Merge pull request #45 from axelwalter/main

update README and main page

README.md

@@ -1,73 +1,19 @@
-# OpenMS streamlit template [![Open Template!](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://abi-services.cs.uni-tuebingen.de/streamlit-template/)
+# OpenMS streamlit template 
 
-This is a template app for OpenMS workflows in a web application.
+[![Open Template!](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://abi-services.cs.uni-tuebingen.de/streamlit-template/)
 
-## Requires
-
-Python <= 3.10
+This repository contains a template app for OpenMS workflows in a web application using the **streamlit** framework. It serves as a foundation for apps ranging from simple workflows with **pyOpenMS** to complex workflows utilizing **OpenMS TOPP tools** with parallel execution. It includes solutions for handling user data and parameters in workspaces as well as deployment with docker-compose.
 
 ## Features
 
 - Workspaces for user data with unique shareable IDs
+- Persistent parameters and input files within a workspace
+- local and online mode
 - Captcha control
-- Deployment with Docker
-- Packaged executables for Windows (built via GitHub action)
-- Automatic removal of unused workspaces
-- Parameters persist within a workspace
-
-## Key concepts
-
-**Workspaces** 
-
-Directories where all data generated and uploaded can be stored as well as a workspace specific parameter file.
-
-**Run the app locally and online**
-
-Launching the app with the `local` argument let's the user create/remove workspaces. In the online the user gets a workspace with a specific ID.
-
-**Parameters**
-
-Parameters (defaults in `assets/default-params.json`) store changing parameters for each workspace. Parameters are loaded via the page_setup function at the start of each page. To track a widget variable via parameters simply give them a key and add a matching entry in the default parameters file. Initialize a widget value from the params dictionary.
-
-```python
-params = page_setup()
-
-st.number_input(label="x dimension", min_value=1, max_value=20,
-value=params["example-y-dimension"], step=1, key="example-y-dimension")
-
-save_params()
-```
-
-
-## Code structure
-
-- **Pages** must be placed in the `pages` directory.
-- It is recommended to use a separate file for defining functions per page in the `src` directory.
-- The `src/common.py` file contains a set of useful functions for common use (e.g. rendering a table with download button).
-
-## App layout
-
-- Main page contains explanatory text on how to use the app and a workspace selector.
-- Sidebar contains the OpenMS logo, settings panel and a workspace indicator. The main page contains a workspace selector as well.
-- See pages in the template app for example use cases. The content of this app serves as a documentation.
+- Packaged executables for Windows
+- framework for workflows with OpenMS TOPP tools
+- Deployment [with docker-compose](https://github.com/OpenMS/streamlit-deployment)
 
-## Modify the template to build your own app
+## Documentation
 
-- in `src/common.py` update the name of your app and the repository name
-- in `clean-up-workspaces.py` update the name of the workspaces directory to `/workspaces-<your-repository-name>`
-    - e.g. for the streamlit template it's "/workspaces-streamlit-template"
-- chose one of the Dockerfiles depending on your use case:
-    - `Dockerfile` build OpenMS including TOPP tools
-    - `Dockerfile_simple` uses pyOpenMS only
-- update the Dockerfile:
-    - with the `GITHUB_USER` owning the streamlit app repository
-    - with the `GITHUB_REPO` name of the streamlit app repository
-    - if your main streamlit file is not called `app.py` modfify the following line
-        - `RUN echo "mamba run --no-capture-output -n streamlit-env streamlit run app.py" >> /app/entrypoint.sh`
-- update Python package dependency files:
-    - `requirements.txt` if using `Dockerfile_simple`
-    - `environment.yml` if using `Dockerfile`
-- update `README.md`
-- for the Windows executable package:
-    - update `datas` in `run_app_temp.spec` with the Python packages required for your app
-    - update main streamlit file name to run in `run_app.py`
+Documentation for **users** and **developers** is included as pages in [this template app](https://abi-services.cs.uni-tuebingen.de/streamlit-template/), indicated by the 📖 icon.

app.py

@@ -34,6 +34,18 @@ def main():
     Display main page content.
     """
     st.title("OpenMS Streamlit Template App")
+    st.info("""
+This repository contains a template app for OpenMS workflows in a web application using the **streamlit** framework. It serves as a foundation for apps ranging from simple workflows with **pyOpenMS** to complex workflows utilizing **OpenMS TOPP tools** with parallel execution. It includes solutions for handling user data and parameters in workspaces as well as deployment with docker-compose.
+""")
+    st.subheader("Features")
+    st.markdown("""
+- Workspaces for user data with unique shareable IDs
+- Persistent parameters and input files within a workspace
+- Captcha control
+- Packaged executables for Windows
+- framework for workflows with OpenMS TOPP tools
+- Deployment [with docker-compose](https://github.com/OpenMS/streamlit-deployment)
+""")
     st.subheader("Quick Start")
     if Path("OpenMS-App.zip").exists():
         st.markdow("""
@@ -50,7 +62,11 @@ def main():
         st.markdown("""
 Extract the zip file and run the executable (.exe) file to launch the app. Since every dependency is compressed and packacked the app will take a while to launch (up to one minute).
 """)
-
+    st.markdown("""
+Check out the documentation for **users** and **developers** is included as pages indicated by the 📖 icon
+
+Try the example pages **📁 mzML file upload**, **👀 visualization** and **example workflows**.
+""")
     save_params(params)