Merge commit 'refs/pull/507/head' of git://github.com/tardis-sn/tardi…

…s into HEAD

conda-requirements

@@ -0,0 +1,13 @@
+numpy==1.10.0
+scipy==0.17.0
+pandas==0.16.2
+pytables==3.2.2
+h5py==2.5
+matplotlib==1.4.3
+astropy==1.0.5
+PyYAML==3.11
+numexpr==2.4.4
+Cython==0.21
+jinja2
+networkx==1.10
+pytest==2.6.3

tardis/tests/test_util.py

@@ -1,60 +1,205 @@
-#tests for util module
-
 import pytest
+import numpy as np
 from astropy import units as u
-from tardis import atomic
-from tardis.util import species_string_to_tuple, species_tuple_to_string, parse_quantity, element_symbol2atomic_number, atomic_number2element_symbol, reformat_element_symbol, MalformedQuantityError
+from io import StringIO
+
+from tardis.util import MalformedSpeciesError, MalformedElementSymbolError, MalformedQuantityError
+from tardis.util import (int_to_roman, roman_to_int, create_synpp_yaml,
+                         calculate_luminosity, intensity_black_body, savitzky_golay,
+                         species_tuple_to_string, species_string_to_tuple, parse_quantity,
+                         element_symbol2atomic_number, atomic_number2element_symbol,
+                         reformat_element_symbol, quantity_linspace)
+
+
+def test_malformed_species_error():
+    malformed_species_error = MalformedSpeciesError('He')
+    assert malformed_species_error.malformed_element_symbol == 'He'
+    assert str(malformed_species_error) == 'Expecting a species notation (e.g. "Si 2", "Si II", "Fe IV") - supplied He'
+
+
+def test_malformed_elements_symbol_error():
+    malformed_elements_symbol_error = MalformedElementSymbolError('Hx')
+    assert malformed_elements_symbol_error.malformed_element_symbol == 'Hx'
+    assert str(malformed_elements_symbol_error) == 'Expecting an atomic symbol (e.g. Fe) - supplied Hx'
+
+
+def test_malformed_quantity_error():
+    malformed_quantity_error = MalformedQuantityError('abcd')
+    assert malformed_quantity_error.malformed_quantity_string == 'abcd'
+    assert str(malformed_quantity_error) == 'Expecting a quantity string(e.g. "5 km/s") for keyword - supplied abcd'
+
+
+@pytest.mark.parametrize(['test_input', 'expected_result'], [
+    (1, 'I'),
+    (5, 'V'),
+    (19, 'XIX'),
+    (556, 'DLVI'),
+    (1400, 'MCD'),
+    (1999, 'MCMXCIX'),
+    (3000, 'MMM')
+])
+def test_int_to_roman(test_input, expected_result):
+    assert int_to_roman(test_input) == expected_result
+
+    with pytest.raises(TypeError):
+        int_to_roman(1.5)
+
+    with pytest.raises(ValueError):
+        int_to_roman(0)
+
+    with pytest.raises(ValueError):
+        int_to_roman(4000)
+
+
+@pytest.mark.parametrize(['test_input', 'expected_result'], [
+    ('I', 1),
+    ('V', 5),
+    ('XIX', 19),
+    ('DLVI', 556),
+    ('MCD', 1400),
+    ('MCMXCIX', 1999),
+    ('MMM', 3000)
+])
+def test_roman_to_int(test_input, expected_result):
+    assert roman_to_int(test_input) == expected_result
+
+    with pytest.raises(TypeError):
+        roman_to_int(1)
+
+    with pytest.raises(ValueError):
+        roman_to_int('IIV')
+
+
+@pytest.mark.parametrize(['string_io', 'distance', 'result'], [
+    (StringIO(u'4000 1e-21\n4500 3e-21\n5000 5e-21'), '100 km', (0.0037699111843077517, 4000.0, 5000.0)),
+    (StringIO(u'7600 2.4e-19\n7800 1.6e-19\n8100 9.1e-20'), '500 km', (2.439446695512474, 7600.0, 8100.0))
+])
+def test_calculate_luminosity(string_io, distance, result):
+    assert calculate_luminosity(string_io, distance) == result
+
+
+@pytest.mark.parametrize(['nu', 't', 'i'], [
+    (10**6, 1000, 3.072357852080765e-22),
+    (10**6, 300, 9.21707305730458e-23),
+    (10**8, 1000, 6.1562660718558254e-24),
+    (10**8, 300, 1.846869480674048e-24),
+])
+def test_intensity_black_body(nu, t, i):
+    assert float(intensity_black_body(nu, t)) == i
+
+
+def test_savitzky_golay():
+    # simple testcase:
+    # time axis sampled into 5 values between 0 and 0.5
+    t = np.linspace(0, 0.5, 5)
+    # y axis represent signal values - time complexed
+    # provided undisturbed signal is ramp input, some disturbances are added randomly
+    y = np.exp(t) + np.array([0.00016543, -0.00011681, -0.00060518, -0.00020232, 0.0006262])
+
+    # applying the filter
+    ysg = savitzky_golay(y, window_size=21, order=5)
+
+    # expected result on application of filter
+    result = np.array([0.62999136, 0.6976977, 0.93429473, 1.23388831, 1.51577056,
+                       1.72441978, 1.82950054, 1.82586363, 1.73354608])
+    assert ysg.all() == result.all()
+
+    with pytest.raises(ValueError):
+        # window_size and order have to be of type int
+        savitzky_golay(y, window_size='a', order='b')
+
+    with pytest.raises(TypeError):
+        # window_size size must be a positive odd number
+        savitzky_golay(y, window_size=10, order=4)
 
-def test_quantity_parser_normal():
+    with pytest.raises(TypeError):
+        # window_size is too small for the polynomials order
+        savitzky_golay(y, window_size=1, order=4)
+
+
+@pytest.mark.parametrize(['species_tuple', 'roman_numerals', 'species_string'], [
+    ((14, 1), True, 'Si II'),
+    ((14, 1), False, 'Si 1'),
+    ((14, 3), True, 'Si IV'),
+    ((14, 3), False, 'Si 3'),
+    ((14, 8), True, 'Si IX'),
+    ((14, 8), False, 'Si 8'),
+])
+def test_species_tuple_to_string(species_tuple, roman_numerals, species_string):
+    assert species_tuple_to_string(species_tuple, roman_numerals=roman_numerals) == species_string
+
+
+@pytest.mark.parametrize(['species_string', 'species_tuple'], [
+    ('si ii', (14, 1)),
+    ('si 2', (14, 1)),
+    ('si ix', (14, 8)),
+])
+def test_species_string_to_tuple(species_string, species_tuple):
+    assert species_string_to_tuple(species_string) == species_tuple
+
+    with pytest.raises(MalformedSpeciesError):
+        species_string_to_tuple('II')
+
+    with pytest.raises(MalformedSpeciesError):
+        species_string_to_tuple('He Si')
+
+    with pytest.raises(ValueError):
+        species_string_to_tuple('He IX')
+
+
+def test_parse_quantity():
     q1 = parse_quantity('5 km/s')
     assert q1.value == 5.
     assert q1.unit == u.Unit('km/s')
 
-def test_quantity_parser_malformed_quantity1():
     with pytest.raises(MalformedQuantityError):
-        q1 = parse_quantity('abcd')
+        parse_quantity(5)
 
-def test_quantity_parser_malformed_quantity2():
     with pytest.raises(MalformedQuantityError):
-        q1 = parse_quantity('5 abcd')
+        parse_quantity('abcd')
 
-def test_atomic_number2element_symbol():
-    assert atomic_number2element_symbol(14) == 'Si'
+    with pytest.raises(MalformedQuantityError):
+        parse_quantity('a abcd')
+
+    with pytest.raises(MalformedQuantityError):
+        parse_quantity('5 abcd')
 
 
-@pytest.mark.parametrize("element_symbol, atomic_number", [
+@pytest.mark.parametrize(['element_symbol', 'atomic_number'], [
     ('sI', 14),
     ('ca', 20),
     ('Fe', 26)
 ])
 def test_element_symbol2atomic_number(element_symbol, atomic_number):
     assert element_symbol2atomic_number(element_symbol) == atomic_number
 
+    with pytest.raises(MalformedElementSymbolError):
+        element_symbol2atomic_number('Hx')
+
+
+def test_atomic_number2element_symbol():
+    assert atomic_number2element_symbol(14) == 'Si'
 
-@pytest.mark.parametrize("unformatted_element_string, formatted_element_string", [
+
+@pytest.mark.parametrize(['unformatted_element_string', 'formatted_element_string'], [
     ('si', 'Si'),
     ('sI', 'Si'),
     ('Si', 'Si'),
     ('c', 'C'),
     ('C', 'C'),
 ])
-def test_element_symbol_reformatter(unformatted_element_string, formatted_element_string):
+def test_reformat_element_symbol(unformatted_element_string, formatted_element_string):
     assert reformat_element_symbol(unformatted_element_string) == formatted_element_string
 
 
-@pytest.mark.parametrize("species_string, species_tuple", [
-    ('si ii', (14, 1)),
-    ('si 2', (14, 1)),
-    ('si ix', (14, 8)),
+@pytest.mark.parametrize(['start', 'stop', 'num', 'expected'], [
+    (u.Quantity(1, 'km/s'), u.Quantity(5, 'km/s'), 5, u.Quantity(np.array([1., 2., 3., 4., 5.]), 'km/s')),
+    (u.Quantity(0.5, 'eV'), u.Quantity(0.6, 'eV'), 3, u.Quantity(np.array([0.5, 0.55, 0.6]), 'eV'))
 ])
-def test_species_string_to_species_tuple(species_string, species_tuple):
-    assert species_string_to_tuple(species_string) == species_tuple
-
+def test_quantity_linspace(start, stop, num, expected):
+    obtained = quantity_linspace(start, stop, num)
+    assert obtained.unit == expected.unit
+    assert obtained.value.all() == expected.value.all()
 
-@pytest.mark.parametrize("species_string, species_tuple", [
-    ('Si II', (14, 1)),
-    ('Si IV', (14, 3)),
-    ('Si IX', (14, 8)),
-])
-def test_species_tuple_to_species_string(species_string, species_tuple):
-    assert species_tuple_to_string(species_tuple) == species_string
+    with pytest.raises(ValueError):
+        quantity_linspace(u.Quantity(0.5, 'eV'), '0.6 eV', 3)