First you need to install xcode from the app store
Then you can run:
xcode-select --installSee Here for why
Then create an install a conda environment for pystan
conda create -n pystan --yes
conda activate pystan
conda install -c conda-forge pystan ipython --yes
Then try running the code from here
import stan
schools_code = """
data {
int<lower=0> J; // number of schools
real y[J]; // estimated treatment effects
real<lower=0> sigma[J]; // standard error of effect estimates
}
parameters {
real mu; // population treatment effect
real<lower=0> tau; // standard deviation in treatment effects
vector[J] eta; // unscaled deviation from mu by school
}
transformed parameters {
vector[J] theta = mu + tau * eta; // school treatment effects
}
model {
target += normal_lpdf(eta | 0, 1); // prior log-density
target += normal_lpdf(y | theta, sigma); // log-likelihood
}
"""
schools_data = {"J": 8,
"y": [28, 8, -3, 7, -1, 1, 18, 12],
"sigma": [15, 10, 16, 11, 9, 11, 10, 18]}
posterior = stan.build(schools_code, data=schools_data)
fit = posterior.sample(num_chains=4, num_samples=1000)
eta = fit["eta"] # array with shape (8, 4000)
df = fit.to_frame() # pandas `DataFrame, requires pandasI got the following error:
ValueError: The JSON document has an improper structure: missing or superfluous commas, braces, missing keys, etc.which appears after this line:
posterior = stan.build(schools_code, data=schools_data)conda create -n test --yes
conda activate test
conda install -c pip --yes
which python3
python3 -m pip install -U pip
python3 -m pip install pystan
conda install -c ipython --yesThen run the model code again (from here)
RuntimeError: Exception while building model extension module: `CompileError(DistutilsExecError("command 'x86_64-apple-darwin13.4.0-clang' failed: No such file or directory"))`, traceback: `[' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/httpstan/views.py", line 114, in handle_create_model\n compiler_output = await httpstan.models.build_services_extension_module(program_code)\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/httpstan/models.py", line 168, in build_services_extension_module\n compiler_output = await asyncio.get_running_loop().run_in_executor(\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/concurrent/futures/thread.py", line 52, in run\n result = self.fn(*self.args, **self.kwargs)\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/httpstan/build_ext.py", line 80, in run_build_ext\n build_extension.run()\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/distutils/command/build_ext.py", line 340, in run\n self.build_extensions()\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/distutils/command/build_ext.py", line 449, in build_extensions\n self._build_extensions_serial()\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/distutils/command/build_ext.py", line 474, in _build_extensions_serial\n self.build_extension(ext)\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/distutils/command/build_ext.py", line 529, in build_extension\n objects = self.compiler.compile(sources,\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/distutils/ccompiler.py", line 574, in compile\n self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)\n', ' File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/distutils/unixccompiler.py", line 120, in _compile\n raise CompileError(msg)\n']`Based on answer here
# Uninstall httpstan in case it's already installed.
pip uninstall -y httpstan pystan
# Install httpstan from source (this will take a while).
pip install -v git+https://github.com/tillahoffmann/httpstan@pip
# Install pystan.
pip install 'pystan>=3'
# Try a dummy program (this should report build and sampling progress).
python -c 'import stan; stan.build("parameters { real x; } model { x ~ normal(0, 1); }").sample()'
The following error (@ line: pip install -v git+https://github.com/tillahoffmann/httpstan@pip)
Using pip 22.0.3 from /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/pip (python 3.9)
Collecting git+https://github.com/tillahoffmann/httpstan@pip
Cloning https://github.com/tillahoffmann/httpstan (to revision pip) to /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d
Running command git version
git version 2.30.0
Running command git clone --filter=blob:none https://github.com/tillahoffmann/httpstan /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d
Cloning into '/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d'...
Running command git show-ref pip
0ba90d4be04967d1a9200a8ccb4be11fab788abd refs/remotes/origin/pip
Running command git symbolic-ref -q HEAD
refs/heads/main
Running command git checkout -b pip --track origin/pip
Switched to a new branch 'pip'
Branch 'pip' set up to track remote branch 'pip' from 'origin'.
Resolved https://github.com/tillahoffmann/httpstan to commit 0ba90d4be04967d1a9200a8ccb4be11fab788abd
Running command pip subprocess to install build dependencies
Collecting setuptools
Downloading setuptools-60.9.2-py3-none-any.whl (1.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 7.8 MB/s eta 0:00:00
Collecting poetry_core>=1.0.0
Downloading poetry_core-1.0.7-py2.py3-none-any.whl (424 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 424.8/424.8 KB 11.7 MB/s eta 0:00:00
Installing collected packages: setuptools, poetry_core
Successfully installed poetry_core-1.0.7 setuptools-60.9.2
Installing build dependencies ... done
Running command Getting requirements to build wheel
Getting requirements to build wheel ... done
Running command Preparing metadata (pyproject.toml)
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: aiohttp<4.0,>=3.7 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from httpstan==4.6.1) (3.8.1)
Requirement already satisfied: marshmallow<4.0,>=3.10 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from httpstan==4.6.1) (3.14.1)
Requirement already satisfied: setuptools>=41.0 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from httpstan==4.6.1) (58.0.4)
Requirement already satisfied: webargs<9.0,>=8.0 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from httpstan==4.6.1) (8.1.0)
Requirement already satisfied: appdirs<2.0,>=1.4 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from httpstan==4.6.1) (1.4.4)
Requirement already satisfied: numpy<2.0,>=1.16 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from httpstan==4.6.1) (1.22.2)
Requirement already satisfied: attrs>=17.3.0 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from aiohttp<4.0,>=3.7->httpstan==4.6.1) (21.4.0)
Requirement already satisfied: frozenlist>=1.1.1 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from aiohttp<4.0,>=3.7->httpstan==4.6.1) (1.3.0)
Requirement already satisfied: aiosignal>=1.1.2 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from aiohttp<4.0,>=3.7->httpstan==4.6.1) (1.2.0)
Requirement already satisfied: multidict<7.0,>=4.5 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from aiohttp<4.0,>=3.7->httpstan==4.6.1) (6.0.2)
Requirement already satisfied: charset-normalizer<3.0,>=2.0 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from aiohttp<4.0,>=3.7->httpstan==4.6.1) (2.0.12)
Requirement already satisfied: yarl<2.0,>=1.0 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from aiohttp<4.0,>=3.7->httpstan==4.6.1) (1.7.2)
Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from aiohttp<4.0,>=3.7->httpstan==4.6.1) (4.0.2)
Requirement already satisfied: packaging in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from webargs<9.0,>=8.0->httpstan==4.6.1) (21.3)
Requirement already satisfied: idna>=2.0 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from yarl<2.0,>=1.0->aiohttp<4.0,>=3.7->httpstan==4.6.1) (3.3)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages (from packaging->webargs<9.0,>=8.0->httpstan==4.6.1) (3.0.7)
Building wheels for collected packages: httpstan
Running command git rev-parse HEAD
0ba90d4be04967d1a9200a8ccb4be11fab788abd
Running command Building wheel for httpstan (pyproject.toml)
running build
running build_py
creating /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build
creating /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9
creating /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/build_ext.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/config.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/fits.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/models.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/openapi.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/cache.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/__init__.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/schemas.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/utils.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/services_stub.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/compile.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/app.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/__main__.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/views.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/routes.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
creating /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan/services
copying httpstan/services/arguments.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan/services
copying httpstan/services/__init__.py -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan/services
copying httpstan/socket_writer.hpp -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/socket_logger.hpp -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/stan_services.cpp -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/empty.cpp -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/stan.pyi -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan
copying httpstan/services/cmdstan-help-all.json -> /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build/lib.macosx-10.9-x86_64-3.9/httpstan/services
running build_ext
downloading build/archives/math-v4.2.1.tar.gz
extracting archive build/archives/math-v4.2.1.tar.gz
tar -C build -zxf build/archives/math-v4.2.1.tar.gz
touch build/math-4.2.1
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.libraries build/math-4.2.1/lib/sundials_5.7.0/lib/libsundials_nvecserial.a
/bin/sh: x86_64-apple-darwin13.4.0-clang++: command not found
x86_64-apple-darwin13.4.0-clang++ -fPIC -pipe -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -O3 -I build/math-4.2.1/lib/sundials_5.7.0/include -DNO_FPRINTF_OUTPUT -O3 -c -x c -include build/math-4.2.1/lib/sundials_5.7.0/include/stan_sundials_printf_override.hpp build/math-4.2.1/lib/sundials_5.7.0/src/nvector/serial/nvector_serial.c -o build/math-4.2.1/lib/sundials_5.7.0/src/nvector/serial/nvector_serial.o
make[1]: x86_64-apple-darwin13.4.0-clang++: No such file or directory
make[1]: *** [build/math-4.2.1/lib/sundials_5.7.0/src/nvector/serial/nvector_serial.o] Error 1
make: *** [build/math-4.2.1/lib/sundials_5.7.0/lib/libsundials_nvecserial.a] Error 2
Traceback (most recent call last):
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/setup.py", line 36, in <module>
setup(**setup_kwargs)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 155, in setup
return distutils.core.setup(**attrs)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 148, in setup
return run_commands(dist)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 163, in run_commands
dist.run_commands()
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
self.run_command(cmd)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build.py", line 26, in run
subprocess.check_call(["make"], cwd=self.build_lib)
File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make']' returned non-zero exit status 2.
Traceback (most recent call last):
File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
main()
File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 261, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/poetry/core/masonry/api.py", line 68, in build_wheel
return unicode(WheelBuilder.make_in(poetry, Path(wheel_directory)))
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 72, in make_in
wb.build()
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 103, in build
self._build(zip_file)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 135, in _build
self._run_build_command(setup)
File "/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-build-env-lvr_ot6t/overlay/lib/python3.9/site-packages/poetry/core/masonry/builders/wheel.py", line 163, in _run_build_command
subprocess.check_call(
File "/Users/tommylees/miniconda3/envs/test/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/Users/tommylees/miniconda3/envs/test/bin/python3', '/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/setup.py', 'build', '-b', '/private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d/build']' returned non-zero exit status 1.
error: subprocess-exited-with-error
× Building wheel for httpstan (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
full command: /Users/tommylees/miniconda3/envs/test/bin/python3 /Users/tommylees/miniconda3/envs/test/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/tmp4r3qtbuf
cwd: /private/var/folders/q3/0lmt64ld10s14_0n0vxpt_m00000gp/T/pip-req-build-gipaio1d
Building wheel for httpstan (pyproject.toml) ... error
ERROR: Failed building wheel for httpstan
Failed to build httpstan
ERROR: Could not build wheels for httpstan, which is required to install pyproject.toml-based projectsCreate a virtualenv instead? Towards Data Science: Creating a VirtualEnv
pip install virtualenv
virtualenv stan
source stan/bin/activate
which pip- Issues with Pystan from Anaconda
- M1 Mac Discussion