How to use the pyani.pyani_jobs.JobGroup function in pyani

def test_create_jobgroup(job_empty_script):
    """create dummy jobgroup."""
    jobgroup = pyani_jobs.JobGroup("empty", "")
    assert jobgroup.script == job_empty_script

def test_1d_jobgroup(job_scripts):
    """create dummy 1-parameter sweep jobgroup."""
    jobgroup = pyani_jobs.JobGroup("1d-sweep", "cat", arguments=job_scripts[0].params)
    assert (jobgroup.script, 3) == (job_scripts[0].script, jobgroup.tasks)

def test_remove_group_dependency(job_scripts):
    """add and remove jobgroup dependency."""
    jg1 = pyani_jobs.JobGroup("1d-sweep", "cat", arguments=job_scripts[0].params)
    jg2 = pyani_jobs.JobGroup("2d-sweep", "myprog", arguments=job_scripts[1].params)
    jg2.add_dependency(jg1)
    dep = jg2.dependencies[0]
    jg2.remove_dependency(dep)

    assert 0 == len(jg2.dependencies)

def test_add_group_dependency(job_scripts):
    """add jobgroup dependency."""
    jg1 = pyani_jobs.JobGroup("1d-sweep", "cat", arguments=job_scripts[0].params)
    jg2 = pyani_jobs.JobGroup("2d-sweep", "myprog", arguments=job_scripts[1].params)
    jg2.add_dependency(jg1)
    dep = jg2.dependencies[0]

    assert (1, 3, 4, "1d-sweep") == (
        len(jg2.dependencies),
        dep.tasks,
        jg2.tasks,
        dep.name,
    )

def test_2d_jobgroup(job_scripts):
    """create dummy 2-parameter sweep jobgroup."""
    jobgroup = pyani_jobs.JobGroup(
        "2d-sweep", "myprog", arguments=job_scripts[1].params
    )
    assert (jobgroup.script, 4) == (job_scripts[1].script, jobgroup.tasks)

def test_remove_group_dependency(job_scripts):
    """add and remove jobgroup dependency."""
    jg1 = pyani_jobs.JobGroup("1d-sweep", "cat", arguments=job_scripts[0].params)
    jg2 = pyani_jobs.JobGroup("2d-sweep", "myprog", arguments=job_scripts[1].params)
    jg2.add_dependency(jg1)
    dep = jg2.dependencies[0]
    jg2.remove_dependency(dep)

    assert 0 == len(jg2.dependencies)

:param jgprefix:  str, prefix for SGE jobgroup
    :param sgegroupsize:  int, number of jobs in each SGE jobgroup
    """
    jobcmds = defaultdict(list)  # type: Dict[str, List[str]]
    for job in joblist:
        jobcmds[job.command.split(" ", 1)[0]].append(job.command)
    jobgroups = []  # type: List
    for cmds in list(jobcmds.items()):
        # Break arglist up into batches of sgegroupsize (default: 10,000)
        sublists = split_seq(cmds[1], sgegroupsize)
        count = 0
        for sublist in sublists:
            count += 1
            sge_jobcmdlist = [f'"{jc}"' for jc in sublist]
            jobgroups.append(
                JobGroup(
                    f"{jgprefix}_{count}", "$cmds", arguments={"cmds": sge_jobcmdlist}
                )
            )
    return jobgroups

job.out = root_dir / "stdout"
        job.err = root_dir / "stderr"

        # Add the job name, current working directory, and SGE stdout/stderr
        # directories to the SGE command line
        args = f" -N {job.name} " % (job.name)
        args += " -cwd "
        args += f" -o {job.out} -e {job.err} "

        # If a queue is specified, add this to the SGE command line
        # LP: This has an undeclared variable, not sure why - delete?
        # if job.queue is not None and job.queue in local_queues:
        #    args += local_queues[job.queue]

        # If the job is actually a JobGroup, add the task numbering argument
        if isinstance(job, JobGroup):
            args += f"-t 1:{job.tasks} "

        # If there are dependencies for this job, hold the job until they are
        # complete
        if job.dependencies:
            args += "-hold_jid "
            for dep in job.dependencies:
                args += dep.name + ","
            args = args[:-1]

        # Build the qsub SGE commandline (passing local environment)
        qsubcmd = f"{pyani_config.QSUB_DEFAULT} -V {args} {job.scriptpath}"
        if sgeargs is not None:
            qsubcmd = f"{qsubcmd} {sgeargs}"
        # We've considered Bandit warnings B404,B603 and silence
        # subprocess.call(qsubcmd, shell=False)  # nosec