Fix style.

Author: tompollard

tests/test_archive.py

@@ -1,13 +1,13 @@
 import os
-import numpy as np
-import pytest
 import tempfile
 import zipfile
 
+import numpy as np
+import pytest
+
 from wfdb import rdrecord, wrsamp
 from wfdb.io.archive import WFDBArchive
 
-
 np.random.seed(1234)
 
 
@@ -132,8 +132,9 @@ def test_wfdb_archive_round_trip(temp_record):
     assert record.p_signal.shape == original_signal.shape
 
     # Add tolerance to account for loss of precision during archive round-trip
-    np.testing.assert_allclose(record.p_signal, original_signal, rtol=1e-2,
-                               atol=3e-3)
+    np.testing.assert_allclose(
+        record.p_signal, original_signal, rtol=1e-2, atol=3e-3
+    )
 
 
 def test_archive_read_subset_channels(temp_record):
@@ -149,8 +150,9 @@ def test_archive_read_subset_channels(temp_record):
     assert record.p_signal.shape[0] == original_signal.shape[0]
 
     # Add tolerance to account for loss of precision during archive round-trip
-    np.testing.assert_allclose(record.p_signal[:, 0], original_signal[:, 1],
-                               rtol=1e-2, atol=3e-3)
+    np.testing.assert_allclose(
+        record.p_signal[:, 0], original_signal[:, 1], rtol=1e-2, atol=3e-3
+    )
 
 
 def test_archive_read_partial_samples(temp_record):
@@ -164,7 +166,9 @@ def test_archive_read_partial_samples(temp_record):
     record = rdrecord(archive_path, sampfrom=start, sampto=stop)
 
     assert record.p_signal.shape == (stop - start, original_signal.shape[1])
-    np.testing.assert_allclose(record.p_signal, original_signal[start:stop], rtol=1e-2, atol=1e-3)
+    np.testing.assert_allclose(
+        record.p_signal, original_signal[start:stop], rtol=1e-2, atol=1e-3
+    )
 
 
 def test_archive_missing_file_error(temp_record):
@@ -178,8 +182,9 @@ def test_archive_missing_file_error(temp_record):
         zf_name = [name for name in zf.namelist() if name.endswith(".dat")][0]
         zf.fp = None  # Prevent auto-close bug in some zipfile implementations
     os.rename(archive_path, archive_path + ".bak")
-    with zipfile.ZipFile(archive_path + ".bak", "r") as zin, \
-         zipfile.ZipFile(archive_path, "w") as zout:
+    with zipfile.ZipFile(archive_path + ".bak", "r") as zin, zipfile.ZipFile(
+        archive_path, "w"
+    ) as zout:
         for item in zin.infolist():
             if not item.filename.endswith(".dat"):
                 zout.writestr(item, zin.read(item.filename))

wfdb/io/_header.py

@@ -5,8 +5,7 @@
 import numpy as np
 import pandas as pd
 
-from wfdb.io import _signal
-from wfdb.io import util
+from wfdb.io import _signal, util
 from wfdb.io.header import HeaderSyntaxError, rx_record, rx_segment, rx_signal
 
 """
@@ -326,8 +325,12 @@ def wrheader(self, write_dir="", expanded=True, wfdb_archive=None):
         self.check_field_cohesion(rec_write_fields, list(sig_write_fields))
 
         # Write the header file using the specified fields
-        self.wr_header_file(rec_write_fields, sig_write_fields, write_dir,
-                            wfdb_archive=wfdb_archive)
+        self.wr_header_file(
+            rec_write_fields,
+            sig_write_fields,
+            write_dir,
+            wfdb_archive=wfdb_archive,
+        )
 
     def get_write_fields(self):
         """
@@ -510,8 +513,9 @@ def check_field_cohesion(self, rec_write_fields, sig_write_fields):
                                 "Each file_name (dat file) specified must have the same byte offset"
                             )
 
-    def wr_header_file(self, rec_write_fields, sig_write_fields, write_dir,
-                       wfdb_archive=None):
+    def wr_header_file(
+        self, rec_write_fields, sig_write_fields, write_dir, wfdb_archive=None
+    ):
         """
         Write a header file using the specified fields. Converts Record
         attributes into appropriate WFDB format strings.

wfdb/io/_signal.py

@@ -1,13 +1,13 @@
-import math
 import io
+import math
 import os
 import posixpath
 import sys
 
 import fsspec
 import numpy as np
 
-from wfdb.io import download, _coreio, util
+from wfdb.io import _coreio, download, util
 from wfdb.io._coreio import CLOUD_PROTOCOLS
 
 MAX_I32 = 2147483647
@@ -163,8 +163,9 @@ def wr_dats(self, expanded, write_dir, wfdb_archive=None):
         self.check_sig_cohesion([], expanded)
 
         # Write each of the specified dat files
-        self.wr_dat_files(expanded=expanded, write_dir=write_dir,
-                          wfdb_archive=wfdb_archive)
+        self.wr_dat_files(
+            expanded=expanded, write_dir=write_dir, wfdb_archive=wfdb_archive
+        )
 
     def check_sig_cohesion(self, write_fields, expanded):
         """
@@ -1401,8 +1402,13 @@ def _rd_dat_signals(
         )
     else:
         data_to_read = _rd_dat_file(
-            file_name, dir_name, pn_dir, fmt, start_byte, n_read_samples,
-            wfdb_archive=wfdb_archive
+            file_name,
+            dir_name,
+            pn_dir,
+            fmt,
+            start_byte,
+            n_read_samples,
+            wfdb_archive=wfdb_archive,
         )
 
     if extra_flat_samples:
@@ -1642,8 +1648,9 @@ def _required_byte_num(mode, fmt, n_samp):
     return int(n_bytes)
 
 
-def _rd_dat_file(file_name, dir_name, pn_dir, fmt, start_byte, n_samp,
-                 wfdb_archive=None):
+def _rd_dat_file(
+    file_name, dir_name, pn_dir, fmt, start_byte, n_samp, wfdb_archive=None
+):
     """
     Read data from a dat file, either local or remote, into a 1d numpy
     array.

wfdb/io/archive.py

@@ -17,6 +17,7 @@ class WFDBArchive:
       - .wfdb is included in the record_name explicitly, or
       - .wfdb is passed directly to the file loading function.
     """
+
     def __init__(self, record_name, mode="r"):
         """
         Initialize a WFDBArchive for a given record name (without extension).
@@ -35,7 +36,9 @@ def __init__(self, record_name, mode="r"):
 
         if mode == "r":
             if not os.path.exists(self.archive_path):
-                raise FileNotFoundError(f"Archive not found: {self.archive_path}")
+                raise FileNotFoundError(
+                    f"Archive not found: {self.archive_path}"
+                )
             if not zipfile.is_zipfile(self.archive_path):
                 raise ValueError(f"Invalid WFDB archive: {self.archive_path}")
             self.zipfile = zipfile.ZipFile(self.archive_path, mode="r")
@@ -60,16 +63,17 @@ def open(self, filename, mode="r"):
         Mode 'r' (text) or 'rb' (binary) supported.
         """
         if self.zipfile and filename in self.zipfile.namelist():
-            with self.zipfile.open(filename, 'r') as f:
+            with self.zipfile.open(filename, "r") as f:
                 if "b" in mode:
                     yield f
                 else:
                     import io
+
                     yield io.TextIOWrapper(f)
         else:
             raise FileNotFoundError(
                 f"Could not find '{filename}' as loose file or inside '{self.archive_path}'."
-                )
+            )
 
     def close(self):
         """
@@ -111,14 +115,17 @@ def create_archive(self, file_list, output_path=None):
                     if file.endswith((".hea", ".hea.json", ".hea.yml"))
                     else zipfile.ZIP_DEFLATED
                 )
-                zf.write(file, arcname=os.path.basename(file), compress_type=compress)
+                zf.write(
+                    file, arcname=os.path.basename(file), compress_type=compress
+                )
 
 
 def get_archive(record_base_name, mode="r"):
     """
     Get or create a WFDBArchive for the given record base name.
     """
     if record_base_name not in _archive_cache:
-        _archive_cache[record_base_name] = WFDBArchive(record_base_name,
-                                                       mode=mode)
+        _archive_cache[record_base_name] = WFDBArchive(
+            record_base_name, mode=mode
+        )
     return _archive_cache[record_base_name]

wfdb/io/record.py

@@ -1,22 +1,16 @@
 import datetime
 import multiprocessing.dummy
-import posixpath
 import os
+import posixpath
 import re
 
 import fsspec
 import numpy as np
 import pandas as pd
 
-from wfdb.io import _header
-from wfdb.io import _signal
-from wfdb.io import _url
-from wfdb.io.archive import get_archive
-from wfdb.io import download
-from wfdb.io import header
-from wfdb.io import util
+from wfdb.io import _header, _signal, _url, download, header, util
 from wfdb.io._coreio import CLOUD_PROTOCOLS
-
+from wfdb.io.archive import get_archive
 
 # -------------- WFDB Signal Calibration and Classification ---------- #
 
@@ -935,13 +929,17 @@ def wrsamp(self, expanded=False, write_dir="", wfdb_archive=None):
 
         # Perform field validity and cohesion checks, and write the
         # header file.
-        self.wrheader(write_dir=write_dir, expanded=expanded,
-                      wfdb_archive=wfdb_archive)
+        self.wrheader(
+            write_dir=write_dir, expanded=expanded, wfdb_archive=wfdb_archive
+        )
         if self.n_sig > 0:
             # Perform signal validity and cohesion checks, and write the
             # associated dat files.
-            self.wr_dats(expanded=expanded, write_dir=write_dir,
-                         wfdb_archive=wfdb_archive)
+            self.wr_dats(
+                expanded=expanded,
+                write_dir=write_dir,
+                wfdb_archive=wfdb_archive,
+            )
 
     def _arrange_fields(self, channels, sampfrom, smooth_frames):
         """
@@ -2046,10 +2044,13 @@ def rdrecord(
         hea_file = os.path.basename(record_base) + ".hea"
 
         import tempfile
+
         with wfdb_archive.open(hea_file, "r") as f:
             header_str = f.read()
 
-        with tempfile.NamedTemporaryFile("w+", suffix=".hea", delete=False) as tmpf:
+        with tempfile.NamedTemporaryFile(
+            "w+", suffix=".hea", delete=False
+        ) as tmpf:
             tmpf.write(header_str)
             tmpf.flush()
             record = rdheader(tmpf.name)
@@ -2074,7 +2075,9 @@ def rdrecord(
             if "." not in pn_dir:
                 dir_list = pn_dir.split("/")
                 pn_dir = posixpath.join(
-                    dir_list[0], download.get_version(dir_list[0]), *dir_list[1:]
+                    dir_list[0],
+                    download.get_version(dir_list[0]),
+                    *dir_list[1:],
                 )
 
         record = rdheader(record_name, pn_dir=pn_dir, rd_segments=False)
@@ -2783,7 +2786,9 @@ def wfdbtime(record_name, input_times, pn_dir=None):
         )
         if not times.startswith("s"):
             sample_num = int(
-                sum(x * 60**i for i, x in enumerate([seconds, minutes, hours]))
+                sum(
+                    x * 60**i for i, x in enumerate([seconds, minutes, hours])
+                )
                 * record.fs
             )
         sample_num = "s" + str(sample_num)
@@ -3080,11 +3085,14 @@ def wrsamp(
         expanded = False
 
     if wfdb_archive:
-        wfdb_archive = get_archive(os.path.join(write_dir, record_name),
-                                   mode="w")
+        wfdb_archive = get_archive(
+            os.path.join(write_dir, record_name), mode="w"
+        )
 
     # Write the record files - header and associated dat
-    record.wrsamp(write_dir=write_dir, expanded=expanded, wfdb_archive=wfdb_archive)
+    record.wrsamp(
+        write_dir=write_dir, expanded=expanded, wfdb_archive=wfdb_archive
+    )
 
 
 def dl_database(