diff --git a/README.md b/README.md index e50363ea..6b92e0d1 100644 --- a/README.md +++ b/README.md @@ -28,10 +28,6 @@ Stan.jl v7.x constitutes the third generation and covers all of cmdstan's method Stan.jl v8.0 is based on StanSample.jl v5, StanOptimize.jl v3 and StanQuap.jl v2. -Note: Future versions of the StanJulia packages, in particular StanSample.jl v5.1, will start to support multithreading in the `cmdstan` binary and will require cmdstan v2.28.1 and up. - -My intention is to continue maintenance of CmdStan.jl at least until late 2021. - ## Requirements Stan's cmdstan executable needs to be installed separatedly. Please see [cmdstan installation](https://stanjulia.github.io/Stan.jl/latest/INSTALLATION/). @@ -42,7 +38,9 @@ For more info on Stan, please go to . ### Version 8.0.0 - +1. Supports both CMDSTAN and JULIA_CMDSTAN_HOME environment variables to point to the cmdstan installation. +2. Thanks to @jfb-h completed testing with using conda to install cmdstan +3. Refactored code between StanBase.jl and the other StanJulia packages. ### Version 7.1.1 diff --git a/docs/src/INSTALLATION.md b/docs/src/INSTALLATION.md index 50b792dc..01f6ad42 100644 --- a/docs/src/INSTALLATION.md +++ b/docs/src/INSTALLATION.md @@ -8,23 +8,22 @@ To install Stan.jl e.g. in the Julia REPL: `] add Stan`. To run this version of the Stan.jl package on your local machine, it assumes that the [cmdstan](http://mc-stan.org/interfaces/cmdstan) executable is properly installed. -In order for Stan.jl to find the cmdstan you need to set the environment variable `JULIA_CMDSTAN_HOME` to point to the cmdstan directory, e.g. add +In order for Stan.jl to find the cmdstan you need to set the environment variable `CMDSTAN` (or `JULIA_CMDSTAN_HOME`) to point to the cmdstan directory, e.g. add ``` -export JULIA_CMDSTAN_HOME=/Users/rob/Projects/Stan/cmdstan -launchctl setenv JULIA_CMDSTAN_HOME /Users/rob/Projects/Stan/cmdstan # Mac specific +export CMDSTAN=/Users/rob/Projects/Stan/cmdstan +launchctl setenv CMDSTAN /Users/rob/Projects/Stan/cmdstan # Mac specific ``` to your `~/.zshrc` or `~/.bash_profile` or simply add - ``` -ENV["JULIA_CMDSTAN_HOME"]="_your absolute path to cmdstan_" +ENV["CMDSTAN"]="_your absolute path to cmdstan_" ``` to `./julia/config/startup.jl`. Remember to use `expanduser()` if you use `~` in above "path to cmdstan" if it is not absolute. I typically prefer cmdstan not to include the cmdstan version number in the above path to cmdstan (no update needed when the cmdstan version is updated). -Currently tested with cmdstan 2.28.1. +Currently tested with cmdstan 2.28.2. -Note: Future versions of the StanJulia packages, in particular StanSample.jl v5.1, will start to support multithreading in the `cmdstan` binary and will require cmdstan v2.28.1 and up. +Note: Future versions of the StanJulia packages, in particular StanSample.jl v5.1, will start to support multithreading in the `cmdstan` binary and will require cmdstan v2.28.2 and up. diff --git a/docs/src/VERSIONS.md b/docs/src/VERSIONS.md index 2b535027..17fbeafb 100644 --- a/docs/src/VERSIONS.md +++ b/docs/src/VERSIONS.md @@ -24,11 +24,11 @@ This version of the package has primarily been tested with GitHub workflows and 1. Change the default output format returned by read_samples to :table. 2. Keyword based cmdline modification. -3. Dropped dependency on StanBase. +3. Refactored code between StanBase.jl and the other StanJulia packages. 4. Will need cmdstan 2.28.1 (for num_threads). 5. `tmpdir` now positional argument when creating a CmdStanModel. - -Note: StanVariational.jl and StanDiagnose.jl have not yet been updated to use keywords in the `stan_variational()` and `stan_diagnose()` calls. They still depend on StanBase.jl. +6. Supports both CMDSTAN and JULIA_CMDSTAN_HOME environment variables to point to the cmdstan installation (for compatibility between cmdstan for R and Python). +7. Thanks to @jfb-h completed testing with using conda to install cmdstan ### Version 7.0 diff --git a/src/Stan.jl b/src/Stan.jl index e813dc9b..f4c6db4d 100644 --- a/src/Stan.jl +++ b/src/Stan.jl @@ -1,5 +1,5 @@ module Stan -using StanSample, StanOptimize, StanDiagnose, StanVariational +using StanSample, StanOptimize, StanDiagnose, StanVariational, StanQuap end # module