Update Sphinx documentation, commit 274d5c1 [skip ci].

bluescarni · Apr 13, 2024 · a2d616b · a2d616b
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diff --git a/_sources/benchmarks.rst b/_sources/benchmarks.rst
@@ -220,7 +220,7 @@ heyoka uses the `MPFR library <https://www.mpfr.org/>`__ for multiprecision floa
 computations under the hood. DifferentialEquations.jl can also use MPFR (via the
 `BigFloat <https://docs.julialang.org/en/v1/manual/integers-and-floating-point-numbers/#Arbitrary-Precision-Arithmetic>`__
 type) or, alternatively the `Arb <https://arblib.org/>`__ library (via the
-`ArbNumerics.jl <https://juliapackages.com/p/arbnumerics>`__ package).
+`ArbNumerics.jl <https://github.com/JeffreySarnoff/ArbNumerics.jl>`__ package).
 
 Here are the results of a numerical integration of the simple pendulum with a 256-bit significand
 and a tolerance of :math:`10^{-77}`:

diff --git a/_sources/changelog.rst b/_sources/changelog.rst
@@ -7,8 +7,35 @@ Changelog
 New
 ~~~
 
+- Add mutable ranges getters for the state and pars data of the adaptive
+  integrators (`#409 <https://github.com/bluescarni/heyoka/pull/409>`__).
 - Support LLVM 18 (`#408 <https://github.com/bluescarni/heyoka/pull/408>`__).
 
+Changes
+~~~~~~~
+
+- Remove the (undocumented) ``taylor_add_jet()`` function and rework
+  the unit test code to use ``taylor_adaptive`` instead
+  (`#409 <https://github.com/bluescarni/heyoka/pull/409>`__).
+
+Fix
+~~~
+
+- Fix test failures on OSX arm64
+  (`#409 <https://github.com/bluescarni/heyoka/pull/409>`__).
+
+4.0.3 (2024-04-04)
+------------------
+
+Fix
+~~~
+
+- Workaround compilation failures in the unit tests
+  when using GCC 13
+  (`#409 <https://github.com/bluescarni/heyoka/pull/409>`__).
+- Fix compilation on FreeBSD
+  (`#407 <https://github.com/bluescarni/heyoka/pull/407>`__).
+
 4.0.2 (2024-03-03)
 ------------------
 

diff --git a/_sources/known_issues.rst b/_sources/known_issues.rst
@@ -1,9 +1,42 @@
 Known issues
 ============
 
+Unsolved
+========
+
+* Under very specific circumstances, C++ code executed right after
+  code that was JIT-compiled by heyoka might produce nonsensical results.
+  This happens only if **all** the following conditions are met:
+
+  * you are on an Intel x86 platform where ``long double`` corresponds
+    to the extended-precision 80-bit x86 floating-point type,
+  * heyoka was compiled with support for quadruple-precision computations
+    via :cpp:class:`mppp::real128`,
+  * JIT-compiled code using **both** 80-bit and quadruple-precision datatypes
+    was executed,
+  * the "fast math" flag was enabled during JIT compilation.
+
+  The root cause is most likely a code-generation/optimisation problem in LLVM.
+  This issue is currently under investigation.
+
+Solved
+======
+
+* In several LLVM versions, attempting to use :ref:`batch mode <tut_batch_mode>`
+  with the extended precision ``long double`` type on x86 processors will lead
+  to incorrect results. This is due to code generation issues in LLVM with
+  ``long double`` vector types. This problem seems to have been rectified in
+  LLVM 18. Note that, in practice, there is no reason to attempt to use batch
+  mode with ``long double`` as currently there are no CPUs implementing SIMD operations
+  on extended-precision datatypes.
 * Due to an upstream bug, if you compile heyoka linking statically against LLVM 17
   while enabling the ``HEYOKA_HIDE_LLVM_SYMBOLS`` option (see the
   :ref:`installation instructions <installation_from_source>`), you may experience
   runtime errors due to missing symbols. This problem should be fixed in LLVM 18.
   A patch fixing the issue in LLVM 17
   is available `here <https://github.com/llvm/llvm-project/commit/122ebe3b500190b1f408e2e6db753853e297ba28>`__.
+* Due to an `upstream bug <https://github.com/conda-forge/mpfr-feedstock/issues/44>`__,
+  multiprecision :ref:`ensemble propagations <tut_ensemble>`
+  crash on OSX arm64 when using heyoka's conda-forge package. This is due to the conda-forge
+  package for the MPFR library not being compiled in thread-safe mode. The solution is to update
+  to the latest version of the MPFR package, which includes a fix for this issue.
diff --git a/_sources/tut_cfunc.rst b/_sources/tut_cfunc.rst
@@ -3,6 +3,8 @@
 Compiled functions
 ==================
 
+.. versionadded:: 4.0.0
+
 .. cpp:namespace-push:: heyoka
 
 heyoka can compile just-in-time (JIT) multivariate vector functions defined

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '4.0.2',
+    VERSION: '4.1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/acknowledgement.html b/acknowledgement.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Acknowledgement &#8212; heyoka 4.0.2 documentation</title>
+    <title>Acknowledgement &#8212; heyoka 4.1.0 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
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-    <script src="_static/documentation_options.js?v=0d40523b"></script>
+    <script src="_static/documentation_options.js?v=5d1265ac"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -133,8 +133,8 @@
 
 
 
-    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.0.2 documentation - Home"/>`);</script>
+    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.1.0 documentation - Home"/>
+    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.1.0 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -198,6 +198,8 @@
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 <li class="toctree-l1"><a class="reference internal" href="breaking_changes.html">Breaking changes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="known_issues.html">Known issues</a></li>
+
+
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Acknowledgement</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>

diff --git a/ad_notes.html b/ad_notes.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Notes on automatic differentiation &#8212; heyoka 4.0.2 documentation</title>
+    <title>Notes on automatic differentiation &#8212; heyoka 4.1.0 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <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=0d40523b"></script>
+    <script src="_static/documentation_options.js?v=5d1265ac"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -134,8 +134,8 @@
 
 
 
-    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.0.2 documentation - Home"/>`);</script>
+    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.1.0 documentation - Home"/>
+    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.1.0 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -199,6 +199,8 @@
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 <li class="toctree-l1"><a class="reference internal" href="breaking_changes.html">Breaking changes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="known_issues.html">Known issues</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgement</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>

diff --git a/advanced_tutorials.html b/advanced_tutorials.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Advanced tutorials &#8212; heyoka 4.0.2 documentation</title>
+    <title>Advanced tutorials &#8212; heyoka 4.1.0 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <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=0d40523b"></script>
+    <script src="_static/documentation_options.js?v=5d1265ac"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -133,8 +133,8 @@
 
 
 
-    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.0.2 documentation - Home"/>`);</script>
+    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.1.0 documentation - Home"/>
+    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.1.0 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -198,6 +198,8 @@
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 <li class="toctree-l1"><a class="reference internal" href="breaking_changes.html">Breaking changes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="known_issues.html">Known issues</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgement</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>

diff --git a/api_reference.html b/api_reference.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>API Reference &#8212; heyoka 4.0.2 documentation</title>
+    <title>API Reference &#8212; heyoka 4.1.0 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <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=0d40523b"></script>
+    <script src="_static/documentation_options.js?v=5d1265ac"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -133,8 +133,8 @@
 
 
 
-    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.0.2 documentation - Home"/>`);</script>
+    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.1.0 documentation - Home"/>
+    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.1.0 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -198,6 +198,8 @@
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 <li class="toctree-l1"><a class="reference internal" href="breaking_changes.html">Breaking changes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="known_issues.html">Known issues</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgement</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>

diff --git a/basic_tutorials.html b/basic_tutorials.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Basic tutorials &#8212; heyoka 4.0.2 documentation</title>
+    <title>Basic tutorials &#8212; heyoka 4.1.0 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <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=0d40523b"></script>
+    <script src="_static/documentation_options.js?v=5d1265ac"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -133,8 +133,8 @@
 
 
 
-    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.0.2 documentation - Home"/>`);</script>
+    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.1.0 documentation - Home"/>
+    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.1.0 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -198,6 +198,8 @@
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 <li class="toctree-l1"><a class="reference internal" href="breaking_changes.html">Breaking changes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="known_issues.html">Known issues</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgement</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>

diff --git a/benchmarks.html b/benchmarks.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Benchmarks &#8212; heyoka 4.0.2 documentation</title>
+    <title>Benchmarks &#8212; heyoka 4.1.0 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
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   <script src="_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
-    <script src="_static/documentation_options.js?v=0d40523b"></script>
+    <script src="_static/documentation_options.js?v=5d1265ac"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -134,8 +134,8 @@
 
 
 
-    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.0.2 documentation - Home"/>`);</script>
+    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.1.0 documentation - Home"/>
+    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.1.0 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -199,6 +199,8 @@
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 <li class="toctree-l1"><a class="reference internal" href="breaking_changes.html">Breaking changes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="known_issues.html">Known issues</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgement</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>
@@ -573,7 +575,7 @@ <h2>Extended and arbitrary precision<a class="headerlink" href="#extended-and-ar
 computations under the hood. DifferentialEquations.jl can also use MPFR (via the
 <a class="reference external" href="https://docs.julialang.org/en/v1/manual/integers-and-floating-point-numbers/#Arbitrary-Precision-Arithmetic">BigFloat</a>
 type) or, alternatively the <a class="reference external" href="https://arblib.org/">Arb</a> library (via the
-<a class="reference external" href="https://juliapackages.com/p/arbnumerics">ArbNumerics.jl</a> package).</p>
+<a class="reference external" href="https://github.com/JeffreySarnoff/ArbNumerics.jl">ArbNumerics.jl</a> package).</p>
 <p>Here are the results of a numerical integration of the simple pendulum with a 256-bit significand
 and a tolerance of <span class="math notranslate nohighlight">\(10^{-77}\)</span>:</p>
 <img alt="Arbitrary-precision pendulum" class="align-center" src="_images/mp_cmp.png" />

diff --git a/bibliography.html b/bibliography.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Bibliography &#8212; heyoka 4.0.2 documentation</title>
+    <title>Bibliography &#8212; heyoka 4.1.0 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <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=0d40523b"></script>
+    <script src="_static/documentation_options.js?v=5d1265ac"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=efea14e4"></script>
@@ -132,8 +132,8 @@
 
 
 
-    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.0.2 documentation - Home"/>`);</script>
+    <img src="_static/white_logo.png" class="logo__image only-light" alt="heyoka 4.1.0 documentation - Home"/>
+    <script>document.write(`<img src="_static/white_logo.png" class="logo__image only-dark" alt="heyoka 4.1.0 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -197,6 +197,8 @@
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 <li class="toctree-l1"><a class="reference internal" href="breaking_changes.html">Breaking changes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="known_issues.html">Known issues</a></li>
+
+
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgement</a></li>
 <li><a class="reference internal" href="#">Bibliography</a></li>
 </ul>