build based on 64a3d7b

previews/PR12/getting_started/biojuliainstallation/index.html

@@ -23,4 +23,4 @@
 # all of the dependencies specified in that file into your Julia environment.
 (@v1.9) pkg> instantiate
 # Exit REPL via the Backspace key
-julia&gt; using &lt;name of package here&gt;</code></pre><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>You can skip straight to <code>(@v1.9) pkg&gt; activate ...</code> if you have already installed the package code locally, simply make sure to point Pkg to the right path as shown above.</p></div></div><p>You can now change your source code and load them into the Julia session with <code>using &lt;name of package here&gt;</code>. To test your code, run <code>(@v1.9) pkg&gt; test</code> to run the package&#39;s test suite to ensure that everything works correctly. When you are done developing the package, enter <code>(@v1.9) pkg&gt; free</code> to stop tracking the package. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../toolsinstallation/">« Installing Development Tools</a><a class="docs-footer-nextpage" href="../casescenarios/">Case Scenarios »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 16 August 2023 03:36">Wednesday 16 August 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia&gt; using &lt;name of package here&gt;</code></pre><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>You can skip straight to <code>(@v1.9) pkg&gt; activate ...</code> if you have already installed the package code locally, simply make sure to point Pkg to the right path as shown above.</p></div></div><p>You can now change your source code and load them into the Julia session with <code>using &lt;name of package here&gt;</code>. To test your code, run <code>(@v1.9) pkg&gt; test</code> to run the package&#39;s test suite to ensure that everything works correctly. When you are done developing the package, enter <code>(@v1.9) pkg&gt; free</code> to stop tracking the package. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../toolsinstallation/">« Installing Development Tools</a><a class="docs-footer-nextpage" href="../casescenarios/">Case Scenarios »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 16 August 2023 03:49">Wednesday 16 August 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR12/getting_started/juliainstallation/index.html

@@ -12,4 +12,4 @@
 # Second option: install juliaup in a Rust image (not recommended)
 FROM rust:latest
 
-RUN cargo install juliaup</code></pre><h2 id="Direct-download"><a class="docs-heading-anchor" href="#Direct-download">Direct download</a><a id="Direct-download-1"></a><a class="docs-heading-anchor-permalink" href="#Direct-download" title="Permalink"></a></h2><p>You can also install Julia as a downloadable executable from the Julia website&#39;s <a href="https://julialang.org/downloads/">Download section</a>.  You must make sure to install the correct Julia build for your machine based on:</p><ul><li>native instruction set (x86_64, i686, ARM, Apple Silicon, PowerPC)</li><li>operating system type (Windows, MacOS, Linux (Glibc), Linux (Musl), FreeBSD)</li><li>bit compute type (32-bit, 64-bit)</li><li>desired level of support (Tier 1 (guaranteed to build and pass all tests) through Tier 4)</li></ul><p>Make sure to follow the exact installation steps for your machine in order to ensure the best experience.</p><h2 id="Build-from-source"><a class="docs-heading-anchor" href="#Build-from-source">Build from source</a><a id="Build-from-source-1"></a><a class="docs-heading-anchor-permalink" href="#Build-from-source" title="Permalink"></a></h2><p>For building/testing purposes, you may build Julia from the source code that is fully available in the <a href="https://github.com/JuliaLang/julia.git">Julia GitHub repository</a>. Simply enter <code>git clone https://github.com/JuliaLang/julia.git</code> to copy the entire source on your machine, create a new git branch via <code>git checkout -b name-of-branch</code>, add your modifications, and run <code>make</code> to start the Makefile build.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« BioJulia: Fast, open, easy, software for biology</a><a class="docs-footer-nextpage" href="../toolsinstallation/">Installing Development Tools »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 16 August 2023 03:36">Wednesday 16 August 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+RUN cargo install juliaup</code></pre><h2 id="Direct-download"><a class="docs-heading-anchor" href="#Direct-download">Direct download</a><a id="Direct-download-1"></a><a class="docs-heading-anchor-permalink" href="#Direct-download" title="Permalink"></a></h2><p>You can also install Julia as a downloadable executable from the Julia website&#39;s <a href="https://julialang.org/downloads/">Download section</a>.  You must make sure to install the correct Julia build for your machine based on:</p><ul><li>native instruction set (x86_64, i686, ARM, Apple Silicon, PowerPC)</li><li>operating system type (Windows, MacOS, Linux (Glibc), Linux (Musl), FreeBSD)</li><li>bit compute type (32-bit, 64-bit)</li><li>desired level of support (Tier 1 (guaranteed to build and pass all tests) through Tier 4)</li></ul><p>Make sure to follow the exact installation steps for your machine in order to ensure the best experience.</p><h2 id="Build-from-source"><a class="docs-heading-anchor" href="#Build-from-source">Build from source</a><a id="Build-from-source-1"></a><a class="docs-heading-anchor-permalink" href="#Build-from-source" title="Permalink"></a></h2><p>For building/testing purposes, you may build Julia from the source code that is fully available in the <a href="https://github.com/JuliaLang/julia.git">Julia GitHub repository</a>. Simply enter <code>git clone https://github.com/JuliaLang/julia.git</code> to copy the entire source on your machine, create a new git branch via <code>git checkout -b name-of-branch</code>, add your modifications, and run <code>make</code> to start the Makefile build.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« BioJulia: Fast, open, easy, software for biology</a><a class="docs-footer-nextpage" href="../toolsinstallation/">Installing Development Tools »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 16 August 2023 03:49">Wednesday 16 August 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR12/getting_started/toolsinstallation/index.html

@@ -21,4 +21,4 @@
 ERROR: invalid redefinition of constant Point
 Stacktrace:
 [1] top-level scope
-@ REPL[2]:1</code></pre></div></div><p>To learn more, see the <a href="https://docs.julialang.org/en/v1/stdlib/REPL/">The Julia REPL</a> section in the Julia manual.</p><h2 id="Visual-Studio-Code-extension"><a class="docs-heading-anchor" href="#Visual-Studio-Code-extension">Visual Studio Code extension</a><a id="Visual-Studio-Code-extension-1"></a><a class="docs-heading-anchor-permalink" href="#Visual-Studio-Code-extension" title="Permalink"></a></h2><p>The Julia organization officially maintains the <a href="https://www.julia-vscode.org/">Julia vscode extension</a>, which provides a complete IDE solution for developing in Julia. This boasts a number of advantages compared to a REPL solution:</p><ul><li>Built-in syntax highlighting and code completion</li><li>GUI interaction for managing options and commands</li><li>Advanced profiling/debugging features </li><li>Additional extensions support </li></ul><p>To install vscode, follow the instructions on how to install the official binary for your development machine from the  <a href="https://code.visualstudio.com/">official website</a>. Next, click on the Extension icon in the side Activity Bar and search for &quot;Julia&quot;. The official Julia extension should be the first extension available. You can also install Julia within the Quick Open input panel by pressing <code>Ctrl + P</code> and entering <code>ext install julialang.language-julia</code>.</p><p>&lt;!– TODO: Move image to assets directory –&gt; <img src="../JuliaVSCodeExtension.png" alt="Julia VSCode Extension"/></p><p>Install the extension and restart vscode. We also recommend installing some additional extensions that will further improve the development experience:</p><ul><li><a href="https://marketplace.visualstudio.com/items?itemName=tamasfe.even-better-toml">Even Better TOML</a>  (<code>ext install tamasfe.even-better-toml</code>) for working with the package TOML  files (Project.toml, Manifest.toml, Artifacts.toml,...)</li><li><a href="https://marketplace.visualstudio.com/items?itemName=eamodio.gitlens">GitLens</a> (<code>ext install eamodio.gitlens</code>) for  enhancing Git workflows</li></ul><p>&lt;!– TODO: some examples of julia-vscode commands–&gt;</p><p>You can experiment with Julia extension features in the Quick Open panel by writing Julia and consulting the available options. To learn more, visit the <a href="https://code.visualstudio.com/docs/languages/julia">Julia in Visual Studio Code</a> page  in the official vscode docs. You can also visit the <a href="https://www.julia-vscode.org/">Julia extension</a> website to learn more about what features are available.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../juliainstallation/">« Installing Julia</a><a class="docs-footer-nextpage" href="../biojuliainstallation/">Installing BioJulia Packages »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 16 August 2023 03:36">Wednesday 16 August 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+@ REPL[2]:1</code></pre></div></div><p>To learn more, see the <a href="https://docs.julialang.org/en/v1/stdlib/REPL/">The Julia REPL</a> section in the Julia manual.</p><h2 id="Visual-Studio-Code-extension"><a class="docs-heading-anchor" href="#Visual-Studio-Code-extension">Visual Studio Code extension</a><a id="Visual-Studio-Code-extension-1"></a><a class="docs-heading-anchor-permalink" href="#Visual-Studio-Code-extension" title="Permalink"></a></h2><p>The Julia organization officially maintains the <a href="https://www.julia-vscode.org/">Julia vscode extension</a>, which provides a complete IDE solution for developing in Julia. This boasts a number of advantages compared to a REPL solution:</p><ul><li>Built-in syntax highlighting and code completion</li><li>GUI interaction for managing options and commands</li><li>Advanced profiling/debugging features </li><li>Additional extensions support </li></ul><p>To install vscode, follow the instructions on how to install the official binary for your development machine from the  <a href="https://code.visualstudio.com/">official website</a>. Next, click on the Extension icon in the side Activity Bar and search for &quot;Julia&quot;. The official Julia extension should be the first extension available. You can also install Julia within the Quick Open input panel by pressing <code>Ctrl + P</code> and entering <code>ext install julialang.language-julia</code>.</p><p>&lt;!– TODO: Move image to assets directory –&gt; <img src="../JuliaVSCodeExtension.png" alt="Julia VSCode Extension"/></p><p>Install the extension and restart vscode. We also recommend installing some additional extensions that will further improve the development experience:</p><ul><li><a href="https://marketplace.visualstudio.com/items?itemName=tamasfe.even-better-toml">Even Better TOML</a>  (<code>ext install tamasfe.even-better-toml</code>) for working with the package TOML  files (Project.toml, Manifest.toml, Artifacts.toml,...)</li><li><a href="https://marketplace.visualstudio.com/items?itemName=eamodio.gitlens">GitLens</a> (<code>ext install eamodio.gitlens</code>) for  enhancing Git workflows</li></ul><p>&lt;!– TODO: some examples of julia-vscode commands–&gt;</p><p>You can experiment with Julia extension features in the Quick Open panel by writing Julia and consulting the available options. To learn more, visit the <a href="https://code.visualstudio.com/docs/languages/julia">Julia in Visual Studio Code</a> page  in the official vscode docs. You can also visit the <a href="https://www.julia-vscode.org/">Julia extension</a> website to learn more about what features are available.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../juliainstallation/">« Installing Julia</a><a class="docs-footer-nextpage" href="../biojuliainstallation/">Installing BioJulia Packages »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 16 August 2023 03:49">Wednesday 16 August 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>