Adds basic tests

- Test for simulated data
- Test likelihood evaluation
- Add gitlab-ci.yml
- Remove lal and lalsim which aren't directly pip installable
- Add coverage and pipeline status to README
- Adds coverage report
- Update README.md with instructions on testing and coverage

.gitlab-ci.yml

+# This script is an edited version of the example found at
+# https://git.ligo.org/lscsoft/example-ci-project/blob/python/.gitlab-ci.yml
+# Each 0th-indendation level is a job that will be run within GitLab CI
+# The only exception are a short list of reserved keywords
+#
+# https://docs.gitlab.com/ee/ci/yaml/#gitlab-ci-yml
+
+# stages is a reserved keyword that defines job dependencies and
+# parallelization. each stage runs in parallel but must complete
+# before the next stage begins
+
+stages:
+  - test
+  - deploy
+
+# test example on Debian 8 "jessie"
+exitcode-jessie:
+  stage: test
+  image: ligo/software:jessie
+  script:
+    - pip install -r requirements.txt
+    - pip install coverage
+    - pip install coverage-badge
+    - coverage run tests.py
+    - coverage html
+    - coverage-badge -o coverage.svg
+  artifacts:
+    paths:
+      - htmlcov/
+      - coverage.svg
+
+pages:
+  stage: deploy
+  dependencies:
+    - exitcode-jessie
+  script:
+    - mv htmlcov/ public/
+    - mv coverage.svg public/
+  artifacts:
+    paths:
+      - public
+    expire_in: 30 days
+  #only:
+    #- master

README.md

+[![pipeline status](https://git.ligo.org/Monash/peyote/badges/master/pipeline.svg)](https://git.ligo.org/Monash/peyote/commits/master)
+[![coverage report](https://monash.docs.ligo.org/peyote/coverage.svg)](
+https://monash.docs.ligo.org/peyote/)
+
 # PEYOte
 
 Fulfilling all your GW dreams.
@@ -34,4 +38,28 @@ $ make; make install
 
 ** warning **: in the configure line here, we have disabled everything except lalsimulation. If you need other modules, see `./configure --help`.
 
-You could also `pip install lal, lalsuite`.
\ No newline at end of file
+You could also `pip install lal, lalsuite`.
+
+## Tests and coverage
+
+To locally test the code
+
+```bash
+$ python tests.py
+```
+
+To locally generate a coverage report
+
+```bash
+$ pip install coverage
+$ coverage run tests.py
+$ coverage html
+```
+
+This will generate a directory `htmlcov`, to see detailed coverage navigate
+from your browser to the file `peyote/htmlcov/index.html`.
+
+The coverage report for master can be seen here:
+[https://monash.docs.ligo.org/peyote/](https://monash.docs.ligo.org/peyote/).
+
+

requirements.txt

@@ -4,8 +4,6 @@ scipy
 gwpy
 pandas
 astropy
-lal
-lalsuite
 pymultinest
 gwsurrogate
 NRSur7dq2

tests.py

+import unittest
+import numpy as np
+import os
+import shutil
+import peyote
+import logging
+
+
+class Test(unittest.TestCase):
+    outdir = 'TestDir'
+    dir_path = os.path.dirname(os.path.realpath(__file__))
+
+    # Run a script to produce standard data
+    msd = {}  # A dictionary of variables saved in make_standard_data.py
+    execfile(dir_path + '/tutorials/make_standard_data.py', msd)
+
+    @classmethod
+    def setUpClass(self):
+        if os.path.isdir(self.outdir):
+            try:
+                shutil.rmtree(self.outdir)
+            except OSError:
+                logging.warning(
+                    "{} not removed prior to tests".format(self.outdir))
+
+    @classmethod
+    def tearDownClass(self):
+        if os.path.isdir(self.outdir):
+            try:
+                shutil.rmtree(self.outdir)
+            except OSError:
+                logging.warning(
+                    "{} not removed prior to tests".format(self.outdir))
+
+    def test_make_standard_data(self):
+        " Load in the saved standard data and compare with new data "
+
+        # Load in the saved standard data
+        frequencies_saved, hf_real_saved, hf_imag_saved = np.loadtxt(
+            self.dir_path + '/tutorials/standard_data.txt').T
+        hf_signal_and_noise_saved = hf_real_saved + 1j * hf_imag_saved
+
+        self.assertTrue(
+            all(self.msd['frequencies'] == frequencies_saved))
+        self.assertTrue(
+            all(self.msd['hf_signal_and_noise'] == hf_signal_and_noise_saved))
+
+    def test_calculate_likelihood_for_standard_data(self):
+        pS = self.msd['simulation_parameters']
+        pN = self.msd['simulation_parameters'].copy()
+        pN['luminosity_distance'] = 1e6
+
+        likelihood = peyote.likelihood.likelihood(
+            [self.msd['IFO']], self.msd['source'])
+        loglS = likelihood.loglikelihood(pS)
+        loglN = likelihood.loglikelihood(pN)
+        self.assertAlmostEqual(
+            loglS - loglN,
+            36573752.328521997, 5)
+
+
+if __name__ == '__main__':
+    unittest.main()

tutorials/make_standard_data.py

+import peyote
+import os
+import numpy as np
+np.random.seed(10)
+
+time_duration = 1.
+sampling_frequency = 4096.
+
+simulation_parameters = dict(
+    mass_1=36.,
+    mass_2=29.,
+    spin_1=[0, 0, 0],
+    spin_2=[0, 0, 0],
+    luminosity_distance=410.,
+    inclination_angle=0.,
+    waveform_phase=0.,
+    waveform_approximant='IMRPhenomPv2',
+    reference_frequency=50.,
+    ra=0,
+    dec=1,
+    geocent_time=0,
+    psi=1
+    )
+
+source = peyote.source.BinaryBlackHole(
+    'BBH', sampling_frequency, time_duration)
+hf_signal = source.frequency_domain_strain(simulation_parameters)
+
+IFO = peyote.detector.H1
+hf_noise, frequencies = IFO.power_spectral_density.get_noise_realisation(
+    sampling_frequency, time_duration)
+IFO.set_data(frequency_domain_strain=hf_noise)
+IFO.inject_signal(source, simulation_parameters)
+IFO.set_spectral_densities(frequencies)
+IFO.whiten_data()
+hf_signal_and_noise = IFO.data
+
+if __name__ == '__main__':
+    dir_path = os.path.dirname(os.path.realpath(__file__))
+    with open(dir_path + '/standard_data.txt', 'w+') as f:
+        np.savetxt(
+            f,
+            np.column_stack([frequencies,
+                             hf_signal_and_noise.view(float).reshape(-1, 2)]),
+            header='frequency hf_real hf_imag')