Merge branch 'main' into development

README.md

@@ -1,18 +1,69 @@
-# opyrability - Process Operability Analysis in Python.
+# Opyrability - Process Operability Analysis in Python.
+
+![PyPI - Downloads](https://img.shields.io/pypi/dm/opyrability)
+
+
+![PyPI - Version](https://img.shields.io/pypi/v/opyrability) 
+![Conda Version](https://img.shields.io/conda/v/codes-group/opyrability)
+
+
+![GitHub forks](https://img.shields.io/github/forks/codes-group/opyrability)
+![GitHub Repo stars](https://img.shields.io/github/stars/codes-group/opyrability)
+
+
+![GitHub top language](https://img.shields.io/github/languages/top/codes-group/opyrability)
+
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/codes-group/opyrability/.github%2Fworkflows%2Fpython-publish.yml)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/codes-group/opyrability/.github%2Fworkflows%2Fpublish_conda.yml)
+
+
+![Website](https://img.shields.io/website?url=https%3A%2F%2Fcodes-group.github.io%2Fopyrability%2F)
+![GitHub License](https://img.shields.io/github/license/codes-group/opyrability)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.05966/status.svg)](https://doi.org/10.21105/joss.05966)
+
 
 Welcome to opyrability, a Python-based package for performing [Process Operability](https://www.sciencedirect.com/science/article/pii/S1474667017338028) analysis.
 
-opyrability is developed by the Control, Optimization and Design for Energy and Sustainability (CODES) Group at West Virginia University under Dr. [Fernando V. Lima](https://fernandolima.faculty.wvu.edu/)'s supervision.
+opyrability is developed by the [Control, Optimization and Design for Energy and Sustainability (CODES) Group](https://fernandolima.faculty.wvu.edu/) at West Virginia University.
 
 ![](/docs/opyrability_overview.png)
 
 Authors:
-[Victor Alves](https://github.com/victoraalves) and [San Dinh](https://github.com/sanqdinh)
+- [Victor Alves](https://github.com/victoraalves)
+- [San Dinh](https://github.com/sanqdinh)
+- [Jonh Kitchin](https://github.com/jkitchin)
+- Vitor Gazzaneo
+- Juan C. Carrasco
+- [Fernando V. Lima](https://github.com/fvlima-codes)
 
 ## Documentation and Process Operability Principles
 
 Full documentation and discussion regarding process operability principles are available in [opyrability's online portal.](https://codes-group.github.io/opyrability/)
 
+## Citing Us
+
+To cite us, please use the following BibTeX entry below:
+
+```
+@article{Alves2024, 
+doi = {10.21105/joss.05966}, 
+url = {https://doi.org/10.21105/joss.05966}, 
+year = {2024}, 
+publisher = {The Open Journal}, 
+volume = {9}, 
+number = {94}, 
+pages = {5966}, 
+author = {Victor Alves and San Dinh and John R. Kitchin and Vitor Gazzaneo and Juan C. Carrasco and Fernando V. Lima}, 
+title = {Opyrability: A Python package for process operability analysis}, journal = {Journal of Open Source Software} 
+}
+```
+
+A paper describing opyrability's main functionalities is available in the Journal of Open Source Software (JOSS):
+
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.05966/status.svg)](https://doi.org/10.21105/joss.05966)
+
+
+
 ## Installation
 
 The Anaconda distribution is needed to have some of opyrability's dependencies.

conda/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "1.4.3" %}
+{% set version = "1.4.7" %}
 
 package:
   name: opyrability
@@ -27,7 +27,7 @@ requirements:
     - scipy
     - cvxopt
     - tqdm
-    - matplotlib
+    - matplotlib <3.8.0
     - polytope >=0.2.4,<0.3.0
     - jaxlib >=0.4.13,<0.5.0
     - jax >=0.4.13,<0.5.0

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 00c670da5a092a5c3323b8cbe6da3f36
+config: 11bcd87491be1937c52ddd12119e33c5
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_autosummary/opyrability.html

@@ -152,13 +152,14 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../intro.html">
-                    Opyrability Documentation - v1.4.3
+                    Opyrability Documentation -  
                 </a>
             </li>
         </ul>
         <ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 
+
 <li class="toctree-l1"><a class="reference internal" href="../operability_overview.html">Process Operability Overview</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../algorithms.html">Process Operability Algorithms</a></li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../api.html">API Documentation</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
@@ -482,7 +483,7 @@ <h1>opyrability</h1>
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2022-2024.
       <br/>
 
   </p>

docs/_build/html/_modules/index.html

@@ -149,13 +149,14 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../intro.html">
-                    Opyrability Documentation - v1.4.3
+                    Opyrability Documentation  
                 </a>
             </li>
         </ul>
         <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 
+
 <li class="toctree-l1"><a class="reference internal" href="../operability_overview.html">Process Operability Overview</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../algorithms.html">Process Operability Algorithms</a></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../api.html">API Documentation</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
@@ -355,7 +356,7 @@ <h1>All modules for which code is available</h1>
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2022-2024.
       <br/>
 
   </p>

docs/_build/html/_modules/opyrability.html

@@ -149,13 +149,14 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../intro.html">
-                    Opyrability Documentation - v1.4.3
+                    Opyrability Documentation -  
                 </a>
             </li>
         </ul>
         <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 
+
 <li class="toctree-l1"><a class="reference internal" href="../operability_overview.html">Process Operability Overview</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../algorithms.html">Process Operability Algorithms</a></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../api.html">API Documentation</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
@@ -319,7 +320,7 @@ <h1>Source code for opyrability</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">permutations</span> <span class="k">as</span> <span class="n">perms</span>
 <span class="kn">import</span> <span class="nn">string</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Callable</span><span class="p">,</span><span class="n">Union</span>
-<span class="kn">from</span> <span class="nn">tqdm.auto</span> <span class="kn">import</span> <span class="n">tqdm</span>
+<span class="kn">from</span> <span class="nn">tqdm.notebook</span> <span class="kn">import</span> <span class="n">tqdm</span>
 
 <span class="c1"># Linear Algebra</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -1030,6 +1031,8 @@ <h1>Source code for opyrability</h1><div class="highlight"><pre>
 <span class="sd">    https://doi.org/10.1016/j.compchemeng.2016.12.010</span>
 
 <span class="sd">    &#39;&#39;&#39;</span>
+
+
     <span class="kn">from</span> <span class="nn">scipy.optimize</span> <span class="kn">import</span> <span class="n">NonlinearConstraint</span>
     <span class="c1"># Use JAX.numpy if differentiable programming is available.</span>
     <span class="k">if</span> <span class="n">ad</span> <span class="ow">is</span> <span class="kc">False</span><span class="p">:</span>
@@ -1061,6 +1064,11 @@ <h1>Source code for opyrability</h1><div class="highlight"><pre>
         <span class="kn">import</span> <span class="nn">jax.numpy</span> <span class="k">as</span> <span class="nn">np</span>
         <span class="kn">from</span> <span class="nn">jax</span> <span class="kn">import</span> <span class="n">jacrev</span><span class="p">,</span> <span class="n">grad</span>
 
+        <span class="c1"># Make sure that the arrays contain floats (Reviewer #2 bug @ JOSS)</span>
+        <span class="n">u0</span> <span class="o">=</span> <span class="n">u0</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>
+        <span class="n">lb</span> <span class="o">=</span> <span class="n">lb</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>
+        <span class="n">ub</span> <span class="o">=</span> <span class="n">ub</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>
+        <span class="n">DOS_bounds</span> <span class="o">=</span> <span class="n">DOS_bounds</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>
 
         <span class="k">def</span> <span class="nf">p1</span><span class="p">(</span><span class="n">u</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
                <span class="n">model</span><span class="p">:</span> <span class="n">Callable</span><span class="p">[</span><span class="o">...</span><span class="p">,</span> <span class="n">Union</span><span class="p">[</span><span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]],</span>
@@ -2559,7 +2567,7 @@ <h1>Source code for opyrability</h1><div class="highlight"><pre>
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2022-2024.
       <br/>
 
   </p>

docs/_build/html/_sources/api.md

@@ -59,14 +59,14 @@ y_1 = 0\rightarrow y_2 = 90
 Defining the AIS bounds, as well as the discretization resolution:
 ```{code-cell}
     AIS_bounds =  np.array([[0, 10], [0, 10]])
-    resolution =  [5, 5]
+    resolution =  [25, 25]
 ```
 
 Obtain discretized AIS/AOS.
 
 ```{code-cell}
     AIS, AOS =  AIS2AOS_map(shower_problem, AIS_bounds,  resolution, plot = True)
-    print(AOS)
+    
 ```
 
 ### Inverse mapping (AOS/DOS to AIS/DIS)
@@ -299,8 +299,17 @@ Generating paired simplicial polytopes for the AIS/AOS generated for the
 shower problem example.
 
 ```{code-cell}
+    from opyrability import AIS2AOS_map
     from opyrability import points2simplices
 
+    # Obtain an input-output mapping using AIS2AOS_map
+    AIS_bounds =  np.array([[0, 10], [0, 10]])
+    resolution =  [5, 5]
+
+    # The shower_problem function is the same one from the AIS2AOS_map example.
+    AIS, AOS =  AIS2AOS_map(shower_problem, AIS_bounds,  resolution, plot = False)
+    
+    # Obtain simplices.
     AIS_poly, AOS_poly = points2simplices(AIS,AOS)
 
     print('AIS Simplices \n', AIS_poly)

docs/_build/html/_sources/installation.md

@@ -25,6 +25,17 @@ The single command below will install opyrability and all requirements/dependenc
 conda install -c codes-group -c conda-forge opyrability
 ```
 
+## Using in a Google Colab environment:
+
+You can set up opyrability in your Google Colab session as follows:
+```console
+!pip install -q condacolab
+import condacolab
+condacolab.install()
+!conda install -c codes-group -c conda-forge opyrability
+```
+
+
 ## Dependencies
 
 Opyrability is allowed to exist thanks to the following libraries that are dependencies:

docs/_build/html/_sources/intro.md

@@ -1,4 +1,16 @@
-# Opyrability Documentation - v1.4.3
+# Opyrability Documentation ![PyPI - Version](https://img.shields.io/pypi/v/opyrability) ![Conda Version](https://img.shields.io/conda/vn/codes-group/opyrability)
+
+
+
+![PyPI - Downloads](https://img.shields.io/pypi/dm/opyrability) ![GitHub License](https://img.shields.io/github/license/codes-group/opyrability) [![DOI](https://joss.theoj.org/papers/10.21105/joss.05966/status.svg)](https://doi.org/10.21105/joss.05966)
+
+![GitHub forks](https://img.shields.io/github/forks/codes-group/opyrability)
+![GitHub Repo stars](https://img.shields.io/github/stars/codes-group/opyrability)
+
+
+
+
+
 
 **Opyrability** - A **Py**thon-based package for process **o**pe**rability** analysis - is an open-source project for advanced process operability analyses. The opyrability codebase includes the main operability algorithms, supplementary analysis and visualization methods to allow for the assessment of simultaneous design and control objectives early in the conceptual phase.
 
@@ -16,25 +28,24 @@ and find examples on how to use the package!
 
 # Citing us
 
-This initiative has the objective of supporting process systems applications and promoting the dissemination, discussion and improvement of operability approaches and algorithms. Information about the developed approaches can be found at reference {cite}`gazzaneo20`. Please cite this reference if you use opyrability for your own research.
+This initiative has the objective of supporting process systems applications and promoting the dissemination, discussion and improvement of operability approaches and algorithms. Information about the developed approaches can be found at reference {cite}`Alves2024`. Please cite this reference if you use opyrability for your own research.
+
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.05966/status.svg)](https://doi.org/10.21105/joss.05966)
 
 ```{eval-rst}
 
 .. code-block:: none
 
-    @article{gazzaneo20,
-    author = {Gazzaneo, Vitor and Carrasco, Juan C. and Vinson, David R. and Lima, Fernando V.},
-    title = {Process Operability Algorithms: Past, Present, and Future Developments},
-    journal = {Industrial \& Engineering Chemistry Research},
-    volume = {59},
-    number = {6},
-    pages = {2457-2470},
-    year = {2020},
-    doi = {10.1021/acs.iecr.9b05181},
-
-    URL = {https://doi.org/10.1021/acs.iecr.9b05181},
-    eprint = {https://doi.org/10.1021/acs.iecr.9b05181}
-
+    @article{Alves2024, 
+    doi = {10.21105/joss.05966}, 
+    url = {https://doi.org/10.21105/joss.05966}, 
+    year = {2024}, 
+    publisher = {The Open Journal}, 
+    volume = {9}, 
+    number = {94}, 
+    pages = {5966}, 
+    author = {Victor Alves and San Dinh and John R. Kitchin and Vitor Gazzaneo and Juan C. Carrasco and Fernando V. Lima}, 
+    title = {Opyrability: A Python package for process operability analysis}, journal = {Journal of Open Source Software} 
     }
 
 ```

docs/_build/html/_sources/process_model.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "0c574d21",
+   "id": "f8a0fef3",
    "metadata": {},
    "source": [
     "## The Process Model (M) - Programming Aspects \n",
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "3f67c125",
+   "id": "e92da346",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "790e7897",
+   "id": "761b11a8",
    "metadata": {},
    "source": [
     "### Process Model Defined as a Set of Algebraic Equations\n",
@@ -67,7 +67,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "eccd0ece",
+   "id": "17614507",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ea7a59c9",
+   "id": "ac2059c3",
    "metadata": {},
    "source": [
     "### Process Model Defined as a Set of Ordinary Differential (ODE) Equations:\n",
@@ -106,7 +106,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "b1a4e520",
+   "id": "9bde8dac",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,7 +225,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dde6990a",
+   "id": "bad18fa4",
    "metadata": {},
    "source": [
     "This system needs to be numerically integrated. Afterward, the AOS variables\n",
@@ -237,7 +237,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "5d6580ae",
+   "id": "c839698e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -266,7 +266,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b8c61d30",
+   "id": "60f875a1",
    "metadata": {},
    "source": [
     "In the function `dma_mr_design` above, the function input `u` is a two-dimensional vector\n",