Merge pull request #253 from EIT-ALIVE/233_documention_jwisse

docs: build documentation using mkdocs
EIT-ALIVE · Oct 16, 2024 · 4082346 · 4082346
2 parents 4bc88e1 + c946919
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diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -3,25 +3,21 @@ permissions:
   contents: write
 
 on:
+  workflow_dispatch:
   push:
     branches:
       - main
-      - drcandacemakedamoore/improve_docu
-  pull_request:
-    types: [opened, synchronize, reopened, ready_for_review]
-    branches:
-      - main
-      - drcandacemakedamoore/improve_docu
 
 jobs:
   build-documentation:
-    if: github.event.pull_request.draft == false
     name: Build documentation
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with: 
+          fetch-depth: 0
       - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
@@ -34,14 +30,8 @@ jobs:
       - name: Upgrade pip and install dependencies
         run: |
           python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install .[dev,publishing]
-      - name: Install pandoc using apt
-        run: sudo apt install pandoc
+          python3 -m pip install .[docs]
       - name: Build documentation
-        run: make html
-        working-directory: docs
-      - name: Publish Docs to Pages
-        uses: JamesIves/github-pages-deploy-action@4.1.1
-        with:
-          branch: gh-pages
-          folder: docs/_build/html
+        run: mkdocs build
+      - name: Deploy documentation
+        run: mkdocs gh-deploy
diff --git a/.gitignore b/.gitignore
@@ -36,3 +36,5 @@ venv3
 **/test_data/*
 .helpers/dock_test_data/*
 .helpers/dock_test_add/*
+
+/site/
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
@@ -6,22 +6,20 @@
 | License        | [![github license badge](https://img.shields.io/github/license/EIT-ALIVE/eitprocessing)](git@github.com:EIT-ALIVE/eitprocessing)                                                                                                                                                                                                                                                                                                                                                                             |
 | Citation       | [![DOI](https://zenodo.org/badge/617944717.svg)](https://zenodo.org/badge/latestdoi/617944717)                                                                                                                                                                                                                                                                                                                                                                                                               |
 | Fairness       | [![OpenSSF Best Practices](https://www.bestpractices.dev/projects/9147/badge)](https://www.bestpractices.dev/projects/9147) [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu)                                                                                                                                                                                                  |
-| GitHub Actions | ![build](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/build.yml/badge.svg) ![dash_actions](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/dash_actions.yml/badge.svg) ![lint](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/lint.yml/badge.svg) ![documentation](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/documentation.yml/badge.svg) ![cffconvert](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/cffconvert.yml/badge.svg) |
+| GitHub Actions | ![build](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/build.yml/badge.svg) ![lint](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/lint.yml/badge.svg) ![documentation](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/documentation.yml/badge.svg) ![cffconvert](https://github.com/EIT-ALIVE/eitprocessing/actions/workflows/cffconvert.yml/badge.svg) |
 | Python         | ![Python](https://img.shields.io/badge/python-3.10-blue.svg)                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
 
 # Contents <!-- omit in toc -->
 
-- [What is eitprocessing?](#what-is-eitprocessing)
+- [Introduction](#introduction)
 - [Installation](#installation)
-  - [Virtual environment](#virtual-environment)
-  - [Install using `pip`](#install-using-pip)
+  - [Install from PyPi](#install-from-pypi)
+    - [Developer install](#developer-install)
 - [Documentation](#documentation)
 - [Contributing](#contributing)
 - [Credits](#credits)
 
-# What is eitprocessing?
-
-Processing of data from electrical impedance tomography and other respiratory monitoring tools.
+# Introduction
 
 [Electrical Impedance Tomography](https://en.wikipedia.org/wiki/Electrical_impedance_tomography) (EIT) is a noninvasive
 and radiation-free continuous imaging tool for monitoring respiratory mechanics. eitprocessing aims to provide a
@@ -36,40 +34,39 @@ and Timpel, as well as data from other sources. Several pre-processing tools and
 
 [eit_dash](https://github.com/EIT-ALIVE/eit_dash) provides an accompanying GUI.
 
-We welcome any [contributions or suggestions](CONTRIBUTING.md)
 
-# Installation
 
-## Virtual environment
+# Installation
 
 It is advised to install eitprocessing in a dedicated virtual environment. See e.g. [Install packages in a virtual
 environment using pip and
 venv](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/) or [Getting started
 with conda](https://docs.conda.io/projects/conda/en/stable/user-guide/getting-started.html).
 
-For conda (using 'eit-alive' as example environment name; you can choose your own):
+## Install from PyPi
+
+eitprocessing can be installed from PyPi as follows:
+
 ```
-conda create -n eit-alive python=3.10
-conda activate eit-alive
+pip install eitprocessing
 ```
 
-## Install using `pip`
-
-eitprocessing can be installed from PyPi as follows:
+### Developer install
+For full developer options (testing, etc): 
 
-- For basic use: `pip install eitprocessing`
-- For full developer options (testing, etc): 
-  - `git clone git@github.com:EIT-ALIVE/eitprocessing.git`
-  - `cd eitprocessing`
-  - `pip install -e ".[dev]"`
+```
+git clone git@github.com:EIT-ALIVE/eitprocessing.git
+cd eitprocessing
+pip install -e ".[dev]"
+```
 
 # Documentation
 
-Please see our [usage documentation](https://eit-alive.github.io/eitprocessing/) for a detailed explanation of the package.
+Please see our [user documentation](https://eit-alive.github.io/eitprocessing/) for a detailed explanation of the package.
 
 # Contributing
 
-If you want to contribute to the development of eitprocessing,
+We welcome any contributions or suggestions. If you want to contribute to the development of eitprocessing,
 have a look at the [contribution guidelines](CONTRIBUTING.md) and the [developer documentation](README.dev.md).
 
 # Credits

diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/_templates/.gitignore b/docs/_templates/.gitignore
diff --git a/docs/api/categories.md b/docs/api/categories.md
@@ -0,0 +1,3 @@
+# Categories
+
+::: eitprocessing.categories.Category
diff --git a/docs/api/datacontainers.md b/docs/api/datacontainers.md
@@ -0,0 +1,17 @@
+# Data containers
+
+::: eitprocessing.datahandling.sequence.Sequence
+
+::: eitprocessing.datahandling.eitdata.EITData
+
+::: eitprocessing.datahandling.continuousdata.ContinuousData
+
+::: eitprocessing.datahandling.sparsedata.SparseData
+
+::: eitprocessing.datahandling.intervaldata.IntervalData
+
+::: eitprocessing.datahandling.datacollection.DataCollection
+
+::: eitprocessing.datahandling.breath.Breath
+
+::: eitprocessing.datahandling.event.Event
diff --git a/docs/api/features.md b/docs/api/features.md
@@ -0,0 +1,6 @@
+# Feature extraction
+
+::: eitprocessing.features.breath_detection.BreathDetection
+
+
+::: eitprocessing.features.moving_average.MovingAverage
diff --git a/docs/api/filters.md b/docs/api/filters.md
@@ -0,0 +1,12 @@
+# Filters
+
+::: eitprocessing.filters.butterworth_filters.LowPassFilter
+
+::: eitprocessing.filters.butterworth_filters.HighPassFilter
+
+::: eitprocessing.filters.butterworth_filters.BandStopFilter
+
+::: eitprocessing.filters.butterworth_filters.BandPassFilter
+
+::: eitprocessing.filters.butterworth_filters.ButterworthFilter
+
diff --git a/docs/api/loading.md b/docs/api/loading.md
@@ -0,0 +1,3 @@
+# Loading functions
+
+::: eitprocessing.datahandling.loading.load_eit_data
diff --git a/docs/api/parameters.md b/docs/api/parameters.md
@@ -0,0 +1,3 @@
+# Parameters
+
+::: eitprocessing.parameters.eeli.EELI
diff --git a/docs/basic_example.md b/docs/basic_example.md
@@ -0,0 +1 @@
+Under construction
diff --git a/docs/code_of_conduct_doc.md b/docs/code_of_conduct_doc.md
@@ -0,0 +1,3 @@
+
+
+--8<-- "CODE_OF_CONDUCT.md"
diff --git a/docs/conf.py b/docs/conf.py
diff --git a/docs/contributing_doc.md b/docs/contributing_doc.md
@@ -0,0 +1,3 @@
+
+
+--8<-- "CONTRIBUTING.md"
diff --git a/docs/css/material.css b/docs/css/material.css
@@ -0,0 +1,5 @@
+/* Indentation. */
+div.doc-contents:not(.first) {
+    padding-left: 25px;
+    border-left: .1rem solid var(--md-typeset-table-color);
+}
diff --git a/docs/developers.rst b/docs/developers.rst
diff --git a/docs/index.md b/docs/index.md
@@ -0,0 +1,23 @@
+
+# Welcome to EITprocessing
+
+# Introduction
+
+Welcome to the documentation of the ALIVE software tool designed to load, analyze, and extract parameters from Electrical Impedance Tomography (EIT) data. 
+This software was designed by a joined effort of the Rotterdam Advanced Respiratory Care research group (ROTARC) of the Intensive Care of the Erasmus Medical Center and the Netherlands e-Science center.  [Grant ID: NLESC.OEC.2022.002](https://research-software-directory.org/projects/alive)
+
+EIT is a bedside non-invasive lung imaging tool: it continuously and real-time visualizes changes in lung volume. Our software tool  serves as a comprehensive solution for handling EIT data from multiple leading manufacturers, including Sentec, Dräger, and Timpel.
+
+The software tool includes a back-end for researchers that are familair with programming [eitprocessing](https://github.com/EIT-ALIVE/eitprocessing) and also a user-friendly dashboard [eit_dash](https://github.com/EIT-ALIVE/eit_dash) for clinical researchers allowing to quickly import datasets from various formats and sources and perform processing and analysis. This documentation page concerns eitprocessing. 
+
+Our tool offers robust analysis features. From basic filters to advanced signal processing techniques, you can extract meaningful parameters from your EIT data. With our dashboard we aim to provide default analysis pipelines and many opportunities for customization according to the user needs. Visualizations and interactive graphs make it easy to interpret the results and understand the underlying physiological processes.
+
+It is important to note that the software tool is a work in progress, so not all fuctionalities are available yet. If you would like to contribute to coding you can reach out to us. 
+
+## Getting Started
+To start using our software you can you use the [installation](installation.md) guide to set up the software on your system. Once installed, you can load your first dataset and explore the basic features. 
+We are committed to supporting your journey with EIT data analysis and extraction. If you encounter any issues or have questions you can put a pull request via github or emailadres. 
+
+
+
+