Merge pull request #312 from damar-wicaksono/dev

Merge the dev branch to the main branch

.github/workflows/draft-pdf.yml

@@ -0,0 +1,27 @@
+name: Typesetting draft
+on:
+  push:
+    branches:
+      - dev-joss
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: ./joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: ./joss/paper.pdf

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: Packaging
+name: Testing and packaging
 
 on:
   - push
@@ -52,6 +52,8 @@ jobs:
             toxenv: "py38"
           - version: "3.9"
             toxenv: "py39"
+          - version: "3.11"
+            toxenv: "py311"
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4.0.0

CHANGELOG.md

@@ -5,15 +5,148 @@ All notable changes to the UQTestFuns project is documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.1.1] - 2023-07-03
+## [Unreleased]
+
+## [0.4.1] - 2023-10-27
+
+### Added
+
+- The two-dimensional polynomial function of high-degree for metamodeling
+  exercises from Alemazkoor and Meidani (2008).
+- New tutorials (how the package may be used in a sensitivity analysis or
+  reliability analysis exercises) have been added to the documentation
+  following the review process in the submission of the package
+  to the Journal of Open Source Software (JOSS).
+
+### Changed
+
+- The documentation landing page now includes explicit statement regarding 
+  the purpose of the package.
+
+### Fixed
+
+- Several typos in the documentation have been fixed with an additional
+  minor improvements overall.
+
+## [0.4.0] - 2023-07-07
+
+### Added
+
+- The two-dimensional convex failure domain problem for reliability
+  analysis exercises from Borri and Speranzini (1997).
+- The two-dimensional Quadratic RS problem for reliability analysis
+  exercises from Waarts (2000). This is a variant of the classic RS 
+  problem with one quadratic term.
+- The one-dimensional damped cosine function for metamodeling exercises
+  from an example in Santner et al. (2018).
+- The two-dimensional circular bar RS problem for reliability analysis
+  exercises taken from an example in Verma et al. (2015).
+- The two-dimensional polynomial function with random inputs
+  from Webster et al. (1996) for metamodeling exercises.
+- New instance method for `UnivDist` and `ProbInput` classes
+  called `reset_rng()`. When called (optionally with a seed number), a new
+  instance of NumPy default RNG will be created and attached to the instance.
+- GitHub actions now include testing on Python v3.11 via Tox.
+
+### Changed
+
+- `rng_seed_prob_input` keyword parameter has been removed from the list
+  of parameters to the constructor of all UQ test functions.
+  The accepted way to reset an RNG with a seed is to use the instance
+  method `reset_rng()` (optionally with a seed number)
+  of the `ProbInput` instance attached.
+- Some background information in the documentation has been changed
+  to match the description in the JOSS paper draft.
+
+### Fixed
+
+- A mistake in one the parameter values of the Sobol'-G function
+  has been fixed. 
+
+## [0.3.0] - 2023-07-03
+
+### Added
+
+- The two-dimensional Gayton Hat function from Echard et al. (2013) used
+  in the context of reliability analysis.
+- The eight-dimensional damped oscillator reliability problem from
+  Der Kiureghian and De Stefano (1990); the problem is based on the existing
+  Damped Oscillator model in the code base.
+- The two-dimensional hyper-sphere bound reliability problem
+  from Li et al. (2018).
+- The two-dimensional cantilever beam reliability problem from
+  Rajashekhar and Ellington (1993).
+- The two-dimensional four-branch function for reliability analysis
+  from Katsuki and Frangopol (1994).
+- The five-dimensional speed reducer shaft reliability problem
+  from Du and Sudjianto (2004).
+- The two-dimensional reliability problem of a circular pipe crack
+  under a bending moment under Verma et al. (2015).
+- New docs section on list of functions for reliability analysis including
+  a brief description on the reliability analysis problem.
+
+## [0.2.0] - 2023-06-26
+
+### Added
+
+- The two-dimensional Franke functions (1st, 2nd, 3rd, 4th, 5th, and 6th),
+  relevant for metamodeling exercises, are added as UQ test functions.
+- The two-dimensional McLain functions (S1, S2, S3, S4, and S5),
+  relevant for metamodeling exercises, are added as UQ test functions.
+- An implementation of the Welch et al. (1992) test function, a 20-dimensional
+  function used in the context of metamodeling and sensitivity analysis.
+- Four M-dimensional test functions from Bratley et al. (1992) useful for
+  testing multi-dimensional numerical integrations as well as 
+  global sensitivity analysis methods.
+- Add a new parameterization to the Sobol'-G function taken from
+  Bratley et al. (1992) and Saltelli and Sobol' (1995).
+- An implementation of the one-dimensional function from Forrester et al.
+  (2008). The function was used as a test function for optimization approaches
+  using metamodels.
+- An implementation of the Gramacy (2007) one-dimensional sine function,
+  a function with two regimes.
+- Two base classes are now available `UQTestFunBareABC` and `UQTestFunABC`.
+  The former is used to implement a _bare_ UQ test function
+  (with only `evaluate()` and `ProbInput`), while the latter is used to
+  implement _published_ UQ test functions in the code base (i.e., with 
+  additional metadata such as tags and description).
+- An instance of NumPy random number generator is now attached to instances of
+  `UnivDist` and `ProbInput`. The random seed number may be passed 
+  to the corresponding constructor for reproducibility.
+- CITATION.cff file to the code base.
+
+### Changed
+
+- The date format in CHANGELOG.md has been changed from YYYY-DD-MM to the 
+  ISO format YYYY-MM-DD.
+- The bibliography style in the docs has been changed to 'unsrtalpha'
+  (alphanumeric labels, sorted by order of appearance).
+- When `list_functions()` is called with a `tag` argument,
+  then the application tags are no longer displayed to save terminal spaces.
+- The one-dimensional `OakleyOHagan1D` function has been renamed to
+  `Oakley1D`.
+
+### Fixed
+
+- The original citation for the Sobol'-G function has been fixed;
+  it is now referred to Saltelli and Sobol' (1995).
+- If a function is used as parameters in a test function (e.g., if
+  variable dimension), then it must have the keyword parameter
+  "spatial_dimension" for the function to be called when an instance of
+  a UQ test function is created. This is to allow an arbitrary function
+  (without a parameter named "spatial_dimension") to be a parameter of
+  UQ test function.
+- One-dimensional test function now returns a one-dimensional array.
+
+## [0.1.1] - 2023-03-07
 
 ### Fixed
 
 - v0.1.0 was erroneously already registered at PyPI;
   latest version of UQTestFuns that was planned for v0.1.0 is now v0.1.1
 - Missing link in CHANGELOG.md
 
-## [0.1.0] - 2023-07-03
+## [0.1.0] - 2023-03-07
 
 ### Added
 
@@ -34,7 +167,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Relax the numerical tolerance of a test (i.e., univariate beta distribution)
 - Minor edit in the docs
 
-## [0.0.1] - 2023-06-03
+## [0.0.1] - 2023-03-06
 
 First public release of UQTestFuns.
 
@@ -51,6 +184,11 @@ First public release of UQTestFuns.
 - CI/CD to build and serve the documentation on [ReadTheDocs](https://readthedocs.org/)
 - Mirror GitHub action to the [CASUS organization](https://github.com/casus)
 
+[Unreleased]: https://github.com/damar-wicaksono/uqtestfuns/compare/main...dev
+[0.4.1]: https://github.com/damar-wicaksono/uqtestfuns/compare/v0.4.0...v0.4.1
+[0.4.0]: https://github.com/damar-wicaksono/uqtestfuns/compare/v0.3.0...v0.4.0
+[0.3.0]: https://github.com/damar-wicaksono/uqtestfuns/compare/v0.2.0...v0.3.0
+[0.2.0]: https://github.com/damar-wicaksono/uqtestfuns/compare/v0.1.1...v0.2.0
 [0.1.1]: https://github.com/damar-wicaksono/uqtestfuns/compare/v0.1.0...v0.1.1
 [0.1.0]: https://github.com/damar-wicaksono/uqtestfuns/compare/v0.0.1...v0.1.0
 [0.0.1]: https://github.com/damar-wicaksono/uqtestfuns/releases/tag/v0.0.1

CITATION.cff

@@ -0,0 +1,42 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: UQTestFuns
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Damar
+    family-names: Wicaksono
+    affiliation: CASUS/HZDR
+    orcid: 'https://orcid.org/0000-0001-8587-7730'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.10047512
+    description: The Zenodo URL of version 0.4.1 of the package
+repository-code: 'https://github.com/damar-wicaksono/uqtestfuns'
+url: 'https://uqtestfuns.readthedocs.io/en/latest/'
+repository-artifact: 'https://pypi.org/project/uqtestfuns/'
+abstract: >-
+  UQTestFuns is an open-source Python3 library of test
+  functions commonly used within the uncertainty
+  quantification (UQ) community. The package aims to provide
+  an implementation with minimal dependencies and a common interface
+  of many test functions available in the UQ literature,
+  a single entry point collecting test functions and their probabilistic
+  input specifications in a single Python package,
+  and an opportunity for an open-source contribution,
+  supporting the implementation of new test functions
+  or posting reference results.
+keywords:
+  - uncertainty-quantification
+  - test-functions
+  - sensitivity-analysis
+  - metamodeling
+  - reliability-analysis
+  - surrogate-modeling
+license: MIT
+version: 0.4.1
+date-released: '2023-10-27'

README.md

@@ -1,25 +1,26 @@
 # UQTestFuns
-[![DOI](http://img.shields.io/badge/DOI-10.5281/zenodo.7701904-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.7701904)
+[![DOI](http://img.shields.io/badge/DOI-10.5281/zenodo.10047512-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.10047512)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
-[![Python 3.8](https://img.shields.io/badge/python-3.7-blue.svg?style=flat-square)](https://www.python.org/downloads/release/python-370/)
+[![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg?style=flat-square)](https://www.python.org/downloads/release/python-370/)
 [![License](https://img.shields.io/github/license/damar-wicaksono/uqtestfuns?style=flat-square)](https://choosealicense.com/licenses/mit/)
+[![PyPI](https://img.shields.io/pypi/v/uqtestfuns?style=flat-square)](https://pypi.org/project/uqtestfuns/)
 
 |                                  Branches                                  | Status                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
 |:--------------------------------------------------------------------------:|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| [`main`](https://github.com/damar-wicaksono/uqtestfuns/tree/main) (stable) | ![build](https://img.shields.io/github/actions/workflow/status/damar-wicaksono/uqtestfuns/main.yml?branch=main&style=flat-square) [![codecov](https://img.shields.io/codecov/c/github/damar-wicaksono/uqtestfuns/main?logo=CodeCov&style=flat-square&token=Y6YQEPJ1TT)](https://app.codecov.io/gh/damar-wicaksono/uqtestfuns/tree/main) [![Docs](https://readthedocs.org/projects/uqtestfuns/badge/?version=stable&style=flat-square)](https://uqtestfuns.readthedocs.io/en/latest/?badge=stable) |
+| [`main`](https://github.com/damar-wicaksono/uqtestfuns/tree/main) (stable) | ![build](https://img.shields.io/github/actions/workflow/status/damar-wicaksono/uqtestfuns/main.yml?branch=main&style=flat-square) [![codecov](https://img.shields.io/codecov/c/github/damar-wicaksono/uqtestfuns/main?logo=CodeCov&style=flat-square&token=Y6YQEPJ1TT)](https://app.codecov.io/gh/damar-wicaksono/uqtestfuns/tree/main) [![Docs](https://readthedocs.org/projects/uqtestfuns/badge/?version=stable&style=flat-square)](https://uqtestfuns.readthedocs.io/en/stable/?badge=stable) |
 |  [`dev`](https://github.com/damar-wicaksono/uqtestfuns/tree/dev) (latest)  | ![build](https://img.shields.io/github/actions/workflow/status/damar-wicaksono/uqtestfuns/main.yml?branch=dev&style=flat-square) [![codecov](https://img.shields.io/codecov/c/github/damar-wicaksono/uqtestfuns/dev?logo=CodeCov&style=flat-square&token=Y6YQEPJ1TT)](https://app.codecov.io/gh/damar-wicaksono/uqtestfuns/tree/dev) [![Docs](https://readthedocs.org/projects/uqtestfuns/badge/?version=latest&style=flat-square)](https://uqtestfuns.readthedocs.io/en/latest/?badge=latest)    |
 
 <!--One paragraph description-->
 UQTestFuns is an open-source Python3 library of test functions commonly used
-within the uncertainty quantification (UQ) community.
-The package aims to provide:
+within the applied uncertainty quantification (UQ) community.
+Specifically, the package provides:
 
-- a _lightweight implementation_ (with minimal dependencies) of
-  many test functions available in the UQ literature
-- a _single entry point_ (combining models and their probabilistic input
-  specification) to a wide range of test functions
-- an opportunity for an _open-source contribution_ where new test functions and
-  reference results are posted.
+- an implementation _with minimal dependencies_ (i.e., NumPy and SciPy) and
+  _a common interface_ of many test functions available in the UQ literature
+- a _single entry point_ collecting test functions _and_ their probabilistic
+  input specifications in a single Python package
+- an _opportunity for an open-source contribution_, supporting
+  the implementation of new test functions or posting reference results.
 
 In short, UQTestFuns is an homage
 to the [Virtual Library of Simulation Experiments (VLSE)](https://www.sfu.ca/~ssurjano/).
@@ -32,13 +33,17 @@ To list the available functions:
 ```python-repl
 >>> import uqtestfuns as uqtf
 >>> uqtf.list_functions()
- No.      Constructor       Spatial Dimension          Application          Description
------  ------------------  -------------------  --------------------------  ----------------------------------------------------------------------------
-  1         Ackley()                M           optimization, metamodeling  Ackley function from Ackley (1987)
-  2        Borehole()               8           metamodeling, sensitivity   Borehole function from Harper and Gupta (1983)
-  3    DampedOscillator()           8           metamodeling, sensitivity   Damped oscillator model from Igusa and Der Kiureghian (1985)
-  4         Flood()                 8           metamodeling, sensitivity   Flood model from Iooss and Lemaître (2015)
-  5        Ishigami()               3                  sensitivity          Ishigami function from Ishigami and Homma (1991)
+ No.            Constructor            Dimension                Application                Description
+-----  -----------------------------  -----------  --------------------------------------  ----------------------------------------------------------------------------
+  1              Ackley()                  M             optimization, metamodeling        Optimization test function from Ackley (1987)
+  2           Alemazkoor2D()               2                    metamodeling               Two-dimensional high-degree polynomial from Alemazkoor & Meidani (2018)
+  3             Borehole()                 8             metamodeling, sensitivity         Borehole function from Harper and Gupta (1983)
+  4           Bratley1992a()               M              integration, sensitivity         Integration test function #1 from Bratley et al. (1992)
+  5           Bratley1992b()               M              integration, sensitivity         Integration test function #2 from Bratley et al. (1992)
+  6           Bratley1992c()               M              integration, sensitivity         Integration test function #3 from Bratley et al. (1992)
+  7           Bratley1992d()               M              integration, sensitivity         Integration test function #4 from Bratley et al. (1992)
+  8         CantileverBeam2D()             2                    reliability                Cantilever beam reliability problem from Rajashekhar and Ellington (1993)
+  9         CircularPipeCrack()            2                    reliability                Circular pipe under bending moment from Verma et al. (2015)
 ...
 ```
 
@@ -154,6 +159,9 @@ UQTestFuns is currently maintained by:
 
 - Damar Wicaksono ([HZDR/CASUS](https://www.casus.science/))
 
+under the Mathematical Foundations of Complex System Science Group
+led by Michael Hecht ([HZDR/CASUS](https://www.casus.science/)) at CASUS.
+
 ## License
 
 <!--License-->

docs/_config.yml

@@ -37,3 +37,4 @@ sphinx:
     - 'sphinx.ext.autodoc'
     - 'sphinx.ext.napoleon'
     - 'sphinx.ext.intersphinx'
+    - 'sphinx_proof'