prismWriter 1.0.0__tar.gz

prismwriter-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 smestern
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

prismwriter-1.0.0/MANIFEST.in

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+include LICENSE
+include README.md
+include requirements.txt
+recursive-include prismWriter *.pzfx
+recursive-include prismWriter/schema *.xml

prismwriter-1.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: prismWriter
+Version: 1.0.0
+Summary: Python library for programmatically creating and manipulating GraphPad Prism (.pzfx) files
+Author: smestern
+License: MIT License
+        
+        Copyright (c) 2024 smestern
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/smestern/prismWriter
+Project-URL: Repository, https://github.com/smestern/prismWriter
+Project-URL: Documentation, https://github.com/smestern/prismWriter#readme
+Project-URL: Bug Tracker, https://github.com/smestern/prismWriter/issues
+Keywords: graphpad,prism,pzfx,data visualization,scientific,pandas
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: pandas>=1.3
+Requires-Dist: openpyxl>=3.0
+Provides-Extra: gui
+Requires-Dist: PySide2>=5.15; extra == "gui"
+Provides-Extra: web
+Requires-Dist: streamlit>=1.20; extra == "web"
+Provides-Extra: all
+Requires-Dist: PySide2>=5.15; extra == "all"
+Requires-Dist: streamlit>=1.20; extra == "all"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+
+# prismWriter
+
+Python library and GUI for programmatically creating and manipulating GraphPad Prism (`.pzfx`) files. Convert pandas DataFrames into Prism's XML-based table format with complex grouping structures.
+
+**Version:** 1.0.0
+
+## Features
+
+- Convert pandas DataFrames to GraphPad Prism format
+- Flexible grouping: main groups, sub-columns, row labels
+- Multiple interfaces: Python API, Qt GUI, and Streamlit Web interface
+- Load and modify existing `.pzfx` files
+- Validate table structure with preview functionality
+- Automatic backup creation when loading existing files
+
+## Installation
+
+```bash
+pip install -e .
+```
+
+### Requirements
+
+- Python >= 3.7
+- numpy
+- pandas
+- PySide2 (for Qt GUI)
+- streamlit >= 1.28.0 (for web interface)
+- openpyxl (for Excel file support)
+
+## Quick Start
+
+### Python API
+
+```python
+from prismWriter.prism_writer import PrismFile
+import pandas as pd
+
+# Create a new PrismFile
+pf = PrismFile()
+
+# Load your data
+df = pd.read_csv('data.csv')
+
+# Create a grouped table
+pf.make_group_table(
+    group_name="MyTable",
+    group_values=df,
+    groupby="condition",  # Main grouping column
+    cols=["value1", "value2"],  # Data columns
+    subgroupby="replicate"  # Sub-grouping
+)
+
+# Save to Prism file
+pf.save("output.pzfx")
+```
+
+### Web Interface (Streamlit)
+
+The easiest way to use prismWriter:
+
+```bash
+streamlit run prismWriter/streamlit_app.py
+```
+
+Or use the provided launch script:
+- **Windows**: `run_web.bat`
+
+Or after installation:
+```bash
+prismwriter-web
+```
+
+Features:
+- Upload CSV/Excel files (with multi-sheet Excel support)
+- Live data preview with automatic column type detection
+- Interactive grouping configuration
+- Preview table structure before generating
+- Direct download of generated `.pzfx` files
+- Load and view existing Prism files
+
+### Qt GUI
+
+```bash
+python prismWriter/gui.py
+```
+
+Or after installation:
+```bash
+prismwriter-gui
+```
+
+## API Reference
+
+### PrismFile Class
+
+```python
+pf = PrismFile(file=None)  # Create new or load existing file
+```
+
+**Methods:**
+- `load(file_path, backup=True)` - Load an existing Prism file
+- `smake_group_table(group_name, group_values, groupby=None, cols=None, subgroupby=None, rowgroupby=None, append=True)` - Create a grouped table
+- `get_table_names()` - Get list of all table names
+- `to_dataframe(table_name)` - Convert a table to pandas DataFrame
+- `save(file_path)` - Save to file
+- `write(file_path, xml_declaration=True, encoding='utf-8', pretty_print=True)` - Write with options
+- `remove_table(table_name)` - Remove a table from the file
+
+### Grouping Parameters
+
+- **`groupby`**: Main column grouping - creates separate Y-columns for each category
+- **`subgroupby`**: Sub-columns within each Y-column (string for column name, or list for data columns)
+- **`rowgroupby`**: Row labels on the vertical axis (string for column name, or list for data columns)
+- **`cols`**: Data columns to include
+
+**Note**: Use either column name (`subgroupby='condition'`) OR list of data columns (`subgroupby=['col1', 'col2']`) - not both.
+
+### Example Data Structure
+
+```python
+import pandas as pd
+from prismWriter.prism_writer import PrismFile
+
+# Sample data
+data = {
+    'treatment': ['Control', 'Control', 'Drug A', 'Drug A'],
+    'time': [0, 24, 0, 24],
+    'replicate': [1, 1, 1, 1],
+    'value': [10.5, 15.2, 12.1, 25.8]
+}
+df = pd.DataFrame(data)
+
+# Create Prism file
+pf = PrismFile()
+pf.make_group_table(
+    group_name="Treatment_Data",
+    group_values=df,
+    groupby="treatment",    # Separate columns for Control vs Drug A
+    rowgroupby="time",      # Rows labeled by timepoint
+    cols=["value"]          # Data column
+)
+pf.save("treatment_data.pzfx")
+```
+
+## Loading Existing Files
+
+```python
+from prismWriter.prism_writer import PrismFile
+
+# Load existing Prism file (creates automatic backup)
+pf = PrismFile()
+pf.load("existing.pzfx")
+
+# Or load directly in constructor
+pf = PrismFile(file="existing.pzfx")
+
+# Get table names
+tables = pf.get_table_names()
+print(f"Found tables: {tables}")
+
+# Convert table to DataFrame
+df = pf.to_dataframe("TableName")
+
+# Add new table
+pf.make_group_table(
+    group_name="NewTable",
+    group_values=df,
+    groupby="category",
+    cols=["value"]
+)
+
+# Save (use write() for more options)
+pf.save("modified.pzfx")
+```
+
+## Dependencies
+
+- **Core**: pandas, numpy
+- **GUI**: PySide2 (Qt bindings)
+- **Web**: streamlit >= 1.28.0
+- **Files**: openpyxl for Excel support
+
+## Project Structure
+
+```
+prismWriter/
+├── prismWriter/
+│   ├── __init__.py          # Package exports
+│   ├── prism_writer.py      # Core XML generation engine
+│   ├── gui.py               # PySide2 Qt GUI wrapper
+│   ├── streamlit_app.py     # Streamlit web interface
+│   ├── prism_template2.pzfx # XML structure template
+│   └── schema/              # Prism XML schemas
+├── tests/
+│   ├── test_prism_writer.py
+│   ├── test_gui.py
+│   └── test_data.csv
+├── pyproject.toml
+└── README.md
+```
+
+## Development
+
+### Running Tests
+
+```bash
+pytest tests/
+```
+
+### Key Implementation Details
+
+- Uses `prism_template2.pzfx` as XML structure blueprint
+- XML Namespace: `{http://graphpad.com/prism/Prism.htm}`
+- "Raveling" strategy: transforms DataFrames into flat structure via `melt()`, then rebuilds into nested XML hierarchy
+- Automatic backup files created as `{filename}.backup{timestamp}` when loading existing files
+- Logging enabled at INFO level for debugging table creation
+
+## Known Limitations
+
+- No validation for duplicate table names
+- Row mismatch warnings can occur with sparse data
+- Template system hardcoded to specific Prism XML schema version
+- No undo functionality - backup files are the safety net
+
+## License
+
+MIT License
+
+## Contributing
+
+Contributions welcome! Please feel free to submit a Pull Request.

prismwriter-1.0.0/README.md

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+# prismWriter
+
+Python library and GUI for programmatically creating and manipulating GraphPad Prism (`.pzfx`) files. Convert pandas DataFrames into Prism's XML-based table format with complex grouping structures.
+
+**Version:** 1.0.0
+
+## Features
+
+- Convert pandas DataFrames to GraphPad Prism format
+- Flexible grouping: main groups, sub-columns, row labels
+- Multiple interfaces: Python API, Qt GUI, and Streamlit Web interface
+- Load and modify existing `.pzfx` files
+- Validate table structure with preview functionality
+- Automatic backup creation when loading existing files
+
+## Installation
+
+```bash
+pip install -e .
+```
+
+### Requirements
+
+- Python >= 3.7
+- numpy
+- pandas
+- PySide2 (for Qt GUI)
+- streamlit >= 1.28.0 (for web interface)
+- openpyxl (for Excel file support)
+
+## Quick Start
+
+### Python API
+
+```python
+from prismWriter.prism_writer import PrismFile
+import pandas as pd
+
+# Create a new PrismFile
+pf = PrismFile()
+
+# Load your data
+df = pd.read_csv('data.csv')
+
+# Create a grouped table
+pf.make_group_table(
+    group_name="MyTable",
+    group_values=df,
+    groupby="condition",  # Main grouping column
+    cols=["value1", "value2"],  # Data columns
+    subgroupby="replicate"  # Sub-grouping
+)
+
+# Save to Prism file
+pf.save("output.pzfx")
+```
+
+### Web Interface (Streamlit)
+
+The easiest way to use prismWriter:
+
+```bash
+streamlit run prismWriter/streamlit_app.py
+```
+
+Or use the provided launch script:
+- **Windows**: `run_web.bat`
+
+Or after installation:
+```bash
+prismwriter-web
+```
+
+Features:
+- Upload CSV/Excel files (with multi-sheet Excel support)
+- Live data preview with automatic column type detection
+- Interactive grouping configuration
+- Preview table structure before generating
+- Direct download of generated `.pzfx` files
+- Load and view existing Prism files
+
+### Qt GUI
+
+```bash
+python prismWriter/gui.py
+```
+
+Or after installation:
+```bash
+prismwriter-gui
+```
+
+## API Reference
+
+### PrismFile Class
+
+```python
+pf = PrismFile(file=None)  # Create new or load existing file
+```
+
+**Methods:**
+- `load(file_path, backup=True)` - Load an existing Prism file
+- `smake_group_table(group_name, group_values, groupby=None, cols=None, subgroupby=None, rowgroupby=None, append=True)` - Create a grouped table
+- `get_table_names()` - Get list of all table names
+- `to_dataframe(table_name)` - Convert a table to pandas DataFrame
+- `save(file_path)` - Save to file
+- `write(file_path, xml_declaration=True, encoding='utf-8', pretty_print=True)` - Write with options
+- `remove_table(table_name)` - Remove a table from the file
+
+### Grouping Parameters
+
+- **`groupby`**: Main column grouping - creates separate Y-columns for each category
+- **`subgroupby`**: Sub-columns within each Y-column (string for column name, or list for data columns)
+- **`rowgroupby`**: Row labels on the vertical axis (string for column name, or list for data columns)
+- **`cols`**: Data columns to include
+
+**Note**: Use either column name (`subgroupby='condition'`) OR list of data columns (`subgroupby=['col1', 'col2']`) - not both.
+
+### Example Data Structure
+
+```python
+import pandas as pd
+from prismWriter.prism_writer import PrismFile
+
+# Sample data
+data = {
+    'treatment': ['Control', 'Control', 'Drug A', 'Drug A'],
+    'time': [0, 24, 0, 24],
+    'replicate': [1, 1, 1, 1],
+    'value': [10.5, 15.2, 12.1, 25.8]
+}
+df = pd.DataFrame(data)
+
+# Create Prism file
+pf = PrismFile()
+pf.make_group_table(
+    group_name="Treatment_Data",
+    group_values=df,
+    groupby="treatment",    # Separate columns for Control vs Drug A
+    rowgroupby="time",      # Rows labeled by timepoint
+    cols=["value"]          # Data column
+)
+pf.save("treatment_data.pzfx")
+```
+
+## Loading Existing Files
+
+```python
+from prismWriter.prism_writer import PrismFile
+
+# Load existing Prism file (creates automatic backup)
+pf = PrismFile()
+pf.load("existing.pzfx")
+
+# Or load directly in constructor
+pf = PrismFile(file="existing.pzfx")
+
+# Get table names
+tables = pf.get_table_names()
+print(f"Found tables: {tables}")
+
+# Convert table to DataFrame
+df = pf.to_dataframe("TableName")
+
+# Add new table
+pf.make_group_table(
+    group_name="NewTable",
+    group_values=df,
+    groupby="category",
+    cols=["value"]
+)
+
+# Save (use write() for more options)
+pf.save("modified.pzfx")
+```
+
+## Dependencies
+
+- **Core**: pandas, numpy
+- **GUI**: PySide2 (Qt bindings)
+- **Web**: streamlit >= 1.28.0
+- **Files**: openpyxl for Excel support
+
+## Project Structure
+
+```
+prismWriter/
+├── prismWriter/
+│   ├── __init__.py          # Package exports
+│   ├── prism_writer.py      # Core XML generation engine
+│   ├── gui.py               # PySide2 Qt GUI wrapper
+│   ├── streamlit_app.py     # Streamlit web interface
+│   ├── prism_template2.pzfx # XML structure template
+│   └── schema/              # Prism XML schemas
+├── tests/
+│   ├── test_prism_writer.py
+│   ├── test_gui.py
+│   └── test_data.csv
+├── pyproject.toml
+└── README.md
+```
+
+## Development
+
+### Running Tests
+
+```bash
+pytest tests/
+```
+
+### Key Implementation Details
+
+- Uses `prism_template2.pzfx` as XML structure blueprint
+- XML Namespace: `{http://graphpad.com/prism/Prism.htm}`
+- "Raveling" strategy: transforms DataFrames into flat structure via `melt()`, then rebuilds into nested XML hierarchy
+- Automatic backup files created as `{filename}.backup{timestamp}` when loading existing files
+- Logging enabled at INFO level for debugging table creation
+
+## Known Limitations
+
+- No validation for duplicate table names
+- Row mismatch warnings can occur with sparse data
+- Template system hardcoded to specific Prism XML schema version
+- No undo functionality - backup files are the safety net
+
+## License
+
+MIT License
+
+## Contributing
+
+Contributions welcome! Please feel free to submit a Pull Request.

prismwriter-1.0.0/prismWriter/__init__.py

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+"""
+prismWriter - Python library for creating GraphPad Prism files
+
+This library allows you to programmatically create and manipulate
+GraphPad Prism (.pzfx) files from pandas DataFrames.
+"""
+
+__version__ = "1.0.0"
+__author__ = "smestern"
+
+from .prism_writer import PrismFile
+
+__all__ = ["PrismFile", "__version__"]