From 343fdd20135ebc67c86256515ca53d26838e8b5a Mon Sep 17 00:00:00 2001
From: haeussma <83341109+haeussma@users.noreply.github.com>
Date: Wed, 14 Feb 2024 13:53:04 +0100
Subject: [PATCH] init commit

---
 .github/workflows/documentation.yml | 25 +++++++++++++++
 docs/index.md                       | 20 ++++++++++++
 docs/installation.md                |  3 ++
 docs/status.md                      |  9 ++++++
 mkdocs.yml                          | 50 +++++++++++++++++++++++++++++
 requirements.txt                    |  3 ++
 6 files changed, 110 insertions(+)
 create mode 100644 .github/workflows/documentation.yml
 create mode 100644 docs/index.md
 create mode 100644 docs/installation.md
 create mode 100644 docs/status.md
 create mode 100644 mkdocs.yml
 create mode 100644 requirements.txt

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
new file mode 100644
index 0000000..c511472
--- /dev/null
+++ b/.github/workflows/documentation.yml
@@ -0,0 +1,25 @@
+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - master
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/cache@v2
+        with:
+          path: .cache
+          key: ${{ github.ref }}
+      - run: pip install mkdocs-material
+      - run: mkdocs gh-deploy --force
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..6e68153
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,20 @@
+# EnzymeML Training Course
+
+## ℹ️ About
+The EnzymeML Training Course is a collaborative project between multiple biocatalysis groups. The aim of this project is to jointly develop computational tools, data standards, and best practices for the analysis of enzyme-catalyzed reactions. Furthermore, the project provides training for Python-based data analysis of experimental data.
+
+## 🚀 Motivation
+Current state of data analysis and implications on reproducibility and scalability...
+
+## 📚 Stages
+The project is structured into three stages, dividing the task of implementing generic analysis workflows for biocatalytic data:  
+
+### 1. 🛠️ Making experimental data accessible
+Development of generic Python tools, allowing reading in unprocessed data from various analytical sources such as spectrophotomety, chromatograph, or NMR. The tools facilitate the preprocessing of the data, concentration calculation, and the generation of EnzymeML files.
+
+### 2. 📈 Data Analysis
+Depending on the needs of the project members, existing Python tools will be used or extended to analyze the data. Experimental questions 
+Development of Python-based tools for the analysis of enzyme-catalyzed reactions.  
+
+### 3. 🤝 In-person Training Course
+Development of training materials for the use of the data standard and the Python-based tools.
\ No newline at end of file
diff --git a/docs/installation.md b/docs/installation.md
new file mode 100644
index 0000000..26ac085
--- /dev/null
+++ b/docs/installation.md
@@ -0,0 +1,3 @@
+# Installation of tools
+
+For the installation of the tools, we recommend using the following Docker image, which contains all the necessary tools and dependencies. The Docker image is based on the official Python image and comes with installs JupyterLab locally in your machine:
diff --git a/docs/status.md b/docs/status.md
new file mode 100644
index 0000000..0a46dd5
--- /dev/null
+++ b/docs/status.md
@@ -0,0 +1,9 @@
+# Project Status
+
+## Implemented Spectrophotometers
+- [x] SpectraMax M2
+- [x] Magellan
+- [ ] Infinite M200
+
+## Implemented Chromatography Systems
+- [ ] Agilent 1100
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..b7fa23f
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,50 @@
+site_name: EnzymeML Training Course
+
+nav:
+  - Home: index.md
+  - Project Status: status.md
+  - Installation: installation.md
+
+theme:
+  name: material
+  features:
+    - navigation.tabs
+    - navigation.sections
+    - toc.integrate
+    - navigation.top
+    - search.suggest
+    - search.highlight
+    - content.tabs.links
+    - content.code.select
+    - content.code.copy
+    - content.code.annotation
+  palette: 
+    # Palette toggle for light mode
+    - scheme: default
+      toggle:
+        icon: material/brightness-7 
+        name: Switch to dark mode
+
+    # Palette toggle for dark mode
+    - scheme: slate
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - tables
+  - attr_list
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+  - def_list
+  - pymdownx.tasklist:
+      custom_checkbox: true
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..3ba2daa
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,3 @@
+mkdocs==1.5.3
+mkdocs-material==9.5.9
+mkdocs-material-extensions==1.3.1