D4Xgui 1.0.0__tar.gz

d4xgui-1.0.0/.gitignore

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+
+venv/
+env/
+ENV/
+.venv/
+.env
+.env.local
+.env.*.local
+
+.streamlit/secrets.toml
+.streamlit/cache/
+.streamlit/config.toml.local
+test_assertion_results.txt
+
+docs/build/
+
+__pycache__/
+.idea/
+.vscode/
+*.code-workspace
+.ipynb_checkpoints
+*.ipynb
+
+.DS_Store
+._*
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+
+*.db
+
+*~
+.~*
+
+
+*.pyc

d4xgui-1.0.0/CHANGELOG.md

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+# Changelog
+
+## [1.0.0] - 2025-12-01 – Initial commit
+
++ Initial release of D4Xgui
++ Data I/O functionality for uploading replicate and intensity data
++ Baseline correction using m/z47.5 half-mass cup
++ Processing capabilities for D47, D48, and D49 clumped isotopes
++ Standardization results visualization
++ Dual clumped space plotting
++ Interactive data discovery and analysis
++ D47crunch integration for data processing
++ Database management for storing and retrieving pre-processed d45-d49 data
++ Save and reload functionality for session states
++ Support for multiple calibration methods using D47calib
++ Temperature calculation from D47 values
++ Excel export functionality for results
+
+## [1.0.1] - 2025-12-04
+
++ exclude `Session` and `Sample` from smart_numeric_conversion()
++ Publish D4Xgui to PyPI

d4xgui-1.0.0/D4Xgui/.streamlit/config.toml

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+[theme]
+base="dark"
+primaryColor= '#aa80f7'#aa80f7'#"#7070A0"        # Dark Purple-Blue    primaryColor="#3B4A59"        # Dark Blue for primary elements
+backgroundColor='#0E1117'#"#121212"     # Very Dark Gray for background
+secondaryBackgroundColor="#262730"  # Darker Gray for secondary background
+textColor="#FAFAFA"           # Lightest Gray for text
+font="sans serif"
+
+
+[browser]
+gatherUsageStats = false
+
+[server]
+showEmailPrompt = false
+port = 1337

d4xgui-1.0.0/D4Xgui/Welcome.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import os.path
+from pathlib import Path
+from typing import Dict, Any
+
+import streamlit as st
+import D47crunch
+
+from tools.page_config import set_page_config
+from tools import sidebar_logo
+from tools.database import init_db
+from tools.init_params import INIT_PARAMS
+
+
+
+class WelcomePageManager:
+    """Manages the welcome page content and initialization."""
+    
+    def __init__(self):
+        """Initialize the welcome page manager."""
+        self.app_dir = Path(__file__).parent.absolute()
+        self.session_state = st.session_state
+        self._setup_page()
+        self._initialize_database()
+        self._initialize_session_state()
+    
+    def _setup_page(self) -> None:
+        """Set up the page configuration and sidebar."""
+        set_page_config(0)
+        sidebar_logo.add_logo()
+    
+    def _initialize_database(self) -> None:
+        """Initialize the application database."""
+        init_db()
+    
+    def _initialize_session_state(self) -> None:
+        """Initialize session state with default parameters if not present."""
+        if 'standards_nominal' not in self.session_state:
+            self.session_state['standards_nominal'] = {**INIT_PARAMS['standards_nominal']}
+            #self.session_state['working_gas'] = {**INIT_PARAMS['working_gas']}
+    
+    def _get_info_content(self) -> str:
+        """Generate the welcome page information content.
+        
+        Returns:
+            Formatted markdown string with welcome information.
+        """
+        return rf"""## Welcome to D4Xgui v1.0.0!
+
+[D4Xgui](https://github.com/itsMig/D4Xgui) is developed to enable easy access to state-of-the-art CO₂ clumped isotope (∆₄₇, ∆₄₈ and ∆₄₉) data processing.
+A recently developed optimizer algorithm allows pre-processing of mass spectrometric raw intensities utilizing a m/z47.5 half-mass Faraday cup correction to account for the effect of a negative pressure baseline, which is essential for accurate and highest precision clumped isotope analysis of CO₂ ([Bernecker et al., 2023](https://doi.org/10.1016/j.chemgeo.2023.121803)).
+It is backed with the recently published processing tool [D47crunch (v.{D47crunch.__version__})](https://github.com/mdaeron/D47crunch) (following the methodology outlined in [Daeron, 2021](https://doi.org/10.1029/2020GC009592)), which allows standardization under consideration of full error propagation and has been used for the InterCarb community effort ([Bernasconi et al., 2021](https://doi.org/10.1029/2020GC009588)).
+This web-app allows users to discover replicate- or sample-based processing results in interactive spreadsheets and plots.
+
+<br>
+
+Example data is accessible from the Data-IO page, or can be downloaded from [GitHub](https://github.com/itsMig/D4Xgui/tree/main/D4Xgui/static).
+
+<br>
+
+In order to process post-background corrected data (Data-IO page, Upload δ⁴⁵-δ⁴⁹ replicates tab), the following columns need to be provided (`.xlsx`, `.csv`):
+
+| `UID` | `Sample` | `Session` | `Timetag` | `d45` | `d46` | `d47` | `d48` | `d49` |
+|----|----|----|----|----|----|----|----|----|
+
+$~$
+
+Baseline correction can be performed using a m/z47.5 half-mass cup. For this purpose either a set of equilibrated gases (via heated-gas-line), or carbonate standards (via target values) is used to determine m/z47, m/z48 and m/z49-specific scaling factors. Please upload a cycle-based spreadsheet (`.xlsx`, `.csv`) including the following columns (Data-IO page, Upload m/z44-m/z49 intensities tab):
+
+| `UID` | `Sample` | `Session` | `Timetag` | `Replicate` |
+|----|----|----|----|----|
+
+| `raw_r44` | `raw_r45` | `raw_r46` | `raw_r47` | `raw_r48` | `raw_r49` | `raw_r47.5` |
+|----|----|----|----|----|----|----|
+
+| `raw_s44` | `raw_s45` | `raw_s46` | `raw_s47` | `raw_s48` | `raw_s49` | `raw_s47.5` |
+|----|----|----|----|----|----|----|
+
+
+<br><br>
+Please find the [code documentation here](https://itsmig.github.io/D4Xgui/index.html).
+"""
+    
+    def _save_readme(self, content: str) -> None:
+        """Save the welcome content to README.md file.
+        
+        Args:
+            content: Content to save to README.md.
+        """
+        try:
+            with open(os.path.join(self.app_dir,'../INSTALLATION.md', ),'r') as file:
+                content += f"\n" + file.read()
+
+            readme_path = Path('../README.md')
+            readme_path.write_text(content, encoding='utf-8')
+        except Exception as e:
+            st.warning(f"Could not save README.md: {e}")
+    
+    def display_welcome_page(self) -> None:
+        """Display the welcome page content."""
+        
+        info_content = self._get_info_content()
+        # self._save_readme(info_content)
+        st.markdown(info_content, unsafe_allow_html=True)
+
+
+def main():
+    """Main function to run the welcome page."""
+    welcome_manager = WelcomePageManager()
+    welcome_manager.display_welcome_page()
+
+
+if __name__ == "__main__":
+    main()

d4xgui-1.0.0/D4Xgui/__init__.py

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+"""D4Xgui - Processing app for mass-spectrometric CO₂ clumped isotope (∆₄₇, ∆₄₈ and ∆₄₉) data"""
+
+__version__ = "1.0.0"