diff --git a/docs/search.json b/docs/search.json index c84309d..7dfd3eb 100644 --- a/docs/search.json +++ b/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 git@github.com: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 git@github.com: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" diff --git a/docs/week1.html b/docs/week1.html index 2f5b280..1c43b96 100644 --- a/docs/week1.html +++ b/docs/week1.html @@ -5253,13 +5253,17 @@

Git and ssh

Cmdstanpy and cmdstan

-
from cmdstanpy import CmdStanModel
-filename = "example_stan_program.stan" 
-code = "data {} parameters {real t;} model {t ~ std_normal();}"
-with open(filename, "w") as f:
-    f.write(code)
-model = CmdStanModel(stan_file=filename)
-mcmc = model.sample()
+

First install them:

+
$ pip install cmdstanpy
+$ python -m cmdstanpy.instsall_cmdstan
+

Now test if they work

+
from cmdstanpy import CmdStanModel
+filename = "example_stan_program.stan" 
+code = "data {} parameters {real t;} model {t ~ std_normal();}"
+with open(filename, "w") as f:
+    f.write(code)
+model = CmdStanModel(stan_file=filename)
+mcmc = model.sample()
diff --git a/materials/week1.md b/materials/week1.md index 2c3d70c..ebc0909 100644 --- a/materials/week1.md +++ b/materials/week1.md @@ -289,6 +289,15 @@ git clone git@github.com: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"