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Unit tests for untested methods of tardis/atomic.py #527

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merged 6 commits into from
Apr 6, 2016
Merged

Unit tests for untested methods of tardis/atomic.py #527

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0645546
Refactor data_path() and write its test.
Mar 22, 2016
6da1b9d
Add/ refactor tests for 4 methods in atomic.py
Mar 22, 2016
24c3796
Fix test_read_lines_data, write two new tests.
Mar 22, 2016
de76e5a
Write test for read_collision_data()
Mar 23, 2016
013a625
Write test for read_macro_atom_data()
Mar 23, 2016
9dfb49c
Replace datapaths with fixtures.
Apr 1, 2016
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8 changes: 3 additions & 5 deletions tardis/atomic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,15 +19,13 @@ class AtomDataNotPreparedError(Exception):

logger = logging.getLogger(__name__)

default_atom_h5_path = os.path.join(os.path.dirname(__file__), 'data', 'atom_data.h5')

def data_path(fname):
data_dir = os.path.join(os.path.dirname(__file__), 'data')
return os.path.join(data_dir, fname)
return os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', fname)
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is that more than 140 characters?

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If you are talking about the line length PEP, the value is 80. I'm not sure whether this is too long but line 29 looks like it definitely is to long

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sorry 80 yes. That's I think why I broke it up.

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Is the rule followed as 80 chars or 120 ? Many orgs compromise this PEP8 rule as 120 characters. I'll follow whichever used and push a final cosmetic concluding commit.

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As far as I know we stick with 80. Although we won't do PEP fixes on their own. If I stumble upon code that doesn't follow PEP I'll edit it on the fly.

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I'll take care about it. But why merge if we know of existent PEP8 errors ? I'll include the fixes to cleanup this PR, if we are going with "edit on the fly" way, I'd better squash the PEP8 fixes into previous single commit.

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I'm trying to look out for PEP8 errors but since I'm not doing a checkout of every PR I have a look at I won't see them (I have a pep checker for my editor only).

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I have a built-in PEP8 checker in Pycharm. I had compromised line wrap to 120 characters, but I switched it to 80 characters just now. I removed PEP8 errors from the part of code in this PR. Rest will be "edited on the fly" 😉


atomic_symbols_data = np.recfromtxt(data_path('atomic_symbols.dat'),
names=['atomic_number', 'symbol'])

default_atom_h5_path = data_path('atom_data.h5')
atomic_symbols_data = np.recfromtxt(data_path('atomic_symbols.dat'), names=['atomic_number', 'symbol'])
symbol2atomic_number = OrderedDict(zip(atomic_symbols_data['symbol'], atomic_symbols_data['atomic_number']))
atomic_number2symbol = OrderedDict(atomic_symbols_data)

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116 changes: 103 additions & 13 deletions tardis/tests/test_atomic.py
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@@ -1,32 +1,122 @@
from tardis import atomic
from numpy import testing
import pytest
import os
import pytest
from numpy import testing
from tardis import atomic


chianti_he_db_h5_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data', 'chianti_he_db.h5')


def test_atomic_h5_readin():
def test_data_path():
data_path = atomic.data_path('test')
assert data_path.split('/')[-3:] == ['tardis', 'data', 'test']


def test_read_basic_atom_data():
data = atomic.read_basic_atom_data(atomic.default_atom_h5_path)
assert data['atomic_number'][13] == 14
assert data['symbol'][13] == "Si"
si_mass = data['mass'][13]
testing.assert_almost_equal(si_mass, 28.085, decimal=4)
pass
testing.assert_almost_equal(data['mass'][13], 28.085, decimal=4)

def test_ionization_h5_readin():

def test_read_ionization_data():
data = atomic.read_ionization_data(atomic.default_atom_h5_path)
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I'd suggest using fixtures for the data paths.
That way they could easily be changed for all tests in case something changed.
This goes in line with the DRY principle.

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Yes, I will correct it.

hi_ionization = data['ionization_energy'][0]
testing.assert_almost_equal(hi_ionization, 13.59844, decimal=4)
assert data['atomic_number'][0] == 1
assert data['ion_number'][0] == 1
testing.assert_almost_equal(data['ionization_energy'][0], 13.59844, decimal=4)


def test_levels_h5_readin():
def test_read_levels_data():
data = atomic.read_levels_data(atomic.default_atom_h5_path)
assert data['atomic_number'][4] == 14
assert data['ion_number'][4] == 0
assert data['level_number'][4] == 4
si_energy = data['energy'][4]
testing.assert_almost_equal(si_energy, 1.90865, decimal=4)
testing.assert_almost_equal(data['energy'][4], 1.90865, decimal=4)
assert data['g'][4] == 1
assert data['metastable'][4] == False


def test_read_lines_data():
data = atomic.read_lines_data(atomic.default_atom_h5_path)
assert data['line_id'][0] == 8
assert data['atomic_number'][0] == 14
assert data['ion_number'][0] == 5
testing.assert_almost_equal(data['wavelength'][0], 66.772, decimal=4)
testing.assert_almost_equal(data['f_ul'][0], 0.02703, decimal=4)
testing.assert_almost_equal(data['f_lu'][0], 0.04054, decimal=4)
assert data['level_number_lower'][0] == 0.0
assert data['level_number_upper'][0] == 36.0


def test_read_synpp_refs():
data = atomic.read_synpp_refs(chianti_he_db_h5_path)
assert data['atomic_number'][0] == 1
assert data['ion_number'][0] == 0
testing.assert_almost_equal(data['wavelength'][0], 6562.7973633, decimal=4)
assert data['line_id'][0] == 564995


def test_read_zeta_data():
data = atomic.read_zeta_data(chianti_he_db_h5_path)
testing.assert_almost_equal(data[2000][1][1], 0.339, decimal=4)
testing.assert_almost_equal(data[2000][1][2], 0.000, decimal=4)

with pytest.raises(ValueError):
atomic.read_zeta_data(None)

with pytest.raises(IOError):
atomic.read_zeta_data('fakepath')

with pytest.raises(ValueError):
atomic.read_zeta_data(atomic.default_atom_h5_path)


def test_read_collision_data():
data = atomic.read_collision_data(chianti_he_db_h5_path)
assert data[0]['atomic_number'][0] == 2
assert data[0]['ion_number'][0] == 0
assert data[0]['level_number_upper'][0] == 18
assert data[0]['level_number_lower'][0] == 2
assert data[0]['g_ratio'][0] == 1.0
testing.assert_almost_equal(data[0]['delta_e'][0], 35484.251143, decimal=4)
assert data[1][0] == 2000.0
assert data[1][1] == 4000.0

with pytest.raises(ValueError):
atomic.read_zeta_data(None)

with pytest.raises(IOError):
atomic.read_zeta_data('fakepath')

with pytest.raises(ValueError):
atomic.read_zeta_data(atomic.default_atom_h5_path)


def test_read_macro_atom_data():
data = atomic.read_macro_atom_data(chianti_he_db_h5_path)
assert data[0]['atomic_number'][0] == 2
assert data[0]['ion_number'][0] == 0
assert data[0]['source_level_number'][0] == 0.0
assert data[0]['destination_level_number'][0] == 48.0
assert data[0]['transition_type'][0] == 1
assert data[0]['transition_probability'][0] == 0.0
assert data[0]['transition_line_id'][0] == 564957

assert data[1]['count_down'][0] == 0
assert data[1]['count_up'][0] == 7
assert data[1]['count_total'][0] == 7

with pytest.raises(ValueError):
atomic.read_macro_atom_data(None)

with pytest.raises(IOError):
atomic.read_macro_atom_data('fakepath')

with pytest.raises(ValueError):
atomic.read_macro_atom_data(atomic.default_atom_h5_path)


def test_atom_levels():
atom_data = atomic.AtomData.from_hdf5(atomic.default_atom_h5_path)
with pytest.raises(Exception):
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