build based on 600d49b

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-05-17T07:25:37","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-06-07T09:59:39","documenter_version":"1.4.1"}}

dev/distributed/2_parallel/index.html

@@ -5,4 +5,4 @@
     model,
     optimizer = GLPK.Optimizer,
     workers = workers()
-)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../1_functions/">« Parallel processing overview</a><a class="docs-footer-nextpage" href="../3_slurm/">Working in a HPC environment »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 07:25">Friday 17 May 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../1_functions/">« Parallel processing overview</a><a class="docs-footer-nextpage" href="../3_slurm/">Working in a HPC environment »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 7 June 2024 09:59">Friday 7 June 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/distributed/3_slurm/index.html

@@ -17,4 +17,4 @@
 
 module load lang/Julia   # add Julia to the environment (this may differ on different clusters and installations!)
 
-julia myJob.jl</code></pre><p>To run the computation, run <code>sbatch myJob.sbatch</code> on the cluster access node. The job will be scheduled and eventually executed. It is possible to watch the output of commands <code>sacct</code> and <code>squeue</code> in the meantime, to see the progress.</p><p>Remember that it is necessary to explicitly save the result of the Julia script computation to files, to be able to retrieve them later. Standard outputs of the jobs are often mangled and/or discarded. If we would still want to collect the standard output of the Julia script, we might need to change the last line of the batch script as follows:</p><pre><code class="language-sh hljs">julia myJob.jl &gt; myJob.log</code></pre><p>...and collect the output from <code>myJob.log</code> later. This is convenient especially if the script prints out various computation details using <code>@info</code> and similar macros.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../2_parallel/">« Local parallel processing</a><a class="docs-footer-nextpage" href="../../reference/">Contents »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 07:25">Friday 17 May 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia myJob.jl</code></pre><p>To run the computation, run <code>sbatch myJob.sbatch</code> on the cluster access node. The job will be scheduled and eventually executed. It is possible to watch the output of commands <code>sacct</code> and <code>squeue</code> in the meantime, to see the progress.</p><p>Remember that it is necessary to explicitly save the result of the Julia script computation to files, to be able to retrieve them later. Standard outputs of the jobs are often mangled and/or discarded. If we would still want to collect the standard output of the Julia script, we might need to change the last line of the batch script as follows:</p><pre><code class="language-sh hljs">julia myJob.jl &gt; myJob.log</code></pre><p>...and collect the output from <code>myJob.log</code> later. This is convenient especially if the script prints out various computation details using <code>@info</code> and similar macros.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../2_parallel/">« Local parallel processing</a><a class="docs-footer-nextpage" href="../../reference/">Contents »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 7 June 2024 09:59">Friday 7 June 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/01-loading-and-saving/index.html

@@ -49,4 +49,4 @@
 )
 </code></pre><p><code>CanonicalModel</code> is a newer, cleaned-up version of the <code>StandardModel</code> type used in COBREXA version 1. For all code that relied on <code>StandardModel</code>, the canonical one should work just as well.</p><p>The above command specifies all model types explicitly, leaving least room for guessing-based errors.</p><p>If required, it is also possible to convert all model types to each other simply by using Julia&#39;s <code>convert</code>:</p><pre><code class="language-julia hljs">model_in_json_structure = convert(JSONFBCModels.JSONFBCModel, model_in_julia_structures)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">JSONFBCModels.JSONFBCModel(#= 95 reactions, 72 metabolites =#)</code></pre><h2 id="Saving-models"><a class="docs-heading-anchor" href="#Saving-models">Saving models</a><a id="Saving-models-1"></a><a class="docs-heading-anchor-permalink" href="#Saving-models" title="Permalink"></a></h2><p>The models can be saved to file storage by using <a href="../../reference/core/#COBREXA.save_model-Union{Tuple{T}, Tuple{T, String}} where T&lt;:AbstractFBCModels.AbstractFBCModel"><code>save_model</code></a>:</p><pre><code class="language-julia hljs">save_model(model_converted_to_json, &quot;e_coli_core_from_sbml.json&quot;)</code></pre><p>Expectably, the file will contain the JSON with the model description:</p><pre><code class="language-julia hljs">println(open(&quot;e_coli_core_from_sbml.json&quot;) do f
     read(f, 100)
-end |&gt; String, &quot;...&quot;)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">{&quot;metabolites&quot;:[{&quot;compartment&quot;:&quot;c&quot;,&quot;name&quot;:&quot;3-Phospho-D-glyceroyl phosphate&quot;,&quot;formula&quot;:&quot;C3H4O10P2&quot;,&quot;i...</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Contents</a><a class="docs-footer-nextpage" href="../02-flux-balance-analysis/">Flux balance analysis (FBA) »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 07:25">Friday 17 May 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+end |&gt; String, &quot;...&quot;)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">{&quot;metabolites&quot;:[{&quot;compartment&quot;:&quot;c&quot;,&quot;name&quot;:&quot;3-Phospho-D-glyceroyl phosphate&quot;,&quot;formula&quot;:&quot;C3H4O10P2&quot;,&quot;i...</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Contents</a><a class="docs-footer-nextpage" href="../02-flux-balance-analysis/">Flux balance analysis (FBA) »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 7 June 2024 09:59">Friday 7 June 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/02-flux-balance-analysis/index.html

@@ -33,4 +33,4 @@
      :THD2 => -7.993605777301127e-15
      :TKT1 => 1.496983757261579
      :TKT2 => 1.181498093245977
-      :TPI =&gt; 7.477381962160284</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../01-loading-and-saving/">« Loading and saving models</a><a class="docs-footer-nextpage" href="../02a-optimizer-parameters/">Changing optimizer parameters »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 07:25">Friday 17 May 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+      :TPI =&gt; 7.477381962160284</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../01-loading-and-saving/">« Loading and saving models</a><a class="docs-footer-nextpage" href="../02a-optimizer-parameters/">Changing optimizer parameters »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 7 June 2024 09:59">Friday 7 June 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/02a-optimizer-parameters/index.html

@@ -21,4 +21,4 @@
     settings = [set_optimizer_attribute("IPM_IterationsLimit", 2), set_time_limit(0.1)],
 )
 
-println(solution)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">nothing</code></pre><p>Applicable optimizer attributes are documented in the documentations of the respective optimizers. To browse the possibilities, one might want to see the <a href="https://jump.dev/JuMP.jl/stable/installation/#Supported-solvers">JuMP documentation page that summarizes the references to the available optimizers</a>.</p><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../02-flux-balance-analysis/">« Flux balance analysis (FBA)</a><a class="docs-footer-nextpage" href="../02b-model-modifications/">Making adjustments to the model »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 07:25">Friday 17 May 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+println(solution)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">nothing</code></pre><p>Applicable optimizer attributes are documented in the documentations of the respective optimizers. To browse the possibilities, one might want to see the <a href="https://jump.dev/JuMP.jl/stable/installation/#Supported-solvers">JuMP documentation page that summarizes the references to the available optimizers</a>.</p><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../02-flux-balance-analysis/">« Flux balance analysis (FBA)</a><a class="docs-footer-nextpage" href="../02b-model-modifications/">Making adjustments to the model »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 7 June 2024 09:59">Friday 7 June 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>