apscale-gui 3.2.0__tar.gz → 3.2.2__tar.gz

{apscale_gui-3.2.0/apscale_gui.egg-info → apscale_gui-3.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apscale_gui
-Version: 3.2.0
+Version: 3.2.2
 Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
 Home-page: https://github.com/TillMacher/apscale_gui
 Author: Till-Hendrik Macher
@@ -26,6 +26,7 @@ Requires-Dist: streamlit-file-browser>=3.2.22
 Requires-Dist: scipy>=1.16.1
 Requires-Dist: cutadapt>=5.1
 Requires-Dist: update-checker>=0.18.0
+Requires-Dist: update_checker
 Requires-Dist: powerlaw>=1.5
 Requires-Dist: requests>=2.32.3
 Requires-Dist: beautifulsoup4>=4.13.4

{apscale_gui-3.2.0 → apscale_gui-3.2.2}/apscale_gui/apscale_gui.py

@@ -5,6 +5,7 @@ import streamlit as st
 from streamlit_file_browser import st_file_browser
 import importlib
 from update_checker import update_check
+from update_checker import UpdateChecker
 from pathlib import Path
 import glob
 import pandas as pd
@@ -129,6 +130,21 @@ large datasets—potentially billions of sequences—at high speed, without requ
 memory. This makes it especially useful for scaling up analyses.
                     """
 
+def check_package_update_disp(packages):
+    for pkg in packages:
+        installed_version = importlib.metadata.version(pkg)
+        checker = UpdateChecker()
+        result = checker.check(pkg, installed_version)
+        if result:
+            st.sidebar.info(f'{result}\n\n$ pip install --upgrade {pkg}')
+
+def get_package_versions_disp(pkg):
+    try:
+        version = importlib.metadata.version(pkg)
+        return version
+    except importlib.metadata.PackageNotFoundError:
+        return
+
 def check_dependencies(tools=["cutadapt", "vsearch", "swarm", "blastn"]):
     missing = []
     for tool in tools:
@@ -612,7 +628,10 @@ def main():
 
     # Sidebar inputs & outputs
     with st.sidebar:
-        st.subheader("APSCALE projects")
+        apscale_gui_version = get_package_versions_disp("apscale_gui")
+        st.markdown(f"# APSCALE-GUI v{apscale_gui_version}")
+        check_package_update_disp(["apscale_gui", "apscale", "apscale_blast", "boldigger3"])
+        st.divider()
 
         # read user_data.txt
         script_path = Path(__file__).resolve()
@@ -923,6 +942,8 @@ def main():
 
                 if st.session_state["P5 Primer (5' - 3')"] == '' or st.session_state["P7 Primer (5' - 3')"] == '' or st.session_state['min length'] == '' or st.session_state['max length'] =='':
                     st.error('Please fill out all required fields!')
+                elif float(st.session_state["sequence group threshold"]) >= 1:
+                    st.error('Please choose a sequence group threshold > 1.\n\nESVs are generated seperately!')
                 else:
                     if st.session_state['run_apscale_mode'] == 'Run apscale (basic mode)':
                         st.info('The "Basic mode" mode skips "Replicate merging" and "NC removal".')
@@ -1021,19 +1042,16 @@ def main():
                             subprocess.Popen(cmd, creationflags=subprocess.DETACHED_PROCESS | subprocess.CREATE_NEW_PROCESS_GROUP)
                         st.success("APSCALE analysis module started — it will open in a new browser tab.")
 
-                with st.expander("🧩 TaxonTableTools Table Conversion", expanded=False):
+                with st.expander("🧩 TaxonTableTools2", expanded=False):
                     st.write(
-                        "Combine your read and taxonomy tables into a single, merged table. "
-                        "This format is fully compatible with TaxonTableTools for downstream analyses "
-                        "and provides a more convenient structure for working with your data."
-                    )
-                    available_read_tables = {Path(i).name: Path(i) for i in glob.glob(str(project_folder / '11_read_table' / 'data' / '*_read_table_*.xlsx'))}
-                    available_taxonomy_tables = {Path(i).name: Path(i) for i in glob.glob(str(project_folder / '11_read_table' / 'data' / 'blastn_*' / 'blastn_*.xlsx'))}
-                    st.selectbox(label='Read table', key='TTT_read_table', options=list(available_read_tables.keys()))
-                    st.selectbox(label='Taxonomy table', key='TTT_taxonomy_table', options=list(available_taxonomy_tables.keys()))
-
-                    if st.button('Merge tables'):
-                        merge_tables(available_read_tables[st.session_state['TTT_read_table']], available_taxonomy_tables[st.session_state['TTT_taxonomy_table']])
+                        "Combine your read and taxonomy tables into a single, merged table for TaxonTableTools2.\n\n"
+                        "TaxonTableTools2 (TTT) is an easy-to-use graphical software designed for the analysis"
+                        "and visualization of DNA metabarcoding data. It enables biologists and researchers"
+                        "without bioinformatics experience to explore taxonomic datasets quickly, reproducibly,"
+                        "and interactively through a modern graphical user interface."
+                        )
+                    if st.button('Learn More'):
+                        webbrowser.open("https://github.com/TillMacher/TaxonTableTools2")
 
         ############################################################################################################
         st.markdown("---")

{apscale_gui-3.2.0 → apscale_gui-3.2.2/apscale_gui.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apscale_gui
-Version: 3.2.0
+Version: 3.2.2
 Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
 Home-page: https://github.com/TillMacher/apscale_gui
 Author: Till-Hendrik Macher
@@ -26,6 +26,7 @@ Requires-Dist: streamlit-file-browser>=3.2.22
 Requires-Dist: scipy>=1.16.1
 Requires-Dist: cutadapt>=5.1
 Requires-Dist: update-checker>=0.18.0
+Requires-Dist: update_checker
 Requires-Dist: powerlaw>=1.5
 Requires-Dist: requests>=2.32.3
 Requires-Dist: beautifulsoup4>=4.13.4

{apscale_gui-3.2.0 → apscale_gui-3.2.2}/apscale_gui.egg-info/requires.txt

@@ -12,6 +12,7 @@ streamlit-file-browser>=3.2.22
 scipy>=1.16.1
 cutadapt>=5.1
 update-checker>=0.18.0
+update_checker
 powerlaw>=1.5
 requests>=2.32.3
 beautifulsoup4>=4.13.4

{apscale_gui-3.2.0 → apscale_gui-3.2.2}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="apscale_gui",
-    version="3.2.0",
+    version="3.2.2",
     author="Till-Hendrik Macher",
     author_email="macher@uni-trier.de",
     description="Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface",
@@ -29,6 +29,7 @@ setuptools.setup(
                         "scipy>=1.16.1",
                         "cutadapt>=5.1",
                         "update-checker>=0.18.0",
+                        "update_checker",
                         "powerlaw>=1.5",
                         "requests>=2.32.3",
                         "beautifulsoup4>=4.13.4",