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<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _resource_index(self, resource): """Get index for given resource. by default it will be `self.index`, but it can be overriden via app.config :param resource:...
datasource = self.get_datasource(resource) indexes = self._resource_config(resource, 'INDEXES') or {} default_index = self._resource_config(resource, 'INDEX') return indexes.get(datasource[0], default_index)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _refresh_resource_index(self, resource): """Refresh index for given resource. :param resource: resource name """
if self._resource_config(resource, 'FORCE_REFRESH', True): self.elastic(resource).indices.refresh(self._resource_index(resource))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _resource_prefix(self, resource=None): """Get elastic prefix for given resource. Resource can specify ``elastic_prefix`` which behaves same like ``mongo_pref...
px = 'ELASTICSEARCH' if resource and config.DOMAIN[resource].get('elastic_prefix'): px = config.DOMAIN[resource].get('elastic_prefix') return px
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def elastic(self, resource=None): """Get ElasticSearch instance for given resource."""
px = self._resource_prefix(resource) if px not in self.elastics: url = self._resource_config(resource, 'URL') assert url, 'no url for %s' % px self.elastics[px] = get_es(url, **self.kwargs) return self.elastics[px]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_md5sum(fname, chunk_size=1024): """ Returns the MD5 checksum of a file. Args: fname (str): Filename chunk_size (Optional[int]): Size (in Bytes) of the ...
def iter_chunks(f): while True: chunk = f.read(chunk_size) if not chunk: break yield chunk sig = hashlib.md5() with open(fname, 'rb') as f: for chunk in iter_chunks(f): sig.update(chunk) # data = f.read() # ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def download_and_verify(url, md5sum, fname=None, chunk_size=1024, clobber=False, verbose=True): """ Download a file and verify the MD5 sum. Args: url (str): The...
# Determine the filename if fname is None: fname = url.split('/')[-1] # Check if the file already exists on disk if (not clobber) and os.path.isfile(fname): print('Checking existing file to see if MD5 sum matches ...') md5_existing = get_md5sum(fname, chunk_size=chunk_size) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def download(url, fname=None): """ Downloads a file. Args: url (str): The URL to download. fname (Optional[str]): The filename to store the downloaded file in....
# Determine the filename if fname is None: fname = url.split('/')[-1] # Stream the URL as a file, copying to local disk with contextlib.closing(requests.get(url, stream=True)) as r: try: r.raise_for_status() except requests.exceptions.HTTPError as error: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def dataverse_download_doi(doi, local_fname=None, file_requirements={}, clobber=False): """ Downloads a file from the Dataverse, using a DOI and set of metadata ...
metadata = dataverse_search_doi(doi) def requirements_match(metadata): for key in file_requirements.keys(): if metadata['dataFile'].get(key, None) != file_requirements[key]: return False return True for file_metadata in metadata['data']['latestVersion']['files'...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def address_reencode(address, blockchain='bitcoin', **blockchain_opts): """ Reencode an address """
if blockchain == 'bitcoin': return btc_address_reencode(address, **blockchain_opts) else: raise ValueError("Unknown blockchain '{}'".format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_multisig(privkey_info, blockchain='bitcoin', **blockchain_opts): """ Is the given private key bundle a multisig bundle? """
if blockchain == 'bitcoin': return btc_is_multisig(privkey_info, **blockchain_opts) else: raise ValueError('Unknown blockchain "{}"'.format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_multisig_address(addr, blockchain='bitcoin', **blockchain_opts): """ Is the given address a multisig address? """
if blockchain == 'bitcoin': return btc_is_multisig_address(addr, **blockchain_opts) else: raise ValueError('Unknown blockchain "{}"'.format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_multisig_script(script, blockchain='bitcoin', **blockchain_opts): """ Is the given script a multisig script? """
if blockchain == 'bitcoin': return btc_is_multisig_script(script, **blockchain_opts) else: raise ValueError('Unknown blockchain "{}"'.format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_singlesig(privkey_info, blockchain='bitcoin', **blockchain_opts): """ Is the given private key bundle a single-sig key bundle? """
if blockchain == 'bitcoin': return btc_is_singlesig(privkey_info, **blockchain_opts) else: raise ValueError('Unknown blockchain "{}"'.format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_singlesig_address(addr, blockchain='bitcoin', **blockchain_opts): """ Is the given address a single-sig address? """
if blockchain == 'bitcoin': return btc_is_singlesig_address(addr, **blockchain_opts) else: raise ValueError('Unknown blockchain "{}"'.format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_privkey_address(privkey_info, blockchain='bitcoin', **blockchain_opts): """ Get the address from a private key bundle """
if blockchain == 'bitcoin': return btc_get_privkey_address(privkey_info, **blockchain_opts) else: raise ValueError('Unknown blockchain "{}"'.format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_grad_cartesian_tensor(grad_X, zmat_dist): """Apply the gradient for transformation to cartesian space onto zmat_dist. Args: grad_X (:class:`numpy.ndarr...
columns = ['bond', 'angle', 'dihedral'] C_dist = zmat_dist.loc[:, columns].values.T try: C_dist = C_dist.astype('f8') C_dist[[1, 2], :] = np.radians(C_dist[[1, 2], :]) except (TypeError, AttributeError): C_dist[[1, 2], :] = sympy.rad(C_dist[[1, 2], :]) cart_dist = np.tensord...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def register_model_converter(model, app): """Add url converter for model Example: class Student(db.model): id = Column(Integer, primary_key=True) name = Column(...
if hasattr(model, 'id'): class Converter(_ModelConverter): _model = model app.url_map.converters[model.__name__] = Converter
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def iupacify(self): """Give the IUPAC conform representation. Mathematically speaking the angles in a zmatrix are representations of an equivalence class. We wil...
def convert_d(d): r = d % 360 return r - (r // 180) * 360 new = self.copy() new.unsafe_loc[:, 'angle'] = new['angle'] % 360 select = new['angle'] > 180 new.unsafe_loc[select, 'angle'] = new.loc[select, 'angle'] - 180 new.unsafe_loc[select, 'dihe...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def minimize_dihedrals(self): r"""Give a representation of the dihedral with minimized absolute value. Mathematically speaking the angles in a zmatrix are repres...
new = self.copy() def convert_d(d): r = d % 360 return r - (r // 180) * 360 new.unsafe_loc[:, 'dihedral'] = convert_d(new.loc[:, 'dihedral']) return new
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def change_numbering(self, new_index=None): """Change numbering to a new index. Changes the numbering of index and all dependent numbering The user has to make s...
if (new_index is None): new_index = range(len(self)) elif len(new_index) != len(self): raise ValueError('len(new_index) has to be the same as len(self)') c_table = self.loc[:, ['b', 'a', 'd']] # Strange bug in pandas where .replace is transitive for object colum...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _insert_dummy_cart(self, exception, last_valid_cartesian=None): """Insert dummy atom into the already built cartesian of exception """
def get_normal_vec(cartesian, reference_labels): b_pos, a_pos, d_pos = cartesian._get_positions(reference_labels) BA = a_pos - b_pos AD = d_pos - a_pos N1 = np.cross(BA, AD) n1 = N1 / np.linalg.norm(N1) return n1 def insert_dummy(...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_cartesian(self): """Return the molecule in cartesian coordinates. Raises an :class:`~exceptions.InvalidReference` exception, if the reference of the i-th...
def create_cartesian(positions, row): xyz_frame = pd.DataFrame(columns=['atom', 'x', 'y', 'z'], index=self.index[:row], dtype='f8') xyz_frame['atom'] = self.loc[xyz_frame.index, 'atom'] xyz_frame.loc[:, ['x', 'y', 'z']] = positions[:row] ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_grad_cartesian(self, as_function=True, chain=True, drop_auto_dummies=True): r"""Return the gradient for the transformation to a Cartesian. If ``as_functi...
zmat = self.change_numbering() c_table = zmat.loc[:, ['b', 'a', 'd']] c_table = c_table.replace(constants.int_label).values.T C = zmat.loc[:, ['bond', 'angle', 'dihedral']].values.T if C.dtype == np.dtype('i8'): C = C.astype('f8') C[[1, 2], :] = np.radians(C[...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def tx_extend(partial_tx_hex, new_inputs, new_outputs, blockchain='bitcoin', **blockchain_opts): """ Add a set of inputs and outputs to a tx. Return the new tx o...
if blockchain == 'bitcoin': return btc_tx_extend(partial_tx_hex, new_inputs, new_outputs, **blockchain_opts) else: raise ValueError('Unknown blockchain "{}"'.format(blockchain))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def setcontext(context, _local=local): """ Set the current context to that given. Attributes provided by ``context`` override those in the current context. If ``...
oldcontext = getcontext() _local.__bigfloat_context__ = oldcontext + context
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _apply_function_in_context(cls, f, args, context): """ Apply an MPFR function 'f' to the given arguments 'args', rounding to the given context. Returns a new...
rounding = context.rounding bf = mpfr.Mpfr_t.__new__(cls) mpfr.mpfr_init2(bf, context.precision) args = (bf,) + args + (rounding,) ternary = f(*args) with _temporary_exponent_bounds(context.emin, context.emax): ternary = mpfr.mpfr_check_range(bf, ternary, rounding) if context.su...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_logger(name=None): """ Get virtualchain's logger """
level = logging.CRITICAL if DEBUG: logging.disable(logging.NOTSET) level = logging.DEBUG if name is None: name = "<unknown>" log = logging.getLogger(name=name) log.setLevel( level ) console = logging.StreamHandler() console.setLevel( level ) log_format = ('[%(...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_config_filename(impl, working_dir): """ Get the absolute path to the config file. """
config_filename = impl.get_virtual_chain_name() + ".ini" return os.path.join(working_dir, config_filename)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_db_filename(impl, working_dir): """ Get the absolute path to the last-block file. """
db_filename = impl.get_virtual_chain_name() + ".db" return os.path.join(working_dir, db_filename)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_snapshots_filename(impl, working_dir): """ Get the absolute path to the chain's consensus snapshots file. """
snapshots_filename = impl.get_virtual_chain_name() + ".snapshots" return os.path.join(working_dir, snapshots_filename)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_lockfile_filename(impl, working_dir): """ Get the absolute path to the chain's indexing lockfile """
lockfile_name = impl.get_virtual_chain_name() + ".lock" return os.path.join(working_dir, lockfile_name)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_bitcoind_config(config_file=None, impl=None): """ Set bitcoind options globally. Call this before trying to talk to bitcoind. """
loaded = False bitcoind_server = None bitcoind_port = None bitcoind_user = None bitcoind_passwd = None bitcoind_timeout = None bitcoind_regtest = None bitcoind_p2p_port = None bitcoind_spv_path = None regtest = None if config_file is not None: parser = SafeConfi...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_empty(self): """Returns True if all child date elements present are empty and other nodes are not set. Returns False if any child date elements are not em...
return all(date.is_empty() for date in [self.created, self.issued]) \ and not self.publisher
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def is_empty(self): '''Returns True if all titleInfo subfields are not set or empty; returns False if any of the fields are not empty.''' return not bool(self.title or self.subtitle or self.part_number \ or self.part_name or self.non_sort or self.type)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def is_empty(self): '''Returns True if details, extent, and type are not set or return True for ``is_empty``; returns False if any of the fields are not empty.''' return all(field.is_empty() for field in [self.details, self.extent] if field is not None) \ ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def getinfo(self): """ Backwards-compatibility for 0.14 and later """
try: old_getinfo = AuthServiceProxy(self.__service_url, 'getinfo', self.__timeout, self.__conn, True) res = old_getinfo() if 'error' not in res: # 0.13 and earlier return res except JSONRPCException: pass network_...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_make_payment_script( address, segwit=None, **ignored ): """ Make a pay-to-address script. """
if segwit is None: segwit = get_features('segwit') # is address bech32-encoded? witver, withash = segwit_addr_decode(address) if witver is not None and withash is not None: # bech32 segwit address if not segwit: raise ValueError("Segwit is disabled") i...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_make_data_script( data, **ignored ): """ Make a data-bearing transaction output. Data must be a hex string Returns a hex string. """
if len(data) >= MAX_DATA_LEN * 2: raise ValueError("Data hex string is too long") # note: data is a hex string if len(data) % 2 != 0: raise ValueError("Data hex string is not even length") return "6a{:02x}{}".format(len(data)/2, data)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_make_p2sh_address( script_hex ): """ Make a P2SH address from a hex script """
h = hashing.bin_hash160(binascii.unhexlify(script_hex)) addr = bin_hash160_to_address(h, version_byte=multisig_version_byte) return addr
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_make_p2wpkh_address( pubkey_hex ): """ Make a p2wpkh address from a hex pubkey """
pubkey_hex = keylib.key_formatting.compress(pubkey_hex) hash160_bin = hashing.bin_hash160(pubkey_hex.decode('hex')) return segwit_addr_encode(hash160_bin)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_make_p2sh_p2wpkh_redeem_script( pubkey_hex ): """ Make the redeem script for a p2sh-p2wpkh witness script """
pubkey_hash = hashing.bin_hash160(pubkey_hex.decode('hex')).encode('hex') redeem_script = btc_script_serialize(['0014' + pubkey_hash]) return redeem_script
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_make_p2sh_p2wsh_redeem_script( witness_script_hex ): """ Make the redeem script for a p2sh-p2wsh witness script """
witness_script_hash = hashing.bin_sha256(witness_script_hex.decode('hex')).encode('hex') redeem_script = btc_script_serialize(['0020' + witness_script_hash]) return redeem_script
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_is_p2sh_address( address ): """ Is the given address a p2sh address? """
vb = keylib.b58check.b58check_version_byte( address ) if vb == multisig_version_byte: return True else: return False
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_is_p2pkh_address( address ): """ Is the given address a p2pkh address? """
vb = keylib.b58check.b58check_version_byte( address ) if vb == version_byte: return True else: return False
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_is_p2wpkh_address( address ): """ Is the given address a p2wpkh address? """
wver, whash = segwit_addr_decode(address) if whash is None: return False if len(whash) != 20: return False return True
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_is_p2wsh_address( address ): """ Is the given address a p2wsh address? """
wver, whash = segwit_addr_decode(address) if whash is None: return False if len(whash) != 32: return False return True
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_is_p2sh_script( script_hex ): """ Is the given scriptpubkey a p2sh script? """
if script_hex.startswith("a914") and script_hex.endswith("87") and len(script_hex) == 46: return True else: return False
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_address_reencode( address, **blockchain_opts ): """ Depending on whether or not we're in testnet or mainnet, re-encode an address accordingly. """
# re-encode bitcoin address network = blockchain_opts.get('network', None) opt_version_byte = blockchain_opts.get('version_byte', None) if btc_is_segwit_address(address): # bech32 address hrp = None if network == 'mainnet': hrp = 'bc' elif network == 'testn...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_is_singlesig_segwit(privkey_info): """ Is the given key bundle a p2sh-p2wpkh key bundle? """
try: jsonschema.validate(privkey_info, PRIVKEY_MULTISIG_SCHEMA) if len(privkey_info['private_keys']) > 1: return False return privkey_info.get('segwit', False) except ValidationError: return False
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def segwit_addr_encode(witprog_bin, hrp=bech32_prefix, witver=bech32_witver): """ Encode a segwit script hash to a bech32 address. Returns the bech32-encoded str...
witprog_bytes = [ord(c) for c in witprog_bin] ret = bech32_encode(hrp, [int(witver)] + convertbits(witprog_bytes, 8, 5)) assert segwit_addr_decode(hrp, ret) is not (None, None) return ret
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def format_git_describe(git_str, pep440=False): """format the result of calling 'git describe' as a python version"""
if git_str is None: return None if "-" not in git_str: # currently at a tag return git_str else: # formatted as version-N-githash # want to convert to version.postN-githash git_str = git_str.replace("-", ".post", 1) if pep440: # does not allow git hash afte...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def update_release_version(): """Update VERSION file"""
version = get_version(pep440=True) with open(VERSION_FILE, "w") as outfile: outfile.write(version) outfile.write("\n")
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_version(pep440=False): """Tracks the version number. pep440: bool When True, this function returns a version string suitable for a release as defined by ...
git_version = format_git_describe(call_git_describe(), pep440=pep440) if git_version is None: # not a git repository return read_release_version() return git_version
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def call_git_branch(): """return the string output of git desribe"""
try: with open(devnull, "w") as fnull: arguments = [GIT_COMMAND, 'rev-parse', '--abbrev-ref', 'HEAD'] return check_output(arguments, cwd=CURRENT_DIRECTORY, stderr=fnull).decode("ascii").strip() except (OSError, CalledProcessError): return ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def load_xmlobject_from_string(string, xmlclass=XmlObject, validate=False, resolver=None): """Initialize an XmlObject from a string. If an xmlclass is specified,...
parser = _get_xmlparser(xmlclass=xmlclass, validate=validate, resolver=resolver) element = etree.fromstring(string, parser) return xmlclass(element)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def load_xmlobject_from_file(filename, xmlclass=XmlObject, validate=False, resolver=None): """Initialize an XmlObject from a file. See :meth:`load_xmlobject_from...
parser = _get_xmlparser(xmlclass=xmlclass, validate=validate, resolver=resolver) tree = etree.parse(filename, parser) return xmlclass(tree.getroot())
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def read_zmat(cls, inputfile, implicit_index=True): """Reads a zmat file. Lines beginning with ``#`` are ignored. Args: inputfile (str): implicit_index (bool): ...
cols = ['atom', 'b', 'bond', 'a', 'angle', 'd', 'dihedral'] if implicit_index: zmat_frame = pd.read_table(inputfile, comment='#', delim_whitespace=True, names=cols) zmat_frame.index = range(1, len(zmat...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def to_zmat(self, buf=None, upper_triangle=True, implicit_index=True, float_format='{:.6f}'.format, overwrite=True, header=False): """Write zmat-file Args: buf (...
out = self.copy() if implicit_index: out = out.change_numbering(new_index=range(1, len(self) + 1)) if not upper_triangle: out = out._remove_upper_triangle() output = out.to_string(index=(not implicit_index), float_format=float_form...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def to_xyz(self, buf=None, sort_index=True, index=False, header=False, float_format='{:.6f}'.format, overwrite=True): """Write xyz-file Args: buf (str): StringI...
if sort_index: molecule_string = self.sort_index().to_string( header=header, index=index, float_format=float_format) else: molecule_string = self.to_string(header=header, index=index, float_format=float_format) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def read_xyz(cls, buf, start_index=0, get_bonds=True, nrows=None, engine=None): """Read a file of coordinate information. Reads xyz-files. Args: inputfile (str):...
frame = pd.read_table(buf, skiprows=2, comment='#', nrows=nrows, delim_whitespace=True, names=['atom', 'x', 'y', 'z'], engine=engine) remove_digits = partial(re.sub, r'[0-9]+', '') frame['atom'] = frame['...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def to_cjson(self, buf=None, **kwargs): """Write a cjson file or return dictionary. The cjson format is specified `here <https://github.com/OpenChemistry/chemica...
cjson_dict = {'chemical json': 0} cjson_dict['atoms'] = {} atomic_number = constants.elements['atomic_number'].to_dict() cjson_dict['atoms'] = {'elements': {}} cjson_dict['atoms']['elements']['number'] = [ int(atomic_number[x]) for x in self['atom']] cjson...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def read_cjson(cls, buf): """Read a cjson file or a dictionary. The cjson format is specified `here <https://github.com/OpenChemistry/chemicaljson>`_. Args: buf ...
if isinstance(buf, dict): data = buf.copy() else: with open(buf, 'r') as f: data = json.load(f) assert data['chemical json'] == 0 n_atoms = len(data['atoms']['coords']['3d']) metadata = {} _metadata = {} coords = np.a...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def view(self, viewer=None, use_curr_dir=False): """View your molecule. .. note:: This function writes a temporary file and opens it with an external viewer. If ...
if viewer is None: viewer = settings['defaults']['viewer'] if use_curr_dir: TEMP_DIR = os.path.curdir else: TEMP_DIR = tempfile.gettempdir() def give_filename(i): filename = 'ChemCoord_' + str(i) + '.xyz' return os.path.join(T...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_pymatgen_molecule(self): """Create a Molecule instance of the pymatgen library .. warning:: The `pymatgen library <http://pymatgen.org>`_ is imported loc...
from pymatgen import Molecule return Molecule(self['atom'].values, self.loc[:, ['x', 'y', 'z']].values)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def from_pymatgen_molecule(cls, molecule): """Create an instance of the own class from a pymatgen molecule Args: molecule (:class:`pymatgen.core.structure.Molecu...
new = cls(atoms=[el.value for el in molecule.species], coords=molecule.cart_coords) return new._to_numeric()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def from_ase_atoms(cls, atoms): """Create an instance of the own class from an ase molecule Args: molecule (:class:`ase.atoms.Atoms`): Returns: Cartesian: """
return cls(atoms=atoms.get_chemical_symbols(), coords=atoms.positions)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _convert_eq(self, eq): """WORKS INPLACE on eq """
rename = dict(enumerate(self.index)) eq['eq_sets'] = {rename[k]: {rename[x] for x in v} for k, v in eq['eq_sets'].items()} eq['sym_ops'] = {rename[k]: {rename[x]: v[x] for x in v} for k, v in eq['sym_ops'].items()} try: sym_m...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_pointgroup(self, tolerance=0.3): """Returns a PointGroup object for the molecule. Args: tolerance (float): Tolerance to generate the full set of symmetr...
PA = self._get_point_group_analyzer(tolerance=tolerance) return PointGroupOperations(PA.sch_symbol, PA.symmops)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_equivalent_atoms(self, tolerance=0.3): """Returns sets of equivalent atoms with symmetry operations Args: tolerance (float): Tolerance to generate the f...
PA = self._get_point_group_analyzer(tolerance=tolerance) eq = PA.get_equivalent_atoms() self._convert_eq(eq) return eq
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_serialize(_txobj): """ Given a transaction dict returned by btc_tx_deserialize, convert it back into a hex-encoded byte string. Derived from code writ...
# output buffer o = [] txobj = None if encoding.json_is_base(_txobj, 16): # txobj is built from hex strings already. deserialize them txobj = encoding.json_changebase(_txobj, lambda x: binascii.unhexlify(x)) else: txobj = copy.deepcopy(_txobj) # version o.app...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_witness_strip( tx_serialized ): """ Strip the witness information from a serialized transaction """
if not btc_tx_is_segwit(tx_serialized): # already strippped return tx_serialized tx = btc_tx_deserialize(tx_serialized) for inp in tx['ins']: del inp['witness_script'] tx_stripped = btc_tx_serialize(tx) return tx_stripped
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_script_to_asm( script_hex ): """ Decode a script into assembler """
if len(script_hex) == 0: return "" try: script_array = btc_script_deserialize(script_hex) except: log.error("Failed to convert '%s' to assembler" % script_hex) raise script_tokens = [] for token in script_array: if token is None: token = 0 ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_extend(partial_tx_hex, new_inputs, new_outputs, **blockchain_opts): """ Given an unsigned serialized transaction, add more inputs and outputs to it. @...
# recover tx tx = btc_tx_deserialize(partial_tx_hex) tx_inputs, tx_outputs = tx['ins'], tx['outs'] locktime, version = tx['locktime'], tx['version'] tx_inputs += new_inputs tx_outputs += new_outputs new_tx = { 'ins': tx_inputs, 'outs': tx_outputs, 'locktime': lock...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_der_encode_length(l): """ Return a DER-encoded length field Based on code from python-ecdsa (https://github.com/warner/python-ecdsa) by Brian Warner. ...
if l < 0: raise ValueError("length cannot be negative") if l < 0x80: return int2byte(l) s = ("%x" % l).encode() if len(s) % 2: s = b("0") + s s = binascii.unhexlify(s) llen = len(s) return int2byte(0x80 | llen) + s
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_der_encode_sequence(*encoded_pieces): """ Return a DER-encoded sequence Based on code from python-ecdsa (https://github.com/warner/python-ecdsa) by Br...
# borrowed from python-ecdsa total_len = sum([len(p) for p in encoded_pieces]) return b('\x30') + btc_tx_der_encode_length(total_len) + b('').join(encoded_pieces)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_sighash( tx, idx, script, hashcode=SIGHASH_ALL): """ Calculate the sighash of a non-segwit transaction. If it's SIGHASH_NONE, then digest the inputs b...
txobj = btc_tx_deserialize(tx) idx = int(idx) hashcode = int(hashcode) newtx = copy.deepcopy(txobj) # remove all scriptsigs in all inputs, except for the ith input's scriptsig. # the other inputs will be 'partially signed', except for SIGHASH_ANYONECANPAY mode. for i in xrange(0, len(new...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_sign_multisig_segwit(tx, idx, prevout_amount, witness_script, private_keys, hashcode=SIGHASH_ALL, hashcodes=None, native=False): """ Sign a native p2w...
from .multisig import parse_multisig_redeemscript if hashcodes is None: hashcodes = [hashcode] * len(private_keys) txobj = btc_tx_deserialize(str(tx)) privs = {} for pk in private_keys: pubk = ecdsalib.ecdsa_private_key(pk).public_key().to_hex() compressed_pubkey = keyli...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_privkey_scriptsig_classify(private_key_info): """ What kind of scriptsig can this private key make? """
if btc_is_singlesig(private_key_info): return 'p2pkh' if btc_is_multisig(private_key_info): return 'p2sh' if btc_is_singlesig_segwit(private_key_info): return 'p2sh-p2wpkh' if btc_is_multisig_segwit(private_key_info): return 'p2sh-p2wsh' return None
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def btc_tx_sign_all_unsigned_inputs(private_key_info, prev_outputs, unsigned_tx_hex, scriptsig_type=None, segwit=None, **blockchain_opts): """ Sign all unsigned ...
if segwit is None: segwit = get_features('segwit') txobj = btc_tx_deserialize(unsigned_tx_hex) inputs = txobj['ins'] if scriptsig_type is None: scriptsig_type = btc_privkey_scriptsig_classify(private_key_info) tx_hex = unsigned_tx_hex prevout_index = 0 # impo...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def block_header_serialize( inp ): """ Given block header information, serialize it and return the hex hash. inp has: * version (int) * prevhash (str) * merkle_r...
# concatenate to form header o = encoding.encode(inp['version'], 256, 4)[::-1] + \ inp['prevhash'].decode('hex')[::-1] + \ inp['merkle_root'].decode('hex')[::-1] + \ encoding.encode(inp['timestamp'], 256, 4)[::-1] + \ encoding.encode(inp['bits'], 256, 4)[::-1] + \ e...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def block_header_to_hex( block_data, prev_hash ): """ Calculate the hex form of a block's header, given its getblock information from bitcoind. """
header_info = { "version": block_data['version'], "prevhash": prev_hash, "merkle_root": block_data['merkleroot'], "timestamp": block_data['time'], "bits": int(block_data['bits'], 16), "nonce": block_data['nonce'], "hash": block_data['hash'] } return block_h...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def block_header_verify( block_data, prev_hash, block_hash ): """ Verify whether or not bitcoind's block header matches the hash we expect. """
serialized_header = block_header_to_hex( block_data, prev_hash ) candidate_hash_bin_reversed = hashing.bin_double_sha256(binascii.unhexlify(serialized_header)) candidate_hash = binascii.hexlify( candidate_hash_bin_reversed[::-1] ) return block_hash == candidate_hash
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save(self, force=False): """ Saves the configuration to a JSON, in the standard config location. Args: force (Optional[:obj:`bool`]): Continue writing, even...
if (not self._success) and (not force): raise ConfigError(( 'The config file appears to be corrupted:\n\n' ' {fname}\n\n' 'Before attempting to save the configuration, please either ' 'fix the config file manually, or overwrite it w...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def reset(self): """ Resets the configuration, and overwrites the existing configuration file. """
self._options = {} self.save(force=True) self._success = True
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def run( self ): """ Interact with the blockchain peer, until we get a socket error or we exit the loop explicitly. The order of operations is: * send version * ...
log.debug("Segwit support: {}".format(get_features('segwit'))) self.begin() try: self.loop() except socket.error, se: if not self.finished: # unexpected log.exception(se) return False # fetch rem...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def have_all_block_data(self): """ Have we received all block data? """
if not (self.num_blocks_received == self.num_blocks_requested): log.debug("num blocks received = %s, num requested = %s" % (self.num_blocks_received, self.num_blocks_requested)) return False return True
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fetch_sender_txs(self): """ Fetch all sender txs via JSON-RPC, and merge them into our block data. Try backing off (up to 5 times) if we fail to fetch transa...
# fetch remaining sender transactions if len(self.sender_info.keys()) > 0: sender_txids = self.sender_info.keys()[:] sender_txid_batches = [] batch_size = 20 for i in xrange(0, len(sender_txids), batch_size ): sender_txid_batche...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def block_data_sanity_checks(self): """ Verify that the data we received makes sense. Return True on success Raise on error """
assert self.have_all_block_data(), "Still missing block data" assert self.num_txs_received == len(self.sender_info.keys()), "Num TXs received: %s; num TXs requested: %s" % (self.num_txs_received, len(self.sender_info.keys())) for (block_hash, block_info) in self.block_info.items(): ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def begin(self): """ This method will implement the handshake of the Bitcoin protocol. It will send the Version message, and block until it receives a VerAck. On...
log.debug("handshake (version %s)" % PROTOCOL_VERSION) version = Version() version.services = 0 # can't send blocks log.debug("send Version") self.send_message(version)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def add_sender_info( self, sender_txhash, nulldata_vin_outpoint, sender_out_data ): """ Record sender information in our block info. @sender_txhash: txid of the ...
assert sender_txhash in self.sender_info.keys(), "Missing sender info for %s" % sender_txhash assert nulldata_vin_outpoint in self.sender_info[sender_txhash], "Missing outpoint %s for sender %s" % (nulldata_vin_outpoint, sender_txhash) block_hash = self.sender_info[sender_txhash][nulldata_vin_...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def make_sender_info( self, block_hash, txn, i, block_height ): """ Make sender information bundle for a particular input of a nulldata transaction. We'll use it...
inp = txn['ins'][i] ret = { # to be filled in... 'scriptPubKey': None, 'addresses': None, # for matching the input and sender funded "txindex": txn['txindex'], "relindex": txn['relindex'], "output_index": inp['outpoin...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fetch_txs_rpc( self, bitcoind_opts, txids ): """ Fetch the given list of transactions via the JSON-RPC interface. Return a dict of parsed transactions on suc...
headers = {'content-type': 'application/json'} reqs = [] ret = {} for i in xrange(0, len(txids)): txid = txids[i] if txid == "0000000000000000000000000000000000000000000000000000000000000000": # coinbase; we never send these ret[t...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def read_config(config_file=CONFIG_FILE_DEFAULT, override_url=None): ''' Read configuration file, perform sanity check and return configuration dictionary used by other functions.''' config = ConfigParser() config.read_dict(DEFAULT_SETTINGS) try: config.readfp(open(config_file)) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def check_config(config): ''' Check the executor config file for consistency. ''' # Check server URL url = config.get("Server", "url") try: urlopen(url) except Exception as e: logger.error( "The configured OpenSubmit server URL ({0}) seems to be invalid: {1}"....
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def has_config(config_fname): ''' Determine if the given config file exists. ''' config = RawConfigParser() try: config.readfp(open(config_fname)) return True except IOError: return False
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def create_config(config_fname, override_url=None): ''' Create the config file from the defaults under the given name. ''' config_path = os.path.dirname(config_fname) os.makedirs(config_path, exist_ok=True) # Consider override URL. Only used by test suite runs settings = DEFAULT_SETTINGS_FL...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def make_student(user): ''' Makes the given user a student. ''' tutor_group, owner_group = _get_user_groups() user.is_staff = False user.is_superuser = False user.save() owner_group.user_set.remove(user) owner_group.save() tutor_group.user_set.remove(user) tutor_group.save()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def make_tutor(user): ''' Makes the given user a tutor. ''' tutor_group, owner_group = _get_user_groups() user.is_staff = True user.is_superuser = False user.save() owner_group.user_set.remove(user) owner_group.save() tutor_group.user_set.add(user) tutor_group.save()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def make_owner(user): ''' Makes the given user a owner and tutor. ''' tutor_group, owner_group = _get_user_groups() user.is_staff = True user.is_superuser = False user.save() owner_group.user_set.add(user) owner_group.save() tutor_group.user_set.add(user) tutor_group.save()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def make_admin(user): ''' Makes the given user an admin. ''' tutor_group, owner_group = _get_user_groups() user.is_staff = True user.is_superuser = True user.save() owner_group.user_set.add(user) owner_group.save() tutor_group.user_set.add(user) tutor_group.save()