Remove unnecessary type-ignores

For more context, see Click issue:
pallets/click#2558
At this point, click 8.1.6 is released and fixes can be reverted.

src/rnanorm/cli.py

@@ -71,7 +71,7 @@ def write_out(self, out: file_type, result: pd.DataFrame, force: bool = False) -
 def common_params(func: Callable[..., Any]) -> Callable[..., Any]:
  """Set common parameters for all normalization methods."""
 
- @click.argument("exp", type=click.File("r"), default=sys.stdin) # type: ignore
+ @click.argument("exp", type=click.File("r"), default=sys.stdin)
  @click.option(
  "--out",
  type=click.File("w"),
@@ -89,7 +89,7 @@ def wrapper(*args: Any, **kwargs: Any) -> Callable[..., Any]:
 def gtf_param(func: Callable[..., Any]) -> Callable[..., Any]:
  """Set parameters for normalization methods that require a GTF file."""
 
- @click.option( # type: ignore
+ @click.option(
  "--gtf",
  type=click.File("r"),
  required=False,
@@ -111,7 +111,7 @@ def wrapper(*args: Any, **kwargs: Any) -> Callable[..., Any]:
 def tmm_params(func: Callable[..., Any]) -> Callable[..., Any]:
  """Set parameters for TMM and CTF normalization."""
 
- @click.option("--m_trim", default=0.3, help="Two sided cutoff for M-values") # type: ignore
+ @click.option("--m_trim", default=0.3, help="Two sided cutoff for M-values")
  @click.option("--a_trim", default=0.05, help="Two sided cutoff for A-values")
  @functools.wraps(func)
  def wrapper(*args: Any, **kwargs: Any) -> Callable[..., Any]:
@@ -192,10 +192,10 @@ def main() -> None:
 
 
 # Add sub-commands to the main command
-main.add_command(cpm) # type: ignore
-main.add_command(fpkm) # type: ignore
-main.add_command(tpm) # type: ignore
-main.add_command(uq) # type: ignore
-main.add_command(cuf) # type: ignore
-main.add_command(tmm) # type: ignore
-main.add_command(ctf) # type: ignore
+main.add_command(cpm)
+main.add_command(fpkm)
+main.add_command(tpm)
+main.add_command(uq)
+main.add_command(cuf)
+main.add_command(tmm)
+main.add_command(ctf)