Instruction stringlengths 362 7.83k | output_code stringlengths 1 945 |
|---|---|
Here is a snippet: <|code_start|> assert bs > 0
return bs
@property
def nsites(self):
"""See docs for `Model` abstract base class."""
return self._nsites
@property
def freeparams(self):
"""See docs for `Model` abstract base class."""
return self._freepara... | for x in range(N_STOP): |
Given the following code snippet before the placeholder: <|code_start|> Element `r` is diagonal of :math:`\mathbf{D_r}` diagonal matrix,
:math:`\mathbf{P_r} = \mathbf{A_r}^{-1} \mathbf{D_r} \mathbf{A_r}`
`A` (`numpy.ndarray` floats, shape `(nsites, N_CODON, N_CODON)`)
Element ... | 'eta': (numpy.ndarray, (N_NT - 1,)), |
Given snippet: <|code_start|> minimum value for {0}, {1}, is equal to or \
larger than the new maximum value, {2}"\
.format(param, value[param][0], value[param][1])
self._PARAMLIMITS = value.copy()
def __init__(self, prefs, kappa=2.0, omega=0.5, be... | self.pi = numpy.ndarray((self.nsites, N_AA), dtype='float') |
Here is a snippet: <|code_start|>
@property
def logprior(self):
"""Is zero, as no prior is defined over this model."""
return 0.0
def dlogprior(self, param):
"""Zero for all `param`, as no prior defined over this model."""
assert param in self.freeparams, "Invalid param: {0}... | report['{0}{1}'.format(param, INDEX_TO_NT[w])] = pvalue[w] |
Next line prediction: <|code_start|> for j in range(paramlength):
dM_param[j] = (broadcastMatrixVectorMultiply(self.A,
broadcastGetCols(broadcastMatrixMultiply(self.B[param][j] * V, self.Ainv), tips))) # noqa: E501
if gap... | numpy.copyto(self.Qxy, self.phi[w], where=CODON_NT_MUT[w]) |
Using the snippet: <|code_start|> self.beta, dx=dbeta,
n=1, order=5)
dphi_dbeta_halfdx = scipy.misc.derivative(self._compute_empirical_phi,
self.beta, dx=dbeta / 2,
... | phiprod *= phifull[w]**CODON_NT_COUNT[w] |
Using the snippet: <|code_start|> for w in range(N_NT - 1):
self.eta[w] = 1.0 - self.phi[w] / etaprod
etaprod *= self.eta[w]
_checkParam('eta', self.eta, self.PARAMLIMITS, self.PARAMTYPES)
def _update_phi(self):
"""Update `phi` using current `eta`."""
etaprod ... | self.pi_codon[r] = self.pi[r][CODON_TO_AA] |
Here is a snippet: <|code_start|>
Args:
`prefs` (list)
List of dicts giving amino-acid preferences for
each site. Each dict keyed by amino acid letter
codes, value is pref > 0 and < 1. Must sum to 1
at each site.
`kappa`, `o... | for (a, aa) in INDEX_TO_AA.items(): |
Here is a snippet: <|code_start|> def __init__(self, prefs, kappa=2.0, omega=0.5, beta=1.0, mu=1.0,
phi=numpy.ones(N_NT) / N_NT,
freeparams=('kappa', 'omega', 'beta', 'mu', 'eta')):
"""Initialize an `ExpCM` object.
Args:
`prefs` (list)
Li... | assert set(prefs[r].keys()) == set(AA_TO_INDEX.keys()),\ |
Given the code snippet: <|code_start|> where=CODON_NONSYN)
def _update_Prxy(self):
"""Update `Prxy` using current `Frxy` and `Qxy`."""
self.Prxy = self.Frxy * self.Qxy
_fill_diagonals(self.Prxy, self._diag_indices)
def _update_Prxy_diag(self):
"""Update `D`,... | qx[CODON_NT[j][w]] *= self.phi[w] |
Predict the next line for this snippet: <|code_start|> kappa=self.kappa,
omega=self.omega,
mu=10.0,
phi=self.phi)
treefi... | self.aacounts[r][CODON_TO_AA[CODON_TO_INDEX[seq[i: i+3]]]] += 1 |
Given the code snippet: <|code_start|> kappa=self.kappa,
omega=self.omega,
mu=10.0,
phi=self.phi)
treefile = os.path.abs... | self.aacounts[r][CODON_TO_AA[CODON_TO_INDEX[seq[i: i+3]]]] += 1 |
Predict the next line after this snippet: <|code_start|>Written by Jesse Bloom.
"""
class test_TreeLikelihood_ExpCM_fitprefs(unittest.TestCase):
"""Test `ExpCM_fitprefs` in `TreeLikelihood`."""
MODEL = phydmslib.models.ExpCM_fitprefs
def setUp(self):
"""Set up for tests."""
numpy.rando... | self.phi = numpy.random.dirichlet([5] * N_NT) |
Predict the next line for this snippet: <|code_start|>"""Tests `TreeLikelihood` with `ExpCM_fitprefs` and `ExpCM_fitprefs2`.
Written by Jesse Bloom.
"""
class test_TreeLikelihood_ExpCM_fitprefs(unittest.TestCase):
"""Test `ExpCM_fitprefs` in `TreeLikelihood`."""
MODEL = phydmslib.models.ExpCM_fitprefs
... | rprefs = numpy.random.dirichlet([0.5] * N_AA) |
Given the code snippet: <|code_start|> self.model = self.MODEL(self.prefs,
prior=None,
kappa=self.kappa,
omega=self.omega,
phi=self.phi)
self.realmodel = phydmslib.models.ExpCM(... | self.codoncounts = {r: {INDEX_TO_CODON[c]: 0 for c in range(N_CODON)} |
Continue the code snippet: <|code_start|>"""Tests `TreeLikelihood` with `ExpCM_fitprefs` and `ExpCM_fitprefs2`.
Written by Jesse Bloom.
"""
class test_TreeLikelihood_ExpCM_fitprefs(unittest.TestCase):
"""Test `ExpCM_fitprefs` in `TreeLikelihood`."""
MODEL = phydmslib.models.ExpCM_fitprefs
def setUp(s... | self.prefs.append(dict(zip(sorted(AA_TO_INDEX.keys()), rprefs))) |
Next line prediction: <|code_start|> self.model = self.MODEL(self.prefs,
prior=None,
kappa=self.kappa,
omega=self.omega,
phi=self.phi)
self.realmodel = phydmslib.models.ExpCM(se... | self.codoncounts = {r: {INDEX_TO_CODON[c]: 0 for c in range(N_CODON)} |
Using the snippet: <|code_start|> self.assertTrue(numpy.allclose(kappa, self.expcm.kappa))
self.assertTrue(numpy.allclose(beta, self.expcm.beta))
self.assertTrue(
numpy.allclose(
numpy.repeat(1.0, self.nsites),
self.expcm.stationarystate.sum(axis=1)))
... | diag = numpy.eye(N_CODON, dtype="bool") |
Continue the code snippet: <|code_start|> self.expcm.Prxy[r])))
if r > 0:
self.assertFalse(
numpy.allclose(
0,
numpy.dot(self.expcm.prx[r], self.expcm.Prxy[r - 1])))
def check_ExpCM_derivat... | w = NT_TO_INDEX[ |
Given the following code snippet before the placeholder: <|code_start|> self.assertTrue(numpy.allclose(1, self.expcm.prx[r].sum()))
# prx is eigenvector or Prxy for the same r, but not different r
for r in range(self.nsites):
self.assertTrue(
numpy.allclose(0, num... | pirAx = self.prefs[r][INDEX_TO_AA[CODON_TO_AA[x]]] |
Here is a snippet: <|code_start|> if r > 0:
self.assertFalse(
numpy.allclose(
0,
numpy.dot(self.expcm.prx[r], self.expcm.Prxy[r - 1])))
def check_ExpCM_derivatives(self):
"""Use `sympy` to check values & derivati... | [ynt for (xnt, ynt) in zip(INDEX_TO_CODON[x], |
Continue the code snippet: <|code_start|> self.assertTrue(numpy.allclose(1, self.expcm.prx[r].sum()))
# prx is eigenvector or Prxy for the same r, but not different r
for r in range(self.nsites):
self.assertTrue(
numpy.allclose(0, numpy.dot(self.expcm.prx[r],
... | pirAx = self.prefs[r][INDEX_TO_AA[CODON_TO_AA[x]]] |
Using the snippet: <|code_start|> for r in range(self.nsites):
self.assertTrue(
numpy.allclose(0, numpy.dot(self.expcm.prx[r],
self.expcm.Prxy[r])))
if r > 0:
self.assertFalse(
numpy.allclose(
... | if not CODON_SINGLEMUT[x][y]: |
Given the code snippet: <|code_start|> "eta0": self.params["eta"][0],
"eta1": self.params["eta"][1],
"eta2": self.params["eta"][2]}
# check Prxy
for r in range(self.nsites):
for x in range(N_CODON):
pirAx = self.prefs[r][I... | if CODON_TRANSITION[x][y]: |
Predict the next line after this snippet: <|code_start|> pirAx = self.prefs[r][INDEX_TO_AA[CODON_TO_AA[x]]]
for y in [yy for yy in range(N_CODON) if yy != x]:
pirAy = self.prefs[r][INDEX_TO_AA[CODON_TO_AA[y]]]
if not CODON_SINGLEMUT[x][y]:
... | if CODON_NONSYN[x][y]: |
Given snippet: <|code_start|>"""Tests `phydmslib.models.ExpCM` class.
Written by Jesse Bloom.
Uses `sympy` to make sure attributes and derivatives of attributes
are correct for `ExpCM` implemented in `phydmslib.models`.
"""
class testExpCM(unittest.TestCase):
"""Tests ``ExpCM`` model."""
def test_ExpCM(s... | phi = numpy.random.dirichlet([2] * N_NT) |
Predict the next line after this snippet: <|code_start|>"""Tests `phydmslib.models.ExpCM` class.
Written by Jesse Bloom.
Uses `sympy` to make sure attributes and derivatives of attributes
are correct for `ExpCM` implemented in `phydmslib.models`.
"""
class testExpCM(unittest.TestCase):
"""Tests ``ExpCM`` mode... | self.prefs.append(dict(zip(sorted(AA_TO_INDEX.keys()), rprefs))) |
Continue the code snippet: <|code_start|>"""Tests `phydmslib.models.ExpCM` class.
Written by Jesse Bloom.
Uses `sympy` to make sure attributes and derivatives of attributes
are correct for `ExpCM` implemented in `phydmslib.models`.
"""
class testExpCM(unittest.TestCase):
"""Tests ``ExpCM`` model."""
def ... | rprefs = numpy.random.dirichlet([0.5] * N_AA) |
Predict the next line after this snippet: <|code_start|>"""Tests invquadratic prior in `ExpCM_fitprefs`.
Written by Jesse Bloom.
"""
class test_fitprefs_invquadraticprior(unittest.TestCase):
"""Test `ExpCM_fitprefs` with inverse quadratic prior."""
MODEL = phydmslib.models.ExpCM_fitprefs
def setUp(se... | rprefs = numpy.random.dirichlet([0.7] * N_AA) |
Next line prediction: <|code_start|>"""Tests invquadratic prior in `ExpCM_fitprefs`.
Written by Jesse Bloom.
"""
class test_fitprefs_invquadraticprior(unittest.TestCase):
"""Test `ExpCM_fitprefs` with inverse quadratic prior."""
MODEL = phydmslib.models.ExpCM_fitprefs
def setUp(self):
"""Set ... | phi=numpy.random.dirichlet([5] * N_NT) |
Based on the snippet: <|code_start|>"""Tests invquadratic prior in `ExpCM_fitprefs`.
Written by Jesse Bloom.
"""
class test_fitprefs_invquadraticprior(unittest.TestCase):
"""Test `ExpCM_fitprefs` with inverse quadratic prior."""
MODEL = phydmslib.models.ExpCM_fitprefs
def setUp(self):
"""Set ... | self.prefs.append(dict(zip(sorted(AA_TO_INDEX.keys()), rprefs))) |
Next line prediction: <|code_start|> beta=beta,
omega2=omega2)
# now check ExpCM attributes / derivates, updating several times
for _update in range(2):
self.params = {
"omega": random.uniform(0.1, 2),
"kappa": random.uniform(0.5, 10),
... | for x in range(N_CODON): |
Based on the snippet: <|code_start|>"""Tests `phydmslib.models.ExpCM_empirical_phi_divpressure` class.
Written by Jesse Bloom.
Edited by Sarah Hilton
"""
class test_compare_ExpCM_emp_phi_with_without_divpress(unittest.TestCase):
"""Tests ``ExpCM`` with and without div pressure."""
def test_compare(self):
... | g = numpy.random.dirichlet([3] * N_NT) |
Predict the next line for this snippet: <|code_start|>"""Tests `phydmslib.models.ExpCM_empirical_phi_divpressure` class.
Written by Jesse Bloom.
Edited by Sarah Hilton
"""
class test_compare_ExpCM_emp_phi_with_without_divpress(unittest.TestCase):
"""Tests ``ExpCM`` with and without div pressure."""
def te... | prefs.append(dict(zip(sorted(AA_TO_INDEX.keys()), rprefs))) |
Next line prediction: <|code_start|>"""Tests `phydmslib.models.ExpCM_empirical_phi_divpressure` class.
Written by Jesse Bloom.
Edited by Sarah Hilton
"""
class test_compare_ExpCM_emp_phi_with_without_divpress(unittest.TestCase):
"""Tests ``ExpCM`` with and without div pressure."""
def test_compare(self):
... | rprefs = numpy.random.dirichlet([0.5] * N_AA) |
Next line prediction: <|code_start|> # now check ExpCM attributes / derivates, updating several times
for _update in range(2):
self.params = {
"omega": random.uniform(0.1, 2),
"kappa": random.uniform(0.5, 10),
"beta": random.uniform(0.5, 3),
... | nt_freqs[w] += self.model.prx[r][x] * CODON_NT_COUNT[w][x] |
Given the following code snippet before the placeholder: <|code_start|> subject = ("ITP: bugwarrior -- Pull tickets from github, "
"bitbucket, bugzilla, jira, trac, and others into "
"taskwarrior")
severity = "wishlist"
source = ""
forwarded = ""
pending = "pending"
cl... | self.service = self.get_mock_service(bts.BTSService) |
Here is a snippet: <|code_start|>
class FakeBTSBug:
bug_num = 810629
package = "wnpp"
subject = ("ITP: bugwarrior -- Pull tickets from github, "
"bitbucket, bugzilla, jira, trac, and others into "
"taskwarrior")
severity = "wishlist"
source = ""
forwarded = ""
... | class TestBTSService(AbstractServiceTest, ServiceTest): |
Based on the snippet: <|code_start|>
class FakeBTSBug:
bug_num = 810629
package = "wnpp"
subject = ("ITP: bugwarrior -- Pull tickets from github, "
"bitbucket, bugzilla, jira, trac, and others into "
"taskwarrior")
severity = "wishlist"
source = ""
forwarded = ""... | class TestBTSService(AbstractServiceTest, ServiceTest): |
Next line prediction: <|code_start|>
class TestTaigaIssue(AbstractServiceTest, ServiceTest):
SERVICE_CONFIG = {
'service': 'taiga',
'taiga.base_uri': 'https://one',
'taiga.auth_token': 'two',
}
record = {
'id': 400,
'project': 4,
'ref': 40,
'subject... | self.service = self.get_mock_service(TaigaService) |
Based on the snippet: <|code_start|>
class TestGerritIssue(AbstractServiceTest, ServiceTest):
SERVICE_CONFIG = {
'service': 'gerrit',
'gerrit.base_uri': 'https://one.com',
'gerrit.username': 'two',
'gerrit.password': 'three',
}
record = {
'project': 'nova',
... | self.service = self.get_mock_service(GerritService) |
Based on the snippet: <|code_start|> "id": 35546,
"name": "Adam Coddington"
},
"created_on": arbitrary_created.isoformat(),
"due_on": "2016-12-30T16:40:29Z",
"description": "This is a test issue.",
"done_ratio": 0,
"id": 363901,
"priority": ... | self.service = self.get_mock_service(RedMineService) |
Given snippet: <|code_start|>
class StringCompatTest(unittest.TestCase):
"""This class implements method to test correct and compatible
implementation of __str__ and __repr__ methods"""
def test_issue_str(self):
"check Issue class"
record = {}
origin = {'target': 'target',
... | issue = DumbIssue(record, origin) |
Given snippet: <|code_start|> if main_config.merge_tags:
if main_config.replace_tags:
replace_left('tags', task, issue_dict, main_config.static_tags)
else:
merge_left('tags', task, issue_dict)
issue_dict.pop('annotations', N... | send_notification(issue, 'Created', conf['notifications']) |
Predict the next line after this snippet: <|code_start|> arbitrary_issue = {
'priority': 0,
'project': 'something',
'due_on': {
'formatted_date': arbitrary_due_on.isoformat(),
},
'permalink': 'http://wherever/',
'task_id': 10,
'project_name': 'somet... | self.service = self.get_mock_service(ActiveCollabService) |
Continue the code snippet: <|code_start|>
class FakeActiveCollabLib:
def __init__(self, arbitrary_issue):
self.arbitrary_issue = arbitrary_issue
def get_my_tasks(self):
return {'arbitrary_key': {'assignments': {
self.arbitrary_issue['task_id']: self.arbitrary_issue}}}
def g... | class TestActiveCollabIssues(AbstractServiceTest, ServiceTest): |
Given the following code snippet before the placeholder: <|code_start|>
class FakeActiveCollabLib:
def __init__(self, arbitrary_issue):
self.arbitrary_issue = arbitrary_issue
def get_my_tasks(self):
return {'arbitrary_key': {'assignments': {
self.arbitrary_issue['task_id']: self... | class TestActiveCollabIssues(AbstractServiceTest, ServiceTest): |
Given the code snippet: <|code_start|> self.config.add_section('general')
self.config.set('general', 'targets', 'my_service')
self.config.set('general', 'static_fields', 'project, priority')
self.config.set('general', 'taskrc', self.taskrc)
self.config.add_section('my_service')
... | self.runner.invoke(command.pull, args=('--debug')) |
Continue the code snippet: <|code_start|>
def fake_github_issues(self):
yield from [self.get_issue_for_record(ARBITRARY_ISSUE, ARBITRARY_EXTRA)]
def fake_bz_issues(self):
yield from [{
'annotations': [],
'bugzillabugid': 1234567,
'bugzillastatus': 'NEW',
'bu... | self.config = BugwarriorConfigParser() |
Predict the next line for this snippet: <|code_start|>
def fake_github_issues(self):
yield from [self.get_issue_for_record(ARBITRARY_ISSUE, ARBITRARY_EXTRA)]
def fake_bz_issues(self):
yield from [{
'annotations': [],
'bugzillabugid': 1234567,
'bugzillastatus': 'NEW',
... | class TestPull(ConfigTest): |
Predict the next line after this snippet: <|code_start|> 'activecollab2.projects': '1:one, 2:two'
}
arbitrary_due_on = (
datetime.datetime.now() - datetime.timedelta(hours=1)
).replace(tzinfo=pytz.UTC)
arbitrary_created_on = (
datetime.datetime.now() - datetime.timedelta(hours=2)... | self.service = self.get_mock_service(ActiveCollab2Service) |
Using the snippet: <|code_start|>
class TestLoggingPath(unittest.TestCase):
def setUp(self):
self.dir = os.getcwd()
os.chdir(os.path.expanduser('~'))
def test_log_relative_path(self):
self.assertEqual(
<|code_end|>
, determine the next line of code. You have imports:
import os
impor... | schema.LoggingPath.validate('bugwarrior.log'), |
Based on the snippet: <|code_start|> )
def test_log_envvar(self):
self.assertEqual(
schema.LoggingPath.validate('$HOME/bugwarrior.log'),
'bugwarrior.log',
)
def tearDown(self):
os.chdir(self.dir)
class TestConfigList(unittest.TestCase):
def test_con... | self.config = load.BugwarriorConfigParser() |
Predict the next line for this snippet: <|code_start|> self.assertEqual(
schema.LoggingPath.validate('~/bugwarrior.log'),
'bugwarrior.log',
)
def test_log_envvar(self):
self.assertEqual(
schema.LoggingPath.validate('$HOME/bugwarrior.log'),
'bug... | class TestValidation(ConfigTest): |
Given the code snippet: <|code_start|>
class TestTeamworkIssue(AbstractServiceTest, ServiceTest):
SERVICE_CONFIG = {
'service': 'teamwork_projects',
'teamwork_projects.host': 'https://test.teamwork_projects.com',
'teamwork_projects.token': 'arbitrary_token',
}
@responses.activate
... | self.service = self.get_mock_service(TeamworkService) |
Based on the snippet: <|code_start|>
class TestTemplates(ServiceTest):
def setUp(self):
super().setUp()
self.arbitrary_default_description = 'Construct Library on Terminus'
self.arbitrary_issue = {
'project': 'end_of_empire',
'priority': 'H',
}
def get_i... | issue = DumbIssue({}, origin) |
Predict the next line for this snippet: <|code_start|>
class TestTeamlabIssue(AbstractServiceTest, ServiceTest):
SERVICE_CONFIG = {
'service': 'teamlab',
'teamlab.hostname': 'something',
'teamlab.login': 'alkjdsf',
'teamlab.password': 'lkjklj',
'teamlab.project_name': 'ab... | self.service = self.get_mock_service(TeamLabService) |
Given snippet: <|code_start|>
class TestGetConfigPath(ConfigTest):
def create(self, path):
"""
Create an empty file in the temporary directory, return the full path.
"""
fpath = os.path.join(self.tempdir, path)
if not os.path.exists(os.path.dirname(fpath)):
os... | self.assertEqual(load.get_config_path(), rc) |
Given snippet: <|code_start|>
class TestData(ConfigTest):
def setUp(self):
super().setUp()
<|code_end|>
, continue by predicting the next line. Consider current file imports:
import os
import json
from bugwarrior.config import data, load, schema
from ..base import ConfigTest
and context:
# Path: bugwa... | self.data = data.BugwarriorData(self.lists_path) |
Next line prediction: <|code_start|> permissions = oct(os.stat(self.data.datafile).st_mode & 0o777)
# python2 -> 0600, python3 -> 0o600
self.assertIn(permissions, ['0600', '0o600'])
def test_get_set(self):
# "touch" data file.
with open(self.data.datafile, 'w+') as handle:
... | rawconfig = load.BugwarriorConfigParser() |
Here is a snippet: <|code_start|>
self.data.set('key', 'value')
self.assertEqual(self.data.get('key'), 'value')
self.assertEqual(
self.data.get_data(), {'old': 'stuff', 'key': 'value'})
self.assert0600()
def test_set_first_time(self):
self.data.set('key', 'value... | self.config = schema.validate_config( |
Using the snippet: <|code_start|> server = FakeTracServer()
def __init__(self, record):
self.record = record
@staticmethod
def query_tickets(query):
return ['something']
def get_ticket(self, ticket):
return (1, None, None, self.record)
class TestTracIssue(AbstractServiceT... | self.service = self.get_mock_service(TracService) |
Given the following code snippet before the placeholder: <|code_start|>
class FakeTracTicket:
@staticmethod
def changeLog(issuenumber):
return []
class FakeTracServer:
ticket = FakeTracTicket()
class FakeTracLib:
server = FakeTracServer()
def __init__(self, record):
self.recor... | class TestTracIssue(AbstractServiceTest, ServiceTest): |
Next line prediction: <|code_start|>
class FakeTracTicket:
@staticmethod
def changeLog(issuenumber):
return []
class FakeTracServer:
ticket = FakeTracTicket()
class FakeTracLib:
server = FakeTracServer()
def __init__(self, record):
self.record = record
@staticmethod
d... | class TestTracIssue(AbstractServiceTest, ServiceTest): |
Based on the snippet: <|code_start|>#!/usr/bin/env python
"""Perform object finding and association."""
components = ['label','objects','associate','candidate','plot','www']
def load_candidates(filename,threshold=0):
""" Load candidates for plotting """
candidates = fitsio.read(filename,lower=True,trim_str... | logger.info("Running 'label'...") |
Given the following code snippet before the placeholder: <|code_start|>#!/usr/bin/env python
try:
except ImportError:
DATABASES = {
'sdss':['dr10'],
'des' :['sva1','sva1_gold','y1a1','y2n','y2q1'],
}
def databaseFactory(survey,release):
if survey == 'sdss':
return SDSSDatabase(release = r... | logger.error("Unrecognized survey: %s"%survey) |
Predict the next line after this snippet: <|code_start|>
matplotlib.use('Agg')
#try: os.environ['DISPLAY']
#except KeyError: matplotlib.use('Agg')
components = ['mcmc','membership','results','plot','collect','scan']
components = ['mcmc','membership','results','plot']
def make_filenames(config,label):
... | logger.warning("Couldn't find %s; skipping..."%srcfile) |
Based on the snippet: <|code_start|> return np.savetxt(filename,data,header=','.join(data.dtype.names),delimiter=',',**kwargs)
elif ext in ('.txt','.dat'):
return np.savetxt(filename,data,**kwargs)
msg = "Unrecognized file type: %s"%filename
raise ValueError(msg)
def check_formula(formula):... | logger.info("Running file: %s"%filename) |
Predict the next line after this snippet: <|code_start|>#!/usr/bin/env python
"""
Simulate the likelihood search.
"""
#components = ['simulate','analyze','merge','plot']
components = ['analyze','merge']
def run(self):
outdir=mkdir(self.config['output']['simdir'])
logdir=mkdir(join(outdir,'log'))
# Act... | logger.info("Running 'simulate'...") |
Continue the code snippet: <|code_start|> Initialize a configuration object from a filename or a dictionary.
Provides functionality to merge with a default configuration.
Parameters:
config: filename, dict, or Config object (deep copied)
default: default configuration to m... | logger.warning("%s %s"%(exc_type,exc_value)) |
Next line prediction: <|code_start|> (10,('r',float)),
(11,('i',float)),
(12,('z',float)),
(13,('y',float)),
(16,('stage',float))
]),
lsst = odict([
(2, ('mass_init',float)),
(3, ('... | logger.warning('Unrecognized survey: %s'%(self.survey)) |
Using the snippet: <|code_start|># MESA Isochrones
# http://waps.cfa.harvard.edu/MIST/iso_form.php
# survey system
dict_output = odict([
('des','DECam'),
('sdss','SDSSugriz'),
('ps1','PanSTARRS'),
('lsst','LSST'),
])
mesa_defaults = {
'version':'1.0',
'v_div_vcrit':'vvcrit... | class Dotter2016(Isochrone): |
Continue the code snippet: <|code_start|>dict_output = odict([
('des','DECam'),
('sdss','SDSSugriz'),
('ps1','PanSTARRS'),
('lsst','LSST'),
])
mesa_defaults = {
'version':'1.0',
'v_div_vcrit':'vvcrit0.4',
'age_scale':'linear',
'age_type':'single',
'a... | _dirname = os.path.join(get_iso_dir(),'{survey}','dotter2016') |
Given the following code snippet before the placeholder: <|code_start|>class Projector:
"""
Class for performing two-dimensional map projections from the celestial sphere.
"""
def __init__(self, lon_ref, lat_ref, proj_type = 'ait'):
self.lon_ref = lon_ref
self.lat_ref = lat_ref
... | logger.warn('%s not recognized'%(proj_type)) |
Given the code snippet: <|code_start|>#!/usr/bin/env python
if __name__ == "__main__":
usage = "Usage: %prog [options] results1.fits results2.fits ... "
description = "Script for merging multiple results files."
parser = OptionParser(usage=usage,description=description)
parser.add_option('-o','--outf... | if opts.verbose: logger.setLevel(logger.DEBUG) |
Given snippet: <|code_start|> -------
None
"""
assert mc_source_id_start >= 1, "Starting mc_source_id must be >= 1"
assert n % n_chunk == 0, "Total number of satellites must be divisible by the chunk size"
nside_pix = 256 # NSIDE = 128 -> 27.5 arcmin, NSIDE = 256 -> 13.7 arcmin
if not... | m_fracdet = read_map(infile_fracdet, nest=False) #.astype(np.float16) |
Given the code snippet: <|code_start|> for k,v in header.items():
fitshdr.add_record({'name':k,'value':v})
# ADW: Should this be a debug?
logger.info("Writing %s..."%filename)
fitsio.write(filename,data,extname='PIX_DATA',header=fitshdr,clobber=True)
def read_partial_map(filenames, colum... | data = fileio.load_files(filenames,**kwargs) |
Based on the snippet: <|code_start|> -----------
filename : output file name
data : dictionary or recarray of data to write (must contain 'PIXEL')
nside : healpix nside of data
coord : 'G'alactic, 'C'elestial, 'E'cliptic
ordering : 'RING' or 'NEST'
kwargs : Passed to fitsio.write
... | logger.info("Writing %s..."%filename) |
Predict the next line for this snippet: <|code_start|> 'output_kind': 0,
'photsys_file': photsys_dict['des'],
#'photsys_version': 'yang',
'submit_form': 'Submit'}
defaults_27 = dict(defaults_cmd,cmd_version='2.7')
defaults_28 = dict(defaults_cmd,cmd_versio... | logger.info(msg) |
Continue the code snippet: <|code_start|>#!/usr/bin/env python
"""Run the likelihood search."""
components = ['scan','merge','tar','plot','check']
defaults = ['scan','merge']
def run(self):
if 'scan' in self.opts.run:
<|code_end|>
. Use current file imports:
import glob
import os
import numpy as np
import uga... | logger.info("Running 'scan'...") |
Based on the snippet: <|code_start|>#!/usr/bin/env python
"""Run the likelihood search."""
components = ['scan','merge','tar','plot','check']
defaults = ['scan','merge']
def run(self):
if 'scan' in self.opts.run:
logger.info("Running 'scan'...")
farm = Farm(self.config,verbose=self.opts.verbose... | superpixel = healpix.superpixel(pixels, |
Predict the next line after this snippet: <|code_start|>NSIDE = 4096
FACTOR = 4
PIX = np.array([104582830, 43361203, 142027178])
U_GRADE_PIX_NEST = np.array([[418331320, 418331321, 418331322, 418331323],
[173444812, 173444813, 173444814, 173444815],
[568108712,... | np.testing.assert_equal(healpix.ud_grade_ipix(PIX,NSIDE,NSIDE),PIX) |
Predict the next line after this snippet: <|code_start|> if opts.verbose: logger.setLevel(logger.DEBUG)
map = ugali.utils.skymap.readSparseHealpixMaps(args,opts.field)
if opts.coord.upper() == "GAL":
coord = 'G'
elif opts.coord.upper() == "CEL":
coord = 'GC'
if opts.proj.upper() == "... | glon,glat = celToGal(target[1],target[2]) |
Next line prediction: <|code_start|>leo_II = ["Leo II" ,dict(default_kwargs,xytext=(-4,0),ha='right'), ],
leo_IV = ["Leo IV" ,dict(default_kwargs,xytext=(5,-1),ha='left'), ],
leo_T = ["Leo T" ,dict(default_kwargs,xytext=(4,5),ha='left'), ],
leo_V = ["Leo V" ,dic... | if opts.verbose: logger.setLevel(logger.DEBUG) |
Here is a snippet: <|code_start|>#!/usr/bin/env python
#import mangle
if __name__ == "__main__":
usage = "Usage: %prog [options] mangle1.ply [mangle2.ply ...]"
description = "python script"
parser = OptionParser(usage=usage,description=description)
(opts, args) = parser.parse_args()
nside = 2**8... | inside = inMangle(infile,ra,dec) |
Given the following code snippet before the placeholder: <|code_start|>#!/usr/bin/env python
#import mangle
if __name__ == "__main__":
usage = "Usage: %prog [options] mangle1.ply [mangle2.ply ...]"
description = "python script"
parser = OptionParser(usage=usage,description=description)
(opts, args) =... | ra,dec = pixToAng(nside,pix) |
Predict the next line for this snippet: <|code_start|>"""
Documentation.
"""
pylab.ion()
############################################################
def validateSatellite(config, isochrone, kernel, stellar_mass, distance_modulus, trials=1, debug=False, seed=0):
"""
Tool for simple MC validation studies -... | logger.info('=== Validate Satellite ===') |
Here is a snippet: <|code_start|> epsilon = 1.e-10
if config.params['catalog']['band_1_detection']:
bins_mag_1 = numpy.arange(config.params['mag']['min'] - mag_buffer,
config.params['mag']['max'] + mag_buffer + epsilon,
delta_mag)
... | logger.debug('(%i/%i)'%(index_distance_modulus, len(distance_modulus_array))) |
Here is a snippet: <|code_start|> def add_seed(self,**kwargs):
self.add_argument('--seed',default=None,type=int,
help='Random seed.',**kwargs)
def add_version(self,**kwargs):
self.add_argument('-V','--version',action='version',
version='ugali '... | gal = pix2ang(*opts.hpx) |
Continue the code snippet: <|code_start|> help='Force the overwrite of files',**kwargs)
def add_seed(self,**kwargs):
self.add_argument('--seed',default=None,type=int,
help='Random seed.',**kwargs)
def add_version(self,**kwargs):
self.add_argum... | gal = cel2gal(*opts.cel) |
Next line prediction: <|code_start|> help="Batch queue for execution.",**kwargs)
def add_ncores(self,**kwargs):
self.add_argument('--ncores',
help="Number of cores to use.",**kwargs)
def add_config(self,**kwargs):
sel... | logger.setLevel(logger.DEBUG) |
Using the snippet: <|code_start|> 'FeH_value':-3.0,
'theory_output':'basic',
'output_option':'photometry',
'output':'DECam',
'Av_value':0,
}
mesa_defaults_10 = dict(mesa_defaults,version='1.0')
class Dotter2008(Download):
""" Dartmouth isochrones from Dotter et al. 2008:
... | logger.debug(query) |
Based on the snippet: <|code_start|># MESA Isochrones
# http://waps.cfa.harvard.edu/MIST/iso_form.php
# survey system
dict_output = odict([
('des' ,'DECam'),
('sdss','SDSSugriz'),
('ps1' ,'PanSTARRS'),
('lsst','LSST'),
])
mesa_defaults = {
'version':'1.0',
'v_div_vcrit':'vvcri... | class Dotter2008(Download): |
Predict the next line after this snippet: <|code_start|>#!/usr/bin/env python
#CATALOGS = ['McConnachie12','Rykoff14', 'Harris96', 'Corwen04', 'Nilson73', 'Webbink85', 'Kharchenko13', 'WEBDA14']
CATALOGS = ['McConnachie12', 'Harris96', 'Corwen04', 'Nilson73', 'Webbink85', 'Kharchenko13', 'Bica08', 'WEBDA14', 'ExtraDwa... | ra,dec = gal2cel(glon,glat) |
Next line prediction: <|code_start|>#!/usr/bin/env python
#CATALOGS = ['McConnachie12','Rykoff14', 'Harris96', 'Corwen04', 'Nilson73', 'Webbink85', 'Kharchenko13', 'WEBDA14']
CATALOGS = ['McConnachie12', 'Harris96', 'Corwen04', 'Nilson73', 'Webbink85', 'Kharchenko13', 'Bica08', 'WEBDA14', 'ExtraDwarfs','ExtraClusters'... | const = ang2const(glon,glat)[0] |
Using the snippet: <|code_start|>#!/usr/bin/env python
#CATALOGS = ['McConnachie12','Rykoff14', 'Harris96', 'Corwen04', 'Nilson73', 'Webbink85', 'Kharchenko13', 'WEBDA14']
CATALOGS = ['McConnachie12', 'Harris96', 'Corwen04', 'Nilson73', 'Webbink85', 'Kharchenko13', 'Bica08', 'WEBDA14', 'ExtraDwarfs','ExtraClusters']
... | iau = ang2iau(glon,glat) |
Based on the snippet: <|code_start|> ra1950 = ugali.utils.projector.hms2dec(ra)
dec1950 = ugali.utils.projector.dms2dec(dec)
ra2000,dec2000 = ugali.utils.idl.jprecess(ra1950,dec1950)
self.data['ra'] = ra2000
self.data['dec'] = dec2000
glon,glat = cel2gal(self.data['ra'],s... | ra,dec = gal2cel(self.data['glon'],self.data['glat']) |
Given the code snippet: <|code_start|> if np.isnan([self.data['glon'],self.data['glat']]).any():
raise ValueError("Incompatible values")
def __getitem__(self, key):
"""
Support indexing, slicing and direct access.
"""
try:
return self.data[key]
... | glon, glat = cel2gal(lon,lat) |
Given the following code snippet before the placeholder: <|code_start|>class ExtraClusters(SourceCatalog):
"""
Collection of recently discovered star clusters
"""
def _load(self,filename):
kwargs = dict(delimiter=',')
if filename is None:
filename = os.path.join(self.DATADIR... | logger.error(msg) |
Predict the next line after this snippet: <|code_start|> out = self.popen(cmd)
stdout = out.communicate()[0]
# There is an extra newline at the end
return stdout.split('\n')[:-1]
def bcomp(self, path):
""" Return completed logfile(s).
Parameters:
-----------
... | logger.info('%i jobs already in queue, waiting...'%(njobs)) |
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