atoms = 0
 
     for i, line in enumerate(open(filename, "r")):
-
         if i == 0:  # First line in an xyz file is the number of atoms
             n_atoms = _n_atoms_from_first_xyz_line(line)
             continue
@@ -118,7 +117,6 @@ def xyz_file_to_molecules(filename: str) -> Sequence["Molecule"]:
     molecules = []
 
     for i in range(0, len(lines), n_atoms + 2):
-
         atoms = []
         title_line = StringDict(lines[i + 1])
         for j, line in enumerate(lines[i + 2 : i + n_atoms + 2]):
@@ -152,7 +150,6 @@ def attrs_from_xyz_title_line(filename: str) -> StringDict:
 
 
 def _check_xyz_file_exists(filename: str) -> None:
-
     if not os.path.exists(filename):
         raise XYZfileDidNotExist(f"{filename} did not exist")
 
@@ -168,7 +165,6 @@ def _set_attr_from_title_line(
     title_line: StringDict,
     key_in_line: Optional[str] = None,
 ) -> None:
-
     if key_in_line is None:
         key_in_line = attr  # Default to e.g. charge attribute is "charge = 0"
     try:

autode/methods.py

@@ -112,7 +112,6 @@ def get_first_available_method(
         (autode.exceptions.MethodUnavailable):
     """
     for method in possibilities:
-
         if method.is_available:
             return method
 
@@ -137,7 +136,6 @@ def get_defined_method(name, possibilities) -> "Method":
 
     for method in possibilities:
         if method.name.lower() == name.lower():
-
             if method.is_available:
                 return method