Fix the documentation issue #174

.github/workflows/build-windows-executable-app.yaml

@@ -195,6 +195,7 @@ jobs:
         $content.version = $VERSION
         $content | ConvertTo-Json -Depth 100 | Set-Content settings.json
 
+
     - name: Download package as artifact
       uses: actions/download-artifact@v4
       with:
@@ -209,7 +210,7 @@ jobs:
         cp -r openms-package/share ../share
 
     - name: Set up Python (regular distribution)
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ env.PYTHON_VERSION }} # Use the same version as the embeddable version
 
@@ -258,15 +259,7 @@ jobs:
 
     - name: Create .bat file
       run: |
-        echo '@echo off' > ${{ env.APP_NAME }}.bat
-        echo '' >> ${{ env.APP_NAME }}.bat
-        echo 'REM Create .streamlit directory in user''s home if it doesn''t exist' >> ${{ env.APP_NAME }}.bat
-        echo 'if not exist "%USERPROFILE%\.streamlit" mkdir "%USERPROFILE%\.streamlit"' >> ${{ env.APP_NAME }}.bat
-        echo '' >> ${{ env.APP_NAME }}.bat
-        echo 'REM Create credentials.toml with empty email to disable email prompt' >> ${{ env.APP_NAME }}.bat
-        echo 'copy /Y ".streamlit\credentials.toml" "%USERPROFILE%\.streamlit\credentials.toml" > nul' >> ${{ env.APP_NAME }}.bat
-        echo '' >> ${{ env.APP_NAME }}.bat
-        echo 'start /min .\python-${{ env.PYTHON_VERSION }}\python -m streamlit run app.py local' >> ${{ env.APP_NAME }}.bat
+          echo " start /min .\python-${{ env.PYTHON_VERSION }}\python -m streamlit run app.py local" > ${{ env.APP_NAME }}.bat
 
     - name: Create All-in-one executable folder
       run: |

.github/workflows/ci.yml

@@ -28,5 +28,4 @@ jobs:
         pip install pytest
     - name: Test
       run: |
-        python -m pytest test_gui.py tests/
-
+        python -m pytest test_gui.py

.streamlit/config.toml

@@ -1,14 +1,11 @@
-[browser]
-gatherUsageStats = false
-
 [global]
 developmentMode = false
 
 [server]
-maxUploadSize =  200 #MB
 port = 8501 # should be same as configured in deployment repo
 
 [theme]
+
 # The preset Streamlit theme that your custom theme inherits from. One of "light" or "dark".
 # base =
 
@@ -25,4 +22,4 @@ primaryColor = "#29379b"
 # textColor =
 
 # Font family for all text in the app, except code blocks. One of "sans serif", "serif", or "monospace".
-# font =
+# font =

content/file_upload.py

@@ -3,27 +3,14 @@
 import streamlit as st
 import pandas as pd
 
-from src.common.common import (
-    page_setup,
-    save_params,
-    v_space,
-    show_table,
-    TK_AVAILABLE,
-    tk_directory_dialog,
-)
+from src.common.common import page_setup, save_params, v_space, show_table, TK_AVAILABLE, tk_directory_dialog
 from src import fileupload
 
 params = page_setup()
 
 st.title("File Upload")
 
-# Check if there are any files in the workspace
-mzML_dir = Path(st.session_state.workspace, "mzML-files")
-if not any(Path(mzML_dir).iterdir()):
-    # No files present, load example data
-    fileupload.load_example_mzML_files()
-
-tabs = ["File Upload"]
+tabs = ["File Upload", "Example Data"]
 if st.session_state.location == "local":
     tabs.append("Files from local folder")
 
@@ -41,74 +28,55 @@
             else:
                 st.warning("Select files first.")
 
+# Example mzML files
+with tabs[1]:
+    st.markdown("Short information text on example data.")
+    cols = st.columns(3)
+    if cols[1].button("Load Example Data", type="primary"):
+        fileupload.load_example_mzML_files()
+
 # Local file upload option: via directory path
 if st.session_state.location == "local":
-    with tabs[1]:
+    with tabs[2]:
         st_cols = st.columns([0.05, 0.95], gap="small")
         with st_cols[0]:
             st.write("\n")
             st.write("\n")
-            dialog_button = st.button(
-                "📁",
-                key="local_browse",
-                help="Browse for your local directory with MS data.",
-                disabled=not TK_AVAILABLE,
-            )
+            dialog_button = st.button("📁", key='local_browse', help="Browse for your local directory with MS data.", disabled=not TK_AVAILABLE)
             if dialog_button:
-                st.session_state["local_dir"] = tk_directory_dialog(
-                    "Select directory with your MS data",
-                    st.session_state["previous_dir"],
-                )
+                st.session_state["local_dir"] = tk_directory_dialog("Select directory with your MS data", st.session_state["previous_dir"])
                 st.session_state["previous_dir"] = st.session_state["local_dir"]
         with st_cols[1]:
             # with st.form("local-file-upload"):
-            local_mzML_dir = st.text_input(
-                "path to folder with mzML files", value=st.session_state["local_dir"]
-            )
+            local_mzML_dir = st.text_input("path to folder with mzML files", value=st.session_state["local_dir"])
         # raw string for file paths
         local_mzML_dir = rf"{local_mzML_dir}"
         cols = st.columns([0.65, 0.3, 0.4, 0.25], gap="small")
-        copy_button = cols[1].button(
-            "Copy files to workspace", type="primary", disabled=(local_mzML_dir == "")
-        )
-        use_copy = cols[2].checkbox(
-            "Make a copy of files",
-            key="local_browse-copy_files",
-            value=True,
-            help="Create a copy of files in workspace.",
-        )
+        copy_button = cols[1].button("Copy files to workspace", type="primary", disabled=(local_mzML_dir == ""))
+        use_copy = cols[2].checkbox("Make a copy of files", key="local_browse-copy_files", value=True, help="Create a copy of files in workspace.")
         if not use_copy:
-            st.warning(
-                "**Warning**: You have deselected the `Make a copy of files` option. "
-                "This **_assumes you know what you are doing_**. "
-                "This means that the original files will be used instead. "
-            )
+                st.warning(
+        "**Warning**: You have deselected the `Make a copy of files` option. "
+        "This **_assumes you know what you are doing_**. "
+        "This means that the original files will be used instead. "
+    )
         if copy_button:
             fileupload.copy_local_mzML_files_from_directory(local_mzML_dir, use_copy)
 
+mzML_dir = Path(st.session_state.workspace, "mzML-files")
 if any(Path(mzML_dir).iterdir()):
     v_space(2)
     # Display all mzML files currently in workspace
-    df = pd.DataFrame(
-        {
-            "file name": [
-                f.name
-                for f in Path(mzML_dir).iterdir()
-                if "external_files.txt" not in f.name
-            ]
-        }
-    )
-
+    df = pd.DataFrame({"file name": [f.name for f in Path(mzML_dir).iterdir() if "external_files.txt" not in f.name]})
+
     # Check if local files are available
     external_files = Path(mzML_dir, "external_files.txt")
     if external_files.exists():
         with open(external_files, "r") as f_handle:
             external_files = f_handle.readlines()
             external_files = [f.strip() for f in external_files]
-            df = pd.concat(
-                [df, pd.DataFrame({"file name": external_files})], ignore_index=True
-            )
-
+            df = pd.concat([df, pd.DataFrame({"file name": external_files})], ignore_index=True)
+
     st.markdown("##### mzML files in current workspace:")
     show_table(df)
     v_space(1)

docs/installation.md

@@ -11,20 +11,6 @@ Select the latest successfull run and download the zip file from the artifacts s
 
 Clone the [streamlit-template repository](https://github.com/OpenMS/streamlit-template). It includes files to install dependencies via pip or conda.
 
-### via pip in a new Python environment
-
-Create a virtual environment
-
-`python3 -m venv <myenvpath>`
-
-Activate the virtual environment
-
-`source .venv/bin/activate`
-
-To install all required depdencies via pip in the new Python environment, run the following command in the terminal:
-
-`pip install -r requirements.txt`
-
 ### via pip in an existing Python environment
 
 To install all required depdencies via pip in an already existing Python environment, run the following command in the terminal:

docs/user_guide.md

@@ -15,29 +15,18 @@ In the OpenMS web application, workspaces are designed to keep your analysis org
 - **Workspace Specific Parameters and Files**: Each workspace stores parameters and files (uploaded input files and results from workflows).
 - **Persistence**: Your workspaces and parameters are saved, so you can return to your analysis anytime and pick up where you left off. Simply bookmark the page!
 
+## Online and Local Mode Differences
+
+- **File Uploads**:
+  - *Local Mode*: Multiple file uploads are supported, giving you flexibility when working with large datasets.
+  - *Online Mode (Not Enabled in This Deployment)*: When enabled, file uploads may be limited to one file at a time to optimize server performance.
 
-### File Uploads
-- **Online Mode**: You can upload only one file at a time. This helps manage server load and optimizes performance.
-
-- **Local Mode**: Multiple file uploads are supported, giving you flexibility when working with large datasets. Additionally, the file size upload limit can be adjusted in the following ways:
-  1. **Using `.streamlit/config.toml`**:
-     - You can modify the `.streamlit/config.toml` file and set the `maxUploadSize` parameter to your desired value. By default, this is set to 200MB.
-     - Example:
-       ```toml
-       [server]
-       maxUploadSize = 500  # Set the upload limit to 500MB
-       ```
-  2. **Using CLI Command**:
-     - You can customize the file size upload limit directly when running the application using the `--server.maxUploadSize` argument.
-     - Example:
-       ```bash
-       python run_app.py --server.maxUploadSize 500
-       ```
-     - This sets the upload limit to 500MB for the current session.
-
 - **Workspace Access**:
-  - In online mode, workspaces are stored temporarily and will be cleared after seven days of inactivity.
-  - In local mode, workspaces are saved on your local machine, allowing for persistent storage. Workspace directory can be specified in the `settings.json`. Defaults to `..` (parent directory).
+  - *Local Mode*: Workspaces are saved on your local machine, allowing for persistent storage.  
+    - The workspace directory can be specified in `settings.json` .  
+    - Defaults to `..` (parent directory).
+  - *Online Mode (Not Enabled in This Deployment)*: If enabled, workspaces would be temporarily stored and cleared after seven days of inactivity.
+
 
 ## Downloading Results