#503

Committed 14 Sep 2023 05:47PM UTC coverage: 90.035%. Remained the same

Build # #503

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coveralls-python

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web-flow

Commit Message

Merge pull request #382 from California-Planet-Search/next-release

Version 1.4.11

Run Details

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97.37

/radvel/tests/test_api.py

import sys
import copy
import warnings
import types

import radvel
import radvel.driver
import numpy as np
import scipy
import radvel.prior

warnings.simplefilter('ignore')


class _args(types.SimpleNamespace):
    outputdir = '/tmp/'
    decorr = False
    name_in_title = False
    gp = False
    simple = False

    nwalkers = 50
    nsteps = 100
    ensembles = 8
    maxGR = 1.10
    burnGR = 1.30
    burnAfactor = 25
    minAfactor = 50
    maxArchange = .07
    minTz = 1000
    minsteps = 100
    minpercent = 5
    thin = 1
    serial = False
    save = True
    savename = 'rawchains.h5'
    proceed = False
    proceedname = None
    headless=False


def _standard_run(setupfn, arguments):
    """
    Run through all of the standard steps
    """

    args = arguments
    args.setupfn = setupfn

    radvel.driver.fit(args)
    radvel.driver.mcmc(args)
    radvel.driver.derive(args)

    args.type = ['trend', 'jit', 'e', 'nplanets', 'gp']
    args.verbose = True
    radvel.driver.ic_compare(args)

    args.type = ['params', 'priors', 'rv', 'ic_compare', 'derived', 'crit']
    radvel.driver.tables(args)

    args.type = ['rv', 'corner', 'auto', 'trend', 'derived']
    args.plotkw = {'highlight_last': True, 'show_rms': True}
    radvel.driver.plots(args)

    args.comptype = 'ic_compare'
    args.latex_compiler = 'pdflatex'
    radvel.driver.report(args)


def test_k2(setupfn='example_planets/epic203771098.py'):
    """
    Run through K2-24 example
    """
    args = _args()
    args.setupfn = setupfn
    _standard_run(setupfn, args)

    # set the proceed flag and continue
    args.proceed = True
    radvel.driver.mcmc(args)

    args.ensembles = 1
    try:
        radvel.driver.mcmc(args)
    except ValueError:  # expected error when changing number of ensembles with proceed flag
        pass

    args.serial = True
    args.proceed = False
    radvel.driver.mcmc(args)


def test_hd(setupfn='example_planets/HD164922.py'):
    """
    Check multi-instrument fit
    """
    args = _args()
    args.setupfn = setupfn

    radvel.driver.fit(args)
    radvel.driver.mcmc(args)

    args.type = ['rv']
    args.plotkw = {}
    radvel.driver.plots(args)


def test_k2131(setupfn='example_planets/k2-131.py'):
    """
    Check GP fit
    """
    args = _args()
    args.setupfn = setupfn

    radvel.driver.fit(args)

    args.type = ['gp']
    args.verbose = True
    radvel.driver.ic_compare(args)

    args.type = ['rv']
    args.gp = True
    args.plotkw = {}
    radvel.driver.plots(args)


def test_celerite(setupfn='example_planets/k2-131_celerite.py'):
    """
    Check celerite GP fit
    """
    args = _args()
    args.setupfn = setupfn

    radvel.driver.fit(args)

    args.type = ['rv']
    args.gp = True
    args.plotkw = {'plot_likelihoods_separately':True}
    radvel.driver.plots(args)


def test_basis():
    """
    Test basis conversions
    """

    basis_list = radvel.basis.BASIS_NAMES
    default_basis = 'per tc e w k'

    anybasis_params = radvel.Parameters(1, basis=default_basis)

    anybasis_params['per1'] = radvel.Parameter(value=20.885258)
    anybasis_params['tc1'] = radvel.Parameter(value=2072.79438)
    anybasis_params['e1'] = radvel.Parameter(value=0.01)
    anybasis_params['w1'] = radvel.Parameter(value=1.6)
    anybasis_params['k1'] = radvel.Parameter(value=10.0)

    anybasis_params['dvdt'] = radvel.Parameter(value=0.0)
    anybasis_params['curv'] = radvel.Parameter(value=0.0)

    anybasis_params['gamma_j'] = radvel.Parameter(1.0)
    anybasis_params['jit_j'] = radvel.Parameter(value=2.6)

    for new_basis in basis_list:
        iparams = radvel.basis._copy_params(anybasis_params)
        ivector = radvel.Vector(iparams)
        if new_basis != default_basis:
            new_vector = iparams.basis.v_to_any_basis(ivector, new_basis)
            new_params = iparams.basis.to_any_basis(iparams, new_basis)
            tmpv = new_vector.copy()
            tmp = radvel.basis._copy_params(new_params)

            old_vector = tmp.basis.v_to_any_basis(tmpv, default_basis)
            old_params = tmp.basis.to_any_basis(tmp, default_basis)

            for par in iparams:
                before = iparams[par].value
                after = old_params[par].value
                assert (before - after) <= 1e-5,\
                    "Parameters do not match after basis conversion: \
{}, {} != {}".format(par, before, after)

            for i in range(ivector.vector.shape[0]):
                before = ivector.vector[i][0]
                after = old_vector[i][0]
                assert (before - after) <= 1e-5, \
                    "Vectors do not match after basis conversion: \
{} row, {} != {}".format(i, before, after)



def test_kernels():
    """
    Test basic functionality of all standard GP kernels
    """

    kernel_list = radvel.gp.KERNELS

    for kernel in kernel_list:
        hnames = kernel_list[kernel] # gets list of hyperparameter name strings
        hyperparams = {k: radvel.Parameter(value=1.) for k in hnames}
        kernel_call = getattr(radvel.gp, kernel + "Kernel")
        test_kernel = kernel_call(hyperparams)

        x = np.array([1.,2.,3.])
        test_kernel.compute_distances(x,x)
        test_kernel.compute_covmatrix(x.T)

        print("Testing {}".format(kernel_call(hyperparams)))

        sys.stdout.write("Testing error catching with dummy hyperparameters... \n")

        fakeparams1 = {}
        fakeparams1['dummy'] = radvel.Parameter(value=1.0)
        try:
            kernel_call(fakeparams1)
            raise Exception('Test #1 failed for {}'.format(kernel))
        except AssertionError:
            sys.stdout.write("passed #1\n")

        fakeparams2 = copy.deepcopy(hyperparams)
        fakeparams2[hnames[0]] = 1.
        try:
            kernel_call(fakeparams2)
            raise Exception('Test #2 failed for {}'.format(kernel))
        except AttributeError:
            sys.stdout.write("passed #2\n")


def test_priors():
    """
    Test basic functionality of all Priors
    """

    params = radvel.Parameters(1, 'per tc secosw sesinw logk')
    params['per1'] = radvel.Parameter(10.0)
    params['tc1'] = radvel.Parameter(0.0)
    params['secosw1'] = radvel.Parameter(0.0)
    params['sesinw1'] = radvel.Parameter(0.0)
    params['logk1'] = radvel.Parameter(1.5)

    vector = radvel.Vector(params)

    testTex = r'Delta Function Prior on $\sqrt{e}\cos{\omega}_{b}$'

    def userdef_prior_func(inp_list):
        if inp_list[0] >= 0. and inp_list[0] < 1.:
            return 0.
        else:
            return -np.inf

    prior_tests = {
        radvel.prior.EccentricityPrior(1):                  1/.99,
        radvel.prior.EccentricityPrior([1]):                1/.99,
        radvel.prior.PositiveKPrior(1):                     1.0,
        radvel.prior.Gaussian('per1', 9.9, 0.1):            scipy.stats.norm(9.9,0.1).pdf(10.),
        radvel.prior.HardBounds('per1', 1.0, 9.0):          0.,
        radvel.prior.HardBounds('per1', 1.0, 11.0):         1./10.,
        radvel.prior.Jeffreys('per1', 0.1, 100.0):          (1./10.)/np.log(100./0.1),
        radvel.prior.ModifiedJeffreys('per1', 0.1, 100.0, 0.):  (1./10.)/np.log(100./0.1),
        radvel.prior.ModifiedJeffreys('per1', 2., 100.0, 1.):  (1./9.)/np.log(99.),
        radvel.prior.SecondaryEclipsePrior(1, 5.0, 10.0):    1./np.sqrt(2.*np.pi),
        radvel.prior.NumericalPrior(
            ['sesinw1'],
            np.random.randn(1,5000000)
        ):                                                  scipy.stats.norm(0, 1).pdf(0.),
        radvel.prior.UserDefinedPrior(
            ['secosw1'], userdef_prior_func, testTex
        ):                                                  1.0,
        radvel.prior.InformativeBaselinePrior(
            'per1', 5.0, duration=1.0
        ):                                                  6./10.

    }

    for prior, val in prior_tests.items():
        print(prior.__repr__())
        print(prior.__str__())
        tolerance = .01
        print(abs(np.exp(prior(params, vector))))
        print(val)
        assert abs(np.exp(prior(params, vector)) - val) < tolerance, \
            "Prior output does not match expectation"


def test_kepler():
    """
    Profile and test C-based Kepler solver
    """
    radvel.kepler.profile()


def test_model_comp(setupfn='example_planets/HD164922.py'):
    """
    Test some additional model_comp lines
    """

    args = _args()
    args.setupfn = setupfn
    radvel.driver.fit(args)

    # also check some additional lines of model_comp
    args.verbose = True
    args.type = ['trend']
    radvel.driver.ic_compare(args)

    args.simple = True
    args.type = ['e']
    radvel.driver.ic_compare(args)

    args.simple = False
    args.type = ['something_else']
    try:
        radvel.driver.ic_compare(args)
        raise Exception("Unexpected result from model_comp.")
    except AssertionError:  # expected result
        return


if __name__ == '__main__':
    #test_k2()
    #test_hd()
    #test_model_comp()
    test_k2131()
    #test_celerite()
    # test_basis()
    #test_kernels()
    #test_kepler()
    #test_priors()

1	import sys
2	import copy	1✔
3	import warnings	1✔
4	import types	1✔
5
6	import radvel	1✔
7	import radvel.driver	1✔
8	import numpy as np	1✔
9	import scipy	1✔
10	import radvel.prior	1✔
11
12	warnings.simplefilter('ignore')	1✔
13
14
15	class _args(types.SimpleNamespace):	1✔
16	outputdir = '/tmp/'	1✔
17	decorr = False	1✔
18	name_in_title = False	1✔
19	gp = False	1✔
20	simple = False	1✔
21
22	nwalkers = 50	1✔
23	nsteps = 100	1✔
24	ensembles = 8	1✔
25	maxGR = 1.10	1✔
26	burnGR = 1.30	1✔
27	burnAfactor = 25	1✔
28	minAfactor = 50	1✔
29	maxArchange = .07	1✔
30	minTz = 1000	1✔
31	minsteps = 100	1✔
32	minpercent = 5	1✔
33	thin = 1	1✔
34	serial = False	1✔
35	save = True	1✔
36	savename = 'rawchains.h5'	1✔
37	proceed = False	1✔
38	proceedname = None	1✔
39	headless=False	1✔
40
41
42	def _standard_run(setupfn, arguments):	1✔
43	"""
44	Run through all of the standard steps
45	"""
46
47	args = arguments	1✔
48	args.setupfn = setupfn	1✔
49
50	radvel.driver.fit(args)	1✔
51	radvel.driver.mcmc(args)	1✔
52	radvel.driver.derive(args)	1✔
53
54	args.type = ['trend', 'jit', 'e', 'nplanets', 'gp']	1✔
55	args.verbose = True	1✔
56	radvel.driver.ic_compare(args)	1✔
57
58	args.type = ['params', 'priors', 'rv', 'ic_compare', 'derived', 'crit']	1✔
59	radvel.driver.tables(args)	1✔
60
61	args.type = ['rv', 'corner', 'auto', 'trend', 'derived']	1✔
62	args.plotkw = {'highlight_last': True, 'show_rms': True}	1✔
63	radvel.driver.plots(args)	1✔
64
65	args.comptype = 'ic_compare'	1✔
66	args.latex_compiler = 'pdflatex'	1✔
67	radvel.driver.report(args)	1✔
68
69
70	def test_k2(setupfn='example_planets/epic203771098.py'):	1✔
71	"""
72	Run through K2-24 example
73	"""
74	args = _args()	1✔
75	args.setupfn = setupfn	1✔
76	_standard_run(setupfn, args)	1✔
77
78	# set the proceed flag and continue
79	args.proceed = True	1✔
80	radvel.driver.mcmc(args)	1✔
81
82	args.ensembles = 1	1✔
83	try:	1✔
84	radvel.driver.mcmc(args)	1✔
85	except ValueError: # expected error when changing number of ensembles with proceed flag	1✔
86	pass	1✔
87
88	args.serial = True	1✔
89	args.proceed = False	1✔
90	radvel.driver.mcmc(args)	1✔
91
92
93	def test_hd(setupfn='example_planets/HD164922.py'):	1✔
94	"""
95	Check multi-instrument fit
96	"""
97	args = _args()	1✔
98	args.setupfn = setupfn	1✔
99
100	radvel.driver.fit(args)	1✔
101	radvel.driver.mcmc(args)	1✔
102
103	args.type = ['rv']	1✔
104	args.plotkw = {}	1✔
105	radvel.driver.plots(args)	1✔
106
107
108	def test_k2131(setupfn='example_planets/k2-131.py'):	1✔
109	"""
110	Check GP fit
111	"""
112	args = _args()	1✔
113	args.setupfn = setupfn	1✔
114
115	radvel.driver.fit(args)	1✔
116
117	args.type = ['gp']	1✔
118	args.verbose = True	1✔
119	radvel.driver.ic_compare(args)	1✔
120
121	args.type = ['rv']	1✔
122	args.gp = True	1✔
123	args.plotkw = {}	1✔
124	radvel.driver.plots(args)	1✔
125
126
127	def test_celerite(setupfn='example_planets/k2-131_celerite.py'):	1✔
128	"""
129	Check celerite GP fit
130	"""
131	args = _args()	1✔
132	args.setupfn = setupfn	1✔
133
134	radvel.driver.fit(args)	1✔
135
136	args.type = ['rv']	1✔
137	args.gp = True	1✔
138	args.plotkw = {'plot_likelihoods_separately':True}	1✔
139	radvel.driver.plots(args)	1✔
140
141
142	def test_basis():	1✔
143	"""
144	Test basis conversions
145	"""
146
147	basis_list = radvel.basis.BASIS_NAMES	1✔
148	default_basis = 'per tc e w k'	1✔
149
150	anybasis_params = radvel.Parameters(1, basis=default_basis)	1✔
151
152	anybasis_params['per1'] = radvel.Parameter(value=20.885258)	1✔
153	anybasis_params['tc1'] = radvel.Parameter(value=2072.79438)	1✔
154	anybasis_params['e1'] = radvel.Parameter(value=0.01)	1✔
155	anybasis_params['w1'] = radvel.Parameter(value=1.6)	1✔
156	anybasis_params['k1'] = radvel.Parameter(value=10.0)	1✔
157
158	anybasis_params['dvdt'] = radvel.Parameter(value=0.0)	1✔
159	anybasis_params['curv'] = radvel.Parameter(value=0.0)	1✔
160
161	anybasis_params['gamma_j'] = radvel.Parameter(1.0)	1✔
162	anybasis_params['jit_j'] = radvel.Parameter(value=2.6)	1✔
163
164	for new_basis in basis_list:	1✔
165	iparams = radvel.basis._copy_params(anybasis_params)	1✔
166	ivector = radvel.Vector(iparams)	1✔
167	if new_basis != default_basis:	1✔
168	new_vector = iparams.basis.v_to_any_basis(ivector, new_basis)	1✔
169	new_params = iparams.basis.to_any_basis(iparams, new_basis)	1✔
170	tmpv = new_vector.copy()	1✔
171	tmp = radvel.basis._copy_params(new_params)	1✔
172
173	old_vector = tmp.basis.v_to_any_basis(tmpv, default_basis)	1✔
174	old_params = tmp.basis.to_any_basis(tmp, default_basis)	1✔
175
176	for par in iparams:	1✔
177	before = iparams[par].value	1✔
178	after = old_params[par].value	1✔
179	assert (before - after) <= 1e-5,\	1✔
180	"Parameters do not match after basis conversion: \
181	{}, {} != {}".format(par, before, after)
182
183	for i in range(ivector.vector.shape[0]):	1✔
184	before = ivector.vector[i][0]	1✔
185	after = old_vector[i][0]	1✔
186	assert (before - after) <= 1e-5, \	1✔
187	"Vectors do not match after basis conversion: \
188	{} row, {} != {}".format(i, before, after)
189
190
191
192	def test_kernels():	1✔
193	"""
194	Test basic functionality of all standard GP kernels
195	"""
196
197	kernel_list = radvel.gp.KERNELS	1✔
198
199	for kernel in kernel_list:	1✔
200	hnames = kernel_list[kernel] # gets list of hyperparameter name strings	1✔
201	hyperparams = {k: radvel.Parameter(value=1.) for k in hnames}	1✔
202	kernel_call = getattr(radvel.gp, kernel + "Kernel")	1✔
203	test_kernel = kernel_call(hyperparams)	1✔
204
205	x = np.array([1.,2.,3.])	1✔
206	test_kernel.compute_distances(x,x)	1✔
207	test_kernel.compute_covmatrix(x.T)	1✔
208
209	print("Testing {}".format(kernel_call(hyperparams)))	1✔
210
211	sys.stdout.write("Testing error catching with dummy hyperparameters... \n")	1✔
212
213	fakeparams1 = {}	1✔
214	fakeparams1['dummy'] = radvel.Parameter(value=1.0)	1✔
215	try:	1✔
216	kernel_call(fakeparams1)	1✔
217	raise Exception('Test #1 failed for {}'.format(kernel))	×
218	except AssertionError:	1✔
219	sys.stdout.write("passed #1\n")	1✔
220
221	fakeparams2 = copy.deepcopy(hyperparams)	1✔
222	fakeparams2[hnames[0]] = 1.	1✔
223	try:	1✔
224	kernel_call(fakeparams2)	1✔
225	raise Exception('Test #2 failed for {}'.format(kernel))	×
226	except AttributeError:	1✔
227	sys.stdout.write("passed #2\n")	1✔
228
229
230	def test_priors():	1✔
231	"""
232	Test basic functionality of all Priors
233	"""
234
235	params = radvel.Parameters(1, 'per tc secosw sesinw logk')	1✔
236	params['per1'] = radvel.Parameter(10.0)	1✔
237	params['tc1'] = radvel.Parameter(0.0)	1✔
238	params['secosw1'] = radvel.Parameter(0.0)	1✔
239	params['sesinw1'] = radvel.Parameter(0.0)	1✔
240	params['logk1'] = radvel.Parameter(1.5)	1✔
241
242	vector = radvel.Vector(params)	1✔
243
244	testTex = r'Delta Function Prior on $\sqrt{e}\cos{\omega}_{b}$'	1✔
245
246	def userdef_prior_func(inp_list):	1✔
247	if inp_list[0] >= 0. and inp_list[0] < 1.:	1✔
248	return 0.	1✔
249	else:
250	return -np.inf	×
251
252	prior_tests = {	1✔
253	radvel.prior.EccentricityPrior(1): 1/.99,
254	radvel.prior.EccentricityPrior([1]): 1/.99,
255	radvel.prior.PositiveKPrior(1): 1.0,
256	radvel.prior.Gaussian('per1', 9.9, 0.1): scipy.stats.norm(9.9,0.1).pdf(10.),
257	radvel.prior.HardBounds('per1', 1.0, 9.0): 0.,
258	radvel.prior.HardBounds('per1', 1.0, 11.0): 1./10.,
259	radvel.prior.Jeffreys('per1', 0.1, 100.0): (1./10.)/np.log(100./0.1),
260	radvel.prior.ModifiedJeffreys('per1', 0.1, 100.0, 0.): (1./10.)/np.log(100./0.1),
261	radvel.prior.ModifiedJeffreys('per1', 2., 100.0, 1.): (1./9.)/np.log(99.),
262	radvel.prior.SecondaryEclipsePrior(1, 5.0, 10.0): 1./np.sqrt(2.*np.pi),
263	radvel.prior.NumericalPrior(
264	['sesinw1'],
265	np.random.randn(1,5000000)
266	): scipy.stats.norm(0, 1).pdf(0.),
267	radvel.prior.UserDefinedPrior(
268	['secosw1'], userdef_prior_func, testTex
269	): 1.0,
270	radvel.prior.InformativeBaselinePrior(
271	'per1', 5.0, duration=1.0
272	): 6./10.
273
274	}
275
276	for prior, val in prior_tests.items():	1✔
277	print(prior.__repr__())	1✔
278	print(prior.__str__())	1✔
279	tolerance = .01	1✔
280	print(abs(np.exp(prior(params, vector))))	1✔
281	print(val)	1✔
282	assert abs(np.exp(prior(params, vector)) - val) < tolerance, \	1✔
283	"Prior output does not match expectation"
284
285
286	def test_kepler():	1✔
287	"""
288	Profile and test C-based Kepler solver
289	"""
290	radvel.kepler.profile()	1✔
291
292
293	def test_model_comp(setupfn='example_planets/HD164922.py'):	1✔
294	"""
295	Test some additional model_comp lines
296	"""
297
298	args = _args()	1✔
299	args.setupfn = setupfn	1✔
300	radvel.driver.fit(args)	1✔
301
302	# also check some additional lines of model_comp
303	args.verbose = True	1✔
304	args.type = ['trend']	1✔
305	radvel.driver.ic_compare(args)	1✔
306
307	args.simple = True	1✔
308	args.type = ['e']	1✔
309	radvel.driver.ic_compare(args)	1✔
310
311	args.simple = False	1✔
312	args.type = ['something_else']	1✔
313	try:	1✔
314	radvel.driver.ic_compare(args)	1✔
315	raise Exception("Unexpected result from model_comp.")	×
316	except AssertionError: # expected result	1✔
317	return	1✔
318
319
320	if __name__ == '__main__':	1✔
321	#test_k2()
322	#test_hd()
323	#test_model_comp()
324	test_k2131()	×
325	#test_celerite()
326	# test_basis()
327	#test_kernels()
328	#test_kepler()
329	#test_priors()

California-Planet-Search / radvel / #503

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous