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Fix issue #535: Treat rel. paths inside config relative to the config file #543

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merged 5 commits into from
May 3, 2016
Merged

Fix issue #535: Treat rel. paths inside config relative to the config file #543

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b426107
Fix issue 535
lukeshingles Apr 18, 2016
33add7a
Write tests for the issue #535 fix.
ftsamis May 1, 2016
62d6912
Empty commit to trigger a Travis CI build
ftsamis May 2, 2016
f69e95b
Change some relative paths to absolute in order to avoid Travis faili…
ftsamis May 2, 2016
d831c28
Merge pull request #1 from ftsamis/fix-535-tests
lukeshingles May 3, 2016
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5 changes: 4 additions & 1 deletion tardis/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,14 @@ def run_tardis(config, atom_data=None):

from tardis.io import config_reader
from tardis import model, simulation, atomic
import os

try:
config_dict = yaml.load(open(config))
config_dirname = os.path.dirname(config)
except TypeError:
config_dict = config
config_dirname = ''

if atom_data is not None:
try:
Expand All @@ -36,7 +39,7 @@ def run_tardis(config, atom_data=None):
atom_data = atom_data

tardis_config = config_reader.Configuration.from_config_dict(
config_dict, atom_data=atom_data)
config_dict, atom_data=atom_data, config_dirname=config_dirname)
radial1d_mdl = model.Radial1DModel(tardis_config)

simulation.run_radial1d(radial1d_mdl)
Expand Down
33 changes: 27 additions & 6 deletions tardis/io/config_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@

logger = logging.getLogger(__name__)

data_dir = os.path.join(tardis.__path__[0], 'data')
data_dir = os.path.abspath(os.path.join(tardis.__path__[0], 'data'))

default_config_definition_file = os.path.join(data_dir,
'tardis_config_definition.yml')
Expand Down Expand Up @@ -745,11 +745,15 @@ def from_yaml(cls, fname, test_parser=False):
if tardis_config_version != 'v1.0':
raise ConfigurationError('Currently only tardis_config_version v1.0 supported')

return cls.from_config_dict(yaml_dict, test_parser=test_parser)
config_dirname = os.path.dirname(fname)

return cls.from_config_dict(yaml_dict, test_parser=test_parser,
config_dirname=config_dirname)

@classmethod
def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
config_definition_file=None, validate=True):
config_definition_file=None, validate=True,
config_dirname=''):
"""
Validating and subsequently parsing a config file.

Expand Down Expand Up @@ -797,7 +801,11 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
if test_parser:
atom_data = None
elif 'atom_data' in validated_config_dict.keys():
atom_data_fname = validated_config_dict['atom_data']
if os.path.isabs(validated_config_dict['atom_data']):
atom_data_fname = validated_config_dict['atom_data']
else:
atom_data_fname = os.path.join(config_dirname,
validated_config_dict['atom_data'])
validated_config_dict['atom_data_fname'] = atom_data_fname
else:
raise ConfigurationError('No atom_data key found in config or command line')
Expand Down Expand Up @@ -851,9 +859,15 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
validated_config_dict['supernova']['time_explosion']).cgs

elif structure_section['type'] == 'file':
if os.path.isabs(structure_section['filename']):
structure_fname = structure_section['filename']
else:
structure_fname = os.path.join(config_dirname,
structure_section['filename'])

v_inner, v_outer, mean_densities, inner_boundary_index, \
outer_boundary_index = read_density_file(
structure_section['filename'], structure_section['filetype'],
structure_fname, structure_section['filetype'],
validated_config_dict['supernova']['time_explosion'],
structure_section['v_inner_boundary'],
structure_section['v_outer_boundary'])
Expand Down Expand Up @@ -893,7 +907,14 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
abundances.ix[z] = float(abundances_section[element_symbol_string])

elif abundances_section['type'] == 'file':
index, abundances = read_abundances_file(abundances_section['filename'], abundances_section['filetype'],
if os.path.isabs(abundances_section['filename']):
abundances_fname = abundances_section['filename']
else:
abundances_fname = os.path.join(config_dirname,
abundances_section['filename'])

index, abundances = read_abundances_file(abundances_fname,
abundances_section['filetype'],
inner_boundary_index, outer_boundary_index)
if len(index) != no_of_shells:
raise ConfigurationError('The abundance file specified has not the same number of cells'
Expand Down
4 changes: 2 additions & 2 deletions tardis/io/tests/data/tardis_configv1_artis_density.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ atom_data: kurucz_atom_pure_simple.h5
model:
structure:
type: file
filename: tardis/io/tests/data/artis_model.dat
filename: artis_model.dat
filetype: artis

abundances:
Expand Down Expand Up @@ -37,4 +37,4 @@ montecarlo:
spectrum:
start: 500 angstrom
stop: 20000 angstrom
num: 10000
num: 10000
4 changes: 2 additions & 2 deletions tardis/io/tests/data/tardis_configv1_artis_density_v_slice.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ atom_data: kurucz_atom_pure_simple.h5
model:
structure:
type: file
filename: tardis/io/tests/data/artis_model.dat
filename: artis_model.dat
filetype: artis
v_inner_boundary: 9000 km/s
v_outer_boundary: 20000 km/s
Expand Down Expand Up @@ -39,4 +39,4 @@ montecarlo:
spectrum:
start: 500 angstrom
stop: 20000 angstrom
num: 10000
num: 10000
4 changes: 2 additions & 2 deletions tardis/io/tests/data/tardis_configv1_ascii_density.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ atom_data: kurucz_atom_pure_simple.h5
model:
structure:
type: file
filename: tardis/io/tests/data/tardis_simple_ascii_density_test.dat
filename: tardis_simple_ascii_density_test.dat
filetype: simple_ascii

abundances:
Expand Down Expand Up @@ -37,4 +37,4 @@ montecarlo:
spectrum:
start: 500 angstrom
stop: 20000 angstrom
num: 10000
num: 10000
96 changes: 67 additions & 29 deletions tardis/io/tests/test_config_reader.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
# tests for the config reader module
from tardis.io import config_reader
from astropy import units as u
from contextlib import contextmanager
import os
import pytest
import yaml
Expand All @@ -11,7 +12,20 @@

def data_path(filename):
data_dir = os.path.dirname(__file__)
return os.path.join(data_dir, 'data', filename)
return os.path.abspath(os.path.join(data_dir, 'data', filename))

@contextmanager
def change_cwd(directory):
# Function taken from:
# https://github.com/django/django/blob/18d962f2e6cc8829d60d6f6dfb3ee3855fa5362e/tests/test_runner/test_discover_runner.py
current_dir = os.path.abspath(os.path.dirname(__file__))
new_dir = os.path.join(current_dir, directory)
old_cwd = os.getcwd()
os.chdir(new_dir)
try:
yield
finally:
os.chdir(old_cwd)

def test_config_namespace_attribute_test():
namespace = config_reader.ConfigurationNameSpace({'param1':1})
Expand Down Expand Up @@ -134,7 +148,8 @@ def test_last_no_of_packets():
yaml_data = yaml.load(open(data_path('paper1_tardis_configv1.yml')))
del yaml_data['montecarlo']['last_no_of_packets']
config = config_reader.Configuration.from_config_dict(yaml_data,
test_parser=True)
test_parser=True,
config_dirname=data_path(''))
assert (config.montecarlo.last_no_of_packets ==
config.montecarlo.no_of_packets)

Expand All @@ -144,7 +159,7 @@ def setup(self):
#general parsing of the paper config
filename = 'tardis_configv1_ascii_density.yml'
self.config = config_reader.Configuration.from_yaml(data_path(filename),
test_parser=True)
test_parser=True)
self.yaml_data = yaml.load(open(data_path(filename)))


Expand All @@ -163,7 +178,7 @@ def setup(self):
#general parsing of the paper config
filename = 'tardis_configv1_artis_density.yml'
self.config = config_reader.Configuration.from_yaml(data_path(filename),
test_parser=True)
test_parser=True)
self.yaml_data = yaml.load(open(data_path(filename)))


Expand All @@ -186,11 +201,12 @@ def setup(self):

self.yaml_data = yaml.load(open(data_path(filename)))
self.yaml_data['model']['abundances'] = {'type': 'file',
'filename': 'tardis/io/tests/data/artis_abundances.dat',
'filename': 'artis_abundances.dat',
'filetype': 'artis'}

self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
test_parser=True)
test_parser=True,
config_dirname=data_path(''))


def test_velocities(self):
Expand All @@ -209,11 +225,12 @@ def setup(self):

self.yaml_data = yaml.load(open(data_path(filename)))
self.yaml_data['model']['abundances'] = {'type': 'file',
'filename': 'tardis/io/tests/data/artis_abundances.dat',
'filename': 'artis_abundances.dat',
'filetype': 'artis'}

self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
test_parser=True)
test_parser=True,
config_dirname=data_path(''))


def test_velocities(self):
Expand All @@ -234,7 +251,8 @@ def setup(self):
self.yaml_data = yaml.load(open(data_path(filename)))

self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
test_parser=True)
test_parser=True,
config_dirname=data_path(''))

def test_density(self):
assert_array_almost_equal(self.config.structure.mean_densities.to(u.Unit('g / cm3')).value,
Expand All @@ -250,7 +268,8 @@ def setup(self):
self.yaml_data['plasma']['initial_t_inner'] = "2508 K"

self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
test_parser=True)
test_parser=True,
config_dirname=data_path(''))

def test_initial_temperature(self):
assert_almost_equal(self.config.plasma.t_inner.value, 2508)
Expand All @@ -263,11 +282,12 @@ def setup(self):
filename = 'tardis_configv1_ascii_density_abund.yml'

self.yaml_data = yaml.load(open(data_path(filename)))
self.yaml_data['model']['structure']['filename'] = 'tardis/io/tests/data/density.dat'
self.yaml_data['model']['abundances']['filename'] = 'tardis/io/tests/data/abund.dat'
self.yaml_data['model']['structure']['filename'] = 'density.dat'
self.yaml_data['model']['abundances']['filename'] = 'abund.dat'

self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
test_parser=True)
test_parser=True,
config_dirname=data_path(''))


def test_velocities(self):
Expand Down Expand Up @@ -299,8 +319,8 @@ def test_densities(self):
assert_almost_equal(self.config.structure.mean_densities[4].to(u.Unit('g/cm3')).value, 8.5733893e-11/ 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[5].to(u.Unit('g/cm3')).value, 5.3037103e-11/ 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[6].to(u.Unit('g/cm3')).value, 3.3999447e-11/ 13.0**3 )


def test_ascii_reader_power_law():
with open(data_path('tardis_configv1_density_power_law_test.yml')) as f:
yaml_data = yaml.load(f)
Expand All @@ -309,25 +329,26 @@ def test_ascii_reader_power_law():
t_explosion = density_data['time_0']
rho_0 = density_data['rho_0']
exponent = density_data['exponent']

v_inner = yaml_data['model']['structure']['velocity']['start']
v_outer = yaml_data['model']['structure']['velocity']['stop']
my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_power_law_test.yml'),test_parser=True)
my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_power_law_test.yml'),
test_parser=True)
structure = my_conf['structure']

expected_densites = [3.29072513e-14, 2.70357804e-14, 2.23776573e-14,
1.86501954e-14, 1.56435277e-14, 1.32001689e-14, 1.12007560e-14,
9.55397475e-15, 8.18935779e-15, 7.05208050e-15, 6.09916083e-15,
5.29665772e-15, 4.61758699e-15, 4.04035750e-15, 3.54758837e-15,
3.12520752e-15, 2.76175961e-15, 2.44787115e-15, 2.17583442e-15,
1.93928168e-15]

assert structure['no_of_shells'] == 20
for i, mdens in enumerate(expected_densites):
assert_almost_equal(structure['mean_densities'][i].to(
u.Unit('g / (cm3)')).value, mdens)


def test_ascii_reader_exponential_law():
with open(data_path('tardis_configv1_density_exponential_test.yml')) as f:
yaml_data = yaml.load(f)
Expand All @@ -336,20 +357,37 @@ def test_ascii_reader_exponential_law():
t_explosion = density_data['time_0']
rho_0 = density_data['rho_0']
v0 = density_data['v_0']

v_inner = yaml_data['model']['structure']['velocity']['start']
v_outer = yaml_data['model']['structure']['velocity']['stop']
my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_exponential_test.yml'),test_parser=True)
my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_exponential_test.yml'),
test_parser=True)
structure = my_conf['structure']

expected_densites = [5.18114795e-14, 4.45945537e-14, 3.83828881e-14, 3.30364579e-14, 2.84347428e-14, 2.44740100e-14, 2.10649756e-14, 1.81307925e-14, 1.56053177e-14, 1.34316215e-14, 1.15607037e-14, 9.95038990e-15, 8.56437996e-15, 7.37143014e-15, 6.34464872e-15, 5.46088976e-15, 4.70023138e-15, 4.04552664e-15, 3.48201705e-15, 2.99699985e-15]
expected_unit = 'g / (cm3)'

assert structure['no_of_shells'] == 20
for i, mdens in enumerate(expected_densites):
assert_almost_equal(structure['mean_densities'][i].value,mdens)
assert structure['mean_densities'][i].unit == u.Unit(expected_unit)




class TestAbsoluteRelativeConfigFilePaths:
def setup(self):
self.config_filename = 'tardis_configv1_ascii_density_abund.yml'

def test_relative_config_path_same_dir(self):
with change_cwd(data_path('')):
config = config_reader.Configuration.from_yaml(self.config_filename, test_parser=True)

def test_relative_config_path_parent_dir(self):
config_path = os.path.relpath(data_path(self.config_filename), data_path(os.path.pardir))
with change_cwd(data_path(os.path.pardir)):
config = config_reader.Configuration.from_yaml(config_path, test_parser=True)

def test_absolute_config_path(self):
config = config_reader.Configuration.from_yaml(os.path.abspath(data_path(self.config_filename)),
test_parser=True)


#write tests for inner and outer boundary indices