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How to use module_path method in avocado

Best Python code snippet using avocado_python

access.py

Source:access.py

1"""Accessors for Gromacs datasets.2"""3from os.path import dirname, join4from glob import glob5from .. import Bunch6def load_benzene():7    """Load the Gromacs benzene dataset.8    Returns9    -------10    data : Bunch11        Dictionary-like object, the interesting attributes are:12        - 'data' : the data files by alchemical leg13        - 'DESCR': the full description of the dataset14    """15    module_path = dirname(__file__)16    data = {'Coulomb': sorted(glob(join(module_path, 'benzene', 'Coulomb', '*', 'dhdl.xvg.bz2'))),17            'VDW': sorted(glob(join(module_path, 'benzene', 'VDW', '*', 'dhdl.xvg.bz2')))}18    with open(join(module_path, 'benzene', 'descr.rst')) as rst_file:19        fdescr = rst_file.read()20    return Bunch(data=data,21                 DESCR=fdescr)22def load_ABFE():23    """Load the Gromacs ABFE dataset.24    Returns25    -------26    data : Bunch27        Dictionary-like object, the interesting attributes are:28        - 'data' : the data files by alchemical leg29        - 'DESCR': the full description of the dataset30    """31    module_path = dirname(__file__)32    data = {'complex': sorted(glob(join(module_path, 'ABFE', 'complex', 'dhdl_*.xvg'))),33            'ligand': sorted(glob(join(module_path, 'ABFE', 'ligand', 'dhdl_*.xvg')))}34    with open(join(module_path, 'ABFE', 'descr.rst')) as rst_file:35        fdescr = rst_file.read()36    return Bunch(data=data,37                 DESCR=fdescr)38def load_expanded_ensemble_case_1():39    """Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 1 (single simulation visits all states).40    Returns41    -------42    data : Bunch43        Dictionary-like object, the interesting attributes are:44        - 'data' : the data files by alchemical leg45        - 'DESCR': the full description of the dataset46    """47    module_path = dirname(__file__)48    data = {'AllStates': glob(join(module_path, 'expanded_ensemble', 'case_1', 'CB7_Guest3_dhdl.xvg.gz'))}49    with open(join(module_path, 'expanded_ensemble', 'case_1', 'descr.rst')) as rst_file:50        fdescr = rst_file.read()51    return Bunch(data=data,52                 DESCR=fdescr)53def load_expanded_ensemble_case_2():54    """Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 2 (two simulations visit all states independently).55    Returns56    -------57    data : Bunch58        Dictionary-like object, the interesting attributes are:59        - 'data' : the data files by alchemical leg60        - 'DESCR': the full description of the dataset61    """62    module_path = dirname(__file__)63    data = {'AllStates': sorted(glob(join(module_path, 'expanded_ensemble', 'case_2', '*.xvg.gz')))}64    with open(join(module_path, 'expanded_ensemble', 'case_2', 'descr.rst')) as rst_file:65        fdescr = rst_file.read()66    return Bunch(data=data,67                 DESCR=fdescr)68def load_expanded_ensemble_case_3():69    """Load the Gromacs Host CB7 Guest C3 REX dataset, case 3.70    Returns71    -------72    data : Bunch73        Dictionary-like object, the interesting attributes are:74        - 'data' : the data files by alchemical leg75        - 'DESCR': the full description of the dataset76    """77    module_path = dirname(__file__)78    data = {'AllStates': sorted(glob(join(module_path, 'expanded_ensemble', 'case_3', '*.xvg.gz')))}79    with open(join(module_path, 'expanded_ensemble', 'case_3', 'descr.rst')) as rst_file:80        fdescr = rst_file.read()81    return Bunch(data=data,82                 DESCR=fdescr)83def load_water_particle_without_energy():84    """Load the Gromacs water particle without energy dataset.85    Returns86    -------87    data : Bunch88        Dictionary-like object, the interesting attributes are:89        - 'data' : the data files by alchemical leg90        - 'DESCR': the full description of the dataset91    """92    module_path = dirname(__file__)93    data = {'AllStates': sorted(glob(join(module_path, 'water_particle', 'without_energy', '*.xvg.bz2')))}94    with open(join(module_path, 'water_particle', 'descr.rst')) as rst_file:95        fdescr = rst_file.read()96    return Bunch(data=data,97                 DESCR=fdescr)98def load_water_particle_with_potential_energy():99    """Load the Gromacs water particle with potential energy dataset.100    Returns101    -------102    data : Bunch103        Dictionary-like object, the interesting attributes are:104        - 'data' : the data files by alchemical leg105        - 'DESCR': the full description of the dataset106    """107    module_path = dirname(__file__)108    data = {'AllStates': sorted(glob(join(module_path, 'water_particle', 'with_potential_energy', '*.xvg.bz2')))}109    with open(join(module_path, 'water_particle', 'descr.rst')) as rst_file:110        fdescr = rst_file.read()111    return Bunch(data=data,112                 DESCR=fdescr)113def load_water_particle_with_total_energy():114    """Load the Gromacs water particle with total energy dataset.115    Returns116    -------117    data : Bunch118        Dictionary-like object, the interesting attributes are:119        - 'data' : the data files by alchemical leg120        - 'DESCR': the full description of the dataset121    """122    module_path = dirname(__file__)123    data = {'AllStates': sorted(glob(join(module_path, 'water_particle', 'with_total_energy', '*.xvg.bz2')))}124    with open(join(module_path, 'water_particle', 'descr.rst')) as rst_file:125        fdescr = rst_file.read()126    return Bunch(data=data,...

common.py

Source:common.py

...16    if print_traceback:17        eprint(traceback.format_exc())18    if need_exit:19        exit(1)20def list_modules_by_module_path(module_path):21    ret = []22    module = pydoc.importfile(module_path)23    # code below inspired by the pydoc source24    modpkgs_names = set()25    if hasattr(module, '__path__'):26        for importer, modname, ispkg in pkgutil.iter_modules(module.__path__):27            modpkgs_names.add(modname)28    for key, value in inspect.getmembers(module, inspect.ismodule):29        if value.__name__.startswith(module.__name__ + '.') and key not in modpkgs_names:30            ret.append({"name": value.__name__, "module_path": module_path})31    return ret32def list_classes_by_module_path(module_path):33    ret = []34    module = pydoc.importfile(module_path)35    for member in inspect.getmembers(module, inspect.isclass):36        if member[1].__module__ == module.__name__:37            ret.append( {"name": member[1].__name__, "qualname": member[1].__qualname__, "module_path": module_path} )38    return ret39def list_functions_by_module_path(module_path):40    ret = []41    module = pydoc.importfile(module_path)42    try:43        all = module.__all__44    except AttributeError:45        all = None46    for member in inspect.getmembers(module, inspect.isroutine):47        if (all is not None or inspect.isbuiltin(member[1]) or inspect.getmodule(member[1]) is module):48            ret.append( {"name": member[0], "module_path": module_path} )49    return ret50def list_data_by_module_path(module_path):51    ret = []52    module = pydoc.importfile(module_path)53    reserved_names = ["__builtins__", "__cached__", "__doc__", "__file__", "__loader__", "__name__", "__package__", "__spec__"]54    for member in inspect.getmembers(module, pydoc.isdata):55        if member[0] not in reserved_names:56            ret.append( {"name": member[0], "type_name": type(member[1]).__name__, "module_path": module_path} )57    return ret58class Dipper:59    def __init__(self, args):60        self.args = args61        conf_file = "{}/.config/dipperpy.yaml".format(str(Path.home()))62        self.conf_file_object = {"main": {"print_traceback": True}}63        try:64            with open(conf_file, "r") as f:...

table_finder.py

Source:table_finder.py

1import importlib2import inspect3import pkgutil4import sys5from abc import ABC6from os import path7from typing import Iterator, Optional, Set8from bq_schema.bigquery_table import BigqueryTable9def find_tables(module_path: str, ignore_abstract: bool) -> Set[BigqueryTable]:10    tables = {}11    for table in _tables_iterator(module_path, ignore_abstract):12        tables[(table.project, table.dataset, table.name)] = table13    return set(tables.values())14def _tables_iterator(15    root_path: str, ignore_abstract: bool, current_path: Optional[str] = None16) -> Iterator[BigqueryTable]:17    """18    Recursively find all defined bigquery tables.19    """20    if current_path is None:21        module_path = root_path22    else:23        module_path = current_path[current_path.find(root_path) :]24    sys_path = sys.path[0].replace(path.sep, ".")25    module_path_to_iterate = module_path26    module_path = module_path.replace(path.sep, ".")27    for (_, module_name, is_pkg) in pkgutil.iter_modules([module_path_to_iterate]):28        module_path = module_path.replace(sys_path, "")29        module_path = module_path[1:] if module_path.startswith(".") else module_path30        module = importlib.import_module(f"{module_path}.{module_name}")31        if is_pkg and module.__file__:32            sub_path = module.__file__.replace(f"{path.sep}__init__.py", "")33            yield from _tables_iterator(root_path, ignore_abstract, sub_path)34        for attribute_name in dir(module):35            if attribute_name.startswith("__"):36                continue37            attribute = getattr(module, attribute_name)38            if (39                inspect.isclass(attribute)40                and issubclass(attribute, BigqueryTable)41                and attribute != BigqueryTable42                and not (43                    ignore_abstract44                    and attribute45                    in ABC.__subclasses__()  # only direct descendants are in ABC's subclass list46                    # , any concrete implementations shouldn't be here47                )48            ):...

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