Scripts

The following scripts are made available on your command-line by the PSOAP package.

Initialization

!psoap-initialize --help

usage: psoap-initialize [-h] [--check] [--model {SB1,SB2,ST3}]

Initialize a new directory to do inference.

optional arguments:
  -h, --help            show this help message and exit
  --check               To help folks check whether the package was installed
                        properly.
  --model {SB1,SB2,ST3}
                        Which type of model to use, SB1, SB2, ST1, or SB3.

!psoap-generate-chunks --help

/usr/bin/sh: psoap-generate-chunks: command not found

!psoap-process-chunks --help

/usr/bin/sh: psoap-process-chunks: command not found

!psoap-generate-masks --help

/usr/bin/sh: psoap-generate-masks: command not found

!psoap-process-masks --help

/usr/bin/sh: psoap-process-masks: command not found

Sampling

The following scripts are used in sampling the posterior distribution.

!psoap-sample --help

You need to copy a config.yaml file to this directory, and then edit the values to your particular case.
Traceback (most recent call last):
  File "/home/ian/.build/anaconda/bin/psoap-sample", line 11, in <module>
    load_entry_point('psoap==0.0.1', 'console_scripts', 'psoap-sample')()
  File "/home/ian/.build/anaconda/lib/python3.6/site-packages/pkg_resources/__init__.py", line 570, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/ian/.build/anaconda/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2751, in load_entry_point
    return ep.load()
  File "/home/ian/.build/anaconda/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2405, in load
    return self.resolve()
  File "/home/ian/.build/anaconda/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2411, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/ian/.build/anaconda/lib/python3.6/site-packages/psoap-0.0.1-py3.6-linux-x86_64.egg/psoap/sample.py", line 33, in <module>
    f = open("config.yaml")
FileNotFoundError: [Errno 2] No such file or directory: 'config.yaml'

!psoap-sample-parallel --help

usage: psoap-sample-parallel [-h] [--debug] run_index

Sample the distribution across multiple chunks.

positional arguments:
  run_index   Which output subdirectory to save this particular run, in the
              case you may be running multiple concurrently.

optional arguments:
  -h, --help  show this help message and exit
  --debug     Print out debug commands to log.log