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stan_sample defaults depend on state of SampleModel (as potentially modified by previous stan_sample calls) #82

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stan_sample defaults depend on state of SampleModel (as potentially modified by previous stan_sample calls)#82
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bparbhu

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@nsiccha
nsiccha
opened on Nov 14, 2025

I've found that behaviour confusing, as it's also not documented "anywhere" (where it's immediately obvious to the user).

Example code:

sm = Stan.SampleModel(...)
# This runs with engaged=true
Stan.stan_sample(sm; data, num_chains=1) |> display
Stan.stan_sample(sm; data, num_chains=1, engaged=false)
# This runs with engaged=false
Stan.stan_sample(sm; data, num_chains=1) |> display

Output (note engaged=true in the first line and engaged=false in the second line).

Process(`/tmp/jl_K1HcGM/nc_eight_schools_no_gq method=sample adapt engaged=true algorithm=hmc id=1 data file=/tmp/jl_K1HcGM/nc_eight_schools_no_gq_data_1.json output file=/tmp/jl_K1HcGM/nc_eight_schools_no_gq_chain_1.csv`, ProcessExited(0))
Process(`/tmp/jl_K1HcGM/nc_eight_schools_no_gq method=sample adapt engaged=false algorithm=hmc id=1 data file=/tmp/jl_K1HcGM/nc_eight_schools_no_gq_data_1.json output file=/tmp/jl_K1HcGM/nc_eight_schools_no_gq_chain_1.csv`, ProcessExited(0))

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  1. bparbhu
    self-assigned this
    on Dec 19, 2025

  2. penelopeysm commented on Apr 5, 2026

    @penelopeysm
    penelopeysm
    on Apr 5, 2026

    I ran into this issue with thinning as well -- I also find this behaviour really confusing. In most reasonable interfaces, keyword arguments that aren't specified have a fixed default. The current design departs from that convention in two ways:

    1. the default value is inherited from the positional argument
    2. the positional argument is a mutable object, causing the default value to change from call to call

    I would have expected an interface where:

    • SampleModel is a struct that contains (a path to) the compiled model, but not much other info
    • Calling stan_sample on that should not mutate the SampleModel, but instead return a new object, let's call it SampleResults
    • This object could wrap the SampleModel along with all the configuration values that are pertinent to this particular sampling call.

  3. bparbhu commented on Apr 19, 2026

    @bparbhu
    bparbhu
    on Apr 19, 2026
    Contributor

    Understood, and thanks again for filing this. We're in the middle of updating to CmdStan 2.37. We'll take a look into this as soon as that is finished.

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