fix: Fix import error in fa2twobit.py

pyproject.toml

@@ -29,10 +29,10 @@ setuptools = "^68.2.2"
 rich = "^13.3.5"
 pysimdjson = "^5.0.2"
 biopython = "^1.81"
-typer = "^0.9.0"
 deprecated = "^1.2.13"
 mashumaro = "^3.7"
 urllib3 = "2.0.7"
+typer = "^0.9.0"
 
 
 [tool.poetry.group.dev.dependencies]
@@ -225,7 +225,7 @@ allow-star-arg-any = true
 "src/pxblat/server/client.py" = ["PLR0913"]
 "src/pxblat/cli/server.py" = ["PLR0913", "N816", "FBT001", "FBT003"]
 "src/pxblat/cli/client.py" = ["B008", "PLR0913", "FBT001", "FBT003"]
-"src/pxblat/cli/fa2twobit.py" = ["B008", "PLR0913", "FBT001", "FBT003"]
+"src/pxblat/cli/fa2twobit.py" = ["B008", "PLR0913", "FBT001", "FBT003", "FA100"]
 "src/pxblat/cli/cli.py" = ["DTZ005"]
 "src/pxblat/toolkit/__init__.py" = ["PLR0913"]
 "src/pxblat/parser.py" = ["A001", "A002", "ARG001"]

src/pxblat/cli/__init__.py

@@ -1,4 +1,6 @@
 """Command line interface to pxblat."""
+from __future__ import annotations
+
 from .cli import app
 
 __all__ = ["app"]

src/pxblat/cli/fa2twobit.py

@@ -1,16 +1,13 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
+from pathlib import Path
+from typing import List
 
 import typer
+from typing_extensions import Annotated
 
 from pxblat import fa_to_two_bit
 
 from .log import logger
 
-if TYPE_CHECKING:
-    from pathlib import Path
-
 # faToTwoBit - Convert DNA from fasta to 2bit format
 # usage:
 #    faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit
@@ -24,23 +21,29 @@
 
 
 def faToTwoBit(
-    infa: list[Path] = typer.Argument(
-        ...,
-        exists=True,
-        dir_okay=False,
-        readable=True,
-        metavar="in.fa [inf2.fa in3.fa ...]",
-        show_default=False,
-        help="The fasta files",
-    ),
-    out2bit: Path = typer.Argument(
-        ...,
-        dir_okay=False,
-        writable=True,
-        show_default=False,
-        metavar="out.2bit",
-        help="The output file",
-    ),
+    infa: Annotated[
+        List[Path],
+        typer.Argument(
+            ...,
+            exists=True,
+            dir_okay=False,
+            readable=True,
+            metavar="in.fa [inf2.fa in3.fa ...]",
+            show_default=False,
+            help="The fasta files",
+        ),
+    ],
+    out2bit: Annotated[
+        Path,
+        typer.Argument(
+            ...,
+            dir_okay=False,
+            writable=True,
+            show_default=False,
+            metavar="out.2bit",
+            help="The output file",
+        ),
+    ],
     long: bool = typer.Option(
         False,
         "--long",

tests/test_cli.py

@@ -1,6 +1,6 @@
+import pytest
 import filecmp
 
-import pytest
 from pxblat.cli import app
 from pxblat.server import Server
 from typer.testing import CliRunner