Update Sphinx documentation, commit b18dc52 [skip ci].

bluescarni · Jan 26, 2024 · 2ea3f94 · 2ea3f94
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diff --git a/_sources/breaking_changes.rst b/_sources/breaking_changes.rst
@@ -25,7 +25,7 @@ The affected APIs include:
 
 - :ref:`compiled functions <cfunc_tut>`, which now require the list of input
   variables to be always supplied by the user;
-- :func:`~heyoka.diff_tensors()`, which now requires an explicit list of differentiation
+- :func:`~heyoka.diff_tensors()`, which now requires the differentiation
   arguments to be always provided by the user.
 
 The tutorials and the documentation have been updated accordingly.

diff --git a/_sources/changelog.rst b/_sources/changelog.rst
@@ -29,6 +29,8 @@ Changes
   arguments to :func:`~heyoka.diff_tensors()`
   (`#164 <https://github.com/bluescarni/heyoka.py/pull/164>`__).
   This is a :ref:`breaking change <bchanges_4_0_0>`.
+- Improve performance when creating compiled functions
+  (`#162 <https://github.com/bluescarni/heyoka.py/pull/162>`__).
 - **BREAKING**: :ref:`compiled functions <cfunc_tut>` now require
   the list of input variables to be always supplied by the user
   (`#162 <https://github.com/bluescarni/heyoka.py/pull/162>`__).

diff --git a/breaking_changes.html b/breaking_changes.html
@@ -497,7 +497,7 @@ <h4>A more explicit API<a class="headerlink" href="#a-more-explicit-api" title="
 <ul class="simple">
 <li><p><a class="reference internal" href="notebooks/compiled_functions.html#cfunc-tut"><span class="std std-ref">compiled functions</span></a>, which now require the list of input
 variables to be always supplied by the user;</p></li>
-<li><p><a class="reference internal" href="autosummary_generated/heyoka.diff_tensors.html#heyoka.diff_tensors" title="heyoka.diff_tensors"><code class="xref py py-func docutils literal notranslate"><span class="pre">diff_tensors()</span></code></a>, which now requires an explicit list of differentiation
+<li><p><a class="reference internal" href="autosummary_generated/heyoka.diff_tensors.html#heyoka.diff_tensors" title="heyoka.diff_tensors"><code class="xref py py-func docutils literal notranslate"><span class="pre">diff_tensors()</span></code></a>, which now requires the differentiation
 arguments to be always provided by the user.</p></li>
 </ul>
 <p>The tutorials and the documentation have been updated accordingly.</p>

diff --git a/changelog.html b/changelog.html
@@ -628,6 +628,8 @@ <h3>Changes<a class="headerlink" href="#changes" title="Link to this heading">#<
 arguments to <a class="reference internal" href="autosummary_generated/heyoka.diff_tensors.html#heyoka.diff_tensors" title="heyoka.diff_tensors"><code class="xref py py-func docutils literal notranslate"><span class="pre">diff_tensors()</span></code></a>
 (<a class="reference external" href="https://github.com/bluescarni/heyoka.py/pull/164">#164</a>).
 This is a <a class="reference internal" href="breaking_changes.html#bchanges-4-0-0"><span class="std std-ref">breaking change</span></a>.</p></li>
+<li><p>Improve performance when creating compiled functions
+(<a class="reference external" href="https://github.com/bluescarni/heyoka.py/pull/162">#162</a>).</p></li>
 <li><p><strong>BREAKING</strong>: <a class="reference internal" href="notebooks/compiled_functions.html#cfunc-tut"><span class="std std-ref">compiled functions</span></a> now require
 the list of input variables to be always supplied by the user
 (<a class="reference external" href="https://github.com/bluescarni/heyoka.py/pull/162">#162</a>).

diff --git a/notebooks/Batch mode overview.html b/notebooks/Batch mode overview.html
@@ -1384,7 +1384,7 @@ <h2>Ensemble propagations<a class="headerlink" href="#ensemble-propagations" tit
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/0b004f1e2984b9bb68b7d8f68ec5e19d58a7d3e863b7a83f2952faa8b77ef734.png" src="../_images/0b004f1e2984b9bb68b7d8f68ec5e19d58a7d3e863b7a83f2952faa8b77ef734.png" />
+<img alt="../_images/6e6a62c14e57f13d28a9e74d541b1e0c3e10a00f7b9dae1733d5bd99cf523cc6.png" src="../_images/6e6a62c14e57f13d28a9e74d541b1e0c3e10a00f7b9dae1733d5bd99cf523cc6.png" />
 </div>
 </div>
 </section>

diff --git a/notebooks/Customising the adaptive integrator.html b/notebooks/Customising the adaptive integrator.html
@@ -636,8 +636,8 @@ <h2>Compact mode<a class="headerlink" href="#compact-mode" title="Link to this h
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 5.68 s, sys: 4.49 ms, total: 5.69 s
-Wall time: 5.69 s
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 6.04 s, sys: 57.4 ms, total: 6.09 s
+Wall time: 6.09 s
 </pre></div>
 </div>
 </div>
@@ -652,8 +652,8 @@ <h2>Compact mode<a class="headerlink" href="#compact-mode" title="Link to this h
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 203 ms, sys: 0 ns, total: 203 ms
-Wall time: 203 ms
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>CPU times: user 221 ms, sys: 0 ns, total: 221 ms
+Wall time: 221 ms
 </pre></div>
 </div>
 </div>

diff --git a/notebooks/NeuralHamiltonianODEs.html b/notebooks/NeuralHamiltonianODEs.html
@@ -636,10 +636,10 @@ <h1>Neural Hamiltonian ODEs<a class="headerlink" href="#neural-hamiltonian-odes"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7f79086878e0&gt;]
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7efaaa3d7850&gt;]
 </pre></div>
 </div>
-<img alt="../_images/22b6f7cd6fc3dcc789b9dfbdb45d38e24b6a91ff9bf3d55466950276e8d87d40.png" src="../_images/22b6f7cd6fc3dcc789b9dfbdb45d38e24b6a91ff9bf3d55466950276e8d87d40.png" />
+<img alt="../_images/655477f6238b86bc5f8c91aa52d833ba3cba86b1872ba756513535c276b2a626.png" src="../_images/655477f6238b86bc5f8c91aa52d833ba3cba86b1872ba756513535c276b2a626.png" />
 </div>
 </div>
 <p>Clearly, the power and interest of this technique, applied to Hamiltonian systems, lies in the possibility to define some good training for the FFNN weights and biases so that the final system converges to something useful</p>

diff --git a/notebooks/NeuralODEs.html b/notebooks/NeuralODEs.html
@@ -694,7 +694,7 @@ <h3>Taylor Integrator<a class="headerlink" href="#taylor-integrator" title="Link
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.4605686664581299 seconds --- to build (jit) the Taylor integrator
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.4891817569732666 seconds --- to build (jit) the Taylor integrator
 </pre></div>
 </div>
 </div>
@@ -735,7 +735,7 @@ <h3>Taylor Integrator<a class="headerlink" href="#taylor-integrator" title="Link
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.0004184246063232422 seconds --- to propagate using the Taylor scheme
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.00013065338134765625 seconds --- to propagate using the Taylor scheme
 </pre></div>
 </div>
 </div>
@@ -754,7 +754,7 @@ <h3>Taylor Integrator<a class="headerlink" href="#taylor-integrator" title="Link
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/33eb17925f8e880c7eb1f154f3d9fd0cf74f6914a5cde8abcc40ec47a03475da.png" src="../_images/33eb17925f8e880c7eb1f154f3d9fd0cf74f6914a5cde8abcc40ec47a03475da.png" />
+<img alt="../_images/af8c014c60921219e966aafe4c3237fe656fcbbbf9710b30d1bf9924684295da.png" src="../_images/af8c014c60921219e966aafe4c3237fe656fcbbbf9710b30d1bf9924684295da.png" />
 </div>
 </div>
 </section>
@@ -793,7 +793,7 @@ <h3>Scipy Counterpart<a class="headerlink" href="#scipy-counterpart" title="Link
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.0013859272003173828 seconds --- to propagate
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.002370119094848633 seconds --- to propagate
 </pre></div>
 </div>
 </div>
@@ -808,7 +808,7 @@ <h3>Scipy Counterpart<a class="headerlink" href="#scipy-counterpart" title="Link
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/a1c3088f5ba7bfaf5f716eeecea4d130b360aba3706aaa23cd7ac1974d99d514.png" src="../_images/a1c3088f5ba7bfaf5f716eeecea4d130b360aba3706aaa23cd7ac1974d99d514.png" />
+<img alt="../_images/073f0dd9a2a41a29e84bc93e2b4ebea5a440e89a7de8cd4fd50600ca16555893.png" src="../_images/073f0dd9a2a41a29e84bc93e2b4ebea5a440e89a7de8cd4fd50600ca16555893.png" />
 </div>
 </div>
 <p>We see a net advantage in timings using the Taylor integration scheme. Note we are here not using batch propagation, which would add an additional 2-4 factor speedup in performances.</p>

diff --git a/notebooks/Optimal Control of the Lotka-Volterra equations.html b/notebooks/Optimal Control of the Lotka-Volterra equations.html
@@ -1098,9 +1098,9 @@ <h2>Implementing a single shooting method<a class="headerlink" href="#implementi
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_10658/2413872175.py:11: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_10690/2413872175.py:11: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
   ta.pars[6] = np.heaviside(switching_function(x_0,y_0,lx_0,ly_0, ps), 1.)
-/tmp/ipykernel_10658/2413872175.py:14: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
+/tmp/ipykernel_10690/2413872175.py:14: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
   ta.state[0] = x_0; ta.state[1] = y_0; ta.state[2] = lx_0; ta.state[3] = ly_0
 </pre></div>
 </div>
@@ -1142,7 +1142,7 @@ <h2>Implementing a single shooting method<a class="headerlink" href="#implementi
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_10658/3578120629.py:12: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_10690/3578120629.py:12: DeprecationWarning: Conversion of an array with ndim &gt; 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
   ta.pars[6] = np.heaviside(switching_function(x_0,y_0,lx_0,ly_0, ps), 1.)
 </pre></div>
 </div>

diff --git a/notebooks/Periodic orbits in the CR3BP.html b/notebooks/Periodic orbits in the CR3BP.html
@@ -735,7 +735,7 @@ <h2>Putting all together and integrating some initial conditions<a class="header
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 11.18139934539795 seconds --- to build the Taylor integrator
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 14.274664640426636 seconds --- to build the Taylor integrator
 </pre></div>
 </div>
 </div>
@@ -766,7 +766,7 @@ <h2>Putting all together and integrating some initial conditions<a class="header
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.049408674240112305 seconds --- to propagate
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>--- 0.05044221878051758 seconds --- to propagate
 </pre></div>
 </div>
 </div>
@@ -824,7 +824,7 @@ <h2>Putting all together and integrating some initial conditions<a class="header
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;matplotlib.collections.PathCollection at 0x7f58f028ffa0&gt;
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;matplotlib.collections.PathCollection at 0x7fec80311c60&gt;
 </pre></div>
 </div>
 <img alt="../_images/de0d9b784e67d433c81e1c6d68b5b937452559993089914853f0e1f45dbc1669.png" src="../_images/de0d9b784e67d433c81e1c6d68b5b937452559993089914853f0e1f45dbc1669.png" />
@@ -997,22 +997,22 @@ <h2>Finding Periodic Orbits<a class="headerlink" href="#finding-periodic-orbits"
 <div class="cell_output docutils container">
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>error was: 0.0012972874386999722
 condition number is: 16558416262.120907
-new error is: 0.001126849965069169
-error was: 0.001126849965069169
-condition number is: 112029239.50893934
-new error is: 0.005318388912959757
-error was: 0.005318388912959757
-condition number is: 97382195.72485192
-new error is: 0.0008512521425610938
-error was: 0.0008512521425610938
-condition number is: 208596161.6087695
-new error is: 6.615966094672848e-06
-error was: 6.615966094672848e-06
-condition number is: 33988164.67865295
-new error is: 6.542923483972517e-08
-error was: 6.542923483972517e-08
-condition number is: 5547005157.257222
-new error is: 1.844168530369353e-12
+new error is: 0.001126849965099878
+error was: 0.001126849965099878
+condition number is: 112029239.5084326
+new error is: 0.005318388913942381
+error was: 0.005318388913942381
+condition number is: 97382195.71016975
+new error is: 0.0008512521426848299
+error was: 0.0008512521426848299
+condition number is: 208596161.5615835
+new error is: 6.615966335712827e-06
+error was: 6.615966335712827e-06
+condition number is: 33988164.717789754
+new error is: 6.542947405895616e-08
+error was: 6.542947405895616e-08
+condition number is: 5547007072.775402
+new error is: 1.1554575798028065e-12
 </pre></div>
 </div>
 </div>
@@ -1079,8 +1079,8 @@ <h2>Finding Periodic Orbits<a class="headerlink" href="#finding-periodic-orbits"
 </div>
 <div class="cell_output docutils container">
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>mu:  0.01215057
-Initial condition: [-8.3660628428124639e-01, 6.8716716925632383e-05, 0.0000000000000000e+00, -2.3615601898389701e-05, -8.3919863036678266e-01, 0.0000000000000000e+00]
-Period: 2.6915996001662497e+00
+Initial condition: [-8.3660628428621509e-01, 6.8716712682996952e-05, 0.0000000000000000e+00, -2.3615600446411853e-05, -8.3919863032995268e-01, 0.0000000000000000e+00]
+Period: 2.6915996001656333e+00
 </pre></div>
 </div>
 <img alt="../_images/7a44bf7a2547ea1d3bbea540e8a737be4e895a8dd6ff3f10f78a0dd276c3054f.png" src="../_images/7a44bf7a2547ea1d3bbea540e8a737be4e895a8dd6ff3f10f78a0dd276c3054f.png" />
@@ -1239,7 +1239,7 @@ <h2>Continuing into a family of periodic orbits.<a class="headerlink" href="#con
 <div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>(-0.005, 0.005)
 </pre></div>
 </div>
-<img alt="../_images/17680a3a3d7f1a8a033ff5df275db666a9b6bcba60f7eb26009cbcfe441b573d.png" src="../_images/17680a3a3d7f1a8a033ff5df275db666a9b6bcba60f7eb26009cbcfe441b573d.png" />
+<img alt="../_images/70472d6ae6e2f5ad066eebbd6bc45924166576a777451a5d9dd1ba803b9d5ab5.png" src="../_images/70472d6ae6e2f5ad066eebbd6bc45924166576a777451a5d9dd1ba803b9d5ab5.png" />
 </div>
 </div>
 <p>It’s nearly closed, but not that well …. it will need a correction … but we can call the same iterations we made previously when we closed the first initial guess, remember?</p>
@@ -1252,15 +1252,15 @@ <h2>Continuing into a family of periodic orbits.<a class="headerlink" href="#con
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>error was: 0.00027699803739455515
-condition number is: 15781425.08539112
-new error is: 9.461222658847807e-07
-error was: 9.461222658847807e-07
-condition number is: 78777881309.70691
-new error is: 6.062196318473753e-09
-error was: 6.062196318473753e-09
-condition number is: 861551117697.6293
-new error is: 3.427171981558372e-14
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>error was: 0.0002778017858373232
+condition number is: 15736750.479053257
+new error is: 9.515237218310069e-07
+error was: 9.515237218310069e-07
+condition number is: 78502468502.11208
+new error is: 6.172117716412237e-09
+error was: 6.172117716412237e-09
+condition number is: 845787128847.9476
+new error is: 1.794792454124966e-13
 </pre></div>
 </div>
 </div>
@@ -1323,7 +1323,7 @@ <h2>Continuing into a family of periodic orbits.<a class="headerlink" href="#con
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/4632867b8873ae91f7dea3a5da5ed96be650ff335ebe43ce5cb6c1e11aa1bb3f.png" src="../_images/4632867b8873ae91f7dea3a5da5ed96be650ff335ebe43ce5cb6c1e11aa1bb3f.png" />
+<img alt="../_images/c4c731c243dee2aa3fa531af4f930b54a8d1d689cbdf1a2717af57a144c42127.png" src="../_images/c4c731c243dee2aa3fa531af4f930b54a8d1d689cbdf1a2717af57a144c42127.png" />
 </div>
 </div>
 <p>Found it! In order to do this in a loop, though, we will need to do better as eventually this will fail as the continuation parameter

diff --git a/notebooks/ensemble_mode.html b/notebooks/ensemble_mode.html
@@ -636,11 +636,11 @@ <h2>A simple example<a class="headerlink" href="#a-simple-example" title="Link t
  Taylor order            : 20
  Dimension               : 2
  Time                    : 20
- State                   : [0.03802053719173706, 0.052729951339808546],
+ State                   : [0.04274221076606843, 0.05350602824322641],
  &lt;taylor_outcome.time_limit: -4294967299&gt;,
- 0.21012492455291082,
- 0.22280518082508372,
- 93,
+ 0.20598213553603154,
+ 0.2189188676003376,
+ 95,
  None,
  None)
 </pre></div>
@@ -692,7 +692,7 @@ <h2>A simple example<a class="headerlink" href="#a-simple-example" title="Link t
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/6b43e8e06f9db643a118d31dbdc7c91f431836f180f00c7e715d01ab7b254707.png" src="../_images/6b43e8e06f9db643a118d31dbdc7c91f431836f180f00c7e715d01ab7b254707.png" />
+<img alt="../_images/48f6614d5fee834ba9898b1ff4ea18802d7848cf0d1c813cc6c165ddc7b36be0.png" src="../_images/48f6614d5fee834ba9898b1ff4ea18802d7848cf0d1c813cc6c165ddc7b36be0.png" />
 </div>
 </div>
 </section>