build based on c1437ab

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-18T14:20:56","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.7","generation_timestamp":"2025-01-02T21:51:40","documenter_version":"1.8.0"}}

dev/ExampleInstallConfig/index.html

@@ -3,4 +3,4 @@
 julia&gt; Pkg.instantiate()   # download Julia packages</code></pre><p>Individual examples can then be run by eg</p><pre><code class="nohighlight hljs">julia&gt; cd(&quot;CPU&quot;)  # PALEOtutorials.jl/examples/CPU
 julia&gt; include(&quot;CPU_examples.jl&quot;)  # run CPU model example</code></pre><p>See the online <a href="https://paleotoolkit.github.io/PALEOtutorials.jl/">Documentation</a> for details.</p><h2 id="Installing-and-configuring-Julia,-VS-Code,-and-PALEOtutorials.jl"><a class="docs-heading-anchor" href="#Installing-and-configuring-Julia,-VS-Code,-and-PALEOtutorials.jl">Installing and configuring Julia, VS Code, and PALEOtutorials.jl</a><a id="Installing-and-configuring-Julia,-VS-Code,-and-PALEOtutorials.jl-1"></a><a class="docs-heading-anchor-permalink" href="#Installing-and-configuring-Julia,-VS-Code,-and-PALEOtutorials.jl" title="Permalink"></a></h2><h3 id="Install-Julia"><a class="docs-heading-anchor" href="#Install-Julia">Install Julia</a><a id="Install-Julia-1"></a><a class="docs-heading-anchor-permalink" href="#Install-Julia" title="Permalink"></a></h3><p>Download and install Julia from <a href="https://julialang.org/downloads/">https://julialang.org/downloads/</a> (PALEO requires Julia 1.10 or a later version).</p><h3 id="Install-VS-Code"><a class="docs-heading-anchor" href="#Install-VS-Code">Install VS Code</a><a id="Install-VS-Code-1"></a><a class="docs-heading-anchor-permalink" href="#Install-VS-Code" title="Permalink"></a></h3><p>Install VS Code from <a href="https://code.visualstudio.com/download">https://code.visualstudio.com/download</a> Follow instructions at <a href="https://github.com/julia-vscode/julia-vscode">https://github.com/julia-vscode/julia-vscode</a> to install the Julia extension.</p><h3 id="Clone-the-PALEOtutorials.jl-github-repository"><a class="docs-heading-anchor" href="#Clone-the-PALEOtutorials.jl-github-repository">Clone the PALEOtutorials.jl github repository</a><a id="Clone-the-PALEOtutorials.jl-github-repository-1"></a><a class="docs-heading-anchor-permalink" href="#Clone-the-PALEOtutorials.jl-github-repository" title="Permalink"></a></h3><p>This will download <a href="https://github.com/PALEOtoolkit/PALEOtutorials.jl">https://github.com/PALEOtoolkit/PALEOtutorials.jl</a> into a new folder <code>PALEOtutorials.jl</code></p><pre><code class="nohighlight hljs">git clone https://github.com/PALEOtoolkit/PALEOtutorials.jl</code></pre><h3 id="Start-a-Julia-REPL-in-VS-code"><a class="docs-heading-anchor" href="#Start-a-Julia-REPL-in-VS-code">Start a Julia REPL in VS code</a><a id="Start-a-Julia-REPL-in-VS-code-1"></a><a class="docs-heading-anchor-permalink" href="#Start-a-Julia-REPL-in-VS-code" title="Permalink"></a></h3><p>Launch VScode from the <code>PALEOtutorials.jl</code> folder, or use <code>Menu-&gt;File-&gt;Open folder</code> from inside VSCode to change to this folder.</p><p>Start Julia REPL: </p><ul><li>click VScode menu <code>View -&gt; Command Palette</code>, search for Julia, select <code>Julia: Start REPL</code> </li></ul><h3 id="Activate-the-PALEOtutorials.jl/examples-Julia-environment-and-install-Julia-packages"><a class="docs-heading-anchor" href="#Activate-the-PALEOtutorials.jl/examples-Julia-environment-and-install-Julia-packages">Activate the <code>PALEOtutorials.jl/examples</code> Julia environment and install Julia packages</a><a id="Activate-the-PALEOtutorials.jl/examples-Julia-environment-and-install-Julia-packages-1"></a><a class="docs-heading-anchor-permalink" href="#Activate-the-PALEOtutorials.jl/examples-Julia-environment-and-install-Julia-packages" title="Permalink"></a></h3><p>The majority of high-level Julia functionality (numerical solvers, plotting, etc) is provided by <code>Packages</code>. Julia uses <code>environments</code> defined to a <code>Project.toml</code> file to control the loading of <code>Packages</code>, which implement <code>Modules</code> loaded by <code>import</code> or <code>using</code> (eg <code>import DifferentialEquations</code> to use the DifferentialEquations package).</p><p>The environment for using PALEOtutorials.jl is defined by <code>PALEOtutorials.jl/examples/Project.toml</code>. This adds PALEOtoolkit packages including <code>PALEOboxes</code>, <code>PALEOmodel</code> and required dependencies.</p><p>To activate this environment:</p><ul><li>In <code>VS code</code>, right click on any file in the <code>PALEOtutorials.jl/examples</code> folder and select <code>Julia: activate parent environment</code> from the pop-up menu.</li></ul><p>Then download Julia packages: from the Julia REPL,</p><pre><code class="nohighlight hljs">julia&gt; import Pkg
 julia&gt; Pkg.instantiate()  # one-time initialisation for a new installation</code></pre><h2 id="Running-the-examples"><a class="docs-heading-anchor" href="#Running-the-examples">Running the examples</a><a id="Running-the-examples-1"></a><a class="docs-heading-anchor-permalink" href="#Running-the-examples" title="Permalink"></a></h2><p>Start the julia REPL inside VS code, navigate to the <code>PALEOtutorials.jl/examples</code> folder, and activate the correct Julia environment:</p><ul><li>In <code>VS code</code>, right click on any file in the <code>PALEOtutorials.jl/examples</code> folder and select <code>Julia: activate parent environment</code> from the pop-up menu.</li></ul><p>Individual examples can then be run by eg</p><pre><code class="nohighlight hljs">julia&gt; cd(&quot;CPU&quot;)  # PALEOtutorials.jl/examples/CPU
-julia&gt; include(&quot;CPU_examples.jl&quot;)  # run CPU model example</code></pre><p>See the online <a href="https://paleotoolkit.github.io/PALEOtutorials.jl/">Documentation</a> for details.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« PALEOtutorials.jl documentation</a><a class="docs-footer-nextpage" href="../collated_examples/reservoirs/README/">Reservoirs and fluxes »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Thursday 18 July 2024 14:20">Thursday 18 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia&gt; include(&quot;CPU_examples.jl&quot;)  # run CPU model example</code></pre><p>See the online <a href="https://paleotoolkit.github.io/PALEOtutorials.jl/">Documentation</a> for details.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« PALEOtutorials.jl documentation</a><a class="docs-footer-nextpage" href="../collated_examples/reservoirs/README/">Reservoirs and fluxes »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Thursday 2 January 2025 21:51">Thursday 2 January 2025</span>. Using Julia version 1.10.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/HOWTOadditionalconfig/index.html

@@ -7,4 +7,4 @@
 julia> using IJulia  
 julia&gt; notebook(dir=pwd(), detached=true)  # Prompt to install Jupyter, launch an IJulia notebook in your browser</code></pre><p>See <a href="#Configuring-for-Julia-python-interoperability">Configuring for Julia - python interoperability</a> for setup details including how to use an external Python installation.</p><h2 id="Plotting"><a class="docs-heading-anchor" href="#Plotting">Plotting</a><a id="Plotting-1"></a><a class="docs-heading-anchor-permalink" href="#Plotting" title="Permalink"></a></h2><p>Julia has multiple plot backends, and these can either use a standalone window or display &quot;inline&quot; to the VS code plot panel (or Jupyter notebook).</p><h3 id="VS-code-plot-panel"><a class="docs-heading-anchor" href="#VS-code-plot-panel">VS code plot panel</a><a id="VS-code-plot-panel-1"></a><a class="docs-heading-anchor-permalink" href="#VS-code-plot-panel" title="Permalink"></a></h3><p>Enable/disable the VS code plot panel with the <code>Julia: Use plot panel</code> checkbox in VS code settings (search for Julia). If disabled, plotting will use a standalone window.</p><h3 id="GR-backend"><a class="docs-heading-anchor" href="#GR-backend">GR backend</a><a id="GR-backend-1"></a><a class="docs-heading-anchor-permalink" href="#GR-backend" title="Permalink"></a></h3><h4 id="VS-code"><a class="docs-heading-anchor" href="#VS-code">VS code</a><a id="VS-code-1"></a><a class="docs-heading-anchor-permalink" href="#VS-code" title="Permalink"></a></h4><p>Enlarging VS plot window using default GR backend: <code>julia&gt; using Plots; gr(size = (750, 565))</code></p><h4 id="Standalone"><a class="docs-heading-anchor" href="#Standalone">Standalone</a><a id="Standalone-1"></a><a class="docs-heading-anchor-permalink" href="#Standalone" title="Permalink"></a></h4><p>The standalone GR plot window (if not using VS code plot panel) can only display one plot in one window, so not recommended.</p><h3 id="PlotlyJS-backend"><a class="docs-heading-anchor" href="#PlotlyJS-backend">PlotlyJS backend</a><a id="PlotlyJS-backend-1"></a><a class="docs-heading-anchor-permalink" href="#PlotlyJS-backend" title="Permalink"></a></h3><h4 id="VS-code-2"><a class="docs-heading-anchor" href="#VS-code-2">VS code</a><a class="docs-heading-anchor-permalink" href="#VS-code-2" title="Permalink"></a></h4><p>Using PlotlyJS backend in VS code: julia&gt; using Plots; plotlyjs(size=(750, 565)). </p><h4 id="Standalone-2"><a class="docs-heading-anchor" href="#Standalone-2">Standalone</a><a class="docs-heading-anchor-permalink" href="#Standalone-2" title="Permalink"></a></h4><p>See <a href="https://github.com/JuliaPlots/PlotlyJS.jl">https://github.com/JuliaPlots/PlotlyJS.jl</a> for note on Blink install.</p><h3 id="Pyplot-backend"><a class="docs-heading-anchor" href="#Pyplot-backend">Pyplot backend</a><a id="Pyplot-backend-1"></a><a class="docs-heading-anchor-permalink" href="#Pyplot-backend" title="Permalink"></a></h3><p>This requires the Python Matplotlib library, see <a href="https://github.com/JuliaPy/PyPlot.jl">https://github.com/JuliaPy/PyPlot.jl</a> for installation instructions. The simplest configuration is for Julia to install a private (not system provided) Python distribution.  On linux, this requires that you set ENV[&quot;PYTHON&quot;]=&quot;&quot; before adding PyPlot:</p><pre><code class="nohighlight hljs">julia&gt; ENV[&quot;PYTHON&quot;]=&quot;&quot; 
 julia&gt; Pkg.add(&quot;PyPlot&quot;)  # will automatically install python Matplotlib etc as needed and the Qt backend</code></pre><p>or if PyPlot is already installed but failing with a system Python,</p><pre><code class="nohighlight hljs">julia&gt; ENV[&quot;PYTHON&quot;]=&quot;&quot; 
-julia&gt; Pkg.build(&quot;PyCall&quot;)  # will rebuild to use private Python install, and install Matplotlib next time PyPlot is imported.</code></pre><p>See <a href="#Configuring-for-Julia-python-interoperability">Configuring for Julia - python interoperability</a> for setup details including how to use an external Python installation.</p><h4 id="VS-code-3"><a class="docs-heading-anchor" href="#VS-code-3">VS code</a><a class="docs-heading-anchor-permalink" href="#VS-code-3" title="Permalink"></a></h4><p>Using pyplot backend in VS code: julia&gt; using Plots; pyplot()</p><h4 id="Standalone-3"><a class="docs-heading-anchor" href="#Standalone-3">Standalone</a><a class="docs-heading-anchor-permalink" href="#Standalone-3" title="Permalink"></a></h4><p>On linux, install process above will use the Qt backend by default, see <a href="https://github.com/JuliaPy/PyPlot.jl">https://github.com/JuliaPy/PyPlot.jl</a> for instructions for MacOS.</p><h2 id="SIMD-vectorized-math-functions"><a class="docs-heading-anchor" href="#SIMD-vectorized-math-functions">SIMD vectorized math functions</a><a id="SIMD-vectorized-math-functions-1"></a><a class="docs-heading-anchor-permalink" href="#SIMD-vectorized-math-functions" title="Permalink"></a></h2><p>By default, Julia (as of version 1.6) will fall back to slow scalar functions for SIMD exp, log etc, which has a big (x2) impact on the speed of carbonate chemistry and hence run time for large (GENIE size) models that use many small fixed timesteps. As a workaround, PALEO will use the sleef library (<a href="https://sleef.org">https://sleef.org</a>) for fast vectorized versions, supplied by the SLEEF_jll.jl package.  This can be disabled by setting <code>USE_SLEEF = false</code> in LocalPreferences.toml and restarting the Julia REPL.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../HOWTOJuliaUsage/">« Julia and VS code usage</a><a class="docs-footer-nextpage" href="../HOWTOminimalGit/">Minimal git workflow for scientific collaboration and reproducibility »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Thursday 18 July 2024 14:20">Thursday 18 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia&gt; Pkg.build(&quot;PyCall&quot;)  # will rebuild to use private Python install, and install Matplotlib next time PyPlot is imported.</code></pre><p>See <a href="#Configuring-for-Julia-python-interoperability">Configuring for Julia - python interoperability</a> for setup details including how to use an external Python installation.</p><h4 id="VS-code-3"><a class="docs-heading-anchor" href="#VS-code-3">VS code</a><a class="docs-heading-anchor-permalink" href="#VS-code-3" title="Permalink"></a></h4><p>Using pyplot backend in VS code: julia&gt; using Plots; pyplot()</p><h4 id="Standalone-3"><a class="docs-heading-anchor" href="#Standalone-3">Standalone</a><a class="docs-heading-anchor-permalink" href="#Standalone-3" title="Permalink"></a></h4><p>On linux, install process above will use the Qt backend by default, see <a href="https://github.com/JuliaPy/PyPlot.jl">https://github.com/JuliaPy/PyPlot.jl</a> for instructions for MacOS.</p><h2 id="SIMD-vectorized-math-functions"><a class="docs-heading-anchor" href="#SIMD-vectorized-math-functions">SIMD vectorized math functions</a><a id="SIMD-vectorized-math-functions-1"></a><a class="docs-heading-anchor-permalink" href="#SIMD-vectorized-math-functions" title="Permalink"></a></h2><p>By default, Julia (as of version 1.6) will fall back to slow scalar functions for SIMD exp, log etc, which has a big (x2) impact on the speed of carbonate chemistry and hence run time for large (GENIE size) models that use many small fixed timesteps. As a workaround, PALEO will use the sleef library (<a href="https://sleef.org">https://sleef.org</a>) for fast vectorized versions, supplied by the SLEEF_jll.jl package.  This can be disabled by setting <code>USE_SLEEF = false</code> in LocalPreferences.toml and restarting the Julia REPL.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../HOWTOJuliaUsage/">« Julia and VS code usage</a><a class="docs-footer-nextpage" href="../HOWTOminimalGit/">Minimal git workflow for scientific collaboration and reproducibility »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Thursday 2 January 2025 21:51">Thursday 2 January 2025</span>. Using Julia version 1.10.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>