Start applying ruff rules

.github/workflows/codecov.yml

@@ -10,9 +10,9 @@ jobs:
       OS: ${{ matrix.os }}
       PYTHON: '3.9'
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
     - name: Setup Python
-      uses: actions/setup-python@master
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
     - name: Generate coverage report
@@ -23,7 +23,7 @@ jobs:
         pip install -r requirements-test.txt
         pytest --cov=./pyedflib/ --cov-report=xml --cov-config=.coveragerc
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
       with:
         directory: .
         env_vars: OS,PYTHON

.github/workflows/linters.yml

@@ -0,0 +1,15 @@
+name: Lint
+on:
+  pull_request:
+    branches:
+      - '*'
+permissions:
+  contents: read
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps: 
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+      - name: Lint with Ruff
+        run: ruff check --output-format=github

.github/workflows/tests.yml

@@ -12,9 +12,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install packages

.github/workflows/wheels.yml

@@ -22,7 +22,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: Install deps
@@ -45,7 +45,7 @@ jobs:
       - uses: actions/checkout@v4
 
       # Used to host cibuildwheel
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.8'
       - name: Install cibuildwheel

demo/readEDFFile.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-import os
-
 import numpy as np
 
 import pyedflib

demo/streamingEDFFile.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-import time
-
 import matplotlib.animation as animation
 import matplotlib.pyplot as plt
 import numpy as np

doc/source/conf.py

@@ -9,12 +9,12 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
-import datetime
 import re
 
-import jinja2.filters
 import numpy as np
 
+import pyedflib
+
 # FIXME: doctests need the str/repr formatting used in Numpy < 1.14.
 try:
     np.set_printoptions(legacy='1.13')
@@ -63,8 +63,6 @@
 # built documents.
 #
 # The short X.Y version.
-import pyedflib
-
 version = re.sub(r'\.dev0+.*$', r'.dev', pyedflib.__version__)
 release = pyedflib.__version__
 

pyedflib/__init__.py

@@ -1,5 +1,3 @@
-# flake8: noqa
-
 # Copyright (c) 2019 - 2020 Simon Kern
 # Copyright (c) 2015 - 2020 Holger Nahrstaedt
 # Copyright (c) 2016-2017 The pyedflib Developers

pyedflib/_extensions/_pyedflib.pyi

@@ -1,22 +1,61 @@
-from typing import List, Dict, Union, Optional
 import numpy as np
-from datetime import datetime
 
-__all__ = ['lib_version', 'CyEdfReader', 'set_patientcode', 'set_starttime_subsecond',
-           'write_annotation_latin1', 'write_annotation_utf8', 'set_technician', 'EdfAnnotation',
-           'get_annotation', 'read_int_samples', 'blockwrite_digital_samples', 'blockwrite_physical_samples',
-           'set_recording_additional', 'write_physical_samples', 'set_patientname', 'set_physical_minimum',
-           'read_physical_samples', 'close_file', 'set_physical_maximum', 'open_file_writeonly',
-           'set_patient_additional', 'set_digital_maximum', 'set_birthdate', 'set_digital_minimum',
-           'write_digital_samples', 'set_equipment', 'set_samples_per_record', 'set_admincode', 'set_label',
-           'tell', 'rewind', 'set_sex', 'set_gender', 'set_physical_dimension', 'set_transducer',
-           'set_prefilter', 'seek', 'set_startdatetime', 'set_datarecord_duration',
-           'set_number_of_annotation_signals', 'open_errors', 'FILETYPE_EDFPLUS',
-           'FILETYPE_EDF', 'FILETYPE_BDF', 'FILETYPE_BDFPLUS', 'write_errors', 'get_number_of_open_files',
-           'get_handle', 'is_file_used', 'blockwrite_digital_short_samples', 'write_digital_short_samples']
+__all__ = [
+    'FILETYPE_BDF',
+    'FILETYPE_BDFPLUS',
+    'FILETYPE_EDF',
+    'FILETYPE_EDFPLUS',
+    'CyEdfReader',
+    'EdfAnnotation',
+    'blockwrite_digital_samples',
+    'blockwrite_digital_short_samples',
+    'blockwrite_physical_samples',
+    'close_file',
+    'get_annotation',
+    'get_handle',
+    'get_number_of_open_files',
+    'is_file_used',
+    'lib_version',
+    'open_errors',
+    'open_file_writeonly',
+    'read_int_samples',
+    'read_physical_samples',
+    'rewind',
+    'seek',
+    'set_admincode',
+    'set_birthdate',
+    'set_datarecord_duration',
+    'set_digital_maximum',
+    'set_digital_minimum',
+    'set_equipment',
+    'set_gender',
+    'set_label',
+    'set_number_of_annotation_signals',
+    'set_patient_additional',
+    'set_patientcode',
+    'set_patientname',
+    'set_physical_dimension',
+    'set_physical_maximum',
+    'set_physical_minimum',
+    'set_prefilter',
+    'set_recording_additional',
+    'set_samples_per_record',
+    'set_sex',
+    'set_startdatetime',
+    'set_starttime_subsecond',
+    'set_technician',
+    'set_transducer',
+    'tell',
+    'write_annotation_latin1',
+    'write_annotation_utf8',
+    'write_digital_samples',
+    'write_digital_short_samples',
+    'write_errors',
+    'write_physical_samples',
+]
 
-open_errors: Dict[int, str]
-write_errors: Dict[int, str]
+open_errors: dict[int, str]
+write_errors: dict[int, str]
 
 FILETYPE_EDF: int
 FILETYPE_EDFPLUS: int
@@ -35,7 +74,7 @@ class CyEdfReader:
     def check_open_ok(self, result: int) -> bool: ...
     def make_buffer(self) -> np.ndarray: ...
     def open(self, file_name: str, annotations_mode: int = ..., check_file_size: int = ...) -> bool: ...
-    def read_annotation(self) -> List[List[str]]: ...
+    def read_annotation(self) -> list[list[str]]: ...
     def _close(self) -> None: ...
     def read_digital_signal(self, signalnum: int, start: int, n: int, sigbuf: np.ndarray[np.int32_t]) -> None: ...
     def readsignal(self, signalnum: int, start: int, n: int, sigbuf: np.ndarray[np.float64_t]) -> None: ...
@@ -118,19 +157,19 @@ class EdfAnnotation:
     duration: int
     annotation: str
 
-def set_patientcode(handle: int, patientcode: Union[str, bytes]) -> int: ...
-def write_annotation_latin1(handle: int, onset: int, duration: int, description: Union[str, bytes]) -> int: ...
-def write_annotation_utf8(handle: int, onset: int, duration: int, description: Union[str, bytes]) -> int: ...
-def set_technician(handle: int, technician: Union[str, bytes]) -> int: ...
+def set_patientcode(handle: int, patientcode: str | bytes) -> int: ...
+def write_annotation_latin1(handle: int, onset: int, duration: int, description: str | bytes) -> int: ...
+def write_annotation_utf8(handle: int, onset: int, duration: int, description: str | bytes) -> int: ...
+def set_technician(handle: int, technician: str | bytes) -> int: ...
 def get_annotation(handle: int, n: int, edf_annotation: EdfAnnotation) -> int: ...
 def read_int_samples(handle: int, edfsignal: int, n: int, buf: np.ndarray[np.int32_t]) -> int: ...
 def blockwrite_digital_samples(handle: int, buf: np.ndarray[np.int32_t]) -> int: ...
 def blockwrite_digital_short_samples(handle: int, buf: np.ndarray[np.int16_t]) -> int: ...
 def blockwrite_physical_samples(handle: int, buf: np.ndarray[np.float64_t]) -> int: ...
-def set_recording_additional(handle: int, recording_additional: Union[str, bytes]) -> int: ...
+def set_recording_additional(handle: int, recording_additional: str | bytes) -> int: ...
 def write_digital_short_samples(handle: int, buf: np.ndarray[np.int16_t]) -> int: ...
 def write_physical_samples(handle: int, buf: np.ndarray[np.float64_t]) -> int: ...
-def set_patientname(handle: int, name: Union[str,bytes]) -> int: ...
+def set_patientname(handle: int, name: str | bytes) -> int: ...
 def set_physical_minimum(handle: int, edfsignal: int, phys_min: float) -> int: ...
 def read_physical_samples(handle: int, edfsignal: int, n: int, buf: np.ndarray[np.float64_t]) -> int: ...
 def close_file(handle: int) -> int: ...
@@ -139,26 +178,25 @@ def get_handle(file_number: int) -> int: ...
 def is_file_used(path: str) -> bool: ...
 def set_physical_maximum(handle: int, edfsignal: int, phys_max: float) -> int: ...
 def open_file_writeonly(path: str, filetype: int, number_of_signals: int) -> int: ...
-def set_patient_additional(handle: int, patient_additional: Union[str, bytes]) -> int: ...
+def set_patient_additional(handle: int, patient_additional: str | bytes) -> int: ...
 def set_digital_maximum(handle: int, edfsignal: int, dig_max: int) -> int: ...
 def set_birthdate(handle: int, birthdate_year: int, birthdate_month: int, birthdate_day: int) -> int: ...
 def set_digital_minimum(handle: int, edfsignal: int, dig_min: int) -> int: ...
 def write_digital_samples(handle: int, buf: np.ndarray[np.int32_t]) -> int: ...
-def set_equipment(handle: int, equipment: Union[str, bytes]) -> int: ...
+def set_equipment(handle: int, equipment: str | bytes) -> int: ...
 def set_samples_per_record(handle: int, edfsignal: int, smp_per_record: int) -> int: ...
-def set_admincode(handle: int, admincode: Union[str, bytes]) -> int: ...
-def set_label(handle: int, edfsignal: int, label: Union[str, bytes]) -> int: ...
+def set_admincode(handle: int, admincode: str | bytes) -> int: ...
+def set_label(handle: int, edfsignal: int, label: str | bytes) -> int: ...
 def tell(handle: int, edfsignal: int) -> int: ...
 def rewind(handle: int, edfsignal: int) -> None: ...
-def set_sex(handle: int, sex: Optional[int]) -> int: ...
+def set_sex(handle: int, sex: int | None) -> int: ...
 def set_gender(handle: int, gender: int) -> int: ...
-def set_physical_dimension(handle: int, edfsignal: int, phys_dim: Union[str, bytes]) -> int: ...
-def set_transducer(handle: int, edfsignal: int, transducer: Union[str, bytes]) -> int: ...
-def set_prefilter(handle: int, edfsignal: int, prefilter: Union[str, bytes]) -> int: ...
+def set_physical_dimension(handle: int, edfsignal: int, phys_dim: str | bytes) -> int: ...
+def set_transducer(handle: int, edfsignal: int, transducer: str | bytes) -> int: ...
+def set_prefilter(handle: int, edfsignal: int, prefilter: str | bytes) -> int: ...
 def seek(handle: int, edfsignal: int, offset: int, whence: int) -> int: ...
 def set_startdatetime(handle: int, startdate_year: int, startdate_month: int, startdate_day: int,
                       starttime_hour: int, starttime_minute: int, starttime_second: int) -> int: ...
 def set_starttime_subsecond(handle: int, subsecond: int) -> int: ...
-def set_datarecord_duration(handle: int, duration: Union[int, float]) -> int: ...
+def set_datarecord_duration(handle: int, duration: int | float) -> int: ...
 def set_number_of_annotation_signals(handle: int, annot_signals: int) -> int: ...
-

pyedflib/data/_readers.py

@@ -1,7 +1,5 @@
 import os
 
-import numpy as np
-
 import pyedflib
 
 

pyedflib/edfreader.py

@@ -15,13 +15,13 @@
 from ._extensions._pyedflib import CyEdfReader
 
 __all__ = [
-    "EdfReader",
-    "DO_NOT_READ_ANNOTATIONS",
-    "READ_ANNOTATIONS",
-    "READ_ALL_ANNOTATIONS",
     "CHECK_FILE_SIZE",
     "DO_NOT_CHECK_FILE_SIZE",
+    "DO_NOT_READ_ANNOTATIONS",
+    "READ_ALL_ANNOTATIONS",
+    "READ_ANNOTATIONS",
     "REPAIR_FILE_SIZE_IF_WRONG",
+    "EdfReader",
 ]
 
 DO_NOT_READ_ANNOTATIONS = 0
@@ -504,7 +504,7 @@ def getSampleFrequency(self, chn: int) -> float:
             return self.samplefrequency(chn)
         else:
             raise IndexError(
-                "Trying to access channel {}, but only {} " "channels found".format(
+                "Trying to access channel {}, but only {} channels found".format(
                     chn, self.signals_in_file
                 )
             )
@@ -553,7 +553,7 @@ def getLabel(self, chn: int) -> str:
             return self._convert_string(self.signal_label(chn).rstrip())
         else:
             raise IndexError(
-                "Trying to access channel {}, but only {} " "channels found".format(
+                "Trying to access channel {}, but only {} channels found".format(
                     chn, self.signals_in_file
                 )
             )
@@ -580,7 +580,7 @@ def getPrefilter(self, chn: int) -> str:
             return self._convert_string(self.prefilter(chn).rstrip())
         else:
             raise IndexError(
-                "Trying to access channel {}, but only {} " "channels found".format(
+                "Trying to access channel {}, but only {} channels found".format(
                     chn, self.signals_in_file
                 )
             )
@@ -608,7 +608,7 @@ def getPhysicalMaximum(self, chn: Optional[int] = None) -> Union[float, np.ndarr
                 return self.physical_max(chn)
             else:
                 raise IndexError(
-                    "Trying to access channel {}, but only {} " "channels found".format(
+                    "Trying to access channel {}, but only {} channels found".format(
                         chn, self.signals_in_file
                     )
                 )
@@ -641,7 +641,7 @@ def getPhysicalMinimum(self, chn: Optional[int] = None) -> Union[float, np.ndarr
                 return self.physical_min(chn)
             else:
                 raise IndexError(
-                    "Trying to access channel {}, but only {} " "channels found".format(
+                    "Trying to access channel {}, but only {} channels found".format(
                         chn, self.signals_in_file
                     )
                 )
@@ -674,7 +674,7 @@ def getDigitalMaximum(self, chn: Optional[int] = None) -> Union[int, np.ndarray]
                 return self.digital_max(chn)
             else:
                 raise IndexError(
-                    "Trying to access channel {}, but only {} " "channels found".format(
+                    "Trying to access channel {}, but only {} channels found".format(
                         chn, self.signals_in_file
                     )
                 )
@@ -707,7 +707,7 @@ def getDigitalMinimum(self, chn: Optional[int] = None) -> Union[int, np.ndarray]
                 return self.digital_min(chn)
             else:
                 raise IndexError(
-                    "Trying to access channel {}, but only {} " "channels found".format(
+                    "Trying to access channel {}, but only {} channels found".format(
                         chn, self.signals_in_file
                     )
                 )
@@ -739,7 +739,7 @@ def getTransducer(self, chn: int):
             return self._convert_string(self.transducer(chn).rstrip())
         else:
             raise IndexError(
-                "Trying to access channel {}, but only {} " "channels found".format(
+                "Trying to access channel {}, but only {} channels found".format(
                     chn, self.signals_in_file
                 )
             )
@@ -766,7 +766,7 @@ def getPhysicalDimension(self, chn: int) -> str:
             return self._convert_string(self.physical_dimension(chn).rstrip())
         else:
             raise IndexError(
-                "Trying to access channel {}, but only {} " "channels found".format(
+                "Trying to access channel {}, but only {} channels found".format(
                     chn, self.signals_in_file
                 )
             )
@@ -826,7 +826,7 @@ def readSignal(
             return x
         else:
             raise IndexError(
-                "Trying to access channel {}, but only {} " "channels found".format(
+                "Trying to access channel {}, but only {} channels found".format(
                     chn, self.signals_in_file
                 )
             )