added tests and updated version info parser

# /user/HS128/dh00601/.config/tmuxinator/binaryc.yml

name: binarycpython

root: <%= ENV["BINARYC_PYTHON"] %>

windows:

  - binarycpython:

      layout: tiled

      panes:

        - ls

        - subl .

        - cd $BINARYC_DIR/

        - cd $BINARYC_DATA_ROOT/

 No newline at end of file

    version_info_dict = {}

    for line in version_info_string.splitlines():

        line = line.strip()

        if line == "":

            continue

        if " is " in line:

            split = line.split(" is ")

            version_info_dict[split[0].strip()] = split[1].strip()

        else:

            if line.startswith("Binary_c/nucsyn"):

                version_info_dict["intro"] = line

            elif line.startswith("Email"):

                emails = line.split("Email ")[1].split(",")

                cleaned_emails = [email.strip() for email in emails]

                version_info_dict["emails"] = cleaned_emails

            elif line.startswith("DTlimit"):

                split = line.split(" : ")

                version_info_dict[split[0]] = ": ".join(split[1:])

            elif line.startswith("Version"):

                split = line.split("Version ")

                version_number = split[1]

                version_info_dict["version_number"] = version_number

            elif line.startswith("git URL"):

                split = line.split("git URL ")

                git_url = split[1]

                version_info_dict["git_url"] = git_url

            elif line.startswith("Build: "):

                split = line.split("Build: ")

                build = split[1]

                version_info_dict["build"] = build

            elif line.startswith("Compiled for "):

                split = line.split("Compiled for ")

                compiled_for = split[1]

                version_info_dict["compiled_for"] = compiled_for

            elif line.startswith("Stack limit "):

                split = line.split("Stack limit ")

                stack_limit = split[1]

                version_info_dict["stack_limit"] = stack_limit

            elif line.startswith("SVN URL "):

                split = line.split("SVN URL ")

                svn_url = split[1]

                version_info_dict["svn_url"] = svn_url

            elif line.startswith("git branch "):

                split = line.split("git branch ")

                git_branch = split[1]

                version_info_dict["git_branch"] = git_branch

            elif line.startswith("_SC_CLK_TCK"):

                split = line.split(" = ")

                _SC_CLK_TCK = split[1]

                version_info_dict["_SC_CLK_TCK"] = _SC_CLK_TCK

            elif line.startswith("Random number mean "):

                split = line.split("Random number mean ")

                random_number_mean = split[1]

                version_info_dict["Random number mean"] = random_number_mean

            elif line.startswith("SVN revision "):

                split = line.split("SVN revision ")

                svn_revision = split[1]

                version_info_dict["svn_revision"] = svn_revision

            elif line.startswith("Size of :"):

                split = line.split("Size of :")

                data_type_sizes = split[1]

                version_info_dict["data_type_sizes"] = data_type_sizes

            elif line.startswith("git revision "):

                split = line.split("git revision ")

                git_revision = split[1]

                version_info_dict["git_revision"] = git_revision

            elif line.startswith("BINARY_C_PRE_VERSION "):

                split = line.split("BINARY_C_PRE_VERSION ")

                binary_c_pre_version = split[1]

                version_info_dict["binary_c_pre_version"] = binary_c_pre_version

            elif line.startswith("Comenv accretion:"):

                split = line.split("Comenv accretion:")

                comenv_accretion = split[1]

                version_info_dict["comenv_accretion"] = comenv_accretion

            elif line.startswith("Compiled in parameters:"):

                split = line.split("Compiled in parameters:")

                compiled_in_parameters = split[1]

                version_info_dict["compiled_in_parameters"] = compiled_in_parameters

            elif line.startswith("__short__ is"):

                split = line.split("__short__ is")

                short_type = split[1]

                version_info_dict["short_type"] = short_type

    # Clean data and put in correct shape

    splitted = version_info_string.strip().splitlines()

    cleaned = set([el.strip() for el in splitted if not el == ""])

    ##########################

    # Isotopes:

    # Split off

    isotopes = set([el for el in cleaned if el.startswith('Isotope ')])

    cleaned = cleaned - isotopes

    isotope_dict = {}

    for el in isotopes:

        split_info = el.split("Isotope ")[-1].strip().split(" is ")

        isotope_info = split_info[-1]

        name = isotope_info.split(' ')[0].strip()

        # Get details

        mass_g = float(isotope_info.split(",")[0].split('(')[1].split("=")[-1][:-2].strip())

        mass_amu = float(isotope_info.split(",")[0].split('(')[-1].split("=")[-1].strip())

        mass_mev = float(isotope_info.split(",")[-3].split("=")[-1].replace(")", "").strip())

        A = int(isotope_info.split(",")[-1].strip().split("=")[-1].replace(")", ""))

        Z = int(isotope_info.split(",")[-2].strip().split("=")[-1])

        #

        isotope_dict[int(split_info[0])] = {'name': name, 'Z': Z, 'A': A, 'mass_mev': mass_mev, 'mass_g': mass_g, 'mass_amu': mass_amu}

    version_info_dict['isotopes'] = isotope_dict

    ##########################

    # Argpairs:

    # Split off

    argpairs = set([el for el in cleaned if el.startswith('ArgPair')])

    cleaned = cleaned - argpairs

    argpair_dict = {}

    for el in sorted(argpairs):

        split_info = el.split("ArgPair ")[-1].split(" ")

        if not argpair_dict.get(split_info[0], None):

            argpair_dict[split_info[0]] = {split_info[1]: split_info[2]}

        else:

                print("Still found unmatched items!:\n{}".format(repr(line)))

            argpair_dict[split_info[0]][split_info[1]] = split_info[2]

    version_info_dict['argpairs'] = argpair_dict

    ##########################

    # ensembles:

    # Split off

    ensembles = set([el for el in cleaned if el.startswith('Ensemble')])

    cleaned = cleaned - ensembles

    ensemble_dict = {}

    for el in ensembles:

        split_info = el.split("Ensemble ")[-1].split(" is ")

        if len(split_info)>1:

            ensemble_dict[int(split_info[0])] = split_info[-1]

    version_info_dict['ensembles'] = ensemble_dict

    ##########################

    # macros:

    # Split off

    macros = set([el for el in cleaned if el.startswith('macroxyz')])

    cleaned = cleaned - macros

    param_type_dict = {

        'STRING': str,

        'FLOAT': float,

        'MACRO': str,

        'INT': int,

        'LONG_INT': int,

    }

    macros_dict = {}

    for el in macros:

        split_info = el.split("macroxyz ")[-1].split(" : ")

        param_type = split_info[0]

        new_split = "".join(split_info[1:]).split(" is ")

        param_name = new_split[0]

        param_value = " is ".join(new_split[1:])

        # Sometimes the macros have extra information behind it. Needs an update in outputting by binary_c

        try:

            macros_dict[param_name] = param_type_dict[param_type](param_value)

        except ValueError:

            macros_dict[param_name] = str(param_value)

    version_info_dict['macros'] = macros_dict

    ##########################

    # Elements:

    # Split off:

    elements = set([el for el in cleaned if el.startswith('Element')])

    cleaned = cleaned - elements

    # Fill dict:

    elements_dict = {}

    for el in elements:

        split_info = el.split("Element ")[-1].split(" : ")

        name_info = split_info[0].split(" is ")

        # get isotope info

        isotopes = {}

        if not split_info[-1][0]=='0':

            isotope_string = split_info[-1].split(" = ")[-1]

            isotopes = {int(split_isotope.split("=")[0]):split_isotope.split("=")[1] for split_isotope in isotope_string.split(" ")}

        elements_dict[int(name_info[0])] = {'name': name_info[-1], 'atomic_number': int(name_info[0]), 'amt_isotopes': len(isotopes), 'isotopes': isotopes}

    version_info_dict['elements'] = version_info_dict

    ##########################

    # dt_limits:

    # split off

    dt_limits = set([el for el in cleaned if el.startswith('DTlimit')])

    cleaned = cleaned - dt_limits

    # Fill dict

    dt_limits_dict = {}

    for el in dt_limits:

        split_info = el.split("DTlimit ")[-1].split(" : ")

        dt_limits_dict[split_info[1].strip()] = {'index': int(split_info[0]), 'value': float(split_info[-1])}

    version_info_dict['dt_limits'] = dt_limits_dict

    ##########################

    # Nucleosynthesis sources:

    # Split off

    nucsyn_sources = set([el for el in cleaned if el.startswith('Nucleosynthesis')])

    cleaned = cleaned - nucsyn_sources

    # Fill dict

    nucsyn_sources_dict = {}

    for el in nucsyn_sources:

        split_info = el.split("Nucleosynthesis source")[-1].strip().split(" is ")

        nucsyn_sources_dict[int(split_info[0])] = split_info[-1]

    version_info_dict['nucleosynthesis_sources'] = nucsyn_sources_dict

    ##########################

    # miscellaneous:

    # All those that I didnt catch with the above filters. Could try to get some more out though.

    # TODO: filter a bit more.

    misc_dict = {}

    git_revision = [el for el in cleaned if el.startswith('git revision')]

    misc_dict['git_revision'] = git_revision[0].split("git revision ")[-1].replace("\"", '')

    git_branch = [el for el in cleaned if el.startswith('git branch')]

    misc_dict['git_branch'] = git_branch[0].split("git branch ")[-1].replace("\"", '')

    build = [el for el in cleaned if el.startswith('Build')]

    misc_dict['build'] = build[0].split("Build: ")[-1].replace("\"", '')

    email = [el for el in cleaned if el.startswith('Email')]

    misc_dict['email'] = email[0].split("Email ")[-1].split(',')

    misc_dict['uncaught'] = cleaned

    version_info_dict['miscellaneous'] = misc_dict

    return version_info_dict

        if print_structure:

            print("\t" * indent, key, type(value))

        if isinstance(value, dict):

            structure_dict[key] = inspect_dict(value, indent=indent + 1, print_structure=print_structure)

            structure_dict[key] = inspect_dict(

                value, indent=indent + 1, print_structure=print_structure

            )

    return structure_dict

    "main_pid": -1,  # Placeholder for the main process id of the run.

    # "output_dir":

    "commandline_input": "",

    ##########################

    # Execution log:

    ##########################

    "slurm_command": "",  # Command that slurm runs (e.g. evolve or join_datafiles)

    "slurm_dir": "",  # working directory containing scripts output logs etc.

    "slurm_njobs": 0,  # number of scripts; set to 0 as default

    "slurm_jobid": '', # slurm job id (%A)

    "slurm_jobid": "",  # slurm job id (%A)

    "slurm_memory": 512,  # in MB, the memory use of the job

    "slurm_warn_max_memory": 1024,  # in MB : warn if mem req. > this

    "slurm_use_all_node_CPUs": 0,  # 1 = use all of a node's CPUs. 0 = use a given amount of CPUs

    "slurm_postpone_join": 0,  # if 1 do not join on slurm, join elsewhere. want to do it off the slurm grid (e.g. with more RAM)

    "slurm_jobarrayindex": '', # slurm job array index (%a)

    "slurm_jobname": 'binary_grid', # default

    "slurm_jobarrayindex": "",  # slurm job array index (%a)

    "slurm_jobname": "binary_grid",  # default

    "slurm_partition": None,

    "slurm_time": 0,  # total time. 0 = infinite time

    "slurm_postpone_sbatch": 0,  # if 1: don't submit, just make the script

    "slurm_array": None,  # override for --array, useful for rerunning jobs

    "slurm_partition": None,  # MUST be defined

    "slurm_extra_settings": {},  # Place to put extra configuration for the SLURM batch file. The key and value of the dict will become the key and value of the line in te slurm batch file. Will be put in after all the other settings (and before the command). Take care not to overwrite something without really meaning to do so.

    ########################################

    # Condor stuff

    ########################################

    "condor": 0,  # 1 to use condor, 0 otherwise

    "condor_command": '', # condor command e.g. "evolve", "join"

    "condor_dir": '', # working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all)

    "condor_njobs": '', # number of scripts/jobs that CONDOR will run in total

    "condor_jobid": '', # condor job id

    "condor_command": "",  # condor command e.g. "evolve", "join"

    "condor_dir": "",  # working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all)

    "condor_njobs": "",  # number of scripts/jobs that CONDOR will run in total

    "condor_jobid": "",  # condor job id

    "condor_postpone_join": 0,  # if 1, data is not joined, e.g. if you want to do it off the condor grid (e.g. with more RAM)

    # "condor_join_machine": None, # if defined then this is the machine on which the join command should be launched (must be sshable and not postponed)

    "condor_join_pwd": '', # directory the join should be in (defaults to $ENV{PWD} if undef)

    "condor_join_pwd": "",  # directory the join should be in (defaults to $ENV{PWD} if undef)

    "condor_memory": 1024,  # in MB, the memory use (ImageSize) of the job

    "condor_universe": 'vanilla', # usually vanilla universe

    "condor_universe": "vanilla",  # usually vanilla universe

    "condor_extra_settings": {},  # Place to put extra configuration for the CONDOR submit file. The key and value of the dict will become the key and value of the line in te slurm batch file. Will be put in after all the other settings (and before the command). Take care not to overwrite something without really meaning to do so.

    # snapshots and checkpoints

    # condor_snapshot_on_kill=>0, # if 1 snapshot on SIGKILL before exit

    # condor_load_from_snapshot=>0, # if 1 check for snapshot .sv file and load it if found

    # condor_resubmit_submitted=>0,

    # condor_resubmit_running=>0,

    # condor_resubmit_crashed=>0,

    ##########################

    # Unordered. Need to go through this. Copied from the perl implementation.

    ##########################

import subprocess

import __main__ as main

def get_slurm_version():

    """

    Function that checks whether slurm is installed and returns the version if its installed.

    try:

        slurm_version = (

            subprocess.run(['sinfo', "-V"], stdout=subprocess.PIPE, check=True)

            subprocess.run(["sinfo", "-V"], stdout=subprocess.PIPE, check=True)

            .stdout.decode("utf-8")

            .split()

        )[1]

    return slurm_version

def get_condor_version():

    """

    Function that checks whether slurm is installed and returns the version if its installed.

    try:

        condor_version = (

            subprocess.run(['condor_q', "--version"], stdout=subprocess.PIPE, check=True)

            subprocess.run(

                ["condor_q", "--version"], stdout=subprocess.PIPE, check=True

            )

            .stdout.decode("utf-8")

            .split()

        )[1]

    return condor_version

def create_directories_hpc(working_dir):

    """

    Function to create a set of directories, given a root directory

        print("Error. Working directory {} does not exist! Aborting")

        raise ValueError

    directories_list = ['scripts', 'stdout', 'stderr', 'results', 'logs', 'status', 'joining']

    directories_list = [

        "scripts",

        "stdout",

        "stderr",

        "results",

        "logs",

        "status",

        "joining",

    ]

    # Make directories.

    for subdir in directories_list:

                directories_exist = False

    print("..Finished! Directories exist.")

def path_of_calling_script():

    """

    Function to get the name of the script the user executes.

    return main.__file__

def get_python_details():

    """

    Function to get some info about the used python version and virtualenv etc

    python_info_dict = {}

    #

    python_info_dict['virtualenv'] = os.getenv('VIRTUAL_ENV')

    python_info_dict['executable'] = sys.executable

    python_info_dict['version'] = sys.version

    python_info_dict["virtualenv"] = os.getenv("VIRTUAL_ENV")

    python_info_dict["executable"] = sys.executable

    python_info_dict["version"] = sys.version

    return python_info_dict