Merge pull request #311 from damar-wicaksono/dev-304

Prepare the release of v0.4.1
damar-wicaksono · Oct 27, 2023 · 230f257 · 230f257
2 parents 6c3c892 + d7306b1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,10 +7,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [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
 
@@ -169,6 +185,7 @@ First public release of UQTestFuns.
 - 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

diff --git a/CITATION.cff b/CITATION.cff
@@ -14,8 +14,8 @@ authors:
     orcid: 'https://orcid.org/0000-0001-8587-7730'
 identifiers:
   - type: doi
-    value: 10.5281/zenodo.8125015
-    description: The Zenodo URL of version 0.4.0 of the package
+    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/'
@@ -38,5 +38,5 @@ keywords:
   - reliability-analysis
   - surrogate-modeling
 license: MIT
-version: 0.4.0
-date-released: '2023-07-07'
+version: 0.4.1
+date-released: '2023-10-27'
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 # UQTestFuns
-[![DOI](http://img.shields.io/badge/DOI-10.5281/zenodo.8125015-blue.svg?style=flat-square)](https://doi.org/10.5281/zenodo.8125015)
+[![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 3.7](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/)
@@ -33,16 +33,17 @@ To list the available functions:
 ```python-repl
 >>> import uqtestfuns as uqtf
 >>> uqtf.list_functions()
-No.            Constructor            Dimension                Application                Description
+ No.            Constructor            Dimension                Application                Description
 -----  -----------------------------  -----------  --------------------------------------  ----------------------------------------------------------------------------
   1              Ackley()                  M             optimization, metamodeling        Optimization test function from Ackley (1987)
-  2             Borehole()                 8             metamodeling, sensitivity         Borehole function from Harper and Gupta (1983)
-  3           Bratley1992a()               M              integration, sensitivity         Integration test function #1 from Bratley et al. (1992)
-  4           Bratley1992b()               M              integration, sensitivity         Integration test function #2 from Bratley et al. (1992)
-  5           Bratley1992c()               M              integration, sensitivity         Integration test function #3 from Bratley et al. (1992)
-  6           Bratley1992d()               M              integration, sensitivity         Integration test function #4 from Bratley et al. (1992)
-  7         CantileverBeam2D()             2                    reliability                Cantilever beam reliability problem from Rajashekhar and Ellington (1993)
-  8         CircularPipeCrack()            2                    reliability                Circular pipe under bending moment from Verma et al. (2015)
+  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)
 ...
 ```
 
@@ -158,9 +159,8 @@ UQTestFuns is currently maintained by:
 
 - Damar Wicaksono ([HZDR/CASUS](https://www.casus.science/))
 
-with scientific supervision from:
-
-- Michael Hecht ([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
 

diff --git a/docs/fundamentals/metamodeling.md b/docs/fundamentals/metamodeling.md
@@ -17,34 +17,34 @@ kernelspec:
 The table below listed the available test functions typically used
 in the comparison of metamodeling approaches.
 
-|                                Name                                | Spatial Dimension |     Constructor      |
-|:------------------------------------------------------------------:|:-----------------:|:--------------------:|
-|               {ref}`Ackley <test-functions:ackley>`                |         M         |      `Ackley()`      |
-| {ref}`Low-Dimensional High-Degree <test-functions:alemazkoor-2d>`  |         2         |   `Alemazkoor2D()`   |
-|             {ref}`Borehole <test-functions:borehole>`              |         8         |     `Borehole()`     |
-|        {ref}`Damped Cosine <test-functions:damped-cosine>`         |         1         |   `DampedCosine()`   |
-|    {ref}`Damped Oscillator <test-functions:damped-oscillator>`     |         7         | `DampedOscillator()` |
-|                {ref}`Flood <test-functions:flood>`                 |         8         |      `Flood()`       |
-|     {ref}`Forrester et al. (2008) <test-functions:forrester>`      |         1         |  `Forrester2008()`   |
-|           {ref}`(1st) Franke <test-functions:franke-1>`            |         2         |     `Franke1()`      |
-|           {ref}`(2nd) Franke <test-functions:franke-2>`            |         2         |     `Franke2()`      |
-|           {ref}`(3rd) Franke <test-functions:franke-3>`            |         2         |     `Franke3()`      |
-|           {ref}`(4th) Franke <test-functions:franke-4>`            |         2         |     `Franke4()`      |
-|           {ref}`(5th) Franke <test-functions:franke-5>`            |         2         |     `Franke5()`      |
-|           {ref}`(6th) Franke <test-functions:franke-6>`            |         2         |     `Franke6()`      |
-|   {ref}`Gramacy (2007) 1D Sine <test-functions:gramacy-1d-sine>`   |         1         |  `Gramacy1DSine()`   |
-|            {ref}`McLain S1 <test-functions:mclain-s1>`             |         2         |     `McLainS1()`     |
-|            {ref}`McLain S2 <test-functions:mclain-s2>`             |         2         |     `McLainS2()`     |
-|            {ref}`McLain S3 <test-functions:mclain-s3>`             |         2         |     `McLainS3()`     |
-|            {ref}`McLain S4 <test-functions:mclain-s4>`             |         2         |     `McLainS4()`     |
-|            {ref}`McLain S5 <test-functions:mclain-s5>`             |         2         |     `McLainS5()`     |
-|   {ref}`Oakley and O'Hagan (2002) 1D <test-functions:oakley-1d>`   |         1         |     `Oakley1D()`     |
-|          {ref}`OTL Circuit <test-functions:otl-circuit>`           |      6 / 20       |    `OTLCircuit()`    |
-|          {ref}`Piston Simulation <test-functions:piston>`          |      7 / 20       |      `Piston()`      |
-|    {ref}`Webster et al. (1996) 2D <test-functions:webster-2d>`     |         2         |    `Webster2D()`     |
-|               {ref}`Sulfur <test-functions:sulfur>`                |         9         |      `Sulfur()`      |
-|            {ref}`Welch1992 <test-functions:welch1992>`             |        20         |    `Welch1992()`     |
-|          {ref}`Wing Weight <test-functions:wing-weight>`           |        10         |    `WingWeight()`    |
+|                                 Name                                 | Spatial Dimension |     Constructor      |
+|:--------------------------------------------------------------------:|:-----------------:|:--------------------:|
+|                {ref}`Ackley <test-functions:ackley>`                 |         M         |      `Ackley()`      |
+| {ref}`Alemazkoor & Meidani (2018) 2D <test-functions:alemazkoor-2d>` |         2         |   `Alemazkoor2D()`   |
+|              {ref}`Borehole <test-functions:borehole>`               |         8         |     `Borehole()`     |
+|         {ref}`Damped Cosine <test-functions:damped-cosine>`          |         1         |   `DampedCosine()`   |
+|     {ref}`Damped Oscillator <test-functions:damped-oscillator>`      |         7         | `DampedOscillator()` |
+|                 {ref}`Flood <test-functions:flood>`                  |         8         |      `Flood()`       |
+|      {ref}`Forrester et al. (2008) <test-functions:forrester>`       |         1         |  `Forrester2008()`   |
+|            {ref}`(1st) Franke <test-functions:franke-1>`             |         2         |     `Franke1()`      |
+|            {ref}`(2nd) Franke <test-functions:franke-2>`             |         2         |     `Franke2()`      |
+|            {ref}`(3rd) Franke <test-functions:franke-3>`             |         2         |     `Franke3()`      |
+|            {ref}`(4th) Franke <test-functions:franke-4>`             |         2         |     `Franke4()`      |
+|            {ref}`(5th) Franke <test-functions:franke-5>`             |         2         |     `Franke5()`      |
+|            {ref}`(6th) Franke <test-functions:franke-6>`             |         2         |     `Franke6()`      |
+|    {ref}`Gramacy (2007) 1D Sine <test-functions:gramacy-1d-sine>`    |         1         |  `Gramacy1DSine()`   |
+|             {ref}`McLain S1 <test-functions:mclain-s1>`              |         2         |     `McLainS1()`     |
+|             {ref}`McLain S2 <test-functions:mclain-s2>`              |         2         |     `McLainS2()`     |
+|             {ref}`McLain S3 <test-functions:mclain-s3>`              |         2         |     `McLainS3()`     |
+|             {ref}`McLain S4 <test-functions:mclain-s4>`              |         2         |     `McLainS4()`     |
+|             {ref}`McLain S5 <test-functions:mclain-s5>`              |         2         |     `McLainS5()`     |
+|     {ref}`Oakley & O'Hagan (2002) 1D <test-functions:oakley-1d>`     |         1         |     `Oakley1D()`     |
+|           {ref}`OTL Circuit <test-functions:otl-circuit>`            |      6 / 20       |    `OTLCircuit()`    |
+|           {ref}`Piston Simulation <test-functions:piston>`           |      7 / 20       |      `Piston()`      |
+|     {ref}`Webster et al. (1996) 2D <test-functions:webster-2d>`      |         2         |    `Webster2D()`     |
+|                {ref}`Sulfur <test-functions:sulfur>`                 |         9         |      `Sulfur()`      |
+|             {ref}`Welch1992 <test-functions:welch1992>`              |        20         |    `Welch1992()`     |
+|           {ref}`Wing Weight <test-functions:wing-weight>`            |        10         |    `WingWeight()`    |
 
 In a Python terminal, you can list all the available functions relevant
 for metamodeling applications using ``list_functions()`` and filter the results

diff --git a/docs/glossary.md b/docs/glossary.md
@@ -39,15 +39,15 @@ SORM
 
 SS
     Subset simulation
-    
+
 SSRM
     Sequential surrogate reliability method {cite}`Li2018`
 
 Support
     The support of the probability density function, that is, the subset of 
     the function domain whose elements are not mapped to zero;
     denoted by $\mathcal{D}_X$.
-    
+
 SVM
     Support Vector Machines
 ```

diff --git a/docs/test-functions/alemazkoor-2d.md b/docs/test-functions/alemazkoor-2d.md
@@ -13,19 +13,19 @@ kernelspec:
 ---
 
 (test-functions:alemazkoor-2d)=
-# Low-Dimensional High-Degree Function from Alemazkoor and Meidani (2008)
+# Two-dimensional Function from Alemazkoor and Meidani (2018)
 
 ```{code-cell} ipython3
 import numpy as np
 import matplotlib.pyplot as plt
 import uqtestfuns as uqtf
 ```
 
-The low-dimensional high-degree test function
-(or `Alemazkoor2D` for short) is a two-dimensional polynomial function.
-It was introduced in {cite}`Alemazkoor2018` as a test function for
+The test function from {cite}`Alemazkoor2018` (or `Alemazkoor2D` for short)
+is a two-dimensional polynomial function.
+It was used as a test function for
 a metamodeling exercise (i.e., sparse polynomial chaos expansion).
-The function features a low-dimensional polynomial function (2D)
+The function features a low-dimensional polynomial function (two-dimensional)
 with a high degree (a total degree of $20$).
 
 The surface and contour plots of the `Alemazkoor2D` function are shown below.

diff --git a/docs/test-functions/available.md b/docs/test-functions/available.md
@@ -22,7 +22,7 @@ regardless of their typical applications.
 |                                        Name                                         | Spatial Dimension |           Constructor           |
 |:-----------------------------------------------------------------------------------:|:-----------------:|:-------------------------------:|
 |                        {ref}`Ackley <test-functions:ackley>`                        |         M         |           `Ackley()`            |
-|          {ref}`Low-Dimensional High-Degree <test-functions:alemazkoor-2d>`          |         2         |        `Alemazkoor2D()`         |
+|        {ref}`Alemazkoor & Meidani (2018) 2D <test-functions:alemazkoor-2d>`         |         2         |        `Alemazkoor2D()`         |
 |                      {ref}`Borehole <test-functions:borehole>`                      |         8         |          `Borehole()`           |
 |            {ref}`Bratley et al. (1992) A <test-functions:bratley1992a>`             |         M         |        `Bratley1992a()`         |
 |            {ref}`Bratley et al. (1992) B <test-functions:bratley1992b>`             |         M         |        `Bratley1992b()`         |
@@ -52,7 +52,7 @@ regardless of their typical applications.
 |                     {ref}`McLain S3 <test-functions:mclain-s3>`                     |         2         |          `McLainS3()`           |
 |                     {ref}`McLain S4 <test-functions:mclain-s4>`                     |         2         |          `McLainS4()`           |
 |                     {ref}`McLain S5 <test-functions:mclain-s5>`                     |         2         |          `McLainS5()`           |
-|           {ref}`Oakley and O'Hagan (2002) 1D <test-functions:oakley-1d>`            |         1         |          `Oakley1D()`           |
+|            {ref}`Oakley & O'Hagan (2002) 1D <test-functions:oakley-1d>`             |         1         |          `Oakley1D()`           |
 |                   {ref}`OTL Circuit <test-functions:otl-circuit>`                   |      6 / 20       |         `OTLCircuit()`          |
 |                  {ref}`Piston Simulation <test-functions:piston>`                   |      7 / 20       |           `Piston()`            |
 |              {ref}`RS - Circular Bar <test-functions:rs-circular-bar>`              |         2         |        `RSCircularBar()`        |

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = uqtestfuns
-version = 0.4.0
+version = 0.4.1
 url = https://github.com/damar-wicaksono/uqtestfuns
 author = Damar Wicaksono
 author_email = [email protected]

diff --git a/src/uqtestfuns/test_functions/alemazkoor.py b/src/uqtestfuns/test_functions/alemazkoor.py
@@ -25,7 +25,7 @@
 
 AVAILABLE_INPUT_SPECS_2D = {
     "Alemazkoor2018": ProbInputSpecFixDim(
-        name="Alemazkoor2018",
+        name="2D-Alemazkoor2018",
         description=(
             "Input specification for the 2D test function "
             "from Alemazkoor & Meidani (2018)"