Changelog

=========

All notable changes to this project will be documented in this file.

The format is based on `Keep a

Changelog <https://keepachangelog.com/en/1.1.0/>`__, and this project

adheres to `Semantic

Versioning <https://semver.org/spec/v2.0.0.html>`__.

`Unreleased <https://github.com/DeepPSP/torch_ecg/compare/v0.0.31...HEAD>`__

----------------------------------------------------------------------------

Added

~~~~~

Changed

~~~~~~~

- Make the function `remove_spikes_naive` in `torch_ecg.utils.utils_signal`

  support 2D and 3D input signals.

Deprecated

~~~~~~~~~~

Removed

~~~~~~~

Fixed

~~~~~

- Correctly update the `_df_metadata` attribute of the `PTBXL` database reader

  classes after filtering records.

- Enhance the `save` method of the `torch_ecg.utils.utils_nn.CkptMixin` class:

  non-safe items in the configs are removed before saving the model.

- Fix errors when monitor is specified while the validation dataloader is not

  provided in the `torch_ecg.components.BaseTrainer` class.

- Enhance the `save_checkpoint` method of the `torch_ecg.components.BaseTrainer` class:

  non-safe items in the configs are removed before saving the model.

Security

~~~~~~~~

`0.0.31 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.30...v0.0.31>`__ - 2025-01-28

----------------------------------------------------------------------------------------

Added

~~~~~

- Add functions for downloading PhysioNet data from AWS S3. It is now made

  the default way to download data from PhysioNet.

- Add ``easydict`` as a dependency for backward compatibility (loading

  old models using safe-mode ``torch.load`` with ``weights_only=True``.

  Extra dependencies are added with

  ``torch.serialization.add_safe_globals``).

Changed

~~~~~~~

- Test files (in the ``sample-data`` directory) are updated.

- Add keyword argument ``weights_only`` to ``from_checkpoint`` and

  ``from_remote`` methods of the models (indeed the ``CkptMixin``

  class). The default value is ``"auto"``, which means the behavior is

  the same as before. It checks if ``torch.serialization`` has

  ``add_safe_globals`` attribute. If it does, it will use safe-mode

  ``torch.load`` with ``weights_only=True``. Otherwise, it will use

  ``torch.load`` with ``weights_only=False``.

Deprecated

~~~~~~~~~~

- Support for Python 3.7, 3.8 is deprecated. The minimum supported Python

  version is now 3.9. In the ``pyproject.toml`` file, the field

  ``requires-python`` is updated from ``>=3.7`` to ``>=3.9``.

Removed

~~~~~~~

- Restrictions on the version of ``wfdb`` and ``numpy`` packages are

  removed.

Fixed

~~~~~

- Fix IO issues with several PhysioNet databases.

Security

~~~~~~~~

- Models are now loaded using safe-mode ``torch.load`` with

  ``weights_only=True`` by default.

`0.0.30 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.29...v0.0.30>`__ - 2024-10-10

----------------------------------------------------------------------------------------

Added

~~~~~

- Add support for AWS S3 in the download utility function ``http_get``

  in the ``torch_ecg.utils.download`` module. PhysioNet now provides

  data download links from AWS S3, and the download utility function

  can now handle these links if AWS CLI is installed. This feature is

  implemented but not put into use yet.

Changed

~~~~~~~

- Change the default value of the ``method`` argument of the

  ``torch_ecg.utils.utils_signal.resample_irregular_timeseries`` function

  from ``"spline"`` to ``"interp1d"``. The former is probably not

  correctly implemented.

- Update the logger classes: add checking of the write access of the

  ``log_dir``. If the directory is not writable, the default log dir

  ``~/.cache/torch_ecg/logs`` is used (ref. ``torch_ecg.cfg.DEFAULTS.log_dir``).

- Update the selection mechanism of the final model for the trainer

  classes: if no monitor is specified, the last model is selected by

  default (previously, no model was selected and saved).

- The main part of the ``_setup_criterion`` method of the ``BaseTrainer``

  class is moved to the function ``setup_criterion`` in the

  ``torch_ecg.models.loss`` module. The method is simplified and

  enhanced.

Deprecated

~~~~~~~~~~

- Script ``setup.py`` is deprecated. The package building system is

  switched to ``hatch``.

Removed

~~~~~~~

- Remove redundancy in base trainer classes: identical ``if`` blocks

  are removed from the ``_setup_criterion`` method of the ``BaseTrainer``

  class.

Fixed

~~~~~

- Fix potential error in getting model name in the trainer classes.

- Fix bugs in the ``CINC2020`` and ``CINC2021`` database reader classes

  for parsing the header files.

`0.0.29 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.28...v0.0.29>`__ - 2024-07-21

----------------------------------------------------------------------------------------

Added

~~~~~

- Add keyword argument ``with_suffix`` to function

  ``torch_ecg.utils.misc.get_record_list_recursive3``.

- Add function ``_download_from_google_drive`` to the

  ``torch_ecg.utils.download`` module for downloading files from Google

  Drive.

- Add ``gdown`` as a dependency in the ``requirements.txt`` file.

- Add database reader class ``PTBXLPlus`` for the PTB-XL+ database in

  ``torch_ecg.databases.physionet_databases``.

- Add github-release job to the publish action for creating a release

  on GitHub automatically.

Changed

~~~~~~~

- Improve the main training loop method of the base trainer class

  ``torch_ecg.components.trainers.BaseTrainer``.

- Allow passing additional keyword arguments to pass to ``requests.head``

  in the ``url_is_reachable`` function of the ``torch_ecg.utils.download``

  module (via adding the ``**kwargs`` argument).

- Restrict version of ``numpy`` to be ``<=2.0.0`` in the

  ``requirements.txt`` file. ``numpy`` version ``2.0.0`` is a breaking

  update, and a large proportion of the dependencies of this project

  are not compatible with it yet.

- Enhance the ``cls_to_bin`` function and rename it to ``one_hot_encode``

  in the ``torch_ecg.utils.utils_data`` module.

Fixed

~~~~~

- Enhance compatibility for different ``pandas`` versions.

- Fix errors for taking length of an empty database reader class.

Security

~~~~~~~~

- Fix code scanning alert - Incomplete regular expression for hostnames

  `#21 <https://github.com/DeepPSP/torch_ecg/pull/21>`__.

- Fix code scanning alert - Incomplete URL substring sanitization

  `#23 <https://github.com/DeepPSP/torch_ecg/pull/23>`__.

`0.0.28 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.27...v0.0.28>`__ - 2024-04-02

----------------------------------------------------------------------------------------

Added

~~~~~

- Add CD workflow for the publish action with GitHub Action.

- Add an optional argument ``return_fs`` for the ``load_data``

  method for the database reader classes. If ``True``, the sampling

  frequency of the record is returned along with the data as a tuple.

  To keep the behavior consistent, the default value is ``False``.

- Add an optional parameter ``fs`` for the function ``compute_receptive_field``

  in the ``torch_ecg.utils.utils_nn`` module. If ``fs`` is provided, the

  receptive field is computed based on the sampling frequency.

- Add method ``compute_receptive_field`` for several convolutional neural

  network models (layers) in the ``torch_ecg.models._nets`` module.

- Add helper function ``make_serializable`` in the ``torch_ecg.utils.misc``

  module for making an object serializable (with the ``json`` package).

  It will convert all ``numpy`` arrays to ``list`` in an object, and

  also convert ``numpy`` data types to python data types in the object

  recursively.

- Add helper function ``url_is_reachable`` in the ``torch_ecg.utils.download``

  module for checking if a URL is reachable.

- Add database reader class ``PTBXL`` for the PTB-XL database in

  ``torch_ecg.databases.physionet_databases``.

- Add class method ``from_remote`` for ``CkptMixin`` classes. It is used

  to load a model from a remote location (e.g., a URL) directly.

- Add ``sphinx-emoji-favicon`` as a dependency for generating the favicon

  for the documentation.

- Add utility function ``ecg_plot`` from

  `ecg-image-kit <https://github.com/alphanumericslab/ecg-image-kit/.>`__.

- Add ``pyarrow`` as a dependency in the ``requirements.txt`` file.

- Add benchmark study ``train_crnn_cinc2023`` for the CinC2023 challenge.

Changed

~~~~~~~

- Change the default value ``reset_index`` of the utility function

  ``torch_ecg.utils.utils_data.stratified_train_test_split`` from

  ``True`` to ``False``.

- Enhance the decorator ``torch_ecg.utils.misc.add_kwargs`` so that

  the signature of the decorated function is also updated.

- Update the documentation: use ``sphinx_toolbox.collapse`` and

  ``sphinxcontrib.bibtex``; add citation info in the index page.

- Make ``Dataset`` classes accept slice index for the ``__getitem__``

  method.

Deprecated

~~~~~~~~~~

- Support for Python 3.6 is deprecated. The minimum supported Python

  version is updated to 3.7.

Removed

~~~~~~~

- Remove broken links in the docstrings of the database reader classes.

- Remove unused scripts ``formatting.sh`` and ``push2pypi.sh``.

Fixed

~~~~~

- Fix errors in the decorator ``torch_ecg.utils.misc.add_kwargs``

  when a bound method is decorated.

- Fix bugs related to data overflow for preprocessor classes that

  work with ``numpy`` arrays as reported in issue

  `#12 <https://github.com/DeepPSP/torch_ecg/issues/12>`__.

- Fix bugs in augmentor class ``StretchCompress`` in the

  ``torch_ecg.augmenters`` module.

- Fix dtype error when calling ``compute_class_weight`` from

  ``sklearn.utils``.

- Fix the issue when handling nan values in in computing metrics.

- Fix errors for the ``ApneaECG`` database reader class when passing

  a path that does not exist or a path that contains no records at

  initialization.

`0.0.27 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.26...v0.0.27>`__ - 2023-03-14

----------------------------------------------------------------------------------------

Added

~~~~~

- Add default configs for blocks of the ``ResNet`` model in the

  ``torch_ecg.models.cnn`` module.

- Add ``RegNet`` model in the ``torch_ecg.models.cnn`` module.

- Add ``CutMix`` augmentor in the ``torch_ecg.augmenters`` module.

- Add support for ``torch.nn.Dropout1d`` in the models.

- Add ``.readthedocs.yml`` to the project. The documentation is

  now hosted on Read the Docs besides GitHub Pages.

Changed

~~~~~~~

- Move ``torch_ecg.utils.preproc`` to ``torch_ecg.utils._preproc``.

- Allow ``embed_dim`` of ``SelfAttention`` layer not divisible by

  ``num_heads`` via adding a linear projection layer before the

  multi-head attention layer.

- Documentation is largely improved.

Deprecated

~~~~~~~~~~

- Drop compability for older versions of ``torch`` (1.5 and below).

Removed

~~~~~~~

- Remove ``protobuf`` from the ``requirements.txt`` file.

- Clear unused methods in the ``CINC2020`` and ``CINC2021`` database

  reader classes.

- Clear unused layers in the ``torch_ecg.models._nets`` module.

- Remove the ``torch_ecg.utils._pantompkins`` module. It contains

  the implementation of the Pan-Tompkins algorithm for QRS detection,

  modified from old versions of the ``wfdb`` package. It is moved to

  the ``legacy`` folder of the project.

- Remove ``WandbLogger`` class from the ``torch_ecg.components.loggers``

  module.

Fixed

~~~~~

- Fix bugs when passing ``units=None`` for the ``load_data`` method

  of the PhysioNet database reader classes.

`0.0.26 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.25...v0.0.26>`__ - 2022-12-25

----------------------------------------------------------------------------------------

Added

~~~~~

- Add a default ``load_data`` method for physionet databases reader

  classes in the base class ``PhysioNetDataBase``. In most cases,

  in the inherited classes, one does not need to implement the

  ``load_data`` method, as the default method is sufficient. This

  method is a slight improvement over ``wfdb.rdrecord``.

- Add decorator ``add_kwargs`` in the ``torch_ecg.utils.misc`` module

  for adding keyword arguments to a function or method.

- Add functions ``list_databases``, ``list_datasets`` in the

  ``torch_ecg.datasets`` module for listing available databases reader

  classes and ``Dataset`` classes.

- Add ``save`` method for the ``CkptMixin`` class. It is used to save

  the model to a file.

- Add ``_normalize_leads`` a method of the base ``_DataBase`` class

  in the ``torch_ecg.databases.base`` module. It is used to normalize

  the names of the ECG leads.

- Add subsampling functionality for database reader classes.

- Add benchmark study ``train_mtl_cinc2022`` for the CinC2022 challenge.

- Add ``CITATIONS.bib`` file for storing BibTeX entries of the

  papers related to the project.

- Add 10 sample data from the CPSC2018 database for testing in the

  ``sample-data`` directory.

Changed

~~~~~~~

- Use ``CitationMixin`` from the ``bib-lookup`` package as the base

  class for the ``DataBaseInfo`` class in ``torch_ecg.databases.base``.

- Use ``CitationMixin`` as one of the base classes for the models

  in ``torch_ecg.models``.

- Allow dummy (empty) preprocessor managers, a warning instead of an

  error is raised in such cases.

- Enhance error message for the computation of metrics.

- Add keyword argument ``requires_grad`` and ``include_buffers`` to

  the ``torch_ecg.utils.utils_nn.compute_module_size`` function.

  The ``dtype`` argument is removed as the data type of the model

  is now inferred from the model itself.

- Improve several database reader classes: ``CPSC2018``, ``CPSC2021``,

  ``CINC2017``, ``ApneaECG``, ``MITDB``, ``SPH``.

- Add asymmetric zero pad for convolution layers, so that when

  ``stride = 1`` and ``kernel_size`` is even, strict ``"same"``

  padding is conducted.

- Use loggers instead of ``print`` in database reader classes.

- Integrate code coverage into the CI workflow. The coverage report

  is generated and uploaded to Codecov.

- More unit tests are added, and the existing ones are updated.

  Code coverage is largely improved.

Deprecated

~~~~~~~~~~

- Drop compatibility for ``tqdm`` < 4.29.1

Removed

~~~~~~~

- Remove unused rpeaks detection methods in the ``torch_ecg.utils.rpeaks``

  module.

- Remove ``_normalize_leads`` method in ``LUDB`` database reader class.

- Remove unused functions in the file of the ``CPSC2020`` database reader

  class.

Fixed

~~~~~

- Fix bugs in the config class ``torch_ecg.cfg.CFG``.

- Fix errors in the ``plot`` method of ``CINC2020`` and ``CINC2021``

  database reader classes.

Security

~~~~~~~~

- `CVE-2007-4559 <https://github.com/advisories/GHSA-gw9q-c7gh-j9vm>`__

  patch: Fix a potential security vulnerability in the

  ``torch_ecg.utils.download.http_get`` function.

`0.0.25 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.23...v0.0.25>`__ - 2022-10-08

----------------------------------------------------------------------------------------

Added

~~~~~

- Add docstring utility function ``remove_parameters_returns_from_docstring``

  in ``torch_ecg.utils.misc``.

- Add abstract property ``database_info`` to the base class ``_DataBase`` in

  ``torch_ecg.databases.base`` so that when implementing a new database reader

  class that inherits from the base class, its ``DataBaseInfo`` must be

  implemented and assigned to the property.

- Add method ``get_citation`` to the base abstract class ``_DataBase`` in

  ``torch_ecg.databases.base`` which enhances the process for getting citations

  for the databases.

- Add database reader class ``CACHET_CADB`` for the CACHET-CADB database in

  ``torch_ecg.databases.other_databases``.

- Add ``download`` method for the base abstract class ``CPSCDataBase`` in

  ``torch_ecg.databases.base``.

Changed

~~~~~~~

- Improve the warning message for passing an non-existing path when

  initializing a database reader class.

- Change the default behavior of the ``download`` method for

  ``PhysioNetDataBase`` class: default to download the compressed

  version of the database.

- Update the ``README`` file in the ``torch_ecg/databases`` directory.

Fixed

~~~~~

- Use ``register_buffer`` in custom loss classes for constant tensors

  to avoid potential device mismatch issues.

- Rename and update the data file ``physionet_dbs.csv.tar.gz`` to

  ``physionet_dbs.csv.gz`` to comply with the changement of the

  ``pandas.read_csv`` function from version 1.4.x to 1.5.x.

- Fix the incorrect usage of ``NoReturn`` type hints. It is replaced

  with ``None`` to indicate that the function/method does not return

  anything.

0.0.24 - 2022-08-13 [YANKED]

-----------------------------

This release was yanked.

`0.0.23 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.22...v0.0.23>`__ - 2022-08-09

----------------------------------------------------------------------------------------

Added

~~~~~

- Add ``collate_fn`` as an optional argument for ``BaseTrainer`` class

  in ``torch_ecg.components.trainers``.

Changed

~~~~~~~

- Let ``db_dir`` attribute of the database reader classes be absolute

  when instantiated, to avoid potential ``pathlib`` errors.

- Update utility function `torch_ecg.utils.utils_nn.adjust_cnn_filter_lengths``:

  avoid assigning unnecessary fs to dict-type config items; change default

  value of the ``pattern`` argument from ``"filter_length|filt_size"`` to

  ``"filter_length|filter_size"`` to avoid unintended changement of configs

  for ``BlurPool`` (in ``torch_ecg.models._nets``).

- Enhance error message for ``BlurPool`` in ``torch_ecg.models._nets``.

`0.0.22 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.21...v0.0.22>`__ - 2022-08-05

----------------------------------------------------------------------------------------

Changed

~~~~~~~

- Make utility function ``torch_ecg.utils.utils_data.default_collate_fn``

  support ``dict`` type batched data.

- Update docstrings of several metrics utility functions in

  ``torch_ecg.utils.utils_metrics``.

`0.0.21 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.20...v0.0.21>`__ - 2022-08-01

----------------------------------------------------------------------------------------

Added

~~~~~

- Add utility function ``get_kwargs`` in ``torch_ecg.utils.misc`` for

  getting (keyword) arguments from a function/method.

- Add AHA diagnosis statements in ``torch_ecg.databases.aux_data``.

- Add argument ``reset_index`` to the utility function

  ``torch_ecg.utils.utils_data.stratified_train_test_split``.

- Add ``typing-extensions`` as a dependency in the ``requirements.txt``

  file.

- Add database reader class ``QTDB`` for the QTDB database in

  ``torch_ecg.databases.physionet_databases``.

Changed

~~~~~~~

- Enhance data handling (typicall when using the ``load_data`` method of

  the database reader classes) with precise dtypes via

  ``torch_ecg.cfg.DEFAUTLS``.

- Update the setup of optimizer for the base trainer class

  ``torch_ecg.components.trainers.BaseTrainer``.

- Update the ``DataBaseInfo`` class for the ``SPH`` database.

- Update the ``README`` file in the ``torch_ecg/databases`` directory.

- Update plotted figures of the benchmark studies.

- Rename ``SequenceLabelingOutput`` to ``SequenceLabellingOutput``

  (typo fixed) in the ``torch_ecg.components.outputs`` module.

- Enhance docstring of ``LUDB`` database reader class via updating its

  ``DataBaseInfo`` class.

- Append the ``_ls_rec`` method as the last step in the ``download``

  method of the database reader classes.

- Change ``torch_ecg.utils.utils_data.ECGWaveForm`` from a ``namedtuple``

  to a ``dataclass``.

Removed

~~~~~~~

- ``bib_lookup.py`` is removed from the project. It is now delivered in

  an isolated package ``bib_lookup`` published on PyPI, and added as a

  dependency in the ``requirements.txt`` file.

- Remove unnecessary script ``exec_git.py``.

- Remove ``joblib`` in the ``requirements.txt`` file.

`0.0.20 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.19...v0.0.20>`__ - 2022-06-15

----------------------------------------------------------------------------------------

Added

~~~~~

- Add database reader class ``SPH`` for the SPH database in

  ``torch_ecg.databases.other_databases``.

- Add ``dataclass`` ``DataBaseInfo`` for storing information of a

  database. It has attributes ``title``, ``about``, ``note``,

  ``usage``, ``issues``, ``reference``, etc., and has a method

  ``format_database_docstring`` for formatting the docstring of a

  database reader class. The generated docstring can be assigned to

  corresponding database reader class via the ``add_docstring``

  decorator (in ``torch_ecg.utils.misc``).

- Add default cache directory ``~/.cache/torch_ecg`` for storing

  downloaded data files, model weight files, etc.

- Add helper function ``is_compressed_file`` for checking if a file is

  compressed in ``torch_ecg.utils.download``.

`0.0.19 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.18...v0.0.19>`__ - 2022-06-09

----------------------------------------------------------------------------------------

Added

~~~~~

- Add argument ``relative`` to the utility function ``get_record_list_recursive3``.

- Add attribute ``_df_records`` to the database reader classes. The attribute

  stores the DataFrame of the records of the database, containing paths to the

  records and other information (labels, demographics, etc.).

Fixed

~~~~~

- Fix bugs in the download utility function ``http_get``.

- Fix bugs in the database reader classe ``CPSC2021``.

`0.0.18 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.16...v0.0.18>`__ - 2022-06-05

----------------------------------------------------------------------------------------

Added

~~~~~

- Add property ``in_channels`` for the models.The number of input channels

  is stored as a private attribute ``_in_channels``, and the property

  ``in_channels`` makes it easier to access the value.

- Add warning message to the ``download`` method of the ``CPSC2019`` database

  reader class.

- Add ``get_absolute_path`` method for the database reader classes to

  uniformly handle the path operations.

Changed

~~~~~~~

- All all absolute imports are replaced with relative imports.

- Update citation and images for several benchmark studies

- Update the ``downlaod`` link for the ``CPSC2019`` database reader class

  (ref. property ``torch_ecg.databases.CPSC2019.url``).

Removed

~~~~~~~

- Remove the ``torch_ecg.utils.misc.deprecate_kwargs`` decorator. It is

  delivered in an isolated package ``deprecate_kwargs`` published on PyPI,

  and added as a dependency in the ``requirements.txt`` file.

Fixed

~~~~~

- Fix errors in the ``_ls_rec`` method of the ``CPSC2019`` database reader

  class.

- Fix bugs in the ``torch_ecg.utils.misc.deprecate_kwargs`` decorator.

- Fix the issue that ``tensorboardX`` is incompatible with the latest version

  of ``protobuf``.

0.0.17 - 2022-05-03 [YANKED]

-----------------------------

This release was yanked.

`0.0.16 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.15...v0.0.16>`__ - 2022-04-28

----------------------------------------------------------------------------------------

Added

~~~~~

- Add method ``_categorize_records`` for the ``MITDB`` database reader class,

  categorize records by specific attributes. Related helper properties

  ``beat_types_records`` and ``rhythm_types_records`` are added.

- Add method ``_aggregate_stats`` for the ``MITDB`` database reader class.

  Related helper properties ``df_stats`` and ``db_stats`` are added.

- Add  function ``cls_to_bin`` for converting categorical (typically multi-label)

  class labels to binary class labels (2D array with 0/1 values).

- Add context manager ``torch_ecg.utils.misc.timeout`` for setting a timeout for

  a block of code.

- Add context manager ``torch_ecg.utils.misc.Timer`` to time the execution of

  a block of code.

- Add module ``torch_ecg.components.inputs`` for input data classes.

- Add class ``Spectrogram`` (in ``torch_ecg.utils``) for generating spectrogram

  input data. This class is modified from the ``torchaudio.transforms.Spectrogram``.

- Add decorator ``torch_ecg.utils.misc.deprecate_kwargs`` for deprecating keyword

  arguments of a function/method.

- Top-level module ``torch_ecg.ssl`` for self-supervised learning methods and

  models is introduced, but not implemented yet.

- Add helper function ``torch_ecg.utils.utils_nn.compute_sequential_output_shape``

  to simplify the computation of output shape of sequential models.

- ``mobilenet_v3`` model is added to the ``torch_ecg.models`` module. It is

  now available as a cnn backbone choice for the ``ECG_CRNN`` model (and for other

  downstream task models).

Changed

~~~~~~~

- Use ``numpy``'s default ``rng`` for random number generation in place

  of ``np.random`` and Python built-in ``random`` module.

- Update the ``README`` file.

- Move the function ``generate_weight_mask`` from ``CPSC2021`` dataset

  to ``torch_ecg.utils.utils_data``.

- Database reader ``MITDB`` is enhanced: add properties ``df_stats_expanded``;

  add arguments ``beat_types`` and ``rhythm_types`` to the data and annotation

  loading methods.

- Downloading function ``http_get`` is enhanced to support downloading

  normal files other than compressed files.

- Update ``__init__`` file of the ``torch_ecg.utils`` module.

- Database reader class ``CinC2017`` is updated: add property ``_validation_set``.

- The ``ECG_UNET`` model is simplified by removing the unnecessary zero padding

  along the channel axis.

- Update the ``README`` file.

Deprecated

~~~~~~~~~~

- Keyword argument ``batch_norm`` in model building blocks (ref. ``torch_ecg.models``)

  is deprecated. Use ``norm`` instead.

Removed

~~~~~~~

- Redundant functions in ``torch_ecg.utils.utils_interval`` are removed:

  ``diff_with_step``, ``mask_to_intervals``.

Fixed

~~~~~

- Remove redudant code for the ``ECG_UNET`` model which might cause error in

  computing output shapes.

`0.0.15 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.14...v0.0.15>`__ - 2022-04-14

----------------------------------------------------------------------------------------

Changed

~~~~~~~

- Use ``pathlib.Path.parents`` instead of sequence of ``pathlib.Path..parent``

  to get the parent directory of a file path.

- Type hints and docstrings of some database reader classes are enhanced:

  ``ApneaECG``, ``CINC2020``, ``CINC2021``.

- Update the ``README`` file: add citation information for the package.

`0.0.14 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.13...v0.0.14>`__ - 2022-04-10

----------------------------------------------------------------------------------------

Added

~~~~~

- Implements the lead-wise mechanism (as a method ``_assign_weights_lead_wise``)

  for the ``Conv_Bn_Activation`` layer in the ``torch_ecg.models._nets`` module.

- Implements ``assign_weights_lead_wise`` for model ``MultiScopicCNN``

  (in ``torch_ecg.models``).

- Zenodo configuration file ``.zenodo.json`` is added.

Changed

~~~~~~~

- Update the ``README`` file: add ``:point_right: [Back to TOC](#torch_ecg)``

  to the end of long sections.

Fixed

~~~~~

- Fix errors in the computation of classification metrics.

`0.0.13 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.12...v0.0.13>`__ - 2022-04-09

----------------------------------------------------------------------------------------

Added

~~~~~

- Add metrics computation class ``WaveDelineationMetrics`` for evaluating the

  performance of ECG wave delineation models.

- Add methods for computing the metrics to the output classes (in the module

  ``torch_ecg.components.outputs``).

- Add script ``push2pypi.sh`` for pushing the package to PyPI.

- Add attribute ``global_pool_size`` to the configuration of the classification

  models (``torch_ecg.models.ECG_CRNN``).

Changed

~~~~~~~

- ``flake8`` check ignore list is updated.

- ``README`` is updated.

Removed

~~~~~~~

- Usage of ``easydict`` is removed. Now we use ``torch_ecg.cfg.CFG`` for

  configuration.

Fixed

~~~~~

- Computation of the metric of `mean_error` for ECG wave delineation is corrected.

- Fix bugs in ``SpaceToDepth`` layer (``torch_ecg.models.resnet``).

`0.0.12 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.11...v0.0.12>`__ - 2022-04-05

----------------------------------------------------------------------------------------

Changed

~~~~~~~

- Some out-of-date ``sample-data`` files are updated, unnecessary files

  are removed.

- Passing a path that does not exist to a database reader class now raises

  no error, but a warning is issued instead.

- Include ``isort`` and ``flake8`` in the code formatting and linting steps.

  Code are reformatted and linted.

`0.0.11 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.10...v0.0.11>`__ - 2022-04-03

----------------------------------------------------------------------------------------

Changed

~~~~~~~

- Docstrings are cleaned up.

- Unit tests are updated.

`0.0.10 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.9...v0.0.10>`__ - 2022-04-01

----------------------------------------------------------------------------------------

Added

~~~~~

- Add ``BibLookup`` class for looking up BibTeX entries from DOIs

  of papers related to datasets and models.

- Add ``RPeaksDetectionMetrics`` class to the ``torch_ecg.components.metrics``

  module for evaluating the performance of R-peaks detection models.

- Add CI workflow for running tests via GitHub Actions.

Changed

~~~~~~~

- The loading methods (``load_data``, ``load_ann``, etc.) of the database

  reader classes are enhanced to accept ``int`` type record name argument

  (``rec``), which redirects to the record with the corresponding index

  in the ``all_records`` attribute of the database reader class.

`0.0.9 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.8...v0.0.9>`__ - 2023-03-30

----------------------------------------------------------------------------------------

Added

~~~~~

- Add decorator ``add_docstring`` for adding/modifying docstrings of functions

  and classes.

- Add method ``append`` for the ``BaseOutput`` class.

- Add several metrics computation functions in ``torch_ecg/utils/utils_metrics.py``:

   - ``confusion_matrix``

   - ``ovr_confusion_matrix``

   - ``auc``

   - ``accuracy``

   - ``f_measure``

   - ``QRS_score``

- Add top-level module ``torch_ecg.components``.

- Add classes for metrics computation to the ``torch_ecg.components.metrics`` module.

Changed

~~~~~~~

- ``Dataset`` classes and corresponding config classes are added to the

  ``__init__.py`` file of the ``torch_ecg.databases.dataset`` module

  so that they can be imported directly from the module.

- Logger classes, output classes, and trainer classes are moved to the new

  module ``torch_ecg.components``.

- Callbacks in ``BaseTrainer`` are enhanced, allowing empty monitor, and allowing

  non-positive number of checkpoints to be saved (i.e., no checkpoint is saved).

`0.0.8 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.7...v0.0.8>`__ - 2022-03-29

----------------------------------------------------------------------------------------

Fixed

~~~~~

- Bugs in extracting compressed files in the ``http_get`` function

  of the ``utils.download`` module.

Security

~~~~~~~~

`0.0.7 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.6...v0.0.7>`__ - 2022-03-28

----------------------------------------------------------------------------------------

Fixed

~~~~~

- Import errors for early versions of pytorch.

- Cached table of PhysioNet databases is added as ``package_data`` in

  ``setup.py`` to avoid the error of missing the table file when

  installing the package.

Security

~~~~~~~~

`0.0.6 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.5...v0.0.6>`__ - 2022-03-28

----------------------------------------------------------------------------------------

Added

~~~~~

- Add methods ``__len__`` and ``__getitem__`` for the base class

  ``torch_ecg.databases.base._DataBase``.

Changed

~~~~~~~

- The base class of ``CPSC2021`` is changed from ``CPSCDataBase`` to

  ``PhysioNetDataBase``.

- Function ``compute_output_shape`` is enhanced to support different

  paddings in two ends of the input signal.

- ``README`` is updated.

- Docstrings of many classes and functions are updated.

- ``black`` is used for code formatting.

`0.0.5 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.4...v0.0.5>`__ - 2022-03-27

----------------------------------------------------------------------------------------

Added

~~~~~

- Add cached table of PhysioNet databases as a data file

  stored in the package.

- Add ``requests`` as a dependency in the ``requirements.txt`` file.

Changed

~~~~~~~

- An optional argument ``btype`` is added to the function

  ``butter_bandpass_filter`` to specify the type of the filter:

  ``"lohi"``, ``"hilo"``.

- A ``compressed`` argument is added to the ``download`` method of the

  ``PhysioNetDataBase`` class to specify whether to download the

  compressed version of the database.

Fixed

~~~~~

- Fix bugs in the function ``preprocess_multi_lead_signal``.

`0.0.4 <https://github.com/DeepPSP/torch_ecg/compare/v0.0.2...v0.0.4>`__ - 2022-03-26

----------------------------------------------------------------------------------------

Added

~~~~~

- Add ``ReprMixin`` class for better representation of the classes

  (e.g., models, preprocessors, database readers, etc.).

- Added model_dir to default config.

- Add ``Dataset`` classes for generating input data for the models:

   - ``CINC2020``

   - ``CINC2021``

   - ``CPSC2019``

   - ``CPSC2021``

   - ``LUDB``

- Add ``sample-data`` directory for storing sample data for testing.

- Add ``url`` property to the database classes.

- Add utility functions for the computation of metrics.

- Add ``BeatAnn`` class for better annotation of ECG beats.

- Add download utility functions.

- Add ``Output`` classes for the models. The output classes are used to

  store the output of the models and provide methods for post-processing.

Changed

~~~~~~~

- Manipulation of custom preprocessor classes is enhanced.

- ``SizeMixin`` class is improved for better computation of the sizes of the models.

- Replace ``os`` with ``pathlib``, which is more flexible for path operations.

- Several database reader classes are updated: mitdb, ltafdb.

- Improve ``PhysioNetDataBase`` by using wfdb built-in methods of

  getting database version string and downloading the database.

- Update the ``README`` file.

Removed

~~~~~~~

- Unnecessary imports are removed.

Fixed

~~~~~

- Fix bugs in the ``flush`` method of the ``TxtLogger``.

0.0.3 - 2022-03-24 [YANKED]

-----------------------------

This release was yanked.

`0.0.2 <https://github.com/DeepPSP/torch_ecg/releases/tag/v0.0.2>`__ - 2022-03-04

----------------------------------------------------------------------------------------

Added

~~~~~

- Add ``Preprocessor`` classes for ECG data preprocessing (ref.

  ``torch_ecg.preprocessors``).

- Add ``Augmenter`` classes for ECG data augmentation (ref.

  ``torch_ecg.augmenters``).

- Add database reader classes for reading ECG data from different

  sources (ref. ``torch_ecg.databases``).

- Add model classes for ECG signal analysis, including classification,

  segmentation (R-peak detection, wave delineation, etc., ref.

  ``torch_ecg.models``).

- Add several benchmark studies for ECG signal analysis tasks:

   - CinC2020, multi-label classification.

   - CinC2021, multi-label classification.

   - CPSC2019, QRS detection.

   - CPSC2020, single-label classification.

   - CPSC2021, single-label classification.

   - LUDB, wave delineation.

  ref. the ``benchmarks`` directory of the project.

- Add documentation for the project (ref. ``docs`` directory).

- Add CodeQL action for security analysis (ref. ``.github/workflows``).

- Add unit tests for the project (ref. ``test`` directory).

0.0.1 - 2022-03-03 [YANKED]

-----------------------------

This release was yanked.