build based on 9e4be24

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-11-21T19:07:05","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-11-22T09:46:34","documenter_version":"1.8.0"}}

dev/distributed/2_parallel/index.html

@@ -5,4 +5,4 @@
     model,
     optimizer = HiGHS.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><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 21 November 2024 19:07">Thursday 21 November 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><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="Friday 22 November 2024 09:46">Friday 22 November 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><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 21 November 2024 19:07">Thursday 21 November 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><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="Friday 22 November 2024 09:46">Friday 22 November 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

@@ -54,4 +54,4 @@
 end |&gt; String, &quot;...&quot;)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">7JL5
Model|�)�&amp;i!��@��=OZ
AbstractFBCModels
CanonicalModelD5
DictN�D!
Reaction...</code></pre><p>The above code has saved the <code>CanonicalModel</code> in the way specified by the <code>CanonicalModel</code> structure – which is, in this case, a binary dump of the Julia objects, instead of the expected JSON. To prevent this, you can either specify the output type yourself:</p><pre><code class="language-julia hljs">save_model(model_in_julia_structures, &quot;e_coli_saved_right.json&quot;, JSONFBCModel)</code></pre><p>...or use <a href="../../reference/core/#COBREXA.save_converted_model-Union{Tuple{T}, Tuple{T, String}} where T&lt;:AbstractFBCModels.AbstractFBCModel"><code>save_converted_model</code></a> to guess the model type automatically from the extension:</p><pre><code class="language-julia hljs">save_converted_model(model_in_julia_structures, &quot;e_coli_saved_automatically_right.json&quot;)
 println(open(&quot;e_coli_saved_automatically_right.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><p>As with <a href="../../reference/core/#COBREXA.load_model-Tuple{String}"><code>load_model</code></a>, there is some overhead and uncertainty associated with <a href="../../reference/core/#COBREXA.save_converted_model-Union{Tuple{T}, Tuple{T, String}} where T&lt;:AbstractFBCModels.AbstractFBCModel"><code>save_converted_model</code></a> guessing the model type from extension. For that reason, it is adviseable to rely on the guessing functionality only in interactive use in REPL, and avoid it in automated scriptage altogether.</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="../">« Contents</a><a class="docs-footer-nextpage" href="../02a-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><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 21 November 2024 19:07">Thursday 21 November 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><p>As with <a href="../../reference/core/#COBREXA.load_model-Tuple{String}"><code>load_model</code></a>, there is some overhead and uncertainty associated with <a href="../../reference/core/#COBREXA.save_converted_model-Union{Tuple{T}, Tuple{T, String}} where T&lt;:AbstractFBCModels.AbstractFBCModel"><code>save_converted_model</code></a> guessing the model type from extension. For that reason, it is adviseable to rely on the guessing functionality only in interactive use in REPL, and avoid it in automated scriptage altogether.</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="../">« Contents</a><a class="docs-footer-nextpage" href="../02a-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><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="Friday 22 November 2024 09:46">Friday 22 November 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

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

@@ -32,4 +32,4 @@
      :THD2 => 0.0
      :TKT1 => 1.496983757261565
      :TKT2 => 1.1814980932459616
-      :TPI =&gt; 7.477381962160285</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="../02b-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><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 21 November 2024 19:07">Thursday 21 November 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+      :TPI =&gt; 7.477381962160285</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="../02b-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><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="Friday 22 November 2024 09:46">Friday 22 November 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/02b-optimizer-parameters.ipynb

@@ -162,7 +162,7 @@
       "  System       : Augmented system (K2)\n",
       "\n",
       " Itn            PObj            DObj     PFeas    DFeas    GFeas       Mu  Time\n",
-      "   0  -0.0000000e+00  +1.7686535e+05  1.16e+04 8.59e-02 1.77e+05  1.0e+00  0.86\n",
+      "   0  -0.0000000e+00  +1.7686535e+05  1.16e+04 8.59e-02 1.77e+05  1.0e+00  0.87\n",
       "Solver exited with status Trm_TimeLimit\n"
      ]
     }