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‎.gitattributes

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# Auto detect text files and perform LF normalization
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* text=auto

‎.gitignore

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.DS_Store
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.idea/
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### Local dir stuff
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article_figures/
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dev/
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notes/
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my_tests/
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# Created by https://www.toptal.com/developers/gitignore/api/python
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# Edit at https://www.toptal.com/developers/gitignore?templates=python
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### Python ###
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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‎LICENSE.txt

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MIT License
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Copyright (c) 2022 Timothy Pollard
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎MANIFEST.in

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include *.py
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include *.txt
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recursive-include src *.py

‎README.md

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# Pysoplot
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**Pysoplot** is a Python library that contains basic functions and routines
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for geochronology. It implements some of the core functionality
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of the popular (and now defunct) Isoplot/Ex. software, but also
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includes new algorithms and routines. Pysoplot is intended to be
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used to build custom scripts and data processing
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routines in order to meet individual requirements.
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Pysoplot includes functions for:
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* regressing 2-D data using the model 1, 2 and 3 algorithms popularised by Isoplot/Ex.
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* regressing 2-D data using the robust spine algorithm of Powell et al. (2020) and a new robust model 2 algorithm
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* computing weighted averages using algorithms based on classical and robust statistics
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* computing classical isochron and U-Pb concordia-intercept ages
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* plotting isochron diagrams
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* computing disequilibrium U-Pb ages
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* plotting equilibrium and disequilibriam concordia curves, age ellipses, and uncertainty envelopes
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* computing age uncertainties using Monte Carlo methods
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Full code documentation is coming soon!
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## Installation
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Run the following to install:
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```python
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pip install pysoplot
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```
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## Example usage
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```python
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import pysoplot as pp
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# get Tera-Wasserburg test dataset
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dp = pp.data.LA0708
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# transform data point errors from 2 sigma to 1 sigma absolute
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dp = pp.transform.dp_errors(dp, 'abs2s')
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# regress data
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fit = pp.regression.robust_fit(*dp, plot=True, diagram='tw')
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pp.misc.print_result(fit, 'Regression results')
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fit['fig'].show()
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# compute Tera-Wasserburg concordia-intercept age
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result = pp.upb.concint_age(fit, method='Powell')
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print(f"age: {result['age']:.2f} +/- {result['age_95pm']:.2f}")
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```
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## Acknowledgements
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Acknowledgement of all third-party algorithms implemented in Pysoplot with links to
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publications will be added here very soon...
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## License
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Pysoplot is distributed under the MIT license.
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## Contact
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Timothy Pollard - [email protected]
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‎setup.py

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from setuptools import setup
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with open("README.md", "r") as fh:
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long_description = fh.read()
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setup(
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name='pysoplot',
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version='0.0.1',
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description='a Python geochronology library',
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license='MIT',
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packages=['pysoplot', 'pysoplot.uxpb'],
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package_dir={'': 'src'},
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url="https://github.com/timpol/pysoplot",
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author="Timothy Pollard",
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author_email="[email protected]",
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platforms="all",
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classifiers=[
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"Development Status :: 4 - Beta",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Operating System :: OS Independent",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3 :: Only",
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"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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],
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long_description=long_description,
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long_description_content_type="text/markdown",
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install_requires=[
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"numpy",
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"scipy",
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"matplotlib"
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],
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extras_require={
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"dev": []
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}
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)

‎src/pysoplot/__init__.py

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"""
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A Python library for geochronology.
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"""
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from . import uxpb
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from .exceptions import ConvergenceError
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from . import cfg
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from . import concordia
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from . import isochron
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from . import misc
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from . import monte_carlo
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from . import plotting
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from . import regression
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from . import stats
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from . import transform
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from . import upb
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from . import useries
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from . import wtd_average
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