Merge pull request OpenMS#39 from axelwalter/main

Add CI

.github/workflows/build-docker-images.yml

@@ -0,0 +1,27 @@
+name: Docker Image CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+
+  build-full-app:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Build the full Docker image
+      run: docker build . --file Dockerfile --tag streamlitapp:latest
+
+  build-simple-app:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Build the Docker image (pyOpenMS only)
+      run: docker build . --file Dockerfile_simple --tag streamlitapp-simple:latest

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

@@ -1,5 +1,9 @@
 name: Build executable for Windows
-on: [push]
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
 
 jobs:
   build-openms:

.github/workflows/pylint.yml

@@ -0,0 +1,24 @@
+name: Pylint
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files '*.py') --disable=C0103,C0114,C0301,C0411,W0212,W0631,W0602,W1514,W2402,E0401,E1101,F0001,R1732 --errors-only

.github/workflows/workflow-tests.yml

@@ -0,0 +1,25 @@
+name: Test workflow functions
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest
+    - name: Running test cases
+      run: |
+        pytest test.py

README.md

@@ -2,6 +2,10 @@
 
 This is a template app for OpenMS workflows in a web application.
 
+## Requires
+
+Python <= 3.10
+
 ## Features
 
 - Workspaces for user data with unique shareable IDs

app.py

@@ -1,43 +1,65 @@
-import streamlit as st
-from src.common import *
-from pathlib import Path
+"""
+Main page for the OpenMS Template App.
+
+This module sets up and displays the Streamlit app for the OpenMS Template App.
+It includes:
+- Setting the app title.
+- Displaying a description.
+- Providing a download button for the Windows version of the app.
+
+Usage:
+Run this script to launch the OpenMS Template App.
+
+Note:
+- If run in local mode, the CAPTCHA control is not applied.
+- If not in local mode, CAPTCHA control is applied to verify the user.
+
+Returns:
+    None
+"""
+
 import sys
 
-from src.captcha_ import *
+from pathlib import Path
+import streamlit as st
+
+from src.captcha_ import captcha_control
+from src.common import page_setup, save_params
 
 params = page_setup(page="main")
 
+
 def main():
+    """
+    Display main page content.
+    """
     st.title("Template App")
     st.markdown("## A template for an OpenMS streamlit app.")
     if Path("OpenMS-App.zip").exists():
         st.markdown("## Installation")
         with open("OpenMS-App.zip", "rb") as file:
             st.download_button(
-                    label="Download for Windows",
-                    data=file,
-                    file_name="OpenMS-App.zip",
-                    mime="archive/zip",
-                    type="primary"
-                )
+                label="Download for Windows",
+                data=file,
+                file_name="OpenMS-App.zip",
+                mime="archive/zip",
+                type="primary",
+            )
     save_params(params)
 
+
 # Check if the script is run in local mode (e.g., "streamlit run app.py local")
 if "local" in sys.argv:
     # In local mode, run the main function without applying captcha
     main()
 
 # If not in local mode, assume it's hosted/online mode
 else:
-
     # WORK LIKE MULTIPAGE APP
-    if 'controllo' not in st.session_state or st.session_state['controllo'] == False:
-
+    if "controllo" not in st.session_state or st.session_state["controllo"] is False:
         # Apply captcha control to verify the user
         captcha_control()
 
-    else:     
+    else:
         # Run the main function
         main()
-
-

clean-up-workspaces.py

@@ -15,7 +15,9 @@
 threshold = current_time - (86400 * 7)
 
 # Print current time
-print(f"Current Time: {datetime.utcfromtimestamp(current_time).strftime('%Y-%m-%d %H:%M:%S UTC')}\n")
+print(
+    f"Current Time: {datetime.utcfromtimestamp(current_time).strftime('%Y-%m-%d %H:%M:%S UTC')}\n"
+)
 
 # Collect remaining dirctories to print out later
 remaining_directories = []
@@ -25,14 +27,16 @@
     if directory.is_dir():
         # Get the directory's modification time
         modification_time = os.path.getmtime(directory)
-        
+
         # Check if the modification time is less than the threshold
         if modification_time < threshold:
             # Calculate the time difference in seconds
             time_difference = current_time - modification_time
-            
+
             # Print the directory name and the time difference in minutes
-            print(f"Deleting directory: {directory.name}, Last Modified: {time_difference / 86400:.1f} days ago")
+            print(
+                f"Deleting directory: {directory.name}, Last Modified: {time_difference / 86400:.1f} days ago"
+            )
 
             # Remove workspace
             shutil.rmtree(directory)
@@ -43,10 +47,12 @@
 if remaining_directories:
     print(f"\nRemaining directories in {workspaces_directory.name}:")
     for directory in remaining_directories:
-        print(f"{directory.name}, Last Modified: {(current_time - os.path.getmtime(directory)) / 60:.2f} minutes ago")
+        print(
+            f"{directory.name}, Last Modified: {(current_time - os.path.getmtime(directory)) / 60:.2f} minutes ago"
+        )
 else:
     print(f"\n{workspaces_directory.name} is empty.")
 
 
 # Print separator
-print(100*"-")
+print(100 * "-")

environment.yml

@@ -3,15 +3,15 @@ name: streamlit-env
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
-  - plotly
-  - pip
-  - numpy
-  - pandas
-  - mono
+  - python==3.10
+  - plotly==5.18.0
+  - pip==23.3
+  - numpy==1.25.2
+  - pandas==2.1.2
+  - mono==6.12.0.90
   - pip: # dependencies only available through pip
       # streamlit dependencies
-    - streamlit
-    - streamlit-plotly-events
-    - streamlit-aggrid
-    - captcha
+    - streamlit==1.28.0
+    - streamlit-plotly-events==0.0.6
+    - streamlit-aggrid==0.3.4.post3
+    - captcha==0.5.0

hooks/hook-streamlit.py

@@ -1,7 +1,8 @@
 from PyInstaller.utils.hooks import copy_metadata
+
 datas = []
-datas += copy_metadata('streamlit')
-datas += copy_metadata('streamlit_plotly_events')
-datas += copy_metadata('pyopenms') 
-datas += copy_metadata('captcha') 
-datas += copy_metadata('pyarrow')
+datas += copy_metadata("streamlit")
+datas += copy_metadata("streamlit_plotly_events")
+datas += copy_metadata("pyopenms")
+datas += copy_metadata("captcha")
+datas += copy_metadata("pyarrow")

pages/0_📁_File_Upload.py

@@ -3,14 +3,14 @@
 import streamlit as st
 import pandas as pd
 
-from src.common import *
-from src.fileupload import *
-from src.captcha_ import *
+from src.captcha_ import captcha_control
+from src.common import page_setup, save_params, v_space, show_table
+from src import fileupload
 
 params = page_setup()
 
 # If run in hosted mode, show captcha as long as it has not been solved
-if 'controllo' not in st.session_state or params["controllo"] == False:
+if "controllo" not in st.session_state or params["controllo"] is False:
     # Apply captcha by calling the captcha_control function
     captcha_control()
 
@@ -25,11 +25,12 @@
 with tabs[0]:
     with st.form("mzML-upload", clear_on_submit=True):
         files = st.file_uploader(
-            "mzML files", accept_multiple_files=(st.session_state.location == "local"))
+            "mzML files", accept_multiple_files=(st.session_state.location == "local")
+        )
         cols = st.columns(3)
         if cols[1].form_submit_button("Add files to workspace", type="primary"):
             if files:
-                save_uploaded_mzML(files)
+                fileupload.save_uploaded_mzML(files)
             else:
                 st.warning("Select files first.")
 
@@ -38,42 +39,45 @@
     st.markdown("Short information text on example data.")
     cols = st.columns(3)
     if cols[1].button("Load Example Data", type="primary"):
-        load_example_mzML_files()
+        fileupload.load_example_mzML_files()
 
 # Local file upload option: via directory path
 if st.session_state.location == "local":
     with tabs[2]:
         # with st.form("local-file-upload"):
-        local_mzML_dir = st.text_input(
-            "path to folder with mzML files")
+        local_mzML_dir = st.text_input("path to folder with mzML files")
         # raw string for file paths
-        local_mzML_dir = r"{}".format(local_mzML_dir)
+        local_mzML_dir = rf"{local_mzML_dir}"
         cols = st.columns(3)
-        if cols[1].button("Copy files to workspace", type="primary", disabled=(local_mzML_dir == "")):
-            copy_local_mzML_files_from_directory(local_mzML_dir)
+        if cols[1].button(
+            "Copy files to workspace", type="primary", disabled=(local_mzML_dir == "")
+        ):
+            fileupload.copy_local_mzML_files_from_directory(local_mzML_dir)
 
 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()]})
+    df = pd.DataFrame({"file name": [f.name for f in Path(mzML_dir).iterdir()]})
     st.markdown("##### mzML files in current workspace:")
     show_table(df)
     v_space(1)
     # Remove files
     with st.expander("🗑️ Remove mzML files"):
-        to_remove = st.multiselect("select mzML files",
-                                   options=[f.stem for f in sorted(mzML_dir.iterdir())])
+        to_remove = st.multiselect(
+            "select mzML files", options=[f.stem for f in sorted(mzML_dir.iterdir())]
+        )
         c1, c2 = st.columns(2)
-        if c2.button("Remove **selected**", type="primary", disabled=not any(to_remove)):
-            params = remove_selected_mzML_files(to_remove, params)
+        if c2.button(
+            "Remove **selected**", type="primary", disabled=not any(to_remove)
+        ):
+            params = fileupload.remove_selected_mzML_files(to_remove, params)
             save_params(params)
             st.rerun()
 
         if c1.button("⚠️ Remove **all**", disabled=not any(mzML_dir.iterdir())):
-            params = remove_all_mzML_files(params)
+            params = fileupload.remove_all_mzML_files(params)
             save_params(params)
             st.rerun()
 
-save_params(params)
+save_params(params)