update installation instructions

docs/search.json

@@ -202,7 +202,7 @@
     "href": "week1.html#things-to-set-up",
     "title": "Introduction to Bayesian inference",
     "section": "Things to set up",
-    "text": "Things to set up\n\nPython\nFirst get a recent (ideally 3.11+) version of Python This can be very annoying so talk to me if necessary!\nNext get used to Python virtual environments.\nThe method I like is to put the virtual environment in a folder .venv inside the root of my project:\n$ python -m venv .venv --prompt=bscb\nThen to use: Tip: use an ergonomic alias to activate venvs e.g. alias va=\"source .venv/bin/activate\"\n$ source .venv/bin/activate\n# ... do work\n$ deactivate\n\n\nGit and ssh\ngit clone [email protected]:teddygroves/bayesian_statistics_for_systems_biologists.git\n\n\nCmdstanpy and cmdstan\nfrom cmdstanpy import CmdStanModel\nfilename = \"example_stan_program.stan\" \ncode = \"data {} parameters {real t;} model {t ~ std_normal();}\"\nwith open(filename, \"w\") as f:\n    f.write(code)\nmodel = CmdStanModel(stan_file=filename)\nmcmc = model.sample()",
+    "text": "Things to set up\n\nPython\nFirst get a recent (ideally 3.11+) version of Python This can be very annoying so talk to me if necessary!\nNext get used to Python virtual environments.\nThe method I like is to put the virtual environment in a folder .venv inside the root of my project:\n$ python -m venv .venv --prompt=bscb\nThen to use: Tip: use an ergonomic alias to activate venvs e.g. alias va=\"source .venv/bin/activate\"\n$ source .venv/bin/activate\n# ... do work\n$ deactivate\n\n\nGit and ssh\ngit clone [email protected]:teddygroves/bayesian_statistics_for_systems_biologists.git\n\n\nCmdstanpy and cmdstan\nFirst install them:\n$ pip install cmdstanpy\n$ python -m cmdstanpy.instsall_cmdstan\nNow test if they work\nfrom cmdstanpy import CmdStanModel\nfilename = \"example_stan_program.stan\" \ncode = \"data {} parameters {real t;} model {t ~ std_normal();}\"\nwith open(filename, \"w\") as f:\n    f.write(code)\nmodel = CmdStanModel(stan_file=filename)\nmcmc = model.sample()",
     "crumbs": [
       "Course materials",
       "Introduction to Bayesian inference"

docs/week1.html

@@ -5253,13 +5253,17 @@ <h3 class="anchored" data-anchor-id="git-and-ssh">Git and ssh</h3>
 </section>
 <section id="cmdstanpy-and-cmdstan" class="level3">
 <h3 class="anchored" data-anchor-id="cmdstanpy-and-cmdstan">Cmdstanpy and cmdstan</h3>
-<div class="sourceCode" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> cmdstanpy <span class="im">import</span> CmdStanModel</span>
-<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>filename <span class="op">=</span> <span class="st">&quot;example_stan_program.stan&quot;</span> </span>
-<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>code <span class="op">=</span> <span class="st">&quot;data </span><span class="sc">{}</span><span class="st"> parameters {real t;} model {t ~ std_normal();}&quot;</span></span>
-<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(filename, <span class="st">&quot;w&quot;</span>) <span class="im">as</span> f:</span>
-<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>    f.write(code)</span>
-<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>model <span class="op">=</span> CmdStanModel(stan_file<span class="op">=</span>filename)</span>
-<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>mcmc <span class="op">=</span> model.sample()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>First install them:</p>
+<pre class="shell"><code>$ pip install cmdstanpy
+$ python -m cmdstanpy.instsall_cmdstan</code></pre>
+<p>Now test if they work</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> cmdstanpy <span class="im">import</span> CmdStanModel</span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>filename <span class="op">=</span> <span class="st">&quot;example_stan_program.stan&quot;</span> </span>
+<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>code <span class="op">=</span> <span class="st">&quot;data </span><span class="sc">{}</span><span class="st"> parameters {real t;} model {t ~ std_normal();}&quot;</span></span>
+<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(filename, <span class="st">&quot;w&quot;</span>) <span class="im">as</span> f:</span>
+<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>    f.write(code)</span>
+<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>model <span class="op">=</span> CmdStanModel(stan_file<span class="op">=</span>filename)</span>
+<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>mcmc <span class="op">=</span> model.sample()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section>
 </section>
 </section>

materials/week1.md

@@ -289,6 +289,15 @@ git clone [email protected]:teddygroves/bayesian_statistics_for_systems_biologists.
 
 ### Cmdstanpy and cmdstan
 
+First install them:
+
+```shell
+$ pip install cmdstanpy
+$ python -m cmdstanpy.instsall_cmdstan
+```
+
+Now test if they work
+
 ```python
 from cmdstanpy import CmdStanModel
 filename = "example_stan_program.stan"