Merge branch 'master' of https://git.ligo.org/Monash/tupak

.gitlab-ci.yml

@@ -30,18 +30,27 @@ exitcode-jessie:
     - coverage run --include=tupak/* -a test/example_tests.py
     - coverage html
     - coverage-badge -o coverage_badge.svg -f
+
+    # Make the documentation
+    - pip install -r docs/requirements.txt
+    - cd docs
+    - make html
+
   artifacts:
     paths:
       - htmlcov/
       - coverage_badge.svg
+      - docs/_build/html/
 
 pages:
   stage: deploy
   dependencies:
     - exitcode-jessie
   script:
+    - mkdir public/
     - mv htmlcov/ public/
     - mv /builds/Monash/tupak/coverage_badge.svg public/
+    - mv docs/_build/html/* public/
   artifacts:
     paths:
       - public

README.md

 [![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_badge.svg)](
-https://monash.docs.ligo.org/tupak/)
+https://monash.docs.ligo.org/tupak/htmlcov/)
 
 # Tupak
 
@@ -81,6 +81,6 @@ have also written [a shortened tl;dr here](./TLDR_MULTINEST.md).
 
 We have a variety of tests which can be found in the `tests` directory.  You
 can find a [current coverage report for master
-here.](https://monash.docs.ligo.org/tupak/).
+here.](https://monash.docs.ligo.org/tupak/htmlcov/).
 
 

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = tupak
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

docs/conf.py

+# -*- coding: utf-8 -*-
+#
+# tupak documentation build configuration file, created by
+# sphinx-quickstart on Fri May 25 12:08:01 2018.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../tupak/'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.mathjax', 'numpydoc',
+              'nbsphinx', 'sphinx.ext.autosummary']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
+source_suffix = '.txt'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'tupak'
+copyright = u'2018, Paul Lasky'
+author = u'Paul Lasky'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'0.2'
+# The full version, including alpha/beta/rc tags.
+release = u'0.2'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'requirements.txt']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'tupakdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'tupak.tex', u'tupak Documentation',
+     u'Paul Lasky', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'tupak', u'tupak Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'tupak', u'tupak Documentation',
+     author, 'tupak', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/index.txt

+Welcome to tupak's documentation!
+=================================
+
+.. automodule:: tupak
+    :members:
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   likelihood
+   samplers
+   writing-documentation
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/likelihood.txt

+==========
+Likelihood
+==========
+
+`tupak` likelihood objects are used in calculating the likelihood of the data
+for some specific set of parameters. In mathematical notation, the likelihood
+can be generically written as :math:`\mathcal{L}(d| \theta)`. How this is
+coded up will depend on the problem, but `tupak` expects all likelihood
+objects to have a `parameters` attribute (a dictionary of key-value pairs) and
+a `log_likelihood()` method.
+
+The default likelihood we use in the examples is `GravitationalWaveTransient`:
+
+.. autoclass:: tupak.likelihood.GravitationalWaveTransient
+    :members:
+
+We also provide a simpler likelihood
+
+.. autoclass:: tupak.likelihood.BasicGravitationalWaveTransient
+    :members:
+
+We provide an empty parent class which can be subclassed for alternative use
+cases
+
+.. autoclass:: tupak.likelihood.Likelihood
+    :members:
+
+
+
+

docs/requirements.txt

+html5lib==1.0b8  # Hack to ensure documentation generated
+sphinx
+numpydoc
+nbsphinx
+autodoc
+sphinx_rtd_theme

docs/samplers.txt

+==========
+Samplers
+==========
+
+Given a `likelihood` and `prior`, we can run parameter estimation using `run_sampler` 
+
+.. autofunction:: tupak.sampler.run_sampler

docs/writing-documentation.txt

+=====================
+Writing documentation
+=====================
+
+This is a short tutorial on how to contribute to the documentation of ``tupak``.
+
+Writing the basics
+------------------
+
+First, open your terminal and head to the ``docs`` directory in your clone of
+`tupak`. Once here, you'll notice there are a number of `*txt` files. Each one
+is a page of the documentation.
+
+Let's say you want to write documentation about the your new feature (or update
+the existing documentation). Simply open a new file ``a-new-feature.txt`` in
+your text editor. Then add a title and some text::
+
+   ====================
+   A new tupak feature!
+   ====================
+
+   Here we'll put a description of the new feature
+
+Next, in order to get your new page known by the rest of the documentation,
+open ``index.rst`` and, under ``toctree`` add the name of your file (without
+the suffix). For the example above::
+
+   .. toctree::
+      :maxdepth: 3
+      :caption: Contents:
+
+      likelihood
+      samplers
+      writing-documentation
+      a-new-feature
+
+
+Checking the results
+--------------------
+
+You can check what this will look like by (whilst in the ``docs`` directory)
+running the command::
+
+   $ make html
+
+This will create a directory ``./_build/html`` with the documentation. To
+see the result, open the file ``./_build/html/index.html`` in your browser.
+
+
+Pushing your changes to master
+------------------------------
+
+To contribute your documentation changes, you should create a branch and add in
+all of the new/changed files::
+
+   $ git checkout -b adding-my-new-documentation
+   $ git add index.txt
+   $ git add a-new-feature.txt
+   $ git commit -m "Adding my documentation for the feature"
+   $ git push origin adding-my-new-documentation
+
+Then, on the web interface create an merge request.
+
+Using reStructured text
+-----------------------
+
+The help files are written in reStructured text format. To familiarise yourself
+with these features visit http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html.
+
+A useful feature is the ability to `format code examples <http://www.sphinx-doc.org/en/stable/markup/code.html>`_. This is done through the use of ``::`` and indendentation. For
+example, to make this code block::
+
+   import tupak
+
+You would write::
+
+   to make this code block::
+
+      import tupak
+
+reStructured text is very powerful, but can be quite particular. For example,
+**all code blocks must be indented by 3 spaces**.
+
+Sphinx autodoc
+--------------
+
+Most of the documentation for ``tupak`` should be written in the `docstrings
+<https://www.python.org/dev/peps/pep-0257/>`_ of the functions themselves. We
+can add these into the online documentation using `autodoc
+<http://www.sphinx-doc.org/en/master/ext/autodoc.html>`_. To add the documentation
+for a class, add a line such as::
+
+   .. autoclass:: tupak.likelihood.GravitationalWaveTransient
+       :members:
+
+into your documentation file. Similarly, to document a function::
+
+   .. autofunction:: tupak.sampler.run_sampler
+
+

setup.py

@@ -4,17 +4,24 @@ from distutils.core import setup
 import subprocess
 
 # Write a version file containing the git hash and info
-git_log = subprocess.check_output(['git', 'log', '-1', '--pretty=%h %ai']).decode('utf-8')
-git_diff = (subprocess.check_output(['git', 'diff', '.'])
-            + subprocess.check_output(['git', 'diff', '--cached', '.'])).decode('utf-8')
-if git_diff == '':
-    status = '(CLEAN) ' + git_log
-else:
-    status = '(UNCLEAN) ' + git_log
+try:
+    git_log = subprocess.check_output(
+        ['git', 'log', '-1', '--pretty=%h %ai']).decode('utf-8')
+    git_diff = (subprocess.check_output(['git', 'diff', '.'])
+                + subprocess.check_output(
+                    ['git', 'diff', '--cached', '.'])).decode('utf-8')
+    if git_diff == '':
+        status = '(CLEAN) ' + git_log
+    else:
+        status = '(UNCLEAN) ' + git_log
+except subprocess.CalledProcessError:
+    status = "NO VERSION INFORMATION"
+
 version_file = '.version'
 with open('tupak/' + version_file, 'w+') as f:
     f.write(status)
 
+
 setup(name='tupak',
       version='0.1',
       packages=['tupak'],

tupak/__init__.py

+"""
+tupak
+=====
+
+Tupak is The User friendly Parameter estimAtion Kode
+
+FILL IN THE REST
+
+"""
+
+
 from __future__ import print_function, division
 
 # import local files, utils should be imported first

tupak/detector.py

@@ -527,11 +527,16 @@ def get_empty_interferometer(name):
                              minimum_frequency=20, maximum_frequency=2048,
                              latitude=43 + 37. / 60 + 53.0921 / 3600, longitude=10 + 30. / 60 + 16.1878 / 3600,
                              elevation=51.884, xarm_azimuth=70.5674, yarm_azimuth=160.5674),
-        'GEO600': Interferometer(name='GEO600', power_spectral_density=PowerSpectralDensity(asd_file='GEO600_S6e_asd.txt'),
-                                 minimum_frequency=40, maximum_frequency=2048,
-                                 length=0.6, latitude=52 + 14. / 60 + 42.528 / 3600, longitude=9 + 48. / 60 + 25.894 / 3600,
-                                 elevation=114.425,
-                                 xarm_azimuth=115.9431, yarm_azimuth=21.6117)
+        'GEO600': Interferometer(name='GEO600',
+                                 power_spectral_density=PowerSpectralDensity(asd_file='GEO600_S6e_asd.txt'),
+                                 minimum_frequency=40, maximum_frequency=2048, length=0.6,
+                                 latitude=52 + 14. / 60 + 42.528 / 3600, longitude=9 + 48. / 60 + 25.894 / 3600,
+                                 elevation=114.425, xarm_azimuth=115.9431, yarm_azimuth=21.6117),
+        'CE': Interferometer(name='CE', power_spectral_density=PowerSpectralDensity('CE_psd.txt'),
+                             minimum_frequency=10, maximum_frequency=2048,
+                             length=40, latitude=46 + 27. / 60 + 18.528 / 3600,
+                             longitude=-(119 + 24. / 60 + 27.5657 / 3600), elevation=142.554, xarm_azimuth=125.9994,
+                             yarm_azimuth=215.994, xarm_tilt=-6.195e-4, yarm_tilt=1.25e-5),
     }
 
     if name in known_interferometers.keys():

tupak/result.py

@@ -39,7 +39,7 @@ class Result(dict):
     def __init__(self, dictionary=None):
         if type(dictionary) is dict:
             for key in dictionary:
-                setattr(self, key, dictionary[key])
+                setattr(self, key, self._decode_object(dictionary[key]))
 
     def __getattr__(self, name):
         try:
@@ -62,6 +62,22 @@ class Result(dict):
         else:
             return ''
 
+    def _decode_object(self, item):
+        """ When reading in data, ensure all bytes are decoded to strings """
+        try:
+            return item.decode()
+        except AttributeError:
+            pass
+
+        try:
+            return [i.decode() for i in item]
+        except (AttributeError, TypeError):
+            pass
+
+        logging.debug("Unable to decode item")
+        return item
+
+
     def get_result_dictionary(self):
         return dict(self)