Source code for pycif.plugins.models.template.run

import pandas as pd
import datetime
import os
import shutil
import subprocess
import glob
import numpy as np

from logging import info, debug


def run(self, runsubdir, mode, workdir, ddi, nbproc=1, do_simu=True,
        approx_transf=False, ref_fwd_dir="", overlap=False, **kwargs):
    """Run the model in forward, tangent-linear or adjoint mode.
    This includes:

        - executing the model external executable
        - updating ``adj_refdir``
        - moving files needed for chained simulations to
          "{}/../".format(runsubdir)

    Note:
        For model for which the adjoint is not coded, make sure to return
        a clear error if the ``run`` function is called
        in ``adj`` mode and with ``do_simu = True``

    Args:
        self: the model Plugin
        runsubdir (str): working directory for the current run
        mode (str): forward or backward
        workdir (str): pyCIF working directory
        do_simu (bool): re-run or not existing simulation

    """

    if not do_simu:
        # if mode in ["fwd", "tl"]:
        #     self.adj_refdir = "{}/../".format(runsubdir)
        return

    with open("{}/log.std".format(runsubdir), "w") as log:
        process = subprocess.Popen(
            "ls",
            cwd=runsubdir,
            stdout=log,
            stderr=subprocess.PIPE
        )
        _, stderr = process.communicate()

    if stderr != "":
        debug("Deal with exception in executable")

    # If not running the model, copy expected pre-computed output files
    if self.only_outputs:
        debug("Here, one should copy reference files from a directory "
              "given as argument in the Yaml to $runsubdir: {}"
              .format(runsubdir))

    # if mode in ["fwd", "tl"]:
    #     # Adj_refdir is not the runsubdir itself
    #     # (which corresponds to a sub-simulation)
    #     # But the level above, which is the full chained simulation
    #     self.adj_refdir = "{}/../".format(runsubdir)

    # Now move necessary files to the chain directory
    os.system("mv -f {runsubdir}/XXXXX {runsubdir}/../chain/XXX"
              .format(runsubdir=runsubdir))