update url_is_reachable

.github/workflows/run-pytest.yml

@@ -80,7 +80,7 @@ jobs:
           du -sh ~/tmp/*
     - name: Run test with pytest and collect coverage
       run: |
-        pytest -v -s \
+        pytest -vv -s \
         --cov=torch_ecg \
         --ignore=test/test_pipelines \
         test

.github/workflows/test-databases.yml

@@ -79,29 +79,29 @@ jobs:
           du -sh ~/tmp/nsrr-data/*
     - name: Run test SHHS with pytest
       run: |
-        pytest -v -s test/test_databases/test_shhs.py
+        pytest -vv -s test/test_databases/test_shhs.py
     - name: Run test other databases with pytest
       run: |
-        pytest -v -s test/test_databases/test_cachet_cadb.py
-        pytest -v -s test/test_databases/test_sph.py
+        pytest -vv -s test/test_databases/test_cachet_cadb.py
+        pytest -vv -s test/test_databases/test_sph.py
     - name: Run test normal physionet databases with pytest
       run: |
-        pytest -v -s test/test_databases/test_base.py
-        pytest -v -s test/test_databases/test_afdb.py
-        pytest -v -s test/test_databases/test_apnea_ecg.py
-        pytest -v -s test/test_databases/test_cinc2017.py
-        pytest -v -s test/test_databases/test_cinc2018.py
-        pytest -v -s test/test_databases/test_ltafdb.py
-        pytest -v -s test/test_databases/test_ludb.py
-        pytest -v -s test/test_databases/test_mitdb.py
-        pytest -v -s test/test_databases/test_qtdb.py
+        pytest -vv -s test/test_databases/test_base.py
+        pytest -vv -s test/test_databases/test_afdb.py
+        pytest -vv -s test/test_databases/test_apnea_ecg.py
+        pytest -vv -s test/test_databases/test_cinc2017.py
+        pytest -vv -s test/test_databases/test_cinc2018.py
+        pytest -vv -s test/test_databases/test_ltafdb.py
+        pytest -vv -s test/test_databases/test_ludb.py
+        pytest -vv -s test/test_databases/test_mitdb.py
+        pytest -vv -s test/test_databases/test_qtdb.py
     - name: Run test CPSC databases with pytest
       run: |
-        pytest -v -s test/test_databases/test_cpsc2018.py
-        pytest -v -s test/test_databases/test_cpsc2019.py
-        pytest -v -s test/test_databases/test_cpsc2020.py
-        pytest -v -s test/test_databases/test_cpsc2021.py
+        pytest -vv -s test/test_databases/test_cpsc2018.py
+        pytest -vv -s test/test_databases/test_cpsc2019.py
+        pytest -vv -s test/test_databases/test_cpsc2020.py
+        pytest -vv -s test/test_databases/test_cpsc2021.py
     - name: Run test CinC20/21 databases with pytest
       run: |
-        pytest -v -s test/test_databases/test_cinc2020.py
-        pytest -v -s test/test_databases/test_cinc2021.py
+        pytest -vv -s test/test_databases/test_cinc2020.py
+        pytest -vv -s test/test_databases/test_cinc2021.py

.github/workflows/test-models.yml

@@ -56,4 +56,4 @@ jobs:
         python -m pip list
     - name: Run test with pytest
       run: |
-        pytest -v -s test/test_models
+        pytest -vv -s test/test_models

.github/workflows/test-ppl.yml

@@ -56,4 +56,4 @@ jobs:
         python -m pip list
     - name: Run test with pytest
       run: |
-        pytest -v -s test/test_pipelines
+        pytest -vv -s test/test_pipelines

torch_ecg/databases/base.py

@@ -126,6 +126,15 @@
 class _DataBase(ReprMixin, ABC):
     """Universal abstract base class for all databases.
 
+    Abstract methods that should be implemented by the subclass:
+    - `_ls_rec`: Find all records in the database.
+    - `load_data`: Load data from a record.
+    - `load_ann`: Load annotations of a record.
+
+    Abstract properties that should be implemented by the subclass:
+    - `database_info`: The :class:`DataBaseInfo` object of the database.
+    - `url`: URL(s) for downloading the database.
+
     Parameters
     ----------
     db_dir : `path-like`, optional

torch_ecg/databases/nsrr_databases/shhs.py

@@ -317,7 +317,6 @@ class SHHS(NSRRDataBase, PSGDataBaseMixin):
     ----------
     db_dir : `path-like`, optional
         Storage path of the database.
-        If not specified, data will be fetched from Physionet.
     working_dir : `path-like`, optional
         Working directory, to store intermediate files and log files.
     verbose : int, default 1

torch_ecg/utils/download.py

@@ -15,7 +15,7 @@
 import warnings
 import zipfile
 from pathlib import Path
-from typing import Iterable, Optional, Union
+from typing import Any, Iterable, Optional, Union
 
 import requests
 from tqdm.auto import tqdm
@@ -323,13 +323,15 @@ def _safe_tar_extract(
     tar.extractall(dst_dir, members, numeric_owner=numeric_owner)
 
 
-def url_is_reachable(url: str) -> bool:
+def url_is_reachable(url: str, **kwargs: Any) -> bool:
     """Check if a URL is reachable.
 
     Parameters
     ----------
     url : str
         The URL.
+    **kwargs : dict, optional
+        Additional keyword arguments to pass to :meth:`requests.head`.
 
     Returns
     -------
@@ -338,7 +340,8 @@ def url_is_reachable(url: str) -> bool:
 
     """
     try:
-        r = requests.head(url, timeout=3)
+        timeout = kwargs.pop("timeout", 3)
+        r = requests.head(url, timeout=timeout, **kwargs)
         # successful responses and redirection messages
         # https://developer.mozilla.org/en-US/docs/Web/HTTP/Status#information_responses
         # Informational responses (100 – 199)