quends 0.1.0__tar.gz

quends-0.1.0/LICENSE

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+BSD 3-Clause License
+
+Copyright 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains
+certain rights in this software.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

quends-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: quends
+Version: 0.1.0
+Summary: A Python package for quantifying uncertainty in ensembles of data streams.
+License: BSD 3-Clause License
+        
+        Copyright 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+        Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains
+        certain rights in this software.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.3
+Requires-Dist: netcdf4>=1.7
+Requires-Dist: statsmodels>=0.13
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: matplotlib>=3.1
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pre-commit>=2.17.0; extra == "dev"
+Requires-Dist: black>=24.4.2; extra == "dev"
+Requires-Dist: ruff>=0.11.0; extra == "dev"
+Requires-Dist: isort>=5.12.0; extra == "dev"
+Requires-Dist: papermill; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Dynamic: license-file

quends-0.1.0/README.md

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+# Quantification of Uncertainty in ENsembles of Data Streams (QUENDS)
+
+#### Evans Etrue Howard, Abeyah Calpatura, Pieterjan Robbe, Bert Debusschere
+
+[![Coverage Status](https://coveralls.io/repos/github/sandialabs/quends/badge.svg?branch=main)](https://coveralls.io/github/sandialabs/quends?branch=main)
+[![Deploy to GitHub Pages](https://github.com/sandialabs/quends/actions/workflows/deployment.yml/badge.svg)](https://github.com/sandialabs/quends/actions/workflows/deployment.yml)
+[![Run Tests](https://github.com/sandialabs/quends/actions/workflows/python-tests.yml/badge.svg)](https://github.com/sandialabs/quends/actions/workflows/python-tests.yml)
+[![pages-build-deployment](https://github.com/sandialabs/quends/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/sandialabs/quends/actions/workflows/pages/pages-build-deployment)
+
+## Overview
+This project focuses on uncertainty quantification in plasma turbulent simulations. It includes modules for loading and processing NetCDF and CSV datasets, estimating steady states, computing effective sample sizes, and running uncertainty quantification analyses. The project is structured into multiple Python scripts, each handling different aspects of the analysis. To see more information on documentation, etc... visit our website [here](https://sandialabs.github.io/quends/).
+
+## Table of Contents
+
+- [Installation](#installation)
+- [Usage](#usage)
+- [For Developers](#for-developers)
+- [Documentation](#documentation)
+- [Examples](#examples)
+- [Summary](#summary)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Installation
+
+1. **Clone the repository**:
+    - Using SSH:
+    ```bash
+    git clone git@github.com:sandialabs/quends.git
+    cd quends
+    ```
+    - Using HTTPS:
+    ```bash
+    git clone https://github.com/sandialabs/quends.git
+    cd quends
+    ```
+
+2. **Install the package and dependencies**:
+    You can install the package along with its dependencies using pip:
+    ```bash
+    pip install .
+    ```
+
+3. **Verify the installation**:
+    To ensure that the installation was successful, you can run a simple test:
+    ```bash
+    python -c "import quends"
+    ```
+
+
+## Usage
+
+Examples are shown in the `examples/notebooks` directories.
+- `cgyro`: Contains all CGYRO data
+- `gx`: Contains all gx data
+- `gx/ensemble`: Contains all ensemble data
+- `DataStream_Guide-CGRYO.ipynb`: DataStream guide for CGYRO data
+- `DataStream_Guide-GX.ipynb`: DataStream guide for GX data
+- `DataStream_Guide-Ensemble.ipynb`: DataStream guide for Ensembles
+- `DataStream_Guide.ipynb`: DataStream guide
+
+## For Developers
+
+1. **Clone the repository**:
+    - Using SSH:
+    ```bash
+    git clone git@github.com:sandialabs/quends.git
+    cd quends
+    ```
+    - Using HTTPS:
+    ```bash
+    git clone https://github.com/sandialabs/quends.git
+    cd quends
+    ```
+
+2. **Install the package and dependencies**:
+    You can install the package along with its dependencies using pip:
+    ```bash
+    pip install -e .\[dev\]
+    ```
+
+3. **Install pre-commit hooks**
+    To ensure code quality and consistency, install:
+    ```bash
+    pre-commit install
+    ```
+
+4. **Run Ruff**:
+    For linting and fixing issues:
+    ```bash
+    ruff check --fix
+    ```
+
+5. **Run isort**:
+    To format your code with Black:
+    ```bash
+    isort .
+    ```
+
+6. **Run Black**:
+    To format your code with Black:
+    ```bash
+    black .
+    ```
+
+## Documentation
+For comprehensive information on how to use the QUENDS package, please refer to our [official documentation](https://sandialabs.github.io/quends/). 
+
+## Summary
+Key functionalities include:
+- **Data Handling**: Seamlessly load and preprocess data from various formats, including CSV, JSON, and NetCDF.
+- **Statistical Analysis**: Compute essential statistics and assess data quality with built-in methods for effective sample size estimation and confidence interval calculations.
+- **Visualization**: Create informative plots to visualize trends, correlations, and patterns in time series data.
+
+## Contributing
+Feel free to submit issues and merge requests. For major changes, please open an issue first to discuss what you would like to change.
+
+## License
+BSD 3-Clause License
+
+Copyright 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains
+certain rights in this software.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

quends-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "quends"
+version = "0.1.0"
+description = "A Python package for quantifying uncertainty in ensembles of data streams."
+readme = "README.rst"
+license = { file = "LICENSE" }
+requires-python = ">=3.8"
+
+dependencies = [
+    "numpy>=1.21",
+    "pandas>=1.3",
+    "netcdf4>=1.7",
+    "statsmodels>=0.13",
+    "scikit-learn>=1.0",
+    "matplotlib>=3.1",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0",
+    "pytest-cov",
+    "pre-commit>=2.17.0",
+    "black>=24.4.2",
+    "ruff>=0.11.0",
+    "isort>=5.12.0",
+    "papermill",
+    "ipykernel"
+]
+
+[project.scripts]
+quends = "quends.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore"
+]
+
+[tool.coverage.run]
+source = ["quends"]
+omit = [
+    "src/quends/postprocessing/*",
+]
+
+[tool.coverage.paths]
+source = [
+    "src/quends",
+    "*/site-packages/quends",
+]
+
+[tool.coverage.report]
+omit = [
+    "src/quends/postprocessing/*",
+]
+
+[tool.coverage.html]
+omit = [
+    "src/quends/postprocessing/*",
+]

quends-0.1.0/setup.cfg

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

quends-0.1.0/src/quends/__init__.py

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+# quends/__init__.py
+
+__version__ = "0.1.0"
+
+# Importing classes and functions from base module
+from .base.data_stream import DataStream
+from .base.ensemble import Ensemble
+from .base.operations import DataStreamOperation
+from .base.stationary import MakeDataStreamStationaryOperation
+from .base.trim import (
+    IQRTrimStrategy,
+    MeanVariationTrimStrategy,
+    NoiseThresholdTrimStrategy,
+    QuantileTrimStrategy,
+    RollingVarianceThresholdTrimStrategy,
+    RollingVarianceTrimStrategy,
+    SSSStartTrimStrategy,
+    SelfConsistentTrimStrategy,
+    StandardDeviationTrimStrategy,
+    ThresholdTrimStrategy,
+    TrimDataStreamOperation,
+    TrimStrategy,
+    build_trim_strategy,
+)
+
+# Importing classes and functions from postprocessing module
+from .postprocessing.exporter import Exporter
+from .postprocessing.plotter import Plotter
+
+# Importing functions from preprocessing module
+from .preprocessing.csv import from_csv
+from .preprocessing.dictionary import from_dict
+from .preprocessing.gx import from_gx
+from .preprocessing.json import from_json
+from .preprocessing.netcdf import from_netcdf
+from .preprocessing.numpy import from_numpy
+
+# Importing classes from workflow module
+from .workflow.batch_ensemble_workflow import BatchEnsembleWorkflow
+from .workflow.ensemble_average_workflow import EnsembleAverageWorkflow
+from .workflow.ensemble_statistics_workflow import EnsembleStatisticsWorkflow
+from .workflow.robust_workflow import RobustWorkflow
+
+# Optionally, you can define the __all__ variable to specify what is exported
+# when using 'from quends import *'
+__all__ = [
+    # Core data containers
+    "DataStream",
+    "Ensemble",
+    # Postprocessing
+    "Exporter",
+    "Plotter",
+    # Preprocessing loaders
+    "from_csv",
+    "from_dict",
+    "from_gx",
+    "from_json",
+    "from_netcdf",
+    "from_numpy",
+    # Workflow
+    "RobustWorkflow",
+    "EnsembleAverageWorkflow",
+    "EnsembleStatisticsWorkflow",
+    "BatchEnsembleWorkflow",
+    # Trim — canonical entry point
+    "build_trim_strategy",
+    # Trim — strategy classes (concrete)
+    "IQRTrimStrategy",
+    "MeanVariationTrimStrategy",
+    "NoiseThresholdTrimStrategy",
+    "QuantileTrimStrategy",
+    "RollingVarianceThresholdTrimStrategy",
+    "SelfConsistentTrimStrategy",
+    # Trim — aliases (backward compat)
+    "StandardDeviationTrimStrategy",
+    "ThresholdTrimStrategy",
+    "RollingVarianceTrimStrategy",
+    "SSSStartTrimStrategy",
+    # Trim — operation + ABC
+    "TrimStrategy",
+    "TrimDataStreamOperation",
+    # Other operations
+    "DataStreamOperation",
+    "MakeDataStreamStationaryOperation",
+]

quends-0.1.0/src/quends/__main__.py

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+"""Entry point for ``python -m quends``."""
+
+import sys
+
+from .cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())

quends-0.1.0/src/quends/base/__init__.py

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+# base/__init__.py
+
+from .data_stream import DataStream
+from .ensemble import Ensemble
+from .history import DataStreamHistory, DataStreamHistoryEntry
+from .operations import DataStreamOperation
+from .stationary import MakeDataStreamStationaryOperation
+from .trim import (
+    IQRTrimStrategy,
+    MeanVariationTrimStrategy,
+    NoiseThresholdTrimStrategy,
+    QuantileTrimStrategy,
+    RollingVarianceThresholdTrimStrategy,
+    RollingVarianceTrimStrategy,
+    SSSStartTrimStrategy,
+    SelfConsistentTrimStrategy,
+    StandardDeviationTrimStrategy,
+    ThresholdTrimStrategy,
+    TrimDataStreamOperation,
+    TrimStrategy,
+    build_trim_strategy,
+)
+
+__all__ = [
+    "DataStream",
+    "Ensemble",
+    "DataStreamHistory",
+    "DataStreamHistoryEntry",
+    "DataStreamOperation",
+    "MakeDataStreamStationaryOperation",
+    "TrimStrategy",
+    "TrimDataStreamOperation",
+    "build_trim_strategy",
+    "QuantileTrimStrategy",
+    "NoiseThresholdTrimStrategy",
+    "RollingVarianceThresholdTrimStrategy",
+    "MeanVariationTrimStrategy",
+    "SelfConsistentTrimStrategy",
+    "IQRTrimStrategy",
+    "StandardDeviationTrimStrategy",
+    "ThresholdTrimStrategy",
+    "RollingVarianceTrimStrategy",
+    "SSSStartTrimStrategy",
+]