Enable flake8-use-pathlib in ruff

becquerel/parsers/cnf.py

@@ -104,7 +104,7 @@ def read(filename, verbose=False, cal_kwargs=None):
 
     # read all of the file into memory
     file_bytes = []
-    with open(filename, "rb") as f:
+    with Path.open(filename, "rb") as f:
         byte = f.read(1)
         while byte:
             byte_int = struct.unpack("1B", byte)

becquerel/parsers/iec1455.py

@@ -95,7 +95,7 @@ def read(filename, verbose=False, cal_kwargs=None):
     energy_channel_pairs = []
     energy_res_pairs = []  # currently unused
     energy_eff_pairs = []  # currently unused
-    with open(filename) as f:
+    with Path.open(filename) as f:
         record = 1
         # loop over lines
         for line in f:

becquerel/parsers/spc.py

@@ -217,7 +217,7 @@ def read(filename, verbose=False, cal_kwargs=None):
     # initialize a dictionary of spectrum data to populate as we parse
     data = {}
 
-    with open(filename, "rb") as f:
+    with Path.open(filename, "rb") as f:
         # read the file in chunks of 128 bytes
         data_records = []
         binary_data = None

becquerel/parsers/spe.py

@@ -48,7 +48,7 @@ def read(filename, verbose=False, cal_kwargs=None):
     counts = []
     channels = []
     cal_coeff = []
-    with open(filename) as f:
+    with Path.open(filename) as f:
         # read & remove newlines from end of each line
         lines = [line.strip() for line in f]
         i = 0

becquerel/tools/df_cache.py

@@ -1,6 +1,6 @@
 """A simple class for caching a pandas DataFrame."""
 
-import os
+from pathlib import Path
 
 import pandas as pd
 
@@ -42,9 +42,9 @@ def __init__(self):
         """
 
         if self.path is None:
-            self.path = os.path.split(__file__)[0]
+            self.path = Path(__file__).parent
         self.check_path()
-        self.filename = os.path.join(self.path, "__df_cache__" + self.name + ".csv")
+        self.filename = self.path / ("__df_cache__" + self.name + ".csv")
         self.df = None
         self.loaded = False
 
@@ -55,9 +55,10 @@ def check_path(self):
           CacheError: if the path does not exist.
         """
 
-        if not os.path.exists(self.path):
+        self.path = Path(self.path)
+        if not self.path.exists():
             raise CacheError(f"Cache path does not exist: {self.path}")
-        if not os.path.isdir(self.path):
+        if not self.path.is_dir():
             raise CacheError(f"Cache path is not a directory: {self.path}")
 
     def check_file(self):
@@ -67,9 +68,10 @@ def check_file(self):
           CacheError: if the file does not exist.
         """
 
-        if not os.path.exists(self.filename):
+        self.filename = Path(self.filename)
+        if not self.filename.exists():
             raise CacheError(f"Cache filename does not exist: {self.filename}")
-        if not os.path.isfile(self.filename):
+        if not self.filename.is_file():
             raise CacheError(f"Cache filename is not a file: {self.filename}")
 
     def write_file(self):
@@ -113,7 +115,7 @@ def delete_file(self):
 
         self.check_file()
         try:
-            os.remove(self.filename)
+            self.filename.unlink()
         except Exception as exc:
             raise CacheError(f"Problem deleting cache file {self.filename}") from exc
         try:

becquerel/tools/materials.py

@@ -1,16 +1,16 @@
 """Load material data for use in attenuation calculations with XCOM."""
 
 import csv
-import os
 import warnings
+from pathlib import Path
 
 import numpy as np
 
 from .materials_compendium import fetch_compendium_data
 from .materials_error import MaterialsError, MaterialsWarning
 from .materials_nist import fetch_compound_data, fetch_element_data
 
-FILENAME = os.path.join(os.path.split(__file__)[0], "materials.csv")
+FILENAME = Path(__file__).parent / "materials.csv"
 
 
 def _load_and_compile_materials():
@@ -133,13 +133,13 @@ def _write_materials_csv(materials):
     materials : dict
         Dictionary of materials.
     """
-    if os.path.exists(FILENAME):
+    if FILENAME.exists():
         warnings.warn(
             f"Materials data CSV already exists at {FILENAME} and will be overwritten",
             MaterialsWarning,
         )
     mat_list = sorted(materials.keys())
-    with open(FILENAME, "w") as f:
+    with FILENAME.open("w") as f:
         print("%name,formula,density,weight fractions,source", file=f)
         for name in mat_list:
             line = ""
@@ -158,10 +158,10 @@ def _read_materials_csv():
     materials
         Dictionary keyed by material names containing the material data.
     """
-    if not os.path.exists(FILENAME):
+    if not FILENAME.exists():
         raise MaterialsError(f"Materials data CSV does not exist at {FILENAME}")
     materials = {}
-    with open(FILENAME) as f:
+    with FILENAME.open() as f:
         lines = f.readlines()
         for tokens in csv.reader(
             lines,
@@ -218,13 +218,13 @@ def fetch_materials(force=False):
     materials
         Dictionary keyed by material names containing the material data.
     """
-    if force or not os.path.exists(FILENAME):
+    if force or not FILENAME.exists():
         materials = force_load_and_write_materials_csv()
     materials = _read_materials_csv()
     return materials
 
 
 def remove_materials_csv():
     """Remove materials.csv if it exists."""
-    if os.path.exists(FILENAME):
-        os.remove(FILENAME)
+    if FILENAME.exists():
+        FILENAME.unlink()

becquerel/tools/materials_compendium.py

@@ -14,15 +14,15 @@
 """
 
 import json
-import os
 import warnings
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
 
 from .materials_error import MaterialsError, MaterialsWarning
 
-FNAME = os.path.join(os.path.split(__file__)[0], "MaterialsCompendium.json")
+FNAME = Path(__file__).parent / "MaterialsCompendium.json"
 
 
 def json_elements_to_weight_fractions(elements):
@@ -47,7 +47,7 @@ def json_elements_to_atom_fractions(elements):
 def fetch_compendium_data():
     """Read material data from the Compendium."""
     # read the file
-    if not os.path.exists(FNAME):
+    if not FNAME.exists():
         warnings.warn(
             'Material data from the "Compendium of Material Composition Data for '
             'Radiation Transport Modeling" cannot be found. If these data are '
@@ -58,7 +58,7 @@ def fetch_compendium_data():
         )
         data = []
     else:
-        with open(FNAME) as f:
+        with FNAME.open() as f:
             data = json.load(f)
 
     # extract relevant data

examples/autocal.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
+    "from pathlib import Path\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
@@ -217,7 +217,7 @@
    ],
    "source": [
     "counts = []\n",
-    "filename = os.path.join(os.path.dirname(bq.__file__), \"../tests/samples/sim_spec.spe\")\n",
+    "filename = Path(bq.__file__).parent / \"../tests/samples/sim_spec.spe\"\n",
     "spec = bq.Spectrum.from_file(filename)\n",
     "spec = spec.combine_bins(4)\n",
     "spec.bin_edges_raw *= 4\n",
@@ -723,8 +723,9 @@
    ],
    "source": [
     "# read raw HPGe data\n",
-    "filename = os.path.join(\n",
-    "    os.path.dirname(bq.__file__), \"../tests/samples/Mendocino_07-10-13_Acq-10-10-13.Spe\"\n",
+    "filename = (\n",
+    "    Path(bq.__file__).parent /\n",
+    "    \"../tests/samples/Mendocino_07-10-13_Acq-10-10-13.Spe\"\n",
     ")\n",
     "spec = bq.Spectrum.from_file(filename)\n",
     "plot_spec(spec)"
@@ -897,9 +898,7 @@
    ],
    "source": [
     "counts = []\n",
-    "filename = os.path.join(\n",
-    "    os.path.dirname(bq.__file__), \"../tests/samples/nai_detector.spe\"\n",
-    ")\n",
+    "filename = Path(bq.__file__).parent / \"../tests/samples/nai_detector.spe\"\n",
     "spec = bq.Spectrum.from_file(filename)\n",
     "plot_spec(spec)"
    ]
@@ -1121,7 +1120,7 @@
    ],
    "source": [
     "counts = []\n",
-    "filename = os.path.join(os.path.dirname(bq.__file__), \"../tests/samples/SGM102432.spe\")\n",
+    "filename = Path(bq.__file__).parent / \"../tests/samples/SGM102432.spe\"\n",
     "spec = bq.Spectrum.from_file(filename)\n",
     "plot_spec(spec)"
    ]

pyproject.toml

@@ -63,7 +63,7 @@ select = [
   "TCH",     # flake8-type-checking
   "INT",     # flake8-gettext
   # "ARG",     # flake8-unused-arguments
-  # "PTH",     # flake8-use-pathlib
+  "PTH",     # flake8-use-pathlib
   # "TD",      # flake8-todos
   # "FIX",     # flake8-fixme
   # "ERA",     # eradicate

setup.py

@@ -3,6 +3,7 @@
 import importlib.util
 import site
 import sys
+from pathlib import Path
 
 from setuptools import find_packages, setup
 
@@ -21,16 +22,16 @@
 site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
 
 # remove package title from description
-with open("README.md") as fh:
+with Path.open("README.md") as fh:
     README = "\n".join(fh.readlines()[2:])
 
-with open("CONTRIBUTING.md") as fh:
+with Path.open("CONTRIBUTING.md") as fh:
     CONTRIBUTING = fh.read()
 
-with open("requirements.txt") as fh:
+with Path.open("requirements.txt") as fh:
     REQUIREMENTS = [_line for _line in fh if _line]
 
-with open("requirements-dev.txt") as fh:
+with Path.open("requirements-dev.txt") as fh:
     REQUIREMENTS_DEV = [line.strip() for line in fh if not line.startswith("-r")]
 
 # make long description from README and CONTRIBUTING

tests/autocal_test.py

@@ -1,19 +1,17 @@
 """Test PeakFinder and AutoCalibrator classes."""
 
-import os
-
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
+from parsers_test import SAMPLES_PATH
 
 import becquerel as bq
 
 # read in spectra
-SAMPLES_PATH = os.path.join(os.path.dirname(__file__), "samples")
-filename1 = os.path.join(SAMPLES_PATH, "sim_spec.spe")
-filename2 = os.path.join(SAMPLES_PATH, "Mendocino_07-10-13_Acq-10-10-13.Spe")
-filename3 = os.path.join(SAMPLES_PATH, "nai_detector.spe")
-filename4 = os.path.join(SAMPLES_PATH, "SGM102432.spe")
+filename1 = SAMPLES_PATH / "sim_spec.spe"
+filename2 = SAMPLES_PATH / "Mendocino_07-10-13_Acq-10-10-13.Spe"
+filename3 = SAMPLES_PATH / "nai_detector.spe"
+filename4 = SAMPLES_PATH / "SGM102432.spe"
 
 spec1 = bq.Spectrum.from_file(filename1)
 spec2 = bq.Spectrum.from_file(filename2)

tests/calibration_test.py

@@ -1,7 +1,5 @@
 """Test Calibration class."""
 
-import os
-
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
@@ -312,7 +310,7 @@ def make_calibration(name, args):
 @pytest.mark.parametrize("name, args", name_args)
 def test_calibration(name, args):
     """Test the Calibration class."""
-    fname = os.path.join(TEST_OUTPUTS, f"calibration__init__{name}.h5")
+    fname = TEST_OUTPUTS / f"calibration__init__{name}.h5"
     # test __init__()
     cal = make_calibration(name, args)
     # test protections on setting parameters
@@ -338,7 +336,7 @@ def test_calibration(name, args):
 @pytest.mark.parametrize("name, args", name_args)
 def test_calibration_set_add_points(name, args):
     """Test Calibration.set_points and add_points methods."""
-    fname = os.path.join(TEST_OUTPUTS, f"calibration__add_points__{name}.h5")
+    fname = TEST_OUTPUTS / f"calibration__add_points__{name}.h5"
     cal = make_calibration(name, args)
     # test set_points
     cal.set_points()
@@ -448,7 +446,7 @@ def test_calibration_fit_from_points(name, args):
     plt.xlim(0)
     plt.ylim(0)
     plt.legend()
-    plt.savefig(os.path.join(TEST_OUTPUTS, f"calibration__fit__{name}.png"))
+    plt.savefig(TEST_OUTPUTS / f"calibration__fit__{name}.png")
 
     # Test statistics
     assert len(cal1.fit_y) > 0
@@ -503,7 +501,7 @@ def test_calibration_domain_range():
 
 def test_calibration_inverse():
     """Test calibrations with and without inverse expression."""
-    fname = os.path.join(TEST_OUTPUTS, "calibration__inverse.h5")
+    fname = TEST_OUTPUTS / "calibration__inverse.h5"
 
     # cal1 has an explicit inverse expression, cal2 does not
     cal1 = Calibration(
@@ -620,7 +618,7 @@ def test_calibration_interpolation():
 
 def test_calibration_read_failures():
     """Test miscellaneous HDF5 reading failures."""
-    fname = os.path.join(TEST_OUTPUTS, "calibration__read_failures.h5")
+    fname = TEST_OUTPUTS / "calibration__read_failures.h5"
     cal = Calibration.from_linear([2.0, 3.0])
     cal.add_points([0, 1000, 2000], [0, 1000, 2000])
 

tests/fitting_test.py

@@ -1,22 +1,19 @@
-import glob
-import os
 from copy import deepcopy
 
 import lmfit
 import numpy as np
 import pytest
+from parsers_test import SAMPLES_PATH
 
 import becquerel as bq
 
-SAMPLES_PATH = os.path.join(os.path.dirname(__file__), "samples")
-
 # TODO: use these for fitting actual data
 SAMPLES = {}
 for extension in [".spe", ".spc", ".cnf"]:
-    filenames = glob.glob(os.path.join(SAMPLES_PATH, "*.*"))
+    filenames = SAMPLES_PATH.glob("*.*")
     filenames_filtered = []
     for filename in filenames:
-        fname, ext = os.path.splitext(filename)
+        ext = filename.suffix
         if ext.lower() == extension:
             filenames_filtered.append(filename)
     SAMPLES[extension] = filenames_filtered