Remove dependency to pyjams

.zenodo.json

@@ -56,5 +56,5 @@
 	}
     ],
     "access_right": "open",
-    "description": "<p><strong>pyeee</strong> is a Python library for performing parameter screening of computational models. It uses Efficient or Sequential Elementary Effects, an extension of Morris&#39; method of Elementary Effects, published by:</p>\n\n<p>Cuntz M, Mai J, Zink M, Thober S, Kumar R, Sch&auml;fer D, Schr&ouml;n M, Craven J, Rakovec O, Spieler D, Prykhodko V, Dalmasso G, Musuuza J, Langenberg B, Attinger A, and Samaniego L (2015) Computationally inexpensive identification of noninformative model parameters by sequential screening, <em>Water Resources Research</em> 51, 6417-6441, doi:<a href=\"https://doi.org/10.1002/2015WR016907\">10.1002/2015WR016907</a></p>\n\n<p><strong>pyeee</strong> can be used with Python functions as well as external executables using libraries such as <a href=\"https://github.org/mcuntz/partialwrap/\">partialwrap</a>. Function evaluations can be distributed with Python&#39;s multiprocessing or via MPI.</p>\n\n<p>The complete documentation of pyeee is available at: <a href=\"https://mcuntz.github.io/pyeee/\">https://mcuntz.github.io/pyeee/</a></p>\n\n<p>A similar package (EEE) using a combination of bash and Python scripts is presented at: <a href=\"https://doi.org/10.5281/zenodo.3620894\">https://doi.org/10.5281/zenodo.3620894</a></p>\n\n<p>The version 4.0 modernised code structure and documentation, moving everything to Github, and version 4.1 added <strong>pyeee</strong> to conda-forge.</p>"
+    "description": "<p><strong>pyeee</strong> is a Python library for performing parameter screening of computational models. It uses Efficient or Sequential Elementary Effects, an extension of Morris&#39; method of Elementary Effects, published by:</p>\n\n<p>Cuntz M, Mai J, Zink M, Thober S, Kumar R, Sch&auml;fer D, Schr&ouml;n M, Craven J, Rakovec O, Spieler D, Prykhodko V, Dalmasso G, Musuuza J, Langenberg B, Attinger A, and Samaniego L (2015) Computationally inexpensive identification of noninformative model parameters by sequential screening, <em>Water Resources Research</em> 51, 6417-6441, doi:<a href=\"https://doi.org/10.1002/2015WR016907\">10.1002/2015WR016907</a></p>\n\n<p><strong>pyeee</strong> can be used with Python functions as well as external executables using libraries such as <a href=\"https://github.org/mcuntz/partialwrap/\">partialwrap</a>. Function evaluations can be distributed with Python&#39;s multiprocessing or via MPI.</p>\n\n<p>The complete documentation of pyeee is available at: <a href=\"https://mcuntz.github.io/pyeee/\">https://mcuntz.github.io/pyeee/</a></p>\n\n<p>A similar package (EEE) using a combination of bash and Python scripts is presented at: <a href=\"https://doi.org/10.5281/zenodo.3620894\">https://doi.org/10.5281/zenodo.3620894</a></p>\n\n<p>The version 4.0 modernised code structure and documentation, moving everything to Github. Version 4.1 added <strong>pyeee</strong> to conda-forge. Version 5.0 removed the dependency to the general purpose package <a href=\"https://github.com/mcuntz/pyjams\">pyjams</a>.</p>"
 }

CHANGELOG.rst

@@ -4,6 +4,10 @@ Changelog
 All notable changes after its initial development up to January 2020
 (v0.2) are documented in this file.
 
+v5.0 (??? 2024)
+    * Remove dependency to `pyjams` by copying all utilities to `pyeee`.
+      Screening and Morris' Method will be deprecated in `pyjams`.
+
 v4.1 (Mar 2024)
     * Added to conda-forge.
 

docs/html/_modules/index.html

@@ -17,12 +17,12 @@
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+  <link href="../_static/styles/theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+<link href="../_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
 
 
-  <link href="../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
+  <link href="../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
@@ -32,11 +32,11 @@
     <link rel="stylesheet" type="text/css" href="../_static/css/custom.css?v=628480d8" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
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-  <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=bd9e20870c6007c4c509"></script>
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae" />
+<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
+  <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="../_static/documentation_options.js?v=352e9ff0"></script>
+    <script src="../_static/documentation_options.js?v=d9c31d6a"></script>
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@@ -55,7 +55,6 @@
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   <div id="pst-scroll-pixel-helper"></div>
-
 
   <button type="button" class="btn rounded-pill" id="pst-back-to-top">
     <i class="fa-solid fa-arrow-up"></i>
@@ -95,13 +94,10 @@
   <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
 </form></div>
   </div>
-
-  <header>
 
-    <div class="bd-header navbar navbar-expand-lg bd-navbar">
-    </div>
+    <header class="bd-header navbar navbar-expand-lg bd-navbar">
+    </header>
 
-  </header>
 
   <div class="bd-container">
     <div class="bd-container__inner bd-page-width">
@@ -153,7 +149,12 @@
 <li class="toctree-l1"><a class="reference internal" href="../index.html">Quickstart</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../userguide.html">User Guide</a></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../package.html">pyeee API</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>
-<li class="toctree-l2"><a class="reference internal" href="../eee.html">pyeee.eee</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../eee.html">eee</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../functions.html">General functions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../logistic_function.html">Logistic function</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../morris_method.html">Morris Method / Elementary Effects</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../screening.html">screening</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tee.html">tee</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
@@ -309,6 +310,11 @@ <h1></h1>
 
   <h1>All modules for which code is available</h1>
 <ul><li><a href="pyeee/eee.html">pyeee.eee</a></li>
+<li><a href="pyeee/functions.html">pyeee.functions</a></li>
+<li><a href="pyeee/logistic_function.html">pyeee.logistic_function</a></li>
+<li><a href="pyeee/morris_method.html">pyeee.morris_method</a></li>
+<li><a href="pyeee/screening.html">pyeee.screening</a></li>
+<li><a href="pyeee/tee.html">pyeee.tee</a></li>
 </ul>
 
                 </article>
@@ -373,8 +379,8 @@ <h1>All modules for which code is available</h1>
   </div>
 
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docs/html/_modules/pyeee/eee.html

@@ -17,12 +17,12 @@
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+<link href="../../_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
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-  <link href="../../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
+  <link href="../../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
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 <link rel="preload" as="font" type="font/woff2" crossorigin href="../../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
@@ -32,11 +32,11 @@
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   <!-- Pre-loaded scripts that we'll load fully later -->
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-    <script src="../../_static/documentation_options.js?v=352e9ff0"></script>
+    <script src="../../_static/documentation_options.js?v=d9c31d6a"></script>
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     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -55,7 +55,6 @@
   <a id="pst-skip-link" class="skip-link" href="#main-content">Skip to main content</a>
 
   <div id="pst-scroll-pixel-helper"></div>
-
 
   <button type="button" class="btn rounded-pill" id="pst-back-to-top">
     <i class="fa-solid fa-arrow-up"></i>
@@ -95,13 +94,10 @@
   <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
 </form></div>
   </div>
-
-  <header>
 
-    <div class="bd-header navbar navbar-expand-lg bd-navbar">
-    </div>
+    <header class="bd-header navbar navbar-expand-lg bd-navbar">
+    </header>
 
-  </header>
 
   <div class="bd-container">
     <div class="bd-container__inner bd-page-width">
@@ -153,7 +149,12 @@
 <li class="toctree-l1"><a class="reference internal" href="../../index.html">Quickstart</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../userguide.html">User Guide</a></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../../package.html">pyeee API</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>
-<li class="toctree-l2"><a class="reference internal" href="../../eee.html">pyeee.eee</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../eee.html">eee</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../functions.html">General functions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../logistic_function.html">Logistic function</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../morris_method.html">Morris Method / Elementary Effects</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../screening.html">screening</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tee.html">tee</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../../changelog.html">Changelog</a></li>
@@ -318,7 +319,7 @@ <h1>Source code for pyeee.eee</h1><div class="highlight"><pre>
 <span class="sd">Recherche pour l&#39;Agriculture, l&#39;Alimentation et l&#39;Environnement (INRAE), Nancy,</span>
 <span class="sd">France.</span>
 
-<span class="sd">Copyright (c) 2017-2021 Matthias Cuntz - mc (at) macu (dot) de</span>
+<span class="sd">Copyright (c) 2017- Matthias Cuntz - mc (at) macu (dot) de</span>
 <span class="sd">Released under the MIT License; see LICENSE file for details.</span>
 
 <span class="sd">.. moduleauthor:: Matthias Cuntz</span>
@@ -343,14 +344,15 @@ <h1>Source code for pyeee.eee</h1><div class="highlight"><pre>
 <span class="sd">      scipy.stats, Mar 2020, Matthias Cuntz</span>
 <span class="sd">    * Use pyjams package, Oct 2021, Matthias Cuntz</span>
 <span class="sd">    * Make flake8 compatible, Oct 2021, Matthias Cuntz</span>
+<span class="sd">    * Use local routines of pyeee package, Mar 2024, Matthias Cuntz</span>
 
 <span class="sd">&quot;&quot;&quot;</span>
-<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">division</span><span class="p">,</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">scipy.optimize</span> <span class="k">as</span> <span class="nn">opt</span>
-<span class="kn">from</span> <span class="nn">pyjams</span> <span class="kn">import</span> <span class="n">screening</span><span class="p">,</span> <span class="n">tee</span>
-<span class="kn">from</span> <span class="nn">pyjams.functions</span> <span class="kn">import</span> <span class="n">cost_square</span><span class="p">,</span> <span class="n">curvature</span><span class="p">,</span> <span class="n">logistic_offset_p</span>
-<span class="kn">from</span> <span class="nn">pyjams.functions</span> <span class="kn">import</span> <span class="n">dlogistic</span><span class="p">,</span> <span class="n">d2logistic</span>
+<span class="kn">from</span> <span class="nn">.screening</span> <span class="kn">import</span> <span class="n">screening</span>
+<span class="kn">from</span> <span class="nn">.tee</span> <span class="kn">import</span> <span class="n">tee</span>
+<span class="kn">from</span> <span class="nn">.functions</span> <span class="kn">import</span> <span class="n">cost_square</span><span class="p">,</span> <span class="n">curvature</span>
+<span class="kn">from</span> <span class="nn">.logistic_function</span> <span class="kn">import</span> <span class="n">dlogistic</span><span class="p">,</span> <span class="n">d2logistic</span><span class="p">,</span> <span class="n">logistic_offset_p</span>
 
 
 <span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;eee&#39;</span><span class="p">,</span> <span class="s1">&#39;see&#39;</span><span class="p">]</span>
@@ -951,7 +953,7 @@ <h1>Source code for pyeee.eee</h1><div class="highlight"><pre>
     <span class="kn">import</span> <span class="nn">doctest</span>
     <span class="n">doctest</span><span class="o">.</span><span class="n">testmod</span><span class="p">(</span><span class="n">optionflags</span><span class="o">=</span><span class="n">doctest</span><span class="o">.</span><span class="n">NORMALIZE_WHITESPACE</span><span class="p">)</span>
 
-    <span class="c1"># # from pyjams import tee</span>
+    <span class="c1"># # from pyeee import tee</span>
     <span class="c1"># # from pyjams.functions import fmorris</span>
 
     <span class="c1"># # # Morris with MPI</span>
@@ -1327,8 +1329,8 @@ <h1>Source code for pyeee.eee</h1><div class="highlight"><pre>
   </div>
 
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