def setup_model(*, cmdstan_dir, model_dir, name, model, data):
"""Compile Stan model."""
cmdstanpy.set_cmdstan_path(cmdstan_dir)
model = model.replace("<-", "=")
with tempfile.NamedTemporaryFile("w",
prefix=f"{name}_",
suffix=".stan",
dir=model_dir,
delete=False) as f:
print(model, file=f)
model_file = f.name
with tempfile.NamedTemporaryFile("w",
prefix=f"{name}_",
suffix=".json",
dir=model_dir,
delete=False) as f:
json.dump(data, f, indent=2, sort_keys=True)
data_file = f.name
model_object = cmdstanpy.CmdStanModel(stan_file=model_file)
exe_file = model_object.exe_file
return model_file, data_file, exe_file
def build_cmdstan_model(target_dir):
"""
Rebuild cmdstan in the build environment, then use this installation to compile the stan model.
The stan model is copied to {target_dir}/prophet_model.bin
The cmdstan files required to run cmdstanpy commands are copied to {target_dir}/cmdstan-{version}.
Parameters
----------
target_dir: Directory to copy the compiled model executable and core cmdstan files to.
"""
import cmdstanpy
cmdstan_cache = get_cmdstan_cache()
download_cmdstan(cmdstan_cache)
cmdstan_dir = os.path.join(target_dir, f"cmdstan-{CMDSTAN_VERSION}")
if os.path.isdir(cmdstan_dir):
rmtree(cmdstan_dir)
copytree(cmdstan_cache, cmdstan_dir)
with cmdstanpy.utils.pushd(cmdstan_dir):
clean_all_cmdstan()
build_cmdstan()
cmdstanpy.set_cmdstan_path(cmdstan_dir)
model_name = "prophet.stan"
target_name = "prophet_model.bin"
sm = cmdstanpy.CmdStanModel(stan_file=os.path.join(MODEL_DIR, model_name))
copy(sm.exe_file, os.path.join(target_dir, target_name))
# Clean up
for f in Path(MODEL_DIR).iterdir():
if f.is_file() and f.name != model_name:
os.remove(f)
prune_cmdstan(cmdstan_dir)
def init():
"Initialize CmdStan and CmdStanPy"
readme = stan_dir / 'README.md'
if not readme.exists():
_log.error('CmdStan not found, is it checked out?')
_log.info('Try running: git submodule update --init --recursive')
raise RuntimeError('CmdStan not available')
_log.info('initializing local settings')
_local_make.write_text(stan_config)
stanc = stan_dir / 'bin' / 'stanc'
make = 'make'
if platform.system() == 'Windows':
stanc = stanc.with_suffix('.exe')
make = 'mingw32-make' # STAN is picky
_log.info('making sure CmdStan is compiled')
sp.run([make, '-j4', 'build'], cwd=stan_dir, check=True)
res = sp.run([os.fspath(stanc), '--version'],
capture_output=True,
check=True)
_log.info('built Stan version %s', res.stdout.decode('utf8').strip())
cmdstanpy.set_cmdstan_path(os.fspath(stan_dir))
def install_cmdstan_deps(cmdstan_dir: Path):
import cmdstanpy
cmdstan_cache = get_cmdstan_cache()
download_cmdstan(cmdstan_cache)
if cmdstan_dir.is_dir():
rmtree(cmdstan_dir)
copytree(cmdstan_cache, cmdstan_dir)
if PLATFORM == "win":
try:
cmdstanpy.utils.cxx_toolchain_path()
except Exception:
install_cmdstan_toolchain()
with cmdstanpy.utils.pushd(cmdstan_dir):
clean_all_cmdstan()
build_cmdstan()
cmdstanpy.set_cmdstan_path(str(cmdstan_dir))
subprocess.run(["conda", "list"])
subprocess.run(["conda", "info"])
else:
print("pip environment:")
subprocess.run([sys.executable, "-m", "pip", "list"])
# hacky for RTD - which doesn't actually call conda activate
# see: https://github.com/readthedocs/readthedocs.org/issues/5339
if os.environ.get('READTHEDOCS', False):
import cmdstanpy
version = 'v' + cmdstanpy.__version__
cmdstanpy.set_cmdstan_path(
'/home/docs/checkouts/readthedocs.org/user_builds/cmdstanpy/'
'conda/' + version + '/bin/cmdstan')
os.environ['CXX'] = (
'/home/docs/checkouts/readthedocs.org/user_builds/cmdstanpy/'
'conda/' + version + '/bin/x86_64-conda-linux-gnu-c++')
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
sys.path.insert(0, os.path.dirname(os.path.abspath('.')))
# this sets up logging to print all logging messages
# the ipython directive doesn't show logging, so this is a hack
import logging
from logging import StreamHandler
def __init__(self):
super().__init__()
import cmdstanpy
cmdstanpy.set_cmdstan_path(
pkg_resources.resource_filename(
"prophet", f"stan_model/cmdstan-{self.CMDSTAN_VERSION}"))