apply black formatter to package files

setup.py

@@ -1,7 +1,7 @@
 """
-PEP 517 doesn’t support editable installs
+PEP 517 doesn't support editable installs
 so this file is currently here to support "pip install -e ."
-"""
+"""  # noqa: RUF002
 from setuptools import setup
 
 setup(

src/starfile/__init__.py

@@ -1 +1,5 @@
-from .functions import read, write, to_string
+"""STAR file format reader and writer."""
+
+from .functions import read, to_string, write
+
+__all__ = ["read", "write", "to_string"]

src/starfile/__main__.py

@@ -1,35 +1,41 @@
+"""Command-line interface for STAR file reading and inspection."""
+
 try:
-    from IPython.terminal.embed import InteractiveShellEmbed
     import click
+    from IPython.terminal.embed import InteractiveShellEmbed
 except ImportError:
     deps = False
 else:
     deps = True
 
 
 if deps:
-    @click.command()
-    @click.argument('path', type=click.Path(exists=True, dir_okay=False, readable=True))
-    @click.option('--read_n_blocks', type=int)
-    @click.option('--always_dict', is_flag=True)
-    def cli(path, read_n_blocks, always_dict):
-        """
-        Read a star file and open an ipython console to interactively inspect its contents
-        """
-        # imports here will be available in the embedded shell
-        from .functions import read, write
 
-        star = read(path, read_n_blocks, always_dict)
+    @click.command()  # type: ignore[misc]
+    @click.argument("path", type=click.Path(exists=True, dir_okay=False, readable=True))  # type: ignore[misc]
+    @click.option("--read_n_blocks", type=int)  # type: ignore[misc]
+    @click.option("--always_dict", is_flag=True)  # type: ignore[misc]
+    def cli(path: str, read_n_blocks: int | None, always_dict: bool) -> None:
+        """Read a star file and open an ipython console to inspect contents."""
+        from pathlib import Path
 
-        banner = '''=== Starfile ===
-    - access your data with `star`
+        from .functions import read
+
+        _ = read(Path(path), read_n_blocks, always_dict)
+
+        banner = """=== Starfile ===
+    - access your data with `data`
     - write it out with `write(...)`
     - read more with `read(...)`
-        '''
-        # sh.instance() needed due to reggression in ipython
-        # https://github.com/ipython/ipython/issues/13966#issuecomment-1696137868
+        """
         sh = InteractiveShellEmbed.instance(banner2=banner)
         sh()
+
 else:
-    def cli():
-        print('To use the command line utility, install with `pip install starfile[cli]`')
+
+    def cli() -> None:
+        """Print installation instructions."""
+        print(
+            "To use the command line utility, install with "
+            "`pip install starfile[cli]`"
+        )

src/starfile/functions.py

@@ -1,32 +1,29 @@
+"""High-level interface for reading and writing STAR files."""
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Dict, List, Union, Optional
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    import pandas as pd
     from os import PathLike
 
+    from .typing import DataBlock
+
 from .parser import StarParser
 from .writer import StarWriter
-from .typing import DataBlock
-
-if TYPE_CHECKING:
-    import pandas as pd
-    from os import PathLike
 
 
 def read(
     filename: PathLike,
-    read_n_blocks: Optional[int] = None,
+    read_n_blocks: int | None = None,
     always_dict: bool = False,
-    parse_as_string: List[str] = []
-) -> Union[DataBlock, Dict[DataBlock]]:
+    parse_as_string: list[str] | None = None,
+) -> DataBlock | dict[str, DataBlock]:
     """Read data from a STAR file.
 
     Basic data blocks are read as dictionaries. Loop blocks are read as pandas
     dataframes. When multiple data blocks are present a dictionary of datablocks is
     returned. When a single datablock is present only the block is returned by default.
-    To force returning a dectionary even when only one datablock is present set
+    To force returning a dictionary even when only one datablock is present set
     `always_dict=True`.
 
     Parameters
@@ -40,23 +37,26 @@ def read(
     parse_as_string: list[str]
         A list of keys or column names which will not be coerced to numeric values.
     """
-    parser = StarParser(filename, n_blocks_to_read=read_n_blocks, parse_as_string=parse_as_string)
+    if parse_as_string is None:
+        parse_as_string = []
+    parser = StarParser(
+        filename, n_blocks_to_read=read_n_blocks, parse_as_string=parse_as_string
+    )
     if len(parser.data_blocks) == 1 and always_dict is False:
-        return list(parser.data_blocks.values())[0]
-    else:
-        return parser.data_blocks
+        return next(iter(parser.data_blocks.values()))
+    return parser.data_blocks
 
 
 def write(
-    data: Union[DataBlock, Dict[str, DataBlock], List[DataBlock]],
+    data: DataBlock | dict[str, DataBlock] | list[DataBlock],
     filename: PathLike,
-    float_format: str = '%.6f',
-    sep: str = '\t',
-    na_rep: str = '<NA>',
+    float_format: str = "%.6f",
+    sep: str = "\t",
+    na_rep: str = "<NA>",
     quote_character: str = '"',
     quote_all_strings: bool = False,
-    **kwargs
-):
+    **kwargs: object,
+) -> None:
     """Write data to disk in the STAR format.
 
     Parameters
@@ -85,14 +85,14 @@ def write(
 
 
 def to_string(
-    data: Union[DataBlock, Dict[str, DataBlock], List[DataBlock]],
-    float_format: str = '%.6f',
-    sep: str = '\t',
-    na_rep: str = '<NA>',
+    data: DataBlock | dict[str, DataBlock] | list[DataBlock],
+    float_format: str = "%.6f",
+    sep: str = "\t",
+    na_rep: str = "<NA>",
     quote_character: str = '"',
     quote_all_strings: bool = False,
-    **kwargs
-):
+    **kwargs: object,
+) -> str:
     """Represent data in the STAR format.
 
     Parameters