toughanimator 0.1.2__tar.gz

toughanimator-0.1.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: toughanimator
+Version: 0.1.2
+Summary: A tool for visualizing TOUGH simulation outputs.
+Home-page: https://github.com/scarletref/toughanimator
+Author: Your Name
+Author-email: your.email@example.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: vtk
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# ToughAnimator
+
+## Installation
+
+1. **Clone the Repository**:
+
+   ```bash
+   git clone https://stride-c.synology.me:50000/ytkuof/toughanimator.git
+   cd toughanimator
+   ```
+
+2. **Create a Python Virtual Environment**:
+
+   ```bash
+   python -m venv .env
+   ```
+
+3. **Activate the Virtual Environment**:
+
+   - **Windows**:
+     ```bash
+     .env\Scripts\activate.bat
+     ```
+   - **Linux/Mac**:
+     ```bash
+     source .env/bin/activate
+     ```
+
+4. **Install Dependencies**:
+
+   ```bash
+   pip install -r requirements.txt
+   ```
+
+5. **Install ToughAnimator Locally**:
+
+   ```bash
+   pip install .
+   ```
+
+   This will install ToughAnimator in your Python virtual environment.
+
+## Run Your Own Case with ToughAnimator
+
+1. **Create a New Case**:
+
+   - Create a new folder under `unresolve`. Name the folder according to your case (e.g., `unresolve/your_case_name`).
+   - Copy all necessary TOUGH result files into the new folder.
+   - Copy the `config.json` file from an existing case in the `test_cases` directory or create a new `config.json` file in the new folder. The file should have the following structure:
+
+     ```json
+     {
+       "case_name": "your_case_name",
+       "input_files": [
+         "name_of_your_input_file (e.g., flow.inp)",
+         "MESH",  // For a separate mesh file, if applicable
+         "INCON"  // For a separate INCON file, if applicable
+       ],
+       "output_files": [
+         "name_of_your_output_file (e.g., conn.csv)",
+         "name_of_another_output_file (e.g., mesh.csv)",
+         "name_of_other_output_file (add or remove as needed)"
+       ],
+       "corners_file": "name_of_your_corners_file (e.g., corners.csv)",
+       "nas_path": "path/to/nas",
+       "notes": "Any additional notes"
+     }
+     ```
+
+   - The `config.json` file should contain these fields:
+     - **case_name**: The name of your case.
+     - **input_files**: A list of TOUGH input files (e.g., `flow.inp`). You can include multiple input files, but they must contain the `INCON`, `ELEME`, and `CONNE` blocks.
+     - **output_files**: A list of output files (e.g., `conn.csv`, `mesh.csv`). Only CSV format files are currently supported.
+     - **corners_file**: The name of the corners file (e.g., `corners.csv`). This field is optional and can be omitted if not applicable.
+       - To obtain the corners file, open the **3D Results** in your PetraSim project, select **Export Data** from the **File** menu, and on the right side of the file-saving window, set the **Interpolation type** to **Interpolate to cell corners**. Save the file as CSV.
+       
+       ![Exporting corners file from PetraSim](../figures/export_results_data.png)
+       
+     - **nas_path**: The path to the NAS (Network Attached Storage) location where the case files are stored. This field is optional.
+     - **notes**: Any additional notes or comments about the case. This field is optional.
+
+2. **Run the Script**:
+
+   - Ensure the virtual environment is activated.
+   - Open `toughanimator/run.py` in VS Code and select **Run Without Debugging** (Ctrl+F5) or run the script from the command line:
+     
+     ```bash
+     python run.py
+     ```
+
+## Run an Existing Case with ToughAnimator
+
+1. **Set Name and Directory**:
+
+   - Open `toughanimator/run.py`.
+   - Modify the `dir_name` and `case_name` variables to match your case directory and name.
+
+2. **Run the Script**:
+
+   - Ensure the virtual environment is activated.
+   - Open `toughanimator/run.py` in VS Code and select **Run Without Debugging** (Ctrl+F5) or run the script from the command line:
+     
+     ```bash
+     python run.py
+     ```
+
+## Acknowledgments
+
+Special thanks to the TOUGH3 development team for their outstanding work on the TOUGH suite of tools.
+

toughanimator-0.1.2/README.md

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+# ToughAnimator
+
+## Installation
+
+1. **Clone the Repository**:
+
+   ```bash
+   git clone https://stride-c.synology.me:50000/ytkuof/toughanimator.git
+   cd toughanimator
+   ```
+
+2. **Create a Python Virtual Environment**:
+
+   ```bash
+   python -m venv .env
+   ```
+
+3. **Activate the Virtual Environment**:
+
+   - **Windows**:
+     ```bash
+     .env\Scripts\activate.bat
+     ```
+   - **Linux/Mac**:
+     ```bash
+     source .env/bin/activate
+     ```
+
+4. **Install Dependencies**:
+
+   ```bash
+   pip install -r requirements.txt
+   ```
+
+5. **Install ToughAnimator Locally**:
+
+   ```bash
+   pip install .
+   ```
+
+   This will install ToughAnimator in your Python virtual environment.
+
+## Run Your Own Case with ToughAnimator
+
+1. **Create a New Case**:
+
+   - Create a new folder under `unresolve`. Name the folder according to your case (e.g., `unresolve/your_case_name`).
+   - Copy all necessary TOUGH result files into the new folder.
+   - Copy the `config.json` file from an existing case in the `test_cases` directory or create a new `config.json` file in the new folder. The file should have the following structure:
+
+     ```json
+     {
+       "case_name": "your_case_name",
+       "input_files": [
+         "name_of_your_input_file (e.g., flow.inp)",
+         "MESH",  // For a separate mesh file, if applicable
+         "INCON"  // For a separate INCON file, if applicable
+       ],
+       "output_files": [
+         "name_of_your_output_file (e.g., conn.csv)",
+         "name_of_another_output_file (e.g., mesh.csv)",
+         "name_of_other_output_file (add or remove as needed)"
+       ],
+       "corners_file": "name_of_your_corners_file (e.g., corners.csv)",
+       "nas_path": "path/to/nas",
+       "notes": "Any additional notes"
+     }
+     ```
+
+   - The `config.json` file should contain these fields:
+     - **case_name**: The name of your case.
+     - **input_files**: A list of TOUGH input files (e.g., `flow.inp`). You can include multiple input files, but they must contain the `INCON`, `ELEME`, and `CONNE` blocks.
+     - **output_files**: A list of output files (e.g., `conn.csv`, `mesh.csv`). Only CSV format files are currently supported.
+     - **corners_file**: The name of the corners file (e.g., `corners.csv`). This field is optional and can be omitted if not applicable.
+       - To obtain the corners file, open the **3D Results** in your PetraSim project, select **Export Data** from the **File** menu, and on the right side of the file-saving window, set the **Interpolation type** to **Interpolate to cell corners**. Save the file as CSV.
+       
+       ![Exporting corners file from PetraSim](../figures/export_results_data.png)
+       
+     - **nas_path**: The path to the NAS (Network Attached Storage) location where the case files are stored. This field is optional.
+     - **notes**: Any additional notes or comments about the case. This field is optional.
+
+2. **Run the Script**:
+
+   - Ensure the virtual environment is activated.
+   - Open `toughanimator/run.py` in VS Code and select **Run Without Debugging** (Ctrl+F5) or run the script from the command line:
+     
+     ```bash
+     python run.py
+     ```
+
+## Run an Existing Case with ToughAnimator
+
+1. **Set Name and Directory**:
+
+   - Open `toughanimator/run.py`.
+   - Modify the `dir_name` and `case_name` variables to match your case directory and name.
+
+2. **Run the Script**:
+
+   - Ensure the virtual environment is activated.
+   - Open `toughanimator/run.py` in VS Code and select **Run Without Debugging** (Ctrl+F5) or run the script from the command line:
+     
+     ```bash
+     python run.py
+     ```
+
+## Acknowledgments
+
+Special thanks to the TOUGH3 development team for their outstanding work on the TOUGH suite of tools.
+

toughanimator-0.1.2/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

toughanimator-0.1.2/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

toughanimator-0.1.2/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name='toughanimator',  # Package name on PyPI
+    version='0.1.2',
+    description='A tool for visualizing TOUGH simulation outputs.',
+    long_description=open('README.md').read(),
+    long_description_content_type='text/markdown',
+    author='Your Name',
+    author_email='your.email@example.com',
+    url='https://github.com/scarletref/toughanimator',
+    packages=find_packages(),
+    include_package_data=True,
+    install_requires=[
+        'numpy',
+        'pandas',
+        'vtk',
+    ],
+    python_requires='>=3.7',
+    classifiers=[
+        'Programming Language :: Python :: 3',
+        'License :: OSI Approved :: MIT License',
+        'Operating System :: OS Independent',
+    ],
+)

toughanimator-0.1.2/tests/test_all_cases.py

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+import os
+import json
+import pytest
+#from toughanimator.tough_classes import VisSetting, vis_reader
+import logging
+import toughanimator as ta
+import shutil
+
+logging.basicConfig(level=logging.DEBUG)
+
+# Directory containing all test cases
+parent_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+TEST_CASES_DIRS = [
+    #os.path.join(parent_path, "test_cases"),
+    os.path.join(parent_path, "unresolved"),
+    ]
+
+
+def discover_test_cases():
+    """
+    Discover all test cases and load configurations.
+    Each test case must have a config.json file.
+    """
+    logging.debug("This is a debug log")
+    cases = []
+    for test_cases_dir in TEST_CASES_DIRS:
+        logging.debug(f"cases_dir: {test_cases_dir}")
+        if os.path.exists(test_cases_dir):
+            for case_name in os.listdir(test_cases_dir):
+                logging.debug(f"case_name: {case_name}")
+                case_dir = os.path.join(test_cases_dir, case_name)
+                cases.append((case_name, case_dir))
+    return cases
+
+
+@pytest.mark.parametrize("case_name, case_dir", discover_test_cases())
+def test_toughanimator_case(case_name, case_dir):
+    """
+    Test each case using its configuration file.
+    """
+    print(f"Running test for case: {case_name}")
+
+
+
+    try:
+        # Execute the process
+        reader = ta.vis_reader(case_dir)
+        #reader.write_geometry()
+        #reader.write_incon()
+        #reader.write_result()
+        reader.write_all()
+        vis_path = os.path.join(case_dir, "tough_vis")
+        # delete the directory if it exists
+        if os.path.isdir(vis_path):
+            shutil.rmtree(vis_path)
+
+            
+        
+        assert True  # If no exceptions, the test passes
+    except Exception as e:
+        pytest.fail(f"Test failed for case {case_name}: {e}")

toughanimator-0.1.2/toughanimator/__init__.py

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+from .tough_classes import *

toughanimator-0.1.2/toughanimator/run.py

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+import os
+import tough_classes as ta
+import pandas as pd
+import matplotlib.pyplot as plt
+
+dir_name = "unresolved" #"test_cases
+case_name = "3D five spot MINC"
+test_case_dir = os.path.join(os.path.dirname(os.path.dirname(__file__)), dir_name) 
+
+case_dir = os.path.join(test_case_dir, case_name)
+#case_dir = r"D:\Projects\202506\cake"
+
+#case_dir = r"D:\Projects\202504\polygonal\poly_test"
+#case_dir = r"D:\Projects\202501\toughanimator\test_cases\P5_eco2n_1D-radial"
+reader = ta.vis_reader(case_dir)
+#reader.write_eleme_conne()
+#reader.write_geometry()
+#reader.write_incon()
+#reader.write_result()
+#reader.
+reader.write_all()
+
+