nbragg 0.3.0__tar.gz

nbragg-0.3.0/LICENSE

@@ -0,0 +1,19 @@
+Copyright 2024 Tsviki Y. Hirsh
+
+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.

nbragg-0.3.0/PKG-INFO

@@ -0,0 +1,100 @@
+Metadata-Version: 2.4
+Name: nbragg
+Version: 0.3.0
+Summary: Simple yet powerful package for neutron resonance fitting
+Author-email: "Tsviki Y. Hirsh" <tsviki.hirsh@gmail.com>
+Project-URL: Homepage, https://github.com/TsvikiHirsh/nbragg
+Project-URL: Bug Tracker, https://github.com/TsvikiHirsh/nbragg/issues
+Project-URL: Discussions, https://github.com/TsvikiHirsh/nbragg/discussions
+Project-URL: Changelog, https://github.com/TsvikiHirsh/nbragg/releases
+Classifier: Development Status :: 1 - Planning
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+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: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: numpy
+Requires-Dist: lmfit
+Requires-Dist: setuptools
+Requires-Dist: ncrystal
+Requires-Dist: tqdm
+Provides-Extra: dev
+Requires-Dist: pytest>=6; extra == "dev"
+Requires-Dist: pytest-cov>=3; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Dynamic: license-file
+
+# nbragg
+
+<p align="center">
+  <img src="docs/source/_static/nbragg_logo.png" alt="nbragg logo" width="200"/>
+</p>
+
+[![Documentation Status](https://readthedocs.org/projects/nbragg/badge/?version=latest)](https://nbragg.readthedocs.io/en/latest/?badge=latest)
+<!-- [![PyPI version][pypi-version]][pypi-link]
+[![PyPI platforms][pypi-platforms]][pypi-link] -->
+
+nbragg is a package designed for fitting neutron Bragg edge data using NCrystal cross-sections. This tool provides a straightforward way to analyze neutron transmission through polycrystalline materials, leveraging Bragg edges to extract information on material structure and composition.
+
+## Features
+
+- **Flexible Cross-Section Calculations**: Interfaces with NCrystal to fetch cross-sections for crystalline materials.
+- **Built-In Tools for Response and Background Functions**: Includes predefined models for instrument response (e.g., Jorgensen, square) and background components (polynomial functions).
+- **LMFit Integration**: Allows flexible, nonlinear fitting of experimental data using the powerful lmfit library.
+- **Rietveld-type analysis**: Enables iterative, parametric refinement of Bragg edge data using the Rietveld method, accumulating parameters across stages for robust fitting.
+- **Pythonic API**: Simple-to-use, yet flexible enough for custom modeling.
+- **Plotting Utilities**: Provides ready-to-use plotting functions for easy visualization of results.
+- **Bragg Edge Analysis**: Perform Bragg edge fitting to extract information such as d-spacing, strain, and texture.
+
+## Installation
+
+To install from the source:
+
+```bash
+git clone https://github.com/TsvikiHirsh/nbragg
+cd nbragg
+pip install .
+```
+
+Alternatively, you can install directly using pip:
+
+```bash
+pip install git+https://github.com/TsvikiHirsh/nbragg.git
+```
+
+## Usage
+
+Here's a quick example to get started:
+
+```python
+import nbragg
+data = nbragg.Data.from_transmission("iron_powder.csv")                         # read data
+xs = nbragg.CrossSection(iron="Fe_sg229_Iron-alpha.ncmat")                      # define sample
+model = nbragg.TransmissionModel(xs, vary_background=True, vary_response=True)  # define model
+result = model.fit(data)                                                        # perform fit
+result.plot()                                                                   # plot results
+```
+
+![Fit Results](notebooks/fit_results.png)
+
+## Tutorials and Documentation
+
+For more detailed examples and advanced usage, including custom stage definitions and Rietveld fitting, please refer to our [documentation page](https://nbragg.readthedocs.io) and check out the updated [Jupyter notebook tutorial](notebooks/nbragg_tutorial.ipynb).
+
+## License
+
+nbragg is licensed under the MIT License.
+
+[pypi-version]: https://img.shields.io/pypi/v/nbragg.svg
+[pypi-link]: https://pypi.org/project/nbragg/
+[pypi-platforms]: https://img.shields.io/badge/platforms-linux%20%7C%20osx%20%7C%20windows-blue.svg

nbragg-0.3.0/README.md

@@ -0,0 +1,64 @@
+# nbragg
+
+<p align="center">
+  <img src="docs/source/_static/nbragg_logo.png" alt="nbragg logo" width="200"/>
+</p>
+
+[![Documentation Status](https://readthedocs.org/projects/nbragg/badge/?version=latest)](https://nbragg.readthedocs.io/en/latest/?badge=latest)
+<!-- [![PyPI version][pypi-version]][pypi-link]
+[![PyPI platforms][pypi-platforms]][pypi-link] -->
+
+nbragg is a package designed for fitting neutron Bragg edge data using NCrystal cross-sections. This tool provides a straightforward way to analyze neutron transmission through polycrystalline materials, leveraging Bragg edges to extract information on material structure and composition.
+
+## Features
+
+- **Flexible Cross-Section Calculations**: Interfaces with NCrystal to fetch cross-sections for crystalline materials.
+- **Built-In Tools for Response and Background Functions**: Includes predefined models for instrument response (e.g., Jorgensen, square) and background components (polynomial functions).
+- **LMFit Integration**: Allows flexible, nonlinear fitting of experimental data using the powerful lmfit library.
+- **Rietveld-type analysis**: Enables iterative, parametric refinement of Bragg edge data using the Rietveld method, accumulating parameters across stages for robust fitting.
+- **Pythonic API**: Simple-to-use, yet flexible enough for custom modeling.
+- **Plotting Utilities**: Provides ready-to-use plotting functions for easy visualization of results.
+- **Bragg Edge Analysis**: Perform Bragg edge fitting to extract information such as d-spacing, strain, and texture.
+
+## Installation
+
+To install from the source:
+
+```bash
+git clone https://github.com/TsvikiHirsh/nbragg
+cd nbragg
+pip install .
+```
+
+Alternatively, you can install directly using pip:
+
+```bash
+pip install git+https://github.com/TsvikiHirsh/nbragg.git
+```
+
+## Usage
+
+Here's a quick example to get started:
+
+```python
+import nbragg
+data = nbragg.Data.from_transmission("iron_powder.csv")                         # read data
+xs = nbragg.CrossSection(iron="Fe_sg229_Iron-alpha.ncmat")                      # define sample
+model = nbragg.TransmissionModel(xs, vary_background=True, vary_response=True)  # define model
+result = model.fit(data)                                                        # perform fit
+result.plot()                                                                   # plot results
+```
+
+![Fit Results](notebooks/fit_results.png)
+
+## Tutorials and Documentation
+
+For more detailed examples and advanced usage, including custom stage definitions and Rietveld fitting, please refer to our [documentation page](https://nbragg.readthedocs.io) and check out the updated [Jupyter notebook tutorial](notebooks/nbragg_tutorial.ipynb).
+
+## License
+
+nbragg is licensed under the MIT License.
+
+[pypi-version]: https://img.shields.io/pypi/v/nbragg.svg
+[pypi-link]: https://pypi.org/project/nbragg/
+[pypi-platforms]: https://img.shields.io/badge/platforms-linux%20%7C%20osx%20%7C%20windows-blue.svg

nbragg-0.3.0/pyproject.toml

@@ -0,0 +1,120 @@
+[build-system]
+requires = ["setuptools>=61", "wheel>=0.41.0"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "nbragg"
+version = "0.3.0"
+authors = [
+  { name = "Tsviki Y. Hirsh", email = "tsviki.hirsh@gmail.com" },
+]
+description = "Simple yet powerful package for neutron resonance fitting"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+  "Development Status :: 1 - Planning",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering",
+]
+dependencies = [
+  "scipy",
+  "pandas",
+  "numpy",
+  "lmfit",
+  "setuptools",
+  "ncrystal",
+  "tqdm"
+]
+
+[project.optional-dependencies]
+dev = [
+  "pytest >=6",
+  "pytest-cov >=3",
+  "pre-commit",
+]
+
+[project.urls]
+Homepage = "https://github.com/TsvikiHirsh/nbragg"
+"Bug Tracker" = "https://github.com/TsvikiHirsh/nbragg/issues"
+Discussions = "https://github.com/TsvikiHirsh/nbragg/discussions"
+Changelog = "https://github.com/TsvikiHirsh/nbragg/releases"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+filterwarnings = [
+  "error",
+]
+log_cli_level = "INFO"
+testpaths = [
+  "tests",
+]
+
+[tool.coverage]
+run.source = ["nbragg"]
+port.exclude_lines = [
+  'pragma: no cover',
+  '\.\.\.',
+  'if typing.TYPE_CHECKING:',
+]
+
+[tool.mypy]
+files = ["src", "tests"]
+python_version = "3.8"
+show_error_codes = true
+warn_unreachable = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+strict = false
+
+[tool.ruff]
+src = ["src"]
+exclude = []
+line-length = 88
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
+select = [
+  "E", "F", "W", 
+  "B",           
+  "I",           
+  "ARG",         
+  "C4",          
+  "EM",          
+  "ICN",         
+  "ISC",         
+  "G",           
+  "PGH",         
+  "PIE",         
+  "PL",          
+  "PT",          
+  "RET",         
+  "RUF",         
+  "SIM",         
+  "UP",          
+  "YTT",         
+  "EXE",         
+]
+ignore = [
+  "PLR",    
+  "ISC001",
+]
+unfixable = [
+  "F401",   
+  "F841",   
+]
+flake8-unused-arguments.ignore-variadic-names = true
+isort.required-imports = ["from __future__ import annotations"]

nbragg-0.3.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

nbragg-0.3.0/src/nbragg/__init__.py

@@ -0,0 +1,18 @@
+"""
+nbragg: Simple yet powerful package for neutron resonance fitting
+"""
+
+from __future__ import annotations
+from importlib.metadata import version
+
+__all__ = ("__version__",)
+__version__ = version(__name__)
+
+from nbragg.cross_section import CrossSection
+from nbragg.response import Response, Background
+from nbragg.models import TransmissionModel
+from nbragg.data import Data
+import nbragg.utils as utils
+from nbragg.utils import materials, register_material
+
+