Update README and docs (#240)

CONTRIBUTING.md

@@ -1,11 +1,14 @@
 # Contributing to SleepECG
+
 If you want to implement a new feature, fix an existing bug, or help improve SleepECG in any other way (such as adding or improving documentation), please consider submitting a [pull request](https://github.com/cbrnr/sleepecg/pulls) on GitHub. It might be a good idea to open an [issue](https://github.com/cbrnr/sleepecg/issues) beforehand and discuss your planned contributions with the developers.
 
 Before you start working on your contribution, please make sure to follow the guidelines described in this document.
 
 
 ## GitHub workflow
+
 ### Setup
+
 - Create a [fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) of the [repository](https://github.com/cbrnr/sleepecg).
 - Clone the fork to your machine:
     ```
@@ -19,6 +22,7 @@ Before you start working on your contribution, please make sure to follow the gu
 
 
 ### Add a feature or fix a bug
+
 - Create and switch to a new branch (use a self-explanatory branch name).
 - Make changes and commit them.
 - Push the changes to your remote fork.
@@ -27,6 +31,7 @@ Before you start working on your contribution, please make sure to follow the gu
 
 
 ### Rebasing
+
 If another PR is merged while you are working on something, a merge conflict may arise. To resolve it, perform the following steps in your local clone:
 - Fetch the upstream changes: `git fetch upstream`
 - Rebase your commits: `git rebase upstream/main`
@@ -35,7 +40,8 @@ If another PR is merged while you are working on something, a merge conflict may
 
 
 ## Development environment
-Make sure to use Python 3.9. You might want to [create a virtual environment](https://docs.python.org/3/library/venv.html#creating-virtual-environments) instead of working your main environment. In the root of the local clone of your fork, install SleepECG as follows:
+
+Make sure to use a supported Python version. You might want to [create a virtual environment](https://docs.python.org/3/library/venv.html#creating-virtual-environments) instead of working your main environment. In the root of the local clone of your fork, install SleepECG as follows:
 
 ```
 pip install -e ".[dev]"
@@ -45,7 +51,8 @@ When using the flag [`-e`](https://pip.pypa.io/en/stable/cli/pip_install/#instal
 
 
 ## Code style
-SleepECG adheres to [PEP 8](https://www.python.org/dev/peps/pep-0008/) and [Black](https://black.readthedocs.io/en/stable/index.html), with the following exceptions/specifications:
+
+SleepECG adheres to [PEP 8](https://www.python.org/dev/peps/pep-0008/) and [Ruff](https://astral.sh/ruff), with the following exceptions/specifications:
 - Each source file contains the following header:
     ```python
     # © SleepECG developers
@@ -57,13 +64,15 @@ SleepECG adheres to [PEP 8](https://www.python.org/dev/peps/pep-0008/) and [Blac
 
 
 ## Public API
+
 - Every non-public member (i.e. every member not intended to be accessed by an end user) is prefixed with an underscore `_`.
 - Inside a (sub-)package's `__init__.py`, public module members are imported explicitly.
 - `__all__` is never set.
 - To add a function or class to the API reference, list its _public_ name (e.g. `sleepecg.detect_heartbeats`, not `sleepecg.heartbeat_detection.detect_heartbeats`) in `doc/source/api.rst`.
 
 
 ## Documentation
+
 For docstrings, SleepECG mainly follows [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html), with the following exceptions/specifications:
 - The maximum line length is `92`.
 - For parameters that may take multiple types, pipe characters are used instead of the word `or`, for example `param_name : int | float`.
@@ -73,6 +82,7 @@ For docstrings, SleepECG mainly follows [numpydoc](https://numpydoc.readthedocs.
 
 
 ## Pre-commit
+
 Coding and documentation style are checked via a CI job. To make sure your contribution passes those checks, you can use [`pre-commit`](https://pre-commit.com/) locally. To install the hooks configured in `.pre-commit-config.yml`, run
 
 ```
@@ -83,18 +93,23 @@ inside your local clone. After that, the checks required by the CI job will be r
 
 
 ## Tests
-SleepECG uses [`pytest`](https://docs.pytest.org/) for testing. The structure of `sleepecg/test/` follows that of the package itself, e.g. the test module for `sleepecg.io.nsrr` would be `sleepecg/test/io/test_nsrr.py`. If a new test requires a package that is not part of the core dependencies (i.e. listed under `install_requires` in `setup.cfg`), make sure to add it to the optional requirement categories `dev` and `cibw`.
+
+SleepECG uses [`pytest`](https://docs.pytest.org/) for testing. The structure of `sleepecg/tests/` follows that of the package itself, e.g. the test module for `sleepecg.io.nsrr` would be `sleepecg/tests/io/test_nsrr.py`. If a new test requires a package that is not part of the core dependencies, make sure to add it to the optional requirement categories `dev` and `cibw`.
 
 To run the tests, execute
+
 ```
 pytest
 ```
+
 in the project or package root. The tests for the C extension can be excluded using
+
 ```
 pytest -m "not c_extension"
 ```
 
 ## Releases
+
 Follow these steps to release a new version of SleepECG:
 - In `src/sleepecg/__init__.py` remove the `-dev` suffix in `__version__`.
     - In case of a patch release, modify the version number accordingly.

README.md

@@ -1,6 +1,5 @@
 ![Python](https://img.shields.io/pypi/pyversions/sleepecg.svg?logo=python&logoColor=white)
 [![PyPI](https://img.shields.io/pypi/v/sleepecg)](https://pypi.org/project/sleepecg/)
-[![conda-forge](https://img.shields.io/conda/v/conda-forge/sleepecg.svg?label=conda-forge)](https://anaconda.org/conda-forge/sleepecg)
 [![Docs](https://readthedocs.org/projects/sleepecg/badge/?version=latest)](https://sleepecg.readthedocs.io/en/stable/index.html)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.05411/status.svg)](https://doi.org/10.21105/joss.05411)
 [![License](https://img.shields.io/github/license/cbrnr/sleepecg)](LICENSE)
@@ -27,12 +26,6 @@ SleepECG is available on PyPI and can be installed with [pip](https://pip.pypa.i
 pip install sleepecg
 ```
 
-Alternatively, an unofficial [conda](https://docs.conda.io/en/latest/) package is available:
-
-```
-conda install -c conda-forge sleepecg
-```
-
 SleepECG with all optional dependencies can be installed with the following command:
 
 ```
@@ -59,26 +52,6 @@ beats = detect_heartbeats(ecg, fs)  # indices of detected heartbeats
 ```
 
 
-### Dependencies
-
-SleepECG requires Python ≥ 3.9 and the following packages:
-
-- [numpy](https://numpy.org/) ≥ 1.20.0
-- [PyYAML](https://pyyaml.org/) ≥ 5.4.0
-- [requests](https://requests.readthedocs.io/en/latest/) ≥ 2.25.0
-- [scipy](https://scipy.org/) ≥ 1.7.0
-- [tqdm](https://tqdm.github.io/) ≥ 4.60.0
-
-Optional dependencies provide additional features:
-
-- [edfio](https://github.com/the-siesta-group/edfio/) ≥ 0.4.0 (read data from [MESA](https://sleepdata.org/datasets/mesa) and [SHHS](https://sleepdata.org/datasets/shhs))
-- [joblib](https://joblib.readthedocs.io/en/latest/) ≥ 1.0.0 (parallelized feature extraction)
-- [matplotlib](https://matplotlib.org/) ≥ 3.5.0 (plot ECG time courses, hypnograms, and confusion matrices)
-- [numba](https://numba.pydata.org/) ≥ 0.59.1 (JIT-compiled heartbeat detector)
-- [tensorflow](https://www.tensorflow.org/) ≥ 2.16.1 (sleep stage classification with Keras models)
-- [wfdb](https://github.com/MIT-LCP/wfdb-python/) ≥ 3.4.0 (read data from [SLPDB](https://physionet.org/content/slpdb), [MITDB](https://physionet.org/content/mitdb), and [LTDB](https://physionet.org/content/ltdb))
-
-
 ### Contributing
 
 The [contributing guide](https://github.com/cbrnr/sleepecg/blob/main/CONTRIBUTING.md) contains detailed instructions on how to contribute to SleepECG.

docs/index.md

@@ -1,47 +1,30 @@
 # SleepECG
+
 SleepECG provides tools for sleep stage classification when [EEG](https://en.wikipedia.org/wiki/Electroencephalography) signals are not available. Based only on [ECG](https://en.wikipedia.org/wiki/Electrocardiography), SleepECG provides functions for
 
 - downloading and reading open polysomnography datasets,
 - detecting heartbeats from ECG signals, and
 - classifying sleep stages (which includes preprocessing, feature extraction, and classification).
 
+
 ## Documentation
-Documentation for SleepECG is available on [Read the Docs](https://sleepecg.readthedocs.io/en/stable/index.html).
 
-## Changelog
-Check out the [changelog](https://github.com/cbrnr/sleepecg/blob/main/CHANGELOG.md) to learn what we added, changed, or fixed.
+Documentation for SleepECG is available on [Read the Docs](https://sleepecg.readthedocs.io/en/stable/index.html).
 
-## Dependencies
-SleepECG requires Python ≥ 3.9 and the following packages:
 
-- [numpy](https://numpy.org/) ≥ 1.20.0
-- [PyYAML](https://pyyaml.org/) ≥ 5.4.0
-- [requests](https://requests.readthedocs.io/en/latest/) ≥ 2.25.0
-- [scipy](https://scipy.org/) ≥ 1.7.0
-- [tqdm](https://tqdm.github.io/) ≥ 4.60.0
+## Changelog
 
-Optional dependencies provide additional features:
+Check out the [changelog](https://github.com/cbrnr/sleepecg/blob/main/CHANGELOG.md) to learn what we added, changed, or fixed.
 
-- [edfio](https://github.com/the-siesta-group/edfio/) ≥ 0.4.0 (read data from [MESA](https://sleepdata.org/datasets/mesa) and [SHHS](https://sleepdata.org/datasets/shhs))
-- [joblib](https://joblib.readthedocs.io/en/latest/) ≥ 1.0.0 (parallelized feature extraction)
-- [matplotlib](https://matplotlib.org/) ≥ 3.5.0 (plot ECG time courses, hypnograms, and confusion matrices)
-- [numba](https://numba.pydata.org/) ≥ 0.59.1 (JIT-compiled heartbeat detector)
-- [tensorflow](https://www.tensorflow.org/) ≥ 2.16.1 (sleep stage classification with Keras models)
-- [wfdb](https://github.com/MIT-LCP/wfdb-python/) ≥ 3.4.0 (read data from [SLPDB](https://physionet.org/content/slpdb), [MITDB](https://physionet.org/content/mitdb), and [LTDB](https://physionet.org/content/ltdb))
 
 ## Installation
+
 SleepECG is available on PyPI and can be installed with [pip](https://pip.pypa.io/en/stable/):
 
 ```
 pip install sleepecg
 ```
 
-Alternatively, an unofficial [conda](https://docs.conda.io/en/latest/) package is available:
-
-```
-conda install -c conda-forge sleepecg
-```
-
 SleepECG with all optional dependencies can be installed with the following command:
 
 ```
@@ -54,5 +37,7 @@ If you want the latest development version, use the following command:
 pip install git+https://github.com/cbrnr/sleepecg
 ```
 
+
 ## Contributing
+
 The [contributing guide](https://github.com/cbrnr/sleepecg/blob/main/CONTRIBUTING.md) contains detailed instructions on how to contribute to SleepECG.