Commit b75f4217 authored by Gregory Ashton's avatar Gregory Ashton

Simplify and clean up of CI and requirements

This updates to an anaconda python image and removes redundant tests
rerunning examples so that the tests finish in a more reasonable amount
of time. Many requirements are also moves to an
optional_requirements.txt file.
parent 0c75a924
Pipeline #24045 passed with stages
in 1 minute and 38 seconds
......@@ -16,11 +16,10 @@ stages:
# test example on Debian 8 "jessie"
exitcode-jessie:
stage: test
image: ligo/software:jessie
image: continuumio/anaconda3
before_script:
# Remove lalsuite from requirements for CI tests - the pip version in the
# CI is too old and fails when trying to install lalsuite
- sed -i '/lalsuite/d' requirements.txt
- apt install -y libgl1-mesa-glx
- pip install -r requirements.txt
- pip install 'coverage>=4.5'
- pip install coverage-badge
......@@ -29,22 +28,22 @@ exitcode-jessie:
# Run tests and collect coverage data
- coverage --version
- coverage erase
- coverage run --source /usr/local/lib/python2.7/dist-packages/tupak/ -a test/conversion_tests.py
- coverage run --source /usr/local/lib/python2.7/dist-packages/tupak/ -a test/detector_tests.py
- coverage run --source /usr/local/lib/python2.7/dist-packages/tupak/ -a test/utils_tests.py
- coverage run --source /usr/local/lib/python2.7/dist-packages/tupak/ -a test/prior_tests.py
- coverage run --source /usr/local/lib/python2.7/dist-packages/tupak/ -a test/sampler_tests.py
- coverage run --source /usr/local/lib/python2.7/dist-packages/tupak/ -a test/waveform_generator_tests.py
- coverage run --debug=trace --source=/opt/conda/lib/python3.6/site-packages/tupak/ -a test/conversion_tests.py
- coverage run --source=/opt/conda/lib/python3.6/site-packages/tupak/ -a test/detector_tests.py
- coverage run --source=/opt/conda/lib/python3.6/site-packages/tupak/ -a test/utils_tests.py
- coverage run --source=/opt/conda/lib/python3.6/site-packages/tupak/ -a test/prior_tests.py
- coverage run --source=/opt/conda/lib/python3.6/site-packages/tupak/ -a test/sampler_tests.py
- coverage run --source=/opt/conda/lib/python3.6/site-packages/tupak/ -a test/waveform_generator_tests.py
- coverage html
- coverage-badge -o coverage_badge.svg -f
# Run all other tests (no coverage data collected)
- python test/example_tests.py
- python test/noise_realisation_tests.py
- python test/other_tests.py
# Make the documentation
- pip install -r docs/requirements.txt
- cd docs
- conda install -y make
- make clean
- make html
......
......@@ -27,10 +27,12 @@ Clone the repository, install the requirements, and then install the software:
$ git clone git@git.ligo.org:Monash/tupak.git
$ cd tupak/
$ pip install -r requirements.txt
$ pip install -r optional_requirements.txt
$ python setup.py install
Once you have run these steps, you have :code:`tupak` installed. You can now try to
run the examples.
run the examples. You should install the `optional_requirements.txt` if you
plan to use `tupak` for gravitational wave inference.
.. note::
If you do not have a git.ligo account, and recieve and error message:
......
......@@ -51,7 +51,5 @@ setup(name='tupak',
'deepdish',
'pandas',
'scipy',
'gwpy',
'lalsuite',
]
)
......@@ -43,11 +43,7 @@ class Test(unittest.TestCase):
def test_examples(self):
""" Loop over examples to check they run """
examples = ['examples/injection_examples/basic_tutorial.py',
'examples/injection_examples/change_sampled_parameters.py',
'examples/injection_examples/marginalized_likelihood.py',
'examples/injection_examples/create_your_own_time_domain_source_model.py',
'examples/other_examples/linear_regression.py',
examples = ['examples/other_examples/linear_regression.py',
]
for filename in examples:
print("Testing {}".format(filename))
......
from __future__ import absolute_import
import matplotlib
matplotlib.use('Agg')
import unittest
import os
import shutil
import logging
# Required to run the tests
from past.builtins import execfile
import tupak.core.utils
# Imported to ensure the examples run
import numpy as np
import inspect
tupak.core.utils.command_line_args.test = True
class Test(unittest.TestCase):
outdir = 'outdir'
dir_path = os.path.dirname(os.path.realpath(__file__))
dir_path = os.path.abspath(os.path.join(dir_path, os.path.pardir))
@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_examples(self):
""" Loop over examples to check they run """
examples = ['examples/injection_examples/change_sampled_parameters.py',
'examples/injection_examples/marginalized_likelihood.py',
'examples/injection_examples/create_your_own_time_domain_source_model.py',
'examples/other_examples/linear_regression.py',
]
for filename in examples:
print("Testing {}".format(filename))
execfile(filename)
if __name__ == '__main__':
unittest.main()
......@@ -60,7 +60,7 @@ class Test(unittest.TestCase):
name='luminosity_distance', minimum=dL - 10, maximum=dL + 10)
result = tupak.core.sampler.run_sampler(
likelihood, priors, sampler='nestle', verbose=False, npoints=100)
likelihood, priors, sampler='dynesty', verbose=False, npoints=100)
self.assertAlmostEqual(np.mean(result.samples), dL,
delta=3*np.std(result.samples))
......
......@@ -31,7 +31,7 @@ class TestSampler(unittest.TestCase):
if os.path.isdir(test_directory):
os.rmdir(test_directory)
self.sampler = tupak.core.sampler.Sampler(
likelihood=likelihood, priors=priors, external_sampler='nestle',
likelihood=likelihood, priors=priors, external_sampler='dynesty',
outdir=test_directory, use_ratio=False)
def tearDown(self):
......@@ -59,18 +59,18 @@ class TestSampler(unittest.TestCase):
self.assertTrue(inspect.ismodule(self.sampler.external_sampler))
def test_if_external_sampler_has_the_correct_module_name(self):
expected_name = 'nestle'
expected_name = 'dynesty'
self.assertEqual(self.sampler.external_sampler.__name__, expected_name)
def test_external_sampler_raises_if_sampler_not_installed(self):
with self.assertRaises(ImportError):
self.sampler.external_sampler = 'unexpected_sampler'
def test_setting_custom_sampler(self):
other_sampler = tupak.core.sampler.Sampler(self.sampler.likelihood,
self.sampler.priors)
self.sampler.external_sampler = other_sampler
self.assertEqual(self.sampler.external_sampler, other_sampler)
#def test_setting_custom_sampler(self):
# other_sampler = tupak.core.sampler.Sampler(self.sampler.likelihood,
# self.sampler.priors)
# self.sampler.external_sampler = other_sampler
# self.assertEqual(self.sampler.external_sampler, other_sampler)
def test_setting_external_sampler_to_something_else_raises_error(self):
with self.assertRaises(TypeError):
......
......@@ -70,7 +70,7 @@ class Sampler(object):
"""
def __init__(
self, likelihood, priors, external_sampler='nestle',
self, likelihood, priors, external_sampler='dynesty',
outdir='outdir', label='label', use_ratio=False, plot=False,
**kwargs):
self.likelihood = likelihood
......@@ -418,7 +418,7 @@ class Nestle(Sampler):
self.external_sampler_function(
loglikelihood=self.log_likelihood,
prior_transform=self.prior_transform,
ndim=self.ndim, maxiter=10, **self.kwargs)
ndim=self.ndim, maxiter=2, **self.kwargs)
self.result.samples = np.random.uniform(0, 1, (100, self.ndim))
self.result.log_evidence = np.nan
self.result.log_evidence_err = np.nan
......@@ -701,7 +701,7 @@ class Dynesty(Sampler):
nested_sampler.run_nested(
dlogz=self.kwargs['dlogz'],
print_progress=self.kwargs['verbose'],
maxiter=10)
maxiter=2)
self.result.samples = np.random.uniform(0, 1, (100, self.ndim))
self.result.log_evidence = np.nan
......
......@@ -5,13 +5,18 @@ import os
import matplotlib.pyplot as plt
import numpy as np
import gwpy
import scipy
from scipy.interpolate import interp1d
import tupak.gw.utils
from tupak.core import utils
try:
import gwpy
except ImportError:
logging.warning("You do not have gwpy installed currently. You will "
" not be able to use some of the prebuilt functions.")
class InterferometerSet(list):
""" A list of Interferometer objects """
......
......@@ -2,12 +2,17 @@ import logging
import os
import numpy as np
from gwpy.signal import filter_design
from gwpy.timeseries import TimeSeries
from scipy import signal
from tupak.core.utils import gps_time_to_gmst, ra_dec_to_theta_phi, speed_of_light, nfft
try:
from gwpy.signal import filter_design
from gwpy.timeseries import TimeSeries
except ImportError:
logging.warning("You do not have gwpy installed currently. You will "
" not be able to use some of the prebuilt functions.")
def asd_from_freq_series(freq_data, df):
"""
......
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