Merge pull request #315 from tovrstra/ruff

Ruff

.pre-commit-config.yaml

@@ -26,10 +26,12 @@ repos:
   hooks:
     - id: remove-crlf
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.28.3
+  rev: 0.28.4
   hooks:
     - id: check-github-workflows
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.4
+  rev: v0.4.5
   hooks:
     - id: ruff-format
+    - id: ruff
+      args: ["--fix", "--show-fixes"]

doc/conf.py

@@ -22,7 +22,6 @@
 import os
 import subprocess
 
-
 # -- Fragile tricks for RTD -----------------------------------------------
 
 # Normally sphinx-build should be called after iodata is installed somehow.
@@ -86,7 +85,7 @@
 
 # General information about the project.
 project = "IOData"
-copyright = "2019, The IODATA Development Team"
+copyright = "2019, The IODATA Development Team"  # noqa: A001
 author = "The IODATA Development Team"
 
 # The version info for the project yo're documenting, acts as replacement for

doc/gen_formats.py

@@ -22,7 +22,6 @@
 
 from iodata.api import FORMAT_MODULES
 
-
 __all__ = []
 
 
@@ -40,7 +39,7 @@
 
 
 def _format_words(words):
-    return ", ".join("``{}``".format(word) for word in words)
+    return ", ".join(f"``{word}``" for word in words)
 
 
 def _print_section(title, linechar):
@@ -65,7 +64,7 @@ def main():
         # add labels for cross-referencing format (e.g. in formats table)
         print(f".. _format_{modname}:")
         print()
-        _print_section("{} (``{}``)".format(lines[0][:-1], modname), "=")
+        _print_section(f"{lines[0][:-1]} (``{modname}``)", "=")
         print()
         for line in lines[2:]:
             print(line)
@@ -76,7 +75,7 @@ def main():
         for fnname in FNNAMES:
             fn = getattr(module, fnname, None)
             if fn is not None:
-                _print_section(":py:func:`iodata.formats.{}.{}`".format(modname, fnname), "-")
+                _print_section(f":py:func:`iodata.formats.{modname}.{fnname}`", "-")
                 if fnname.startswith("load"):
                     print("- Always loads", _format_words(fn.guaranteed))
                     if fn.ifpresent:

doc/gen_formats_tab.py

@@ -20,12 +20,11 @@
 # pylint: disable=unused-argument,redefined-builtin
 """Generate formats.rst."""
 
-from collections import defaultdict
 import inspect
+from collections import defaultdict
 
 import iodata
 
-
 __all__ = []
 
 

doc/gen_inputs.py

@@ -21,8 +21,8 @@
 """Generate formats.rst."""
 
 from gen_formats import _format_words, _print_section
-from iodata.api import INPUT_MODULES
 
+from iodata.api import INPUT_MODULES
 
 __all__ = []
 
@@ -57,12 +57,12 @@ def main():
         # add labels for cross-referencing format (e.g. in formats table)
         print(f".. _input_{modname}:")
         print()
-        _print_section("{} (``{}``)".format(lines[0][:-1], modname), "=")
+        _print_section(f"{lines[0][:-1]} (``{modname}``)", "=")
         print()
         for line in lines[2:]:
             print(line)
 
-        _print_section(":py:func:`iodata.formats.{}.write_input`".format(modname), "-")
+        _print_section(f":py:func:`iodata.formats.{modname}.write_input`", "-")
         fn = getattr(module, "write_input", None)
         print("- Requires", _format_words(fn.required))
         if fn.optional:
@@ -75,7 +75,7 @@ def main():
         print()
         template = getattr(module, "default_template", None)
         if template:
-            code_block_lines = ["    " + l for l in template.split("\n")]
+            code_block_lines = ["    " + ell for ell in template.split("\n")]
             print(TEMPLATE.format(code_block_lines="\n".join(code_block_lines)))
         print()
         print()

iodata/__init__.py

@@ -19,10 +19,13 @@
 """Input and Output Module."""
 
 try:
-    from ._version import __version__
+    from ._version import __version__, __version_tuple__
 except ImportError:
     __version__ = "0.0.0.post0"
+    __version_tuple__ = (0, 0, 0, "a-dev")
 
 
+from .api import dump_many, dump_one, load_many, load_one, write_input
 from .iodata import IOData
-from .api import *
+
+__all__ = ("IOData", "load_one", "load_many", "dump_one", "dump_many", "write_input")

iodata/__main__.py

@@ -20,9 +20,10 @@
 """CLI for file conversion."""
 
 import argparse
+
 import numpy as np
 
-from .api import load_one, dump_one, load_many, dump_many, FORMAT_MODULES
+from .api import FORMAT_MODULES, dump_many, dump_one, load_many, load_one
 
 try:
     from iodata.version import __version__
@@ -74,7 +75,7 @@ def parse_args():
         "-V",
         "--version",
         action="version",
-        version="%(prog)s (IOData version {})".format(__version__),
+        version=f"%(prog)s (IOData version {__version__})",
     )
     parser.add_argument(
         "-i", "--infmt", help="Select the input format, overrides automatic detection."

iodata/api.py

@@ -19,16 +19,16 @@
 """Functions to be used by end users."""
 
 import os
-from typing import Iterator
-from types import ModuleType
+from collections.abc import Iterator
 from fnmatch import fnmatch
-from pkgutil import iter_modules
 from importlib import import_module
+from pkgutil import iter_modules
+from types import ModuleType
+from typing import Optional
 
 from .iodata import IOData
 from .utils import LineIterator
 
-
 __all__ = ["load_one", "load_many", "dump_one", "dump_many", "write_input"]
 
 
@@ -46,7 +46,7 @@ def _find_format_modules():
 FORMAT_MODULES = _find_format_modules()
 
 
-def _select_format_module(filename: str, attrname: str, fmt: str = None) -> ModuleType:
+def _select_format_module(filename: str, attrname: str, fmt: Optional[str] = None) -> ModuleType:
     """Find a file format module with the requested attribute name.
 
     Parameters
@@ -68,14 +68,13 @@ def _select_format_module(filename: str, attrname: str, fmt: str = None) -> Modu
     basename = os.path.basename(filename)
     if fmt is None:
         for format_module in FORMAT_MODULES.values():
-            if any(fnmatch(basename, pattern) for pattern in format_module.PATTERNS):
-                if hasattr(format_module, attrname):
-                    return format_module
+            if any(fnmatch(basename, pattern) for pattern in format_module.PATTERNS) and hasattr(
+                format_module, attrname
+            ):
+                return format_module
     else:
         return FORMAT_MODULES[fmt]
-    raise ValueError(
-        "Could not find file format with feature {} for file {}".format(attrname, filename)
-    )
+    raise ValueError(f"Could not find file format with feature {attrname} for file {filename}")
 
 
 def _find_input_modules():
@@ -113,7 +112,7 @@ def _select_input_module(fmt: str) -> ModuleType:
     raise ValueError(f"Could not find input format {fmt}!")
 
 
-def load_one(filename: str, fmt: str = None, **kwargs) -> IOData:
+def load_one(filename: str, fmt: Optional[str] = None, **kwargs) -> IOData:
     """Load data from a file.
 
     This function uses the extension or prefix of the filename to determine the
@@ -145,7 +144,7 @@ def load_one(filename: str, fmt: str = None, **kwargs) -> IOData:
     return iodata
 
 
-def load_many(filename: str, fmt: str = None, **kwargs) -> Iterator[IOData]:
+def load_many(filename: str, fmt: Optional[str] = None, **kwargs) -> Iterator[IOData]:
     """Load multiple IOData instances from a file.
 
     This function uses the extension or prefix of the filename to determine the
@@ -170,14 +169,14 @@ def load_many(filename: str, fmt: str = None, **kwargs) -> Iterator[IOData]:
     """
     format_module = _select_format_module(filename, "load_many", fmt)
     lit = LineIterator(filename)
-    for data in format_module.load_many(lit, **kwargs):
-        try:
+    try:
+        for data in format_module.load_many(lit, **kwargs):
             yield IOData(**data)
-        except StopIteration:
-            return
+    except StopIteration:
+        return
 
 
-def dump_one(iodata: IOData, filename: str, fmt: str = None, **kwargs):
+def dump_one(iodata: IOData, filename: str, fmt: Optional[str] = None, **kwargs):
     """Write data to a file.
 
     This routine uses the extension or prefix of the filename to determine
@@ -202,7 +201,7 @@ def dump_one(iodata: IOData, filename: str, fmt: str = None, **kwargs):
         format_module.dump_one(f, iodata, **kwargs)
 
 
-def dump_many(iodatas: Iterator[IOData], filename: str, fmt: str = None, **kwargs):
+def dump_many(iodatas: Iterator[IOData], filename: str, fmt: Optional[str] = None, **kwargs):
     """Write multiple IOData instances to a file.
 
     This routine uses the extension or prefix of the filename to determine
@@ -226,7 +225,7 @@ def dump_many(iodatas: Iterator[IOData], filename: str, fmt: str = None, **kwarg
         format_module.dump_many(f, iodatas, **kwargs)
 
 
-def write_input(iodata: IOData, filename: str, fmt: str, template: str = None, **kwargs):
+def write_input(iodata: IOData, filename: str, fmt: str, template: Optional[str] = None, **kwargs):
     """Write input file using an instance of IOData for the specified software format.
 
     Parameters

iodata/attrutils.py

@@ -20,7 +20,6 @@
 
 import numpy as np
 
-
 __all__ = ["convert_array_to", "validate_shape"]
 
 
@@ -35,7 +34,6 @@ def converter(array):
     return converter
 
 
-# pylint: disable=too-many-branches
 def validate_shape(*shape_requirements: tuple):
     """Return a validator for the shape of an array or the length of an iterable.
 
@@ -87,26 +85,21 @@ def validator(obj, attribute, value):
                 other_name, other_axis = item
                 other = getattr(obj, other_name)
                 if other is None:
-                    raise TypeError("Other attribute '{}' is not set.".format(other_name))
+                    raise TypeError(f"Other attribute '{other_name}' is not set.")
                 if other_axis == 0:
                     expected_shape.append(len(other))
                 else:
                     if other_axis >= other.ndim or other_axis < 0:
                         raise TypeError(
                             "Cannot get length along axis "
-                            "{} of attribute {} with ndim {}.".format(
-                                other_axis, other_name, other.ndim
-                            )
+                            f"{other_axis} of attribute {other_name} with ndim {other.ndim}."
                         )
                     expected_shape.append(other.shape[other_axis])
             else:
                 raise ValueError(f"Cannot interpret item in shape_requirements: {item}")
         expected_shape = tuple(expected_shape)
         # Get the actual shape
-        if isinstance(value, np.ndarray):
-            observed_shape = value.shape
-        else:
-            observed_shape = (len(value),)
+        observed_shape = value.shape if isinstance(value, np.ndarray) else (len(value),)
         # Compare
         match = True
         if len(expected_shape) != len(observed_shape):
@@ -121,9 +114,8 @@ def validator(obj, attribute, value):
         # Raise TypeError if needed.
         if not match:
             raise TypeError(
-                "Expecting shape {} for attribute {}, got {}".format(
-                    expected_shape, attribute.name, observed_shape
-                )
+                f"Expecting shape {expected_shape} for attribute {attribute.name}, "
+                f"got {observed_shape}"
             )
 
     return validator