Fix more ruff nags

.pre-commit-config.yaml

@@ -30,3 +30,7 @@ repos:
     rev: v3.1.0
     hooks:
       - id: prettier
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix

pyproject.toml

@@ -1,32 +1,30 @@
 [build-system]
-requires = ["setuptools", "wheel", "Cython"]
+requires = ["Cython", "setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name="rpgPy"
+name = "rpgPy"
 description = "Cython code for reading binary files from RPG cloud radar."
 authors = [{name = "Simo Tukiainen", email = "[email protected]"}]
 readme = "README.md"
 license = {file = "LICENSE"}
 requires-python = ">=3.8"
 classifiers = [
-    "Development Status :: 4 - Beta",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "License :: OSI Approved :: MIT License",
-    "Intended Audience :: Science/Research",
-    "Topic :: Scientific/Engineering",
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Topic :: Scientific/Engineering",
 ]
-
-dependencies = ["numpy", "cython", "netCDF4", "tqdm", "numba"]
-
+dependencies = ["cython", "netCDF4", "numba", "numpy", "tqdm"]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 test = [
-    "pytest-flakefinder",
-    "mypy",
-    "types-tqdm",
+  "mypy",
+  "pytest-flakefinder",
+  "types-tqdm",
 ]
 dev = ["pre-commit", "release-version"]
 
@@ -39,7 +37,7 @@ Changelog = "https://github.com/actris-cloudnet/rpgpy/blob/main/CHANGELOG.md"
 check_untyped_defs = true
 
 [[tool.mypy.overrides]]
-module = ["Cython.Build", "setuptools", "netCDF4", "numba", "rpgpy.data"]
+module = ["Cython.Build", "netCDF4", "numba", "rpgpy.data", "setuptools"]
 ignore_missing_imports = true
 
 [tool.release-version]
@@ -50,8 +48,35 @@ changelog = "CHANGELOG.md"
 [tool.ruff]
 extend-select = ["I"]
 
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+  "ANN", # missing types, use mypy for this
+  "C9", # too complex, fix me later
+  "COM812", # Formatting
+  "D", # documentation
+  "DTZ00", # do not check timezone info
+  "FIX002", # TODOs
+  "INP",
+  "ISC001", # Formatter wants me
+  "N8", # uppercase variable names
+  "PD011", # false positive
+  "PERF", # try except in loop
+  "PLR", # too many arguments etc.
+  "PTH", # use pathlib, fix me later
+  "RUF002", # unicode in doc string
+  "S101", # use assert
+  "S60",
+  "TD002", # TODOs
+  "TD003", # TODOs
+]
+
 [tool.ruff.lint.extend-per-file-ignores]
 "__init__.py" = ["F401"]
 
 [tool.setuptools.dynamic]
 version = {attr = "rpgpy.version.__version__"}
+
+[tool.tomlsort]
+trailing_comma_inline_array = true
+sort_inline_arrays = true

rpgpy/header.py

@@ -1,11 +1,15 @@
 """Module for reading RPG 94 GHz radar header."""
-from pathlib import Path
-from typing import Iterator
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Iterator
 
 import numpy as np
 
 from rpgpy import utils
 
+if TYPE_CHECKING:
+    from pathlib import Path
+
 
 def read_rpg_header(file_name: Path) -> tuple[dict, int]:
     """Reads header from RPG binary file.
@@ -33,7 +37,7 @@ def read(*fields):
                 header[name] = np.array(array, dtype=_get_dtype(array))
 
     header: dict = {}
-    file = open(file_name, "rb")
+    file = open(file_name, "rb")  # noqa: SIM115
 
     read(("FileCode", "i4"), ("HeaderLen", "i4"))
 

rpgpy/metadata.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import NamedTuple
 
 
@@ -67,7 +69,8 @@ class Meta(NamedTuple):
     "CompEna": Meta(
         name="compression",
         long_name="Compression",
-        comment="0=not compressed, 1=compressed, 2=compressed and polarimetric variables saved",
+        comment="0=not compressed, 1=compressed, 2=compressed and polarimetric "
+        "variables saved",
     ),
     "AntiAlias": Meta(
         name="anti_alias",
@@ -216,7 +219,8 @@ class Meta(NamedTuple):
     "FFTWindow": Meta(
         name="fft_window",
         long_name="FFT Window",
-        comment="FFT window in use: 0=square, 1=parzen, 2=blackman, 3=welch, 4=slepian2, "
+        comment="FFT window in use: 0=square, 1=parzen, 2=blackman, 3=welch, "
+        "4=slepian2, "
         "5=slepian3",
     ),
     "FFTInputRng": Meta(
@@ -240,7 +244,8 @@ class Meta(NamedTuple):
     "QF": Meta(
         name="quality_flag",
         long_name="Quality Flag",
-        comment="Bit 1=ADC saturation, Bit 2=spectral width too high, Bit 3=no transm. power "
+        comment="Bit 1=ADC saturation, Bit 2=spectral width too high, Bit 3=no "
+        "transm. power "
         "leveling",
     ),
     "RR": Meta(name="rain_rate", long_name="Rain Rate", units="mm/h"),
@@ -281,7 +286,8 @@ class Meta(NamedTuple):
     "Status": Meta(
         name="status_flag",
         long_name="Status Flag",
-        comment="mitigation status flags: 0/1=heater switch (ON/OFF) 0/10=blower switch (ON/OFF)",
+        comment="mitigation status flags: 0/1=heater switch (ON/OFF) 0/10=blower "
+        "switch (ON/OFF)",
     ),
     "TotSpec": Meta(
         name="doppler_spectrum",

rpgpy/nc.py

@@ -1,9 +1,11 @@
 """Module for writing netCDF file."""
+from __future__ import annotations
+
 import glob
 import logging
 import os
 import uuid
-from pathlib import Path
+from typing import TYPE_CHECKING
 
 import netCDF4
 import numpy as np
@@ -15,6 +17,9 @@
 from rpgpy import read_rpg, utils, version
 from rpgpy.spcutil import spectra2moments
 
+if TYPE_CHECKING:
+    from pathlib import Path
+
 SKIP_ME = ("ProgName", "CustName", "HAlts", "TAlts", "StartTime", "StopTime")
 
 
@@ -84,16 +89,18 @@ def rpg2nc(
             _append_data(f, data, metadata)
     _create_global_attributes(f, header, global_attr)
     f.close()
-    logging.info(f"Created new file: {output_file}")
+    msg = f"Created new file: {output_file}"
+    logging.info(msg)
 
 
 def rpg2nc_multi(
     file_directory: Path | str | None = None,
     output_directory: Path | str | None = None,
+    global_attr: dict | None = None,
+    base_name: str | None = None,
+    *,
     include_lv0: bool = True,
     recursive: bool = True,
-    base_name: str | None = None,
-    global_attr: dict | None = None,
 ) -> list:
     """Converts several RPG binary files individually.
 
@@ -122,18 +129,21 @@ def rpg2nc_multi(
     new_files = []
     file_directory = utils.str2path(file_directory)
     output_directory = utils.str2path(output_directory)
-    for filepath in _generator_files(file_directory, include_lv0, recursive):
-        logging.info(f"Converting {filepath}")
+    for filepath in _generator_files(
+        file_directory, include_lv0=include_lv0, recursive=recursive
+    ):
+        msg = f"Converting {filepath}"
+        logging.info(msg)
         try:
             prefix = f"{base_name}_" if base_name is not None else ""
             new_filename = f"{output_directory}/{prefix}{_new_filename(filepath)}"
             rpg2nc(filepath, new_filename, global_attr)
             new_files.append(new_filename)
         except IndexError as err:
-            logging.warning(
-                f"############### File {filepath} has not been converted: {err}",
-            )
-    logging.info(f"Converted {len(new_files)} files")
+            msg = f"############### File {filepath} has not been converted: {err}"
+            logging.warning(msg)
+    msg = f"Converted {len(new_files)} files"
+    logging.info(msg)
     return new_files
 
 
@@ -144,11 +154,8 @@ def _check_header_consistency(f: netCDF4.Dataset, header: dict) -> None:
             try:
                 assert_array_almost_equal(array, f.variables[key])
             except AssertionError:
-                print(
-                    "Warning: inconsistent header data in " + key,
-                    array,
-                    f.variables[key][:],
-                )
+                msg = f"Inconsistent header data in {key}, {array}, {f.variables[key]}"
+                logging.warning(msg)
 
 
 def _create_dimensions(f: netCDF4.Dataset, header: dict, level: int) -> None:
@@ -189,13 +196,13 @@ def _append_data(f: netCDF4.Dataset, data: dict, metadata: dict) -> None:
     for key, array in data.items():
         if key in SKIP_ME:
             continue
-        key = metadata[key].name
+        name = metadata[key].name
         if array.ndim == 1:
-            f.variables[key][ind0:ind1] = array
+            f.variables[name][ind0:ind1] = array
         elif array.ndim == 2:
-            f.variables[key][ind0:ind1, :] = array
+            f.variables[name][ind0:ind1, :] = array
         else:
-            f.variables[key][ind0:ind1, :, :] = array
+            f.variables[name][ind0:ind1, :, :] = array
 
 
 def _get_dtype(array: np.ndarray) -> str:
@@ -209,14 +216,16 @@ def _get_rpg_files(path_to_files: Path) -> tuple[list, int]:
     files = glob.glob(str(path_to_files))
     files.sort()
     if not files:
-        raise RuntimeError("No proper RPG binary files found")
+        msg = f"No RPG binary files found in {path_to_files}"
+        raise RuntimeError(msg)
     extension = [file[-4:] for file in files]
     if all(ext.lower() == ".lv1" for ext in extension):
         level = 1
     elif all(ext.lower() == ".lv0" for ext in extension):
         level = 0
     else:
-        raise RuntimeError("No consistent RPG level (0 or 1) files found.")
+        msg = "No consistent RPG level (0 or 1) files found."
+        raise RuntimeError(msg)
     return files, level
 
 
@@ -228,7 +237,9 @@ def _get_dim(f: netCDF4.Dataset, array: np.ndarray) -> tuple:
     file_dims = f.dimensions
     for length in array.shape:
         try:
-            dim = [key for key in file_dims.keys() if file_dims[key].size == length][0]
+            dim = next(
+                (key for key in file_dims if file_dims[key].size == length), None
+            )
         except IndexError:
             dim = "time"
         variable_size.append(dim)
@@ -259,11 +270,12 @@ def _get_measurement_date(file: netCDF4.Dataset) -> list:
     date_times = utils.rpg_seconds2datetime64(time, time_ms)
     dates = np.unique(date_times.astype("datetime64[D]"))
     if len(np.unique(dates)) > 1:
-        raise RuntimeError("More than one date in the file")
+        msg = "More than one date in the file"
+        raise RuntimeError(msg)
     return str(dates[0]).split("-")
 
 
-def _generator_files(dir_name: Path, include_lv0: bool, recursive: bool):
+def _generator_files(dir_name: Path, *, include_lv0: bool, recursive: bool):
     includes = (".lv1",) if include_lv0 is False else (".lv0", "lv1")
     if recursive is False:
         for file in os.listdir(str(dir_name)):

rpgpy/spcutil.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 from numba import jit
 
@@ -11,16 +13,16 @@ def spectra2moments(
 ) -> dict:
     """Calculates radar moments from the main peak.
 
-    This routine calculates the radar moments: reflectivity, mean Doppler velocity, spectrum
-    width, skewness and kurtosis from compressed level 0 spectrum files (NoiseFactor > 0)
-    of the 94 GHz RPG cloud radar. Considering only the largest peak.
+    This routine calculates the radar moments: reflectivity, mean Doppler velocity,
+    spectrum width, skewness and kurtosis from compressed level 0 spectrum files
+    (NoiseFactor > 0) of the 94 GHz RPG cloud radar. Considering only the largest peak.
 
     Args:
     ----
         data: Level 0 nD variables.
         header: Level 0 metadata.
-        spec_var: Name of the spectral variable. Possible names are 'TotSpec', 'VSpec', and 'HSpec'.
-        fill_value: Clear sky fill value.
+        spec_var: Name of the spectral variable. Possible names are 'TotSpec', 'VSpec',
+            and 'HSpec'. fill_value: Clear sky fill value.
         n_points_min: Minimum number of points in a valid spectral line.
 
     Returns:
@@ -66,7 +68,7 @@ def spectra2moments(
         key: moments[:, :, i]
         for i, key in enumerate(["Ze", "MeanVel", "SpecWidth", "Skewn", "Kurt"])
     }
-    for key in output.keys():
+    for key in output:
         output[key][no_signal] = fill_value
     return output
 
@@ -113,7 +115,8 @@ def radar_moment_calculation(signal: np.ndarray, vel_bins: np.ndarray) -> np.nda
 
 @jit(nopython=True, fastmath=True)
 def find_peak_edges(signal: np.ndarray) -> tuple[int, int]:
-    """Returns the indices of left and right edge of the main signal peak in a Doppler spectra.
+    """Returns the indices of left and right edge of the main signal peak in a Doppler
+    spectra.
 
     Args:
     ----

rpgpy/utils.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import datetime
 import os
 from pathlib import Path
@@ -76,7 +78,8 @@ def get_rpg_file_type(header: dict) -> tuple[int, float]:
 
     Returns:
     -------
-        tuple: 2-element tuple containing Level (0 or 1) and Version (1.0, 2.0, 3.5 or 4.0).
+        tuple: 2-element tuple containing Level (0 or 1) and Version (1.0, 2.0, 3.5
+            or 4.0).
 
     Raises:
     ------
@@ -96,7 +99,8 @@ def get_rpg_file_type(header: dict) -> tuple[int, float]:
         return 1, 3.5
     if file_code == 889348:
         return 1, 4.0
-    raise RuntimeError(f"Unsupported RPG binary file. File code: {file_code}")
+    msg = f"Unknown file type. File code: {file_code}"
+    raise RuntimeError(msg)
 
 
 def isscalar(array) -> bool: