Fix warnings (#502)

I've fixed a few warnings related to - deprecated functions - unclosed files - unclosed multiprocessing pool Now all tests pass without warnings (and errors of course).

Author: tompollard

tests/test_annotation.py

@@ -33,7 +33,8 @@ def test_1(self):
  # no null to detect in the output text file of rdann.
 
  # Target data from WFDB software package
- lines = tuple(open("tests/target-output/ann-1", "r"))
+ with open("tests/target-output/ann-1", "r") as f:
+ lines = tuple(f)
  nannot = len(lines)
 
  target_time = [None] * nannot
@@ -108,7 +109,8 @@ def test_2(self):
  annotation = wfdb.rdann("sample-data/12726", "anI")
 
  # Target data from WFDB software package
- lines = tuple(open("tests/target-output/ann-2", "r"))
+ with open("tests/target-output/ann-2", "r") as f:
+ lines = tuple(f)
  nannot = len(lines)
 
  target_time = [None] * nannot
@@ -181,7 +183,8 @@ def test_3(self):
  annotation = wfdb.rdann("sample-data/1003", "atr")
 
  # Target data from WFDB software package
- lines = tuple(open("tests/target-output/ann-3", "r"))
+ with open("tests/target-output/ann-3", "r") as f:
+ lines = tuple(f)
  nannot = len(lines)
 
  target_time = [None] * nannot

wfdb/io/convert/edf.py

@@ -438,6 +438,8 @@ def read_edf(
  int(np.sum(v) % 65536) for v in np.transpose(sig_data)
  ] # not all values correct?
 
+ edf_file.close()
+
  record = Record(
  record_name=record_name_out,
  n_sig=n_sig,

wfdb/io/download.py

@@ -143,7 +143,7 @@ def _stream_dat(file_name, pn_dir, byte_count, start_byte, dtype):
  content = f.read(byte_count)
 
  # Convert to numpy array
- sig_data = np.fromstring(content, dtype=dtype)
+ sig_data = np.frombuffer(content, dtype=dtype)
 
  return sig_data
 
@@ -173,7 +173,7 @@ def _stream_annotation(file_name, pn_dir):
  content = f.read()
 
  # Convert to numpy array
- ann_data = np.fromstring(content, dtype=np.dtype("<u1"))
+ ann_data = np.frombuffer(content, dtype=np.dtype("<u1"))
 
  return ann_data
 
@@ -343,7 +343,7 @@ def get_annotators(db_dir, annotators):
  annotators = ann_list
  else:
  # In case they didn't input a list
- if type(annotators) == str:
+ if type(annotators) is str:
  annotators = [annotators]
  # user input ones. Check validity.
  for a in annotators:
@@ -541,8 +541,6 @@ def dl_files(db, dl_dir, files, keep_subdirs=True, overwrite=False):
  print("Downloading files...")
  # Create multiple processes to download files.
  # Limit to 2 connections to avoid overloading the server
- pool = multiprocessing.dummy.Pool(processes=2)
- pool.map(dl_pn_file, dl_inputs)
+ with multiprocessing.dummy.Pool(processes=2) as pool:
+  pool.map(dl_pn_file, dl_inputs)
  print("Finished downloading files")
-
- return

wfdb/io/record.py

@@ -3117,8 +3117,6 @@ def dl_database(
  print("Downloading files...")
  # Create multiple processes to download files.
  # Limit to 2 connections to avoid overloading the server
- pool = multiprocessing.dummy.Pool(processes=2)
- pool.map(download.dl_pn_file, dl_inputs)
+ with multiprocessing.dummy.Pool(processes=2) as pool:
+  pool.map(download.dl_pn_file, dl_inputs)
  print("Finished downloading files")
-
- return