Try to fix again the py39 isinstance issue.

src/phyling/_abc.py

@@ -6,7 +6,7 @@
 import textwrap
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Generic, Iterable, Iterator, Sequence, TypeVar, Union
+from typing import Generic, Iterable, Iterator, Sequence, TypeVar
 
 import phyling.config as config
 import phyling.exception as exception
@@ -103,7 +103,7 @@ class DataListABC(ABC, Generic[T]):
     def __init__(self, files: Iterator[str | Path | T] | Sequence[str | Path | T]) -> None:
         """Initialize the object and store data into a list."""
         self.data: list[T] = []
-        if not isinstance(files, Union[Iterator, tuple, list]):
+        if not isinstance(files, (Iterator, tuple, list)):
             raise TypeError(f"{self.__class__.__qualname__} is not an iterator/tuple/list")
 
     def __repr__(self) -> str:

src/phyling/libphyling.py

@@ -12,7 +12,7 @@
 from io import BytesIO, StringIO
 from multiprocessing.dummy import Pool
 from pathlib import Path
-from typing import AnyStr, Iterable, Sequence, Union
+from typing import AnyStr, Iterable, Sequence
 
 import numpy as np
 import pyhmmer
@@ -190,7 +190,7 @@ def __init__(self, files: Iterable[str | Path | SampleSeqs]) -> None:
         for item in files:
             if isinstance(item, SampleSeqs):
                 self.data.append(item)
-            elif isinstance(item, Union[str, Path]):
+            elif isinstance(item, (str, Path)):
                 self.data.append(SampleSeqs(item))
             else:
                 raise TypeError(f"{self.__class__.__qualname__} only accepts list of str/Path/SampleSeqs")
@@ -285,7 +285,7 @@ class HMMMarkerSet(_abc.DataListABC[pyhmmer.plan7.HMM]):
 
     def __init__(self, folder: str | Path, cutoff: str | Path | None = None, *, raise_err: bool = True):
         """Initialize the object and perform seqtype and duplicated name checks."""
-        if isinstance(folder, Union[str, Path]):
+        if isinstance(folder, (str, Path)):
             folder = Path(folder)
         else:
             raise TypeError('Argument "folder" only accepts of str or Path.')

src/phyling/phylotree.py

@@ -15,7 +15,7 @@
 from itertools import product
 from multiprocessing.dummy import Pool
 from pathlib import Path
-from typing import Iterable, Union
+from typing import Iterator, Sequence
 
 import matplotlib.pyplot as plt
 from Bio import AlignIO, Phylo, SeqIO
@@ -393,7 +393,7 @@ def __init__(self, files: list[str | Path | MFA2Tree], *, seqtype: str | None =
         """Initialize the wrapper object."""
         super().__init__(files)
         for file in files:
-            if isinstance(file, Union[str, Path]):
+            if isinstance(file, (str, Path)):
                 data = MFA2Tree(file, seqtype=seqtype)
             elif isinstance(file, MFA2Tree):
                 data = file
@@ -512,7 +512,9 @@ def get_consensus_tree(self) -> Tree:
     @_utils.timing
     @Decorator.check_sorted
     @Decorator.check_single_file
-    def concat(self, output: Path, samples: Iterable[str] | None, *, partition: str | None = None, threads: int = 1) -> MFA2Tree:
+    def concat(
+        self, output: Path, samples: Iterator[str] | Sequence[str] | None, *, partition: str | None = None, threads: int = 1
+    ) -> MFA2Tree:
         """Concatenate selected MSAs to a single mfa file and return the corresponding MFA2Tree object."""
         alignmentList = [mfa2tree.msa for mfa2tree in self]
         # Sort by MSA length, since shorter MSA might have higher chances to have missing states
@@ -563,7 +565,7 @@ def concat(self, output: Path, samples: Iterable[str] | None, *, partition: str
         return MFA2Tree(concat_file, partition=partition_file, seqtype=self.seqtype)
 
     @staticmethod
-    def _fill_missing_taxon(samples: Iterable[str], alignment: MultipleSeqAlignment) -> MultipleSeqAlignment:
+    def _fill_missing_taxon(samples: Iterator[str] | Sequence[str], alignment: MultipleSeqAlignment) -> MultipleSeqAlignment:
         """Include empty gap-only strings to the alignment for taxa lacking an ortholog."""
         missing = set(samples) - {seq.id for seq in alignment}
         for sample in missing: