Merge pull request #21 from yardenmezi/docs-update

Docs update
NirLab-TAU · Dec 31, 2024 · 4e8b123 · 4e8b123
2 parents a2dc5da + 61b4d5e
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diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -1,6 +1,9 @@
 {{ name | escape | underline}}
 
 .. currentmodule:: {{ module }}
+.. tip::
+      |{{ name }}|
+
 
 .. autoclass:: {{ objname }}
    :members:

diff --git a/docs/api.rst b/docs/api.rst
@@ -4,5 +4,9 @@ API Reference
 .. toctree::
    :maxdepth: 2
 
-   base
    pipeline
+
+.. toctree::
+   :hidden:
+
+   base
diff --git a/docs/base/sleepeegpy.base.BaseEventPipe.rst b/docs/base/sleepeegpy.base.BaseEventPipe.rst
@@ -3,6 +3,10 @@
 
 .. currentmodule:: sleepeegpy.base
 
+.. tip::
+      |BaseEventPipe|
+
+
 .. autoclass:: BaseEventPipe
    :members:
    :show-inheritance:

diff --git a/docs/base/sleepeegpy.base.BaseHypnoPipe.rst b/docs/base/sleepeegpy.base.BaseHypnoPipe.rst
@@ -3,6 +3,10 @@
 
 .. currentmodule:: sleepeegpy.base
 
+.. tip::
+      |BaseHypnoPipe|
+
+
 .. autoclass:: BaseHypnoPipe
    :members:
    :show-inheritance:

diff --git a/docs/base/sleepeegpy.base.BasePipe.rst b/docs/base/sleepeegpy.base.BasePipe.rst
@@ -3,6 +3,10 @@
 
 .. currentmodule:: sleepeegpy.base
 
+.. tip::
+      |BasePipe|
+
+
 .. autoclass:: BasePipe
    :members:
    :show-inheritance:

diff --git a/docs/base/sleepeegpy.base.SpectrumPlots.rst b/docs/base/sleepeegpy.base.SpectrumPlots.rst
@@ -3,6 +3,10 @@
 
 .. currentmodule:: sleepeegpy.base
 
+.. tip::
+      |SpectrumPlots|
+
+
 .. autoclass:: SpectrumPlots
    :members:
    :show-inheritance:

diff --git a/docs/conf.py b/docs/conf.py
@@ -11,7 +11,7 @@
 import inspect
 import shutil
 from pathlib import Path
-
+sys.path.insert(0, os.path.abspath('./notebooks'))
 sys.path.append(os.path.abspath(".."))
 
 project = "sleepeegpy"
@@ -29,7 +29,31 @@
     "sphinx.ext.linkcode",
     "sphinx.ext.autosummary",
     "myst_nb",
+    "nbsphinx",
 ]
+html_logo = "sleepEEGpy.png"
+
+rst_epilog = """
+.. |AbstractClass| replace:: 🚨 **Abstract Class**  - 
+   This class is **abstract** and cannot be used directly.  
+   Subclass it and implement the required methods.
+
+.. |ExamplePipe| replace:: 💡 **Usage Examples**  - 
+   See the notebook for usage examples and code snippets:
+
+.. |CleaningPipe| replace:: |ExamplePipe| :doc:`/notebooks/1_cleaning`
+.. |ICAPipe| replace:: |ExamplePipe| :doc:`/notebooks/2_ica`
+.. |SpectralPipe| replace:: |ExamplePipe| :doc:`/notebooks/4_spectral`
+.. |GrandSpectralPipe| replace:: |ExamplePipe| :doc:`/notebooks/5_grand spectral`
+.. |SpindlesPipe| replace:: |ExamplePipe| :doc:`/notebooks/6_spindles`
+.. |SlowWavesPipe| replace:: |ExamplePipe| :doc:`/notebooks/7_slow_waves`
+.. |RapidEyeMovementsPipe| replace:: |ExamplePipe| :doc:`/notebooks/8_rems`
+
+.. |BasePipe| replace:: |AbstractClass|
+.. |BaseEventPipe| replace:: |AbstractClass|
+.. |BaseHypnoPipe| replace:: |AbstractClass|
+.. |SpectrumPlots| replace:: |AbstractClass|
+"""
 
 nb_execution_mode = "off"
 # autosummary_generate = False
@@ -42,8 +66,7 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = "furo"
-html_static_path = ["_static"]
+html_theme = 'sphinx_rtd_theme'
 
 intersphinx_mapping = {
     "mne": ("https://mne.tools/stable/", None),

diff --git a/docs/index.rst b/docs/index.rst
@@ -3,18 +3,90 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to sleepeegpy's documentation!
-================================================
+sleepeegpy
+==========
 
+**sleepeegpy** is a high-level package built on top of several powerful libraries, including:
+
+- `MNE-python <https://mne.tools/stable/index.html>`_ for electrophysiological data analysis
+- `yasa <https://raphaelvallat.com/yasa/build/html/index.html>`_ for sleep staging and analysis
+- `PyPREP <https://pyprep.readthedocs.io/en/latest/>`_ for preprocessing EEG data
+- `specparam (fooof) <https://fooof-tools.github.io/fooof/>`_ for spectral analysis and parameter estimation
+
+This package is designed to streamline the preprocessing, analysis, and visualization of sleep EEG data.
+
+Additionally, the repository includes a Jupyter notebook demonstrating how to use this package, along with a ready-made workflow for common use cases.
+
+.. image:: https://github.com/user-attachments/assets/f26c2023-44fc-48d7-ba72-d0de89a5dcee
+   :alt: sleepeegpy workflow
+
+API Reference
+===============
 .. toctree::
    :maxdepth: 1
 
    notebooks
    api
 
-Indices and tables
-==================
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+Installation
+============
+
+Prerequisites
+-----
+Before installing, ensure that you have a compatible version of Python installed:
+
+- **Python Version**: `Python <https://www.python.org/downloads/>`_ version >3.9 and <3.12.
+
+Steps
+-----
+Follow these steps to install and set up **sleepeegpy**:
+
+1. **Create a Python Virtual Environment**:
+   First, create a Python virtual environment. For more information, refer to:
+
+   - `venv <https://docs.python.org/3/tutorial/venv.html>`
+   - `virtualenv <https://virtualenv.pypa.io/en/latest/user_guide.html>`
+   - `conda <https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`
+
+2. **Activate the Environment**
+
+3. **Install sleepeegpy**:
+   Run the following command to install **sleepeegpy**:
+
+   .. code-block:: bash
+      pip install sleepeegpy
+
+Usage Example
+=============
+
+The included notebooks are a great way to get started with **sleepeegpy**. They provide examples and instructions for using the package in common workflows.
+
+Steps to Use the Notebooks
+------------------
+1. **Download the Notebooks**:
+   Download the zip folder of this repository by clicking `Download <https://github.com/NirLab-TAU/sleepeegpy/archive/refs/heads/main.zip>`_. You will only need the notebooks folder.
+
+2. **Run Jupyter**:
+   Navigate to the "Pipeline Notebooks" folder and start Jupyter:
+
+   .. code-block:: bash
+      jupyter notebook
+
+3. **Open the Complete Pipeline Notebook**:
+   Open the `complete_pipeline` notebook using Jupyter Notebook within the activated environment and follow the instructions provided in the notebook.
+
+RAM Requirements
+================
+
+For high-density EEG recordings (256 channels) downsampled to 250 Hz, you will need at least 64 GB of RAM for tasks such as data cleaning, spectral analysis, and event detection.
+
+Citation
+========
+
+To cite **sleepeegpy** in your research, please use the following references:
+
+1. Belonosov, G., Falach, R., Schmidig, J.F., Aderka, M., Zhelezniakov, V., Shani-Hershkovich, R., Bar, E., Nir, Y. "SleepEEGpy: A Python-based software package to organize preprocessing, analysis, and visualization of sleep EEG data." bioRxiv (2023). doi: `https://doi.org/10.1101/2023.12.17.572046 <https://doi.org/10.1101/2023.12.17.572046>`_
+
+2. Belonosov, G., Falach, R., Schmidig, F., Aderka, M., Zhelezniakov, V., Shani-Hershkovich, R., Bar, E., & Nir, Y. (2024). SleepEEGpy: A Python-based package for preprocessing, analysis, and visualization of sleep EEG data [Dataset]. Zenodo. `https://doi.org/10.5281/ZENODO.13903088 <https://doi.org/10.5281/ZENODO.13903088>`_
+