def get_next_ids(test=False):
"""Get the next ids from a file
Parameters
----------
test: bool, optional
If true, the command is run for the ``nepc_test`` database. Otherwise,
it is run for the ``nepc`` database. (Default is the ``nepc`` database.)
Returns
-------
: int
Next cs_id to use
: int
Next csdata_id to use
"""
if test:
nepc_data_home = nepc_config.nepc_home() + '/tests/data/'
else:
nepc_data_home = nepc_config.nepc_cs_home() + '/data/'
filename = nepc_data_home + "/next_id.tsv"
with open(filename) as id_file:
id_line = id_file.readlines()
next_cs_id, next_csdata_id = id_line[1].split('\t')
return int(next_cs_id), int(next_csdata_id)
def format_model(model, type='lxcat', filename='lxcat.txt'):
valid_types = ['lxcat']
if type not in valid_types:
raise Exception(f'type {type} is not supported')
if not isinstance(model, nepc.nepc.Model):
raise Exception(f'model {model} is not supported')
file_process_lxcat = nepc_config.nepc_home(
) + '/tests/data/processes_lxcat.tsv'
with open(file_process_lxcat) as f:
processes_lxcat = pd.read_csv(
f, sep='\t', header=0,
names=['name', 'lxcat']).set_index('name').T.to_dict('records')[0]
def threshold(cs):
if cs.metadata['process'] in ['total', 'elastic', 'elastic_total']:
#TODO: implement m/M fully
return 1.95e-5
else:
return cs.metadata['threshold']
with open(filename, 'w') as f:
for cs in model.cs:
for metadata in [
'process', 'reaction_abbrev', 'threshold', 'reaction_full',
'param', 'header'
]:
if metadata == 'process':
line = f"{str(processes_lxcat[cs.metadata[metadata]]).upper()}\n"
elif metadata == 'reaction_abbrev':
line = f'{cs.reaction_text[0]}\n'
elif metadata == 'threshold':
line = f" {threshold(cs):.6e}\n"
elif metadata == 'reaction_full':
line = (
f'PROCESS: {str(cs.reaction_text[1])}, '
f'{str(processes_lxcat[cs.metadata["process"]]).capitalize()}\n'
)
elif metadata == 'param':
if cs.metadata['process'] in [
'total', 'elastic', 'elastic_total'
]:
line = f'PARAM.: m/M = {threshold(cs)}\n'
# TODO: make sure units_e is not needed here
else:
line = f'PARAM.: E = {threshold(cs)} eV\n'
elif metadata == 'header':
line = (f'COLUMNS: Energy (eV) | Cross section (m2)\n'
f'-----------------------------\n')
else:
line = f"{cs.metadata[metadata]}\n"
f.write(line)
for e, sigma in zip(cs.data['e'], cs.data['sigma']):
f.write(f'{e:.6e}\t{sigma:.6e}\n')
f.write(f'-----------------------------\n\n')
def data_config(github):
if github:
NEPC_HOME = os.getcwd()
else:
NEPC_HOME = config.nepc_home()
NEPC_DATA = NEPC_HOME + "/tests/data/"
DIR_NAMES = [
NEPC_HOME + "/tests/data/cs/lxcat/n2/fict/",
NEPC_HOME + "/tests/data/cs/lumped/n2/fict_total/"
]
yield [NEPC_DATA, DIR_NAMES]
def process_attr(process: str, attr_list: List[str], test=False):
if test:
NEPC_DATA = config.nepc_home() + "/tests/data"
else:
NEPC_DATA = config.nepc_cs_home() + "/data"
proc_df = pd.read_csv(NEPC_DATA + '/processes.tsv', sep='\t', header=0)
process_attr_dict = {}
for attr in attr_list:
process_attr_dict[attr] = proc_df.loc[proc_df.name == process,
attr].values[0]
return process_attr_dict
def get_states(test=False):
"""Get lists of name's and long_name's from states.tsv file."""
if test:
nepc_data_home = nepc_config.nepc_home() + '/tests/data/'
else:
nepc_data_home = nepc_config.nepc_cs_home() + '/data/'
filename = nepc_data_home + 'states.tsv'
with open(filename) as states_f:
states_lines = states_f.readlines()[1:]
states = []
for line in states_lines:
states.append(line.split('\t'))
return ([states[i][1] for i in range(len(states))],
[states[i][2] for i in range(len(states))])
def write_next_id_to_file(next_cs_id, next_csdata_id, test=False):
"""Write out the next id's for the database to a file.
Parameters
----------
next_cs_id : int
The next cs_id to use
next_csdata_id: int
The next csdata_id to use
test: bool, optional
If true, the command is run for the ``nepc_test`` database. Otherwise,
it is run for the ``nepc`` database. (Default is the ``nepc`` database.)
"""
if test:
nepc_data_home = nepc_config.nepc_home() + '/tests/data/'
else:
nepc_data_home = nepc_config.nepc_cs_home() + '/data/'
filename = nepc_data_home + "/next_id.tsv"
id_file = open(filename, "w+")
id_file.write("\t".join(('next_cs_id', 'next_csdata_id')) + "\n")
id_file.write("\t".join((str(next_cs_id), str(next_csdata_id))))
id_file.close()
PARSER.add_argument('--debug',
action='store_true',
help='print additional debug info')
PARSER.add_argument('--test', action='store_true', help='build test database')
ARGS = PARSER.parse_args()
if ARGS.debug:
MAX_CS = 50
MAX_RATE = 50
else:
MAX_CS = 2000000
MAX_RATE = 2000000
if ARGS.test:
database = 'nepc_test'
NEPC_DATA = config.nepc_home() + "/tests/data/"
DIR_NAMES = ["/cs/n2/fict/", "/cs/n2/fict_total/"]
else:
database = 'nepc'
NEPC_DATA = config.nepc_cs_home() + "/data/"
DIR_NAMES = [
"/cs/n2/itikawa/", "/cs/n2/zipf/", "/cs/n/zatsarinny/",
"/cs/n2/phelps/", "/cs/n2/phelps_total/", "/cs/n2/little/"
]
T0 = time.time()
HOME = config.user_home()
def np_str(df, row, name):
help='build test database on GitHub runner')
ARGS = PARSER.parse_args()
if ARGS.debug:
MAX_CS = 50
MAX_RATE = 50
else:
MAX_CS = 2000000
MAX_RATE = 2000000
if ARGS.test and ARGS.github:
raise Exception('can pass only --test or --github, not both')
if ARGS.test:
database = 'nepc_test'
NEPC_HOME = config.nepc_home()
NEPC_DATA = NEPC_HOME + "/tests/data/"
DIR_NAMES = ["/cs/lxcat/n2/fict/", "/cs/lumped/n2/fict_total/"]
HOME = config.user_home()
option_files = HOME + '/.mysql/defaults'
elif ARGS.github:
database = 'nepc_test'
NEPC_HOME = os.getcwd()
NEPC_DATA = NEPC_HOME + "/tests/data/"
DIR_NAMES = ["/cs/lxcat/n2/fict/", "/cs/lumped/n2/fict_total/"]
option_files = NEPC_HOME + '/nepc/mysql/defaults'
else:
database = 'nepc'
NEPC_DATA = config.nepc_cs_home() + "/data/"
DIR_NAMES = [
"/cs/n2/itikawa/", "/cs/n/zatsarinny/", "/cs/lxcat/n2/phelps/",
def test_nepc_home(data_config, travis):
"""Verify whether nepc_home() returns a string
that represents the correct path to the NEPC folder"""
if not travis:
assert isinstance(config.nepc_home(), str)
assert config.nepc_home() == os.environ.get('NEPC_HOME')
