More typing/CI fixes

.github/workflows/ci.yaml

@@ -56,21 +56,16 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e '.[dev]'
 
-      - name: Type check 3.9
-        if: ${{ steps.deps.outcome == 'success' && success() || failure() }}
-        uses: jakebailey/pyright-action@v1
-        with:
-          python-version: "3.9"
       - name: Type check 3.10
         if: ${{ steps.deps.outcome == 'success' && success() || failure() }}
         uses: jakebailey/pyright-action@v1
         with:
           python-version: "3.10"
-      - name: Type check 3.11
+      - name: Type check 3.12
         if: ${{ steps.deps.outcome == 'success' && success() || failure() }}
         uses: jakebailey/pyright-action@v1
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
   success:
     name: Success

atomlib/cli.py

@@ -78,7 +78,7 @@ def cli(verbose: int = 0):
 def run_chain(cmds: t.Sequence[CmdType], verbose: int = 0):
     states: t.Iterable[State] = ()
     for cmd in cmds:
-        if cmd is None:
+        if cmd is None:  # type: ignore reportUnnecessaryComparison
             raise RuntimeError("'cmd' is None. Did a command forget to return a wrapper function?")
         states = cmd(states)
     for _ in states:

atomlib/defect.py

@@ -8,6 +8,7 @@
 import typing as t
 from typing import cast
 
+from typing_extensions import TypeAlias
 import numpy
 from numpy.typing import NDArray, ArrayLike
 import polars
@@ -36,7 +37,7 @@ def ellip_pi(n: NDArray[numpy.float64], m: NDArray[numpy.float64]) -> NDArray[nu
     return rf + rj * n / 3
 
 
-CutType = t.Literal['shift', 'add', 'rm']
+CutType: TypeAlias = t.Literal['shift', 'add', 'rm']
 """Cut plane to use when creating a (non-screw) dislocation."""
 
 

atomlib/expr.py

@@ -420,7 +420,7 @@ def parse_nary(self, lhs: Expr[T_co, V], level: t.Optional[int] = None) -> Expr[
         logging.debug(f"parse_nary({lhs}, level={level})")
         token = self.peek()
         logging.debug(f"token: '{token!r}'")
-        
+
         while token is not None:
             if not isinstance(token, OpToken) or \
                not isinstance(token.op, (NaryOp, BinaryOp)):
@@ -435,7 +435,7 @@ def parse_nary(self, lhs: Expr[T_co, V], level: t.Optional[int] = None) -> Expr[
             logging.debug(f"rhs: '{rhs}'")
 
             inner = self.peek()
-            if not inner is None and isinstance(inner, OpToken):
+            if inner is not None and isinstance(inner, OpToken):
                 inner_op = inner.op
                 if isinstance(inner_op, (NaryOp, BinaryOp)) and \
                     inner_op.precedes(token.op):

atomlib/io/__init__.py

@@ -5,6 +5,7 @@
 import logging
 import typing as t
 
+from typing_extensions import TypeAlias
 import numpy
 import polars
 
@@ -23,7 +24,7 @@
 from ..elem import get_sym, get_elem
 from ..util import FileOrPath
 
-FileType = t.Literal['cif', 'xyz', 'xsf', 'cfg', 'lmp', 'mslice', 'qe']
+FileType: TypeAlias = t.Literal['cif', 'xyz', 'xsf', 'cfg', 'lmp', 'mslice', 'qe']
 
 
 def read_cif(f: t.Union[FileOrPath, CIF, CIFDataBlock], block: t.Union[int, str, None] = None) -> HasAtoms:

atomlib/io/cif.py

@@ -12,6 +12,7 @@
 import logging
 import typing as t
 
+from typing_extensions import TypeAlias
 import numpy
 import polars
 from numpy.typing import NDArray
@@ -26,7 +27,7 @@
     from ..atomcell import HasAtomCell
 
 
-Value = t.Union[int, float, str, None]
+Value: TypeAlias = t.Union[int, float, str, None]
 _INT_RE = re.compile(r'[-+]?\d+')
 # float regex with uncertainty (e.g. '3.14159(3)')
 _FLOAT_RE = re.compile(r'([-+]?\d*(\.\d*)?(e[-+]?\d+)?)(\(\d+\))?', re.I)
@@ -59,7 +60,7 @@ def get_block(self, block: t.Union[int, str]) -> CIFDataBlock:
 
     def write(self, file: FileOrPath):
         with open_file(file, 'w') as f:
-            print(f"# generated by atomlib", file=f, end=None)
+            print("# generated by atomlib", file=f, end=None)
             for data_block in self.data_blocks:
                 print(file=f)
                 data_block._write(f)
@@ -195,7 +196,7 @@ def stack_tags(self, *tags: str, dtype: t.Union[str, numpy.dtype, t.Iterable[t.U
         else:
             dtypes = tuple(map(lambda ty: numpy.dtype(ty), dtype))
             if len(dtypes) != len(tags):
-                raise ValueError(f"dtype list of invalid length")
+                raise ValueError("dtype list of invalid length")
 
         if isinstance(required, bool):
             required = repeat(required)
@@ -218,8 +219,8 @@ def stack_tags(self, *tags: str, dtype: t.Union[str, numpy.dtype, t.Iterable[t.U
         if len(d) == 0:
             return polars.DataFrame({})
 
-        l = len(next(iter(d.values())))
-        if any(len(arr) != l for arr in d.values()):
+        tag_len = len(next(iter(d.values())))
+        if any(len(arr) != tag_len for arr in d.values()):
             raise ValueError(f"Tags of mismatching lengths: {tuple(map(len, d.values()))}")
 
         return polars.DataFrame(d)
@@ -264,7 +265,7 @@ class CIFTable:
     data: t.Dict[str, t.List[Value]]
 
     def _write(self, f: TextIOBase):
-        print(f"\nloop_", file=f)
+        print("\nloop_", file=f)
         for tag in self.data.keys():
             print(f" _{tag}", file=f)
 
@@ -535,7 +536,7 @@ def parse_loop(self) -> CIFTable:
         return CIFTable(dict(zip(tags, vals)))
 
     def parse_value(self) -> Value:
-        logging.debug(f"parse_value")
+        logging.debug("parse_value")
         w = self.peek_word()
         assert w is not None
         if w in ('.', '?'):
@@ -551,17 +552,17 @@ def parse_value(self) -> Value:
         return self.parse_bare()
 
     def parse_text_field(self) -> str:
-        line = self.line
-        l = self.next_line()
-        assert l is not None
-        s = l.lstrip().removeprefix(';').lstrip()
+        start_line = self.line
+        line = self.next_line()
+        assert line is not None
+        s = line.lstrip().removeprefix(';').lstrip()
         while True:
-            l = self.next_line()
-            if l is None:
-                raise ValueError(f"While parsing text field at line {line}: Unexpected EOF")
-            if l.strip() == ';':
+            line = self.next_line()
+            if line is None:
+                raise ValueError(f"While parsing text field at line {start_line}: Unexpected EOF")
+            if line.strip() == ';':
                 break
-            s += l
+            s += line
         return s.rstrip()
 
     def parse_quoted(self) -> str:

atomlib/io/lmp.py

@@ -216,10 +216,10 @@ def write(self, file: FileOrPath):
 
             # print sections
             for section in self.sections:
-                l = section.name
+                line = section.name
                 if section.style is not None:
-                    l += f'  # {section.style}'
-                print(f"\n{l}\n", file=f)
+                    line += f'  # {section.style}'
+                print(f"\n{line}\n", file=f)
 
                 f.writelines(section.body)
 
@@ -361,9 +361,9 @@ def collect_lines(self, n: int) -> t.Optional[t.List[str]]:
         try:
             for _ in range(n):
                 while True:
-                    l = next(self._file)
-                    if not l.isspace():
-                        lines.append(l)
+                    line = next(self._file)
+                    if not line.isspace():
+                        lines.append(line)
                         break
         except StopIteration:
             return None
@@ -385,11 +385,14 @@ def inner(s: str) -> t.Tuple[t.Any, ...]:
 
     return inner
 
-
 _parse_2float = _parse_seq(float, 2)
 _parse_3float = _parse_seq(float, 3)
-_fmt_2float = lambda vals: f"{vals[0]:16.7f} {vals[1]:14.7f}"
-_fmt_3float = lambda vals: f"{vals[0]:16.7f} {vals[1]:14.7f} {vals[2]:14.7f}"
+
+def _fmt_2float(vals: t.Sequence[float]):
+    return f"{vals[0]:16.7f} {vals[1]:14.7f}"
+
+def _fmt_3float(vals: t.Sequence[float]):
+    return f"{vals[0]:16.7f} {vals[1]:14.7f} {vals[2]:14.7f}"
 
 
 _HEADER_KWS = {

atomlib/io/xsf.py

@@ -9,14 +9,15 @@
 import logging
 import typing as t
 
+from typing_extensions import TypeAlias
 import numpy
 from numpy.typing import NDArray
 import polars
 
 from ..transform import LinearTransform3D
 from ..util import open_file, FileOrPath
 
-Periodicity = t.Literal['crystal', 'slab', 'polymer', 'molecule']
+Periodicity: TypeAlias = t.Literal['crystal', 'slab', 'polymer', 'molecule']
 
 if t.TYPE_CHECKING:
     from ..atoms import HasAtoms
@@ -204,7 +205,7 @@ def parse_atoms(self, expected_length: t.Optional[int] = None) -> polars.DataFra
             return polars.DataFrame({}, schema=['elem', 'x', 'y', 'z'])  # type: ignore
 
         coord_lens = list(map(len, coords))
-        if not all(l == coord_lens[0] for l in coord_lens[1:]):
+        if not all(coord_len == coord_lens[0] for coord_len in coord_lens[1:]):
             raise ValueError("Mismatched atom dimensions.")
         if coord_lens[0] < 3:
             raise ValueError("Expected at least 3 coordinates per atom.")

atomlib/io/xyz.py

@@ -13,6 +13,7 @@
 import logging
 import typing as t
 
+from typing_extensions import TypeAlias
 import numpy
 from numpy.typing import NDArray
 import polars
@@ -46,7 +47,7 @@
 }
 
 
-XYZFormat = t.Literal['xyz', 'exyz']
+XYZFormat: TypeAlias = t.Literal['xyz', 'exyz']
 
 T = t.TypeVar('T')
 
@@ -90,7 +91,7 @@ def from_file(file: FileOrPath) -> XYZ:
                 # TODO be more gracious about whitespace here
                 length = int(f.readline())
             except ValueError:
-                raise ValueError(f"Error parsing XYZ file: Invalid length") from None
+                raise ValueError("Error parsing XYZ file: Invalid length") from None
             except IOError as e:
                 raise IOError(f"Error parsing XYZ file: {e}") from None
 

atomlib/make/__init__.py

@@ -8,6 +8,7 @@
 import string
 import typing as t
 
+from typing_extensions import TypeAlias
 import numpy
 
 from ..atomcell import Atoms, AtomCell, HasAtomCellT, IntoAtoms
@@ -20,7 +21,7 @@
 from ..util import proc_seed
 
 
-CellType = t.Literal['conv', 'prim', 'ortho']
+CellType: TypeAlias = t.Literal['conv', 'prim', 'ortho']
 
 
 def fcc(elem: ElemLike, a: Num, *, cell: CellType = 'conv', additional: t.Optional[IntoAtoms] = None) -> AtomCell:

atomlib/util.py

@@ -8,7 +8,7 @@
 import time
 import typing as t
 
-from typing_extensions import ParamSpec, Concatenate
+from typing_extensions import ParamSpec, Concatenate, TypeAlias
 import numpy
 from numpy.typing import NDArray
 import polars
@@ -27,9 +27,9 @@ def map_some(f: t.Callable[[T], U], val: t.Optional[T]) -> t.Optional[U]:
     return None if val is None else f(val)
 
 
-FileOrPath = t.Union[str, Path, TextIOBase, t.TextIO]
+FileOrPath: TypeAlias = t.Union[str, Path, TextIOBase, t.TextIO]
 """Open text file or path to a file. Use with [open_file][atomlib.util.open_file]."""
-BinaryFileOrPath = t.Union[str, Path, t.TextIO, t.BinaryIO, IOBase]
+BinaryFileOrPath: TypeAlias = t.Union[str, Path, t.TextIO, t.BinaryIO, IOBase]
 """Open binary file or path to a file. Use with [open_file_binary][atomlib.util.open_file_binary]."""
 
 

atomlib/vec.py

@@ -225,7 +225,7 @@ def miller_4_to_3_plane(a: NDArray[numpy.number], reduce: bool = True, max_denom
     """Convert a plane in 4-axis Miller-Bravais notation to 3-axis Miller notation."""
     a = numpy.atleast_1d(a)
     assert a.shape[-1] == 4
-    h, k, i, l = numpy.split(a, 4, axis=-1)
+    h, k, i, l = numpy.split(a, 4, axis=-1)  # noqa: E741
     assert numpy.allclose(-i, h + k, equal_nan=True)
     out = numpy.concatenate((h, k, l), axis=-1)
     return reduce_vec(out, max_denom) if reduce else out
@@ -235,8 +235,8 @@ def miller_3_to_4_plane(a: NDArray[numpy.number], reduce: bool = True, max_denom
     """Convert a plane in 3-axis Miller notation to 4-axis Miller-Bravais notation."""
     a = numpy.atleast_1d(a)
     assert a.shape[-1] == 3
-    h, k, l = numpy.split(a, 3, axis=-1)
-    out = numpy.concatenate((h, k, -(h + k), l), axis=-1)  # type: ignore
+    h, k, l = numpy.split(a, 3, axis=-1)  # noqa: E741
+    out = numpy.concatenate((h, k, -(h + k), l), axis=-1)
     return reduce_vec(out, max_denom) if reduce else out
 
 

atomlib/visualize/__init__.py

@@ -4,6 +4,7 @@
 from abc import abstractmethod, ABC
 import typing as t
 
+from typing_extensions import TypeAlias
 import numpy
 from numpy.typing import NDArray
 from matplotlib import pyplot
@@ -25,8 +26,8 @@
 from ..elem import get_radius
 
 
-BackendName = t.Literal['mpl', 'ase']
-AtomStyle = t.Literal['spacefill', 'ballstick', 'small']
+BackendName: TypeAlias = t.Literal['mpl', 'ase']
+AtomStyle: TypeAlias = t.Literal['spacefill', 'ballstick', 'small']
 
 
 class AtomImage(ABC):
@@ -140,9 +141,8 @@ def get_plot_radii(atoms: HasAtoms, min_r: t.Optional[float] = 1.0, style: AtomS
 
 def get_azim_elev(zone: VecLike) -> t.Tuple[float, float]:
     (a, b, c) = -to_vec3(zone)  # look down zone
-    l = numpy.sqrt(a**2 + b**2)
     # todo: aren't these just arctan2s?
-    return (numpy.angle(a + b*1.j, deg=True), numpy.angle(l + c*1.j, deg=True))  # type: ignore
+    return (numpy.angle(a + b*1.j, deg=True), numpy.angle(numpy.sqrt(a**2 + b**2) + c*1.j, deg=True))  # type: ignore
 
 
 def show_atoms_mpl_3d(atoms: HasAtoms, *, fig: t.Optional[Figure] = None,