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Commit 8e63070f authored by Nando Hegemann's avatar Nando Hegemann
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Update README

Fix auto-doc build.
Add citation file and bibtex entry info.

Closes #11
parent 3254260b
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3 merge requests!51Deploy v3.1.0,!46deploy v3.0.1,!43Add dev roadmap
...@@ -29,3 +29,4 @@ python: ...@@ -29,3 +29,4 @@ python:
install: install:
- method: setuptools - method: setuptools
path: . path: .
- requirements: docs/source/requirements.txt
cff-version: 1.2.0
title: PyThia UQ Toolbox
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Nando
family-names: Farchmin
email: nando.farchmin@ptb.de
affiliation: Physikalisch-Technische Bundesanstalt
orcid: 'https://orcid.org/0000-0003-3953-9006'
- given-names: Sebastian
family-names: Heidenreich
email: sebastian.heidenreich@ptb.de
affiliation: Physikalisch-Technische Bundesanstalt
orcid: 'https://orcid.org/0000-0002-1909-5770'
repository-code: 'https://gitlab1.ptb.de/pythia/pythia'
url: 'https://pythia-uq.readthedocs.io/en/v3.0.0/'
abstract: >-
The PyThia UQ toolbox uses polynomial chaos surrogates to
efficiently generate a surrogate of any (parametric)
forward problem. The surrogate is fast to evaluate, allows
analytical differentiation and has a built-in global
sensitivity analysis via Sobol indices. Assembling the
surrogate is done non-intrusive by least-squares
regression, hence only training pairs of parameter
realizations and evaluations of the forward problem are
required to construct the surrogate. No need to compute
any nasty interfaces for lagacy code.
keywords:
- uncertainty quantification
- polynomial chaos
- non-intrusive approximation
- surrogate modelling
license: GPL-3.0+
commit: 1a51c025872bbeb14ec1dfb3bf9331b4bda4fc0a
version: v3.0
date-released: '2022-12-10'
...@@ -35,13 +35,13 @@ For other versions of the documentation, see [https://readthedocs.org/projects/p ...@@ -35,13 +35,13 @@ For other versions of the documentation, see [https://readthedocs.org/projects/p
## How to cite PyThia ## How to cite PyThia
There is no official related article to cite PyThia yet. There is no official related article to cite PyThia yet.
If you make use of PyThia in a publication, please cite it with a BibTeX entry similar to this: If you make use of PyThia in a publication, please use the meta data from the `CITATION.cff` file or cite it with a BibTeX entry similar to this:
```bibtex ```bibtex
@misc{pythia, @software{pythia,
author = {Farchmin, Nando}, author = {Farchmin, Nando and Heidenreich, Sebastian},
title = {PyThia Uncertainty Quantification Toolbox}, title = {PyThia UQ Toolbox},
howpublished = {vers.: 3.0}, version = {3.0},
note = {\url{https://gitlab1.ptb.de/pythia/pythia/}}, url = {https://pythia-uq.readthedocs.io/en/v3.0.0/},
year = {2022}, year = {2022},
month = {12} month = {12}
} }
...@@ -52,17 +52,6 @@ If you make use of PyThia in a publication, please cite it with a BibTeX entry s ...@@ -52,17 +52,6 @@ If you make use of PyThia in a publication, please cite it with a BibTeX entry s
Check out the [contribution guidelines](CONTRIBUTING.md) on how to create issues or file bug reports and feature requests. Check out the [contribution guidelines](CONTRIBUTING.md) on how to create issues or file bug reports and feature requests.
Or ever better start developping the PyThia project yourself after reading the [development guidelines](DEVELOPERS.md). Or ever better start developping the PyThia project yourself after reading the [development guidelines](DEVELOPERS.md).
## Roadmap and TODOs
After making the project public, there are a few necessary user experience changes left that we should make available:
- [ ] create [stack overflow](https://stackoverflow.com/) hashtag for `PyThia`
Finally, here is a roadmap of features that we plan to add to pythia in the future.
- [ ] integrate tensor train representations of coefficients
- [ ] add tensor train regression (VMC)[^vmc-base]
- [ ] add exponentiation of tensor trains (expTT)[^expTT]
- [ ] add efficient posterior rejection sampling for tensor trains posteriors[^TT-posterior-sampling]
## References ## References
Here we list the papers that describe concepts implemented in **PyThia** for the interested user. Here we list the papers that describe concepts implemented in **PyThia** for the interested user.
...@@ -75,9 +64,6 @@ To use a minimal but still sufficient amount of random samples for the regressio ...@@ -75,9 +64,6 @@ To use a minimal but still sufficient amount of random samples for the regressio
[^pythia-scat-B]: [Efficient Bayesian inversion for shape reconstruction of lithography masks](https://arxiv.org/abs/2005.05164) [^pythia-scat-B]: [Efficient Bayesian inversion for shape reconstruction of lithography masks](https://arxiv.org/abs/2005.05164)
[^sobol-indices]: [Global sensitivity analysis using polynomial chaos expansions](https://www.sciencedirect.com/science/article/abs/pii/S0951832007001329) [^sobol-indices]: [Global sensitivity analysis using polynomial chaos expansions](https://www.sciencedirect.com/science/article/abs/pii/S0951832007001329)
[^wls-sampling]: [Optimal weighted least-squares methods](https://arxiv.org/abs/1608.00512) [^wls-sampling]: [Optimal weighted least-squares methods](https://arxiv.org/abs/1608.00512)
[^vmc-base]: [Variational Monte Carlo - Bridging Concepts of Machine Learning and High Dimensional Partial Differential Equations](https://arxiv.org/abs/1810.01348)
[^expTT]: [Efficient approximation of high-dimensional exponentials by tensornetworks](https://arxiv.org/abs/2105.09064)
[^TT-posterior-sampling]: [Computation of the Response Surface in the Tensor Train data format](https://arxiv.org/abs/1406.2816)
## Who paid for this? ## Who paid for this?
......
...@@ -74,4 +74,5 @@ html_theme = 'sphinx_rtd_theme' ...@@ -74,4 +74,5 @@ html_theme = 'sphinx_rtd_theme'
# Add any paths that contain custom static files (such as style sheets) here, # Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files, # relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css". # so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static'] # html_static_path = ['_static']
html_static_path = []
...@@ -20,6 +20,29 @@ Pythia was the title of the high priestess of the temple of Apollo in Delphi. ...@@ -20,6 +20,29 @@ Pythia was the title of the high priestess of the temple of Apollo in Delphi.
Hence you could say she used her prophetic abilities to quantify which was uncertain. Hence you could say she used her prophetic abilities to quantify which was uncertain.
Moreover, the package is written in python, so... Moreover, the package is written in python, so...
How to cite PyThia
==================
There is no official related article to cite PyThia yet.
If you make use of PyThia in a publication, please use the meta data from the ``CITATION.cff`` file or cite it with a BibTeX entry similar to this:
::
@software{pythia,
author = {Farchmin, Nando and Heidenreich, Sebastian},
title = {PyThia UQ Toolbox},
version = {3.0},
url = {https://pythia-uq.readthedocs.io/en/v3.0.0/},
year = {2022},
month = {12}
}
Who paid for this?
==================
The development of PyThia UQ Toolbox vers. 1 and 2 has been funded by the `German Central Innovation Program (ZIM) No. ZF4014017RR7`.
The development of PyThia UQ Toolbox vers. 3 has been funded by the `European project 20IND04-ATMOC`.
Contents Contents
======== ========
...@@ -38,9 +61,3 @@ Indices and tables ...@@ -38,9 +61,3 @@ Indices and tables
* :ref:`modindex` * :ref:`modindex`
* :ref:`search` * :ref:`search`
Who paid for this?
==================
The development of PyThia UQ Toolbox vers. 1 and 2 has been funded by the German Central Innovation Program (ZIM) No. ZF4014017RR7.
The development of PyThia UQ Toolbox vers. 3 has been funded by the European project 20IND04-ATMOC.
# Defining the exact version will make sure things don't break # Defining the exact version will make sure things don't break
sphinx>=4.3.0 sphinx>=4.3.*
sphinx_rtd_theme>=0.4.0 sphinx_rtd_theme>=0.4.*
readthedocs-sphinx-search==0.1.1 readthedocs-sphinx-search==0.1.*
sphinx_autodoc_typehints==1.19.*
[build-system] [build-system]
requires = [ requires = [
"setuptools>=42", "setuptools>=42",
"wheel" "wheel",
"sphinx_autodoc_typehints"
] ]
build-backend = "setuptools.build_meta" build-backend = "setuptools.build_meta"
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