add site_radius parameter, which fixes the site radius for analysis

src/gemdat/dashboard/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .gemdash import gemdash
+
+__all__ = ['gemdash']

src/gemdat/dashboard/_shared.py

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+from __future__ import annotations
+
+import base64
+import os
+from importlib.resources import files
+from pathlib import Path
+from tkinter import filedialog
+
+import streamlit as st
+
+data_directory = Path(files('gemdat') / 'data')  # type: ignore
+
+
+def get_trajectory_location(filename='vasprun.xml'):
+    if trajectory_location := os.environ.get('VASP_XML'):
+        st.info(f'Got `{trajectory_location}` via environment variable.')
+        return Path(trajectory_location)
+
+    trajectory_location = st.session_state.get('trajectory_location',
+                                               default=filename)
+
+    st.markdown('Select input trajectory')
+    col1, col2 = st.columns([0.7, 0.3])
+    with col1:
+        trajectory_location = st.text_input('filename',
+                                            trajectory_location,
+                                            label_visibility='collapsed')
+    with col2:
+        if st.button('Browse'):
+            trajectory_location = filedialog.askopenfilename()
+            st.session_state.trajectory_location = trajectory_location
+            st.experimental_rerun()
+
+    if not trajectory_location:
+        st.info(f'Select `{filename}` to continue')
+        st.stop()
+
+    trajectory_location = Path(trajectory_location).expanduser()
+
+    if not trajectory_location.exists():
+        st.info(
+            f'Could not find `{trajectory_location}`, select `{filename}` to continue'
+        )
+        st.stop()
+
+    return trajectory_location
+
+
+@st.cache_data
+def get_base64_of_bin_file(png_file):
+    with open(png_file, 'rb') as f:
+        data = f.read()
+    return base64.b64encode(data).decode()
+
+
+def build_markup_for_logo(png_file,
+                          background_position='50% 2%',
+                          margin_top='0%',
+                          image_width='60%',
+                          image_height='',
+                          anchor='stSidebar'
+                          # anchor='stSidebarNav'  # Anchor to navigation
+                          ):
+    binary_string = get_base64_of_bin_file(png_file)
+    return f"""
+            <style>
+                [data-testid="{anchor}"] {{
+                    background-image: url("data:image/png;base64,{binary_string}");
+                    background-repeat: no-repeat;
+                    background-position: {background_position};
+                    margin-top: {margin_top};
+                    background-size: {image_width} {image_height};
+                }}
+            </style>
+            """
+
+
+def add_sidebar_logo():
+    """Based on: https://stackoverflow.com/a/73278825."""
+    png_file = data_directory / 'logo.png'
+    logo_markup = build_markup_for_logo(png_file)
+    st.markdown(
+        logo_markup,
+        unsafe_allow_html=True,
+    )

src/gemdat/dashboard/gemdash.py

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+from __future__ import annotations
+
+import argparse
+import sys
+from importlib.resources import files
+from pathlib import Path
+
+from streamlit.web.cli import main
+
+dashboard_directory = Path(files('gemdat') / 'dashboard')  # type: ignore
+
+
+def gemdash():
+    parser = argparse.ArgumentParser(
+        prog='gemdash',
+        add_help=False,
+        description='Streamlit dashboard for easily visualizing gemdat data')
+    parser.add_argument('--file',
+                        '-f',
+                        nargs='?',
+                        default='vasprun.xml',
+                        help='File to load in gemdash')
+    parser.add_argument('--help',
+                        action='count',
+                        default=0,
+                        help='specify twice to print streamlit help')
+
+    arguments, unknown = parser.parse_known_args(sys.argv[1:])
+    if arguments.help == 1:
+        parser.print_help()
+        return
+    if arguments.help == 2:
+        unknown.append('--help')
+
+    run_file = str(dashboard_directory / 'run.py')
+
+    sys.argv = [
+        *('streamlit', 'run', run_file),
+        *('--theme.base', 'light'),
+        *('--theme.primaryColor', 'e03c31'),
+        *('--theme.secondaryBackgroundColor', 'bcd9ec'),
+        *('--browser.gatherUsageStats', 'false'),
+        *unknown,
+        '--',
+        *('--file', arguments.file),
+    ]
+
+    main()