Moritz Huebner: Renamed some more Peyote occurences

.gitlab-ci.yml

@@ -26,7 +26,7 @@ exitcode-jessie:
     - coverage run -a test/tests.py
     - coverage run -a test/waveform_generator_tests.py
     - coverage run -a test/noise_realisation_tests.py
-    - coverage html --include=peyote/*
+    - coverage html --include=tupak/*
     - coverage-badge -o coverage.svg
   artifacts:
     paths:

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/)
+[![pipeline status](https://git.ligo.org/Monash/tupak/badges/master/pipeline.svg)](https://git.ligo.org/Monash/tupak/commits/master)
+[![coverage report](https://monash.docs.ligo.org/tupak/coverage.svg)](
+https://monash.docs.ligo.org/tupak/)
 
-# PEYOte
+# Tupak
 
 Fulfilling all your GW dreams.
 
@@ -11,19 +11,19 @@ Fulfilling all your GW dreams.
 In the following, we assume you have installed
 [pip](https://pip.pypa.io/en/stable/installing/) and [git](https://git-scm.com/).
 
-### Install peyote
-Clone the repository, install the requirements, and then install `peyote`.
+### Install tupak
+Clone the repository, install the requirements, and then install `tupak`.
 ```bash
-$ git clone git@git.ligo.org:Monash/peyote.git
-$ cd peyote/
+$ git clone git@git.ligo.org:Monash/tupak.git
+$ cd tupak/
 $ pip install -r requirements.txt
 $ python setup.py install
 ```
 
-Once you have run these steps, you have `peyote` installed.
+Once you have run these steps, you have `tupak` installed.
 
 ### Install lalsuite
-Many of the `peyote` features rely on having a swig-wrapped `lalsuite`
+Many of the `tupak` features rely on having a swig-wrapped `lalsuite`
 installation. To install this head to
 [https://git.ligo.org/lscsoft/lalsuite](https://git.ligo.org/lscsoft/lalsuite)
 to check you have an account and SSH keys set up. Then,
@@ -66,9 +66,9 @@ $ coverage html
 ```
 
 This will generate a directory `htmlcov`, to see detailed coverage navigate
-from your browser to the file `peyote/htmlcov/index.html`.
+from your browser to the file `tupak/htmlcov/index.html`.
 
 The coverage report for master can be seen here:
-[https://monash.docs.ligo.org/peyote/](https://monash.docs.ligo.org/peyote/).
+[https://monash.docs.ligo.org/tupak/](https://monash.docs.ligo.org/tupak/).
 
 

setup.py

@@ -2,9 +2,9 @@
 
 from distutils.core import setup
 
-setup(name='peyote',
+setup(name='tupak',
       version='0.1',
-      packages=['peyote'],
-      package_dir={'peyote': 'peyote'},
-      package_data={'peyote': ['noise_curves/*.txt']}
+      packages=['tupak'],
+      package_dir={'tupak': 'tupak'},
+      package_data={'tupak': ['noise_curves/*.txt']}
       )

tupak/detector.py

@@ -508,7 +508,7 @@ def get_inteferometer(
 
     Returns
     -------
-    interferometer: `peyote.detector.Interferometer`
+    interferometer: `tupak.detector.Interferometer`
         An Interferometer instance with a PSD and frequency-domain strain data.
     """
 
@@ -603,7 +603,7 @@ def get_inteferometer_with_fake_noise_and_injection(
 
     Returns
     -------
-    interferometer: `peyote.detector.Interferometer`
+    interferometer: `tupak.detector.Interferometer`
         An Interferometer instance with a PSD and frequency-domain strain data.
     """
 

tupak/prior.py

@@ -334,7 +334,7 @@ class FromFile(Interped):
         try:
             self.id = file_name
             if '/' not in self.id:
-                self.id = '{}/peyote/prior_files/{}'.format(os.getcwd(), self.id)
+                self.id = '{}/tupak/prior_files/{}'.format(os.getcwd(), self.id)
             xx, yy = np.genfromtxt(self.id).T
             Interped.__init__(self, xx=xx, yy=yy, minimum=minimum, maximum=maximum, name=name, latex_label=latex_label)
         except IOError:

tupak/sampler.py

@@ -348,7 +348,7 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
 
     Parameters
     ----------
-    likelihood: `peyote.likelihood.Likelihood`
+    likelihood: `tupak.likelihood.Likelihood`
         A `Likelihood` instance
     priors: dict
         A dictionary of the priors for each parameter - missing parameters will
@@ -359,7 +359,7 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
         A string used in defining output files
     sampler: str
         The name of the sampler to use - see
-        `peyote.sampler.get_implemented_samplers()` for a list of available
+        `tupak.sampler.get_implemented_samplers()` for a list of available
         samplers
     use_ratio: bool (False)
         If True, use the likelihood's loglikelihood_ratio, rather than just

tutorials/Compare_samplers.ipynb

@@ -30,9 +30,9 @@
     "\n",
     "%matplotlib inline\n",
     "\n",
-    "import peyote\n",
+    "import tupak\n",
     "\n",
-    "peyote.utils.setup_logger()\n",
+    "tupak.utils.setup_logger()\n",
     "\n",
     "time_duration = 1.\n",
     "sampling_frequency = 4096.\n",
@@ -42,22 +42,22 @@
     "                            reference_frequency=50., ra=1.375, dec=-1.2108, geocent_time=1126259642.413,\n",
     "                            psi=2.659)\n",
     "\n",
-    "waveform_generator = peyote.waveform_generator.WaveformGenerator(\n",
+    "waveform_generator = tupak.waveform_generator.WaveformGenerator(\n",
     "    sampling_frequency=sampling_frequency,\n",
     "    time_duration=time_duration,\n",
-    "    frequency_domain_source_model=peyote.source.lal_binary_black_hole,\n",
+    "    frequency_domain_source_model=tupak.source.lal_binary_black_hole,\n",
     "    parameters=injection_parameters)\n",
     "\n",
     "hf_signal = waveform_generator.frequency_domain_strain()\n",
     "\n",
-    "H1 = peyote.detector.H1\n",
+    "H1 = tupak.detector.H1\n",
     "H1.set_data(sampling_frequency=sampling_frequency, duration=time_duration,\n",
     "            from_power_spectral_density=True)\n",
     "H1.inject_signal(waveform_polarizations=hf_signal, parameters=injection_parameters)\n",
     "\n",
     "IFOs = [H1]\n",
     "\n",
-    "likelihood = peyote.likelihood.Likelihood(IFOs, waveform_generator)"
+    "likelihood = tupak.likelihood.Likelihood(IFOs, waveform_generator)"
    ]
   },
   {
@@ -83,9 +83,9 @@
     }
    ],
    "source": [
-    "priors = peyote.prior.parse_floats_to_fixed_priors(injection_parameters)\n",
-    "priors['ra'] = peyote.prior.Uniform(0, 2*np.pi, 'ra')\n",
-    "priors['dec'] = peyote.prior.Uniform(-np.pi/2, np.pi/2, 'dec')"
+    "priors = tupak.prior.parse_floats_to_fixed_priors(injection_parameters)\n",
+    "priors['ra'] = tupak.prior.Uniform(0, 2*np.pi, 'ra')\n",
+    "priors['dec'] = tupak.prior.Uniform(-np.pi/2, np.pi/2, 'dec')"
    ]
   },
   {
@@ -174,7 +174,7 @@
    ],
    "source": [
     "%%time \n",
-    "result = peyote.sampler.run_sampler(\n",
+    "result = tupak.sampler.run_sampler(\n",
     "    likelihood, priors=priors, sampler='pymultinest', label='pymultinest',\n",
     "    npoints=200, verbose=False, resume=False)\n",
     "fig = result.plot_corner(save=False)\n",
@@ -263,7 +263,7 @@
    ],
    "source": [
     "%%time \n",
-    "result = peyote.sampler.run_sampler(\n",
+    "result = tupak.sampler.run_sampler(\n",
     "    likelihood, priors=priors, sampler='dynesty', label='nestle',\n",
     "    bound='multi', sample='rwalk', npoints=200, walks=1, verbose=False,\n",
     "    update_interval=100)\n",
@@ -335,7 +335,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/user1/anaconda2/lib/python2.7/site-packages/peyote/sampler.py:148: RuntimeWarning: divide by zero encountered in log\n",
+      "/home/user1/anaconda2/lib/python2.7/site-packages/tupak/sampler.py:148: RuntimeWarning: divide by zero encountered in log\n",
       "  zip(self.__search_parameter_keys, theta)])\n"
      ]
     },
@@ -395,7 +395,7 @@
    ],
    "source": [
     "%%time \n",
-    "result = peyote.sampler.run_sampler(\n",
+    "result = tupak.sampler.run_sampler(\n",
     "    likelihood, priors=priors, sampler='ptemcee', label='ptemcee',\n",
     "    nwalkers=100, nsteps=200, nburn=100, ntemps=2,\n",
     "    tqdm='tqdm_notebook')\n",

tutorials/make_standard_data.py

@@ -31,7 +31,7 @@ simulation_parameters = dict(
     geocent_time=1126259642.413,
     psi=2.659
 )
-#sampling_parameters = peyote.parameter.Parameter.parse_floats_to_parameters(simulation_parameters)
+#sampling_parameters = tupak.parameter.Parameter.parse_floats_to_parameters(simulation_parameters)
 waveform_generator = WaveformGenerator(frequency_domain_source_model=tupak.source.lal_binary_black_hole,
                                        sampling_frequency=sampling_frequency,
                                        time_duration=time_duration,