Adding tests

docs/conf.py

@@ -183,3 +183,7 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping['astropy'] = ('http://astropy.readthedocs.io/en/latest/', None)
+intersphinx_mapping['astroquery'] = ('http://astroquery.readthedocs.io/en/latest/', None)
+intersphinx_mapping['matplotlib'] = ('https://matplotlib.org/contents.html', None)
+intersphinx_mapping['numpy'] = ('https://docs.scipy.org/doc/numpy/', None)

mrspoc/__init__.py

@@ -1,8 +1,13 @@
-# Licensed under the MIT License - see LICENSE.rst
-
 from __future__ import (absolute_import, division, print_function,
                         unicode_literals)
 
-from .star import *
-from .tgas import *
-from .gaia import *
+# Packages may add whatever they like to this file, but
+# should keep this content at the top.
+# ----------------------------------------------------------------------------
+from ._astropy_init import *
+# ----------------------------------------------------------------------------
+
+if not _ASTROPY_SETUP_:
+    from .star import *
+    from .tgas import *
+    from .gaia import *

mrspoc/conftest.py

@@ -0,0 +1,46 @@
+# this contains imports plugins that configure py.test for astropy tests.
+# by importing them here in conftest.py they are discoverable by py.test
+# no matter how it is invoked within the source tree.
+
+from astropy.tests.pytest_plugins import *
+
+## Uncomment the following line to treat all DeprecationWarnings as
+## exceptions. For Astropy v2.0 or later, there are 2 additional keywords,
+## as follow (although default should work for most cases).
+## To ignore some packages that produce deprecation warnings on import
+## (in addition to 'compiler', 'scipy', 'pygments', 'ipykernel', and
+## 'setuptools'), add:
+##     modules_to_ignore_on_import=['module_1', 'module_2']
+## To ignore some specific deprecation warning messages for Python version
+## MAJOR.MINOR or later, add:
+##     warnings_to_ignore_by_pyver={(MAJOR, MINOR): ['Message to ignore']}
+# enable_deprecations_as_exceptions()
+
+## Uncomment and customize the following lines to add/remove entries from
+## the list of packages for which version numbers are displayed when running
+## the tests. Making it pass for KeyError is essential in some cases when
+## the package uses other astropy affiliated packages.
+# try:
+#     PYTEST_HEADER_MODULES['Astropy'] = 'astropy'
+#     PYTEST_HEADER_MODULES['scikit-image'] = 'skimage'
+#     del PYTEST_HEADER_MODULES['h5py']
+# except (NameError, KeyError):  # NameError is needed to support Astropy < 1.0
+#     pass
+
+## Uncomment the following lines to display the version number of the
+## package rather than the version number of Astropy in the top line when
+## running the tests.
+# import os
+#
+## This is to figure out the package version, rather than
+## using Astropy's
+# try:
+#     from .version import version
+# except ImportError:
+#     version = 'dev'
+#
+# try:
+#     packagename = os.path.basename(os.path.dirname(__file__))
+#     TESTED_VERSIONS[packagename] = version
+# except NameError:   # Needed to support Astropy <= 1.0.0
+#     pass

mrspoc/star.py

@@ -6,7 +6,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from scipy.integrate import quad
-from matplotlib.patches import Circle
+from matplotlib.patches import Circle, Ellipse
 from matplotlib.collections import PatchCollection
 
 
@@ -90,7 +90,10 @@ def plot(self, ax=None, col=True, col_exaggerate=1):
 
         patches = []
         for spot in self.spots:
-            patches.append(Circle((spot.x, spot.y), spot.r))
+            longitude = np.arcsin(spot.x)
+            width = np.cos(longitude) * spot.r * 2
+            height = spot.r * 2
+            patches.append(Ellipse((spot.x, spot.y), width, height))
 
         p1 = PatchCollection([Circle((0, 0), 1)], alpha=1, color='w')
         p2 = PatchCollection(patches, alpha=(1-spot.contrast), color='k')
@@ -120,20 +123,61 @@ def center_of_light(self):
         y_centroid : float
             Photocenter in the y dimension, in units of stellar radii
         """
+        return self._centroid_analytic()
+
+    def _centroid_analytic(self):
+        """
+        Compute the stellar centroid using an analytic approximation.
+        """
         x_centroid = 0
         y_centroid = 0
+        total_flux = np.pi * self.r**2
 
         for spot in self.spots:
-            def _x_weight(x):
-                return - spot.contrast * 2 * x * np.sqrt(spot.r**2 - (x - spot.x)**2)
+            # spot_longitude = np.arcsin(spot.x)
+            # foreshortened_width = np.cos(spot_longitude)
+            # the above is equivalent to:
+            foreshortened_width = np.sqrt(1 - spot.x**2)
+
+            def _x_weighted(x):
+                return - spot.contrast * x * np.sqrt(spot.r**2 - (x - spot.x)**2 /
+                                                         foreshortened_width**2)
 
-            def _y_weight(y):
-                return - spot.contrast * 2 * y * np.sqrt(spot.r**2 - (y - spot.y)**2)
+            def _y_weighted(y):
+                return - spot.contrast * y * np.sqrt(spot.r**2 - (y - spot.y)**2)
 
-            x_i = quad(_x_weight, spot.x-spot.r, spot.x+spot.r)[0]
-            y_i = quad(_y_weight, spot.y-spot.r, spot.y+spot.r)[0]
+            b = spot.r * foreshortened_width
+            a = spot.r
+            total_flux -= (1 - spot.contrast) * np.pi * a * b
+
+            x_i = quad(_x_weighted, spot.x - spot.r*foreshortened_width,
+                       spot.x + spot.r*foreshortened_width)[0]
+            y_i = quad(_y_weighted, spot.y - spot.r, spot.y + spot.r)[0]
 
             x_centroid += x_i
             y_centroid += y_i
 
-        return x_centroid, y_centroid
+        return x_centroid / total_flux, y_centroid / total_flux
+
+    def _centroid_numerical(self, n=1000):
+        """
+        Compute the stellar centroid using a numerical approximation.
+        """
+        image = np.zeros((n, n))
+        x = np.linspace(-1, 1, n)
+        y = np.linspace(-1, 1, n)
+        x, y = np.meshgrid(x, y)
+
+        on_star = x**2 + y**2 <= 1
+        image[on_star] = 1
+
+        for spot in self.spots:
+            foreshortened_width = np.sqrt(1 - spot.x**2)
+
+            on_spot = ((x - spot.x)**2/foreshortened_width**2 +
+                       (y - spot.y)**2 <= spot.r**2)
+            image[on_spot & on_star] = spot.contrast
+
+        x_centroid = np.sum(image * x)/np.sum(image)
+        y_centroid = np.sum(image * y)/np.sum(image)
+        return x_centroid, y_centroid

mrspoc/tests/coveragerc

@@ -0,0 +1,31 @@
+[run]
+source = {packagename}
+omit =
+   {packagename}/_astropy_init*
+   {packagename}/conftest*
+   {packagename}/cython_version*
+   {packagename}/setup_package*
+   {packagename}/*/setup_package*
+   {packagename}/*/*/setup_package*
+   {packagename}/tests/*
+   {packagename}/*/tests/*
+   {packagename}/*/*/tests/*
+   {packagename}/version*
+
+[report]
+exclude_lines =
+   # Have to re-enable the standard pragma
+   pragma: no cover
+
+   # Don't complain about packages we have installed
+   except ImportError
+
+   # Don't complain if tests don't hit assertions
+   raise AssertionError
+   raise NotImplementedError
+
+   # Don't complain about script hooks
+   def main\(.*\):
+
+   # Ignore branches that don't pertain to this version of Python
+   pragma: py{ignore_python_version}

mrspoc/tests/setup_package.py

@@ -0,0 +1,8 @@
+# import os
+
+# If this package has tests data in the tests/data directory, add them to
+# the paths here, see commented example
+paths = [] #[os.path.join('data', '*fits')]
+
+def get_package_data():
+    return {'mrspoc.tests': paths}

mrspoc/tests/test_centroid.py

@@ -0,0 +1,18 @@
+import numpy as np
+
+from ..star import Star, Spot
+
+
+def test_col_methods():
+    """
+    python -c "from mrspoc.tests.test import test_col_methods as f; f()"
+    """
+
+    star = Star()
+    star.spots = [Spot(x=0.8, y=0.00, r=0.2)]
+
+    x0, y0 = star._centroid_analytic()
+    x1, y1 = star._centroid_numerical()
+
+    diff = np.sqrt((x0 - x1)**2 + (y0 - y1)**2)
+    assert diff < star.r / 100

mrspoc/tgas.py

@@ -135,7 +135,8 @@ def color_cut(b_minus_v):
                      color_cut(2) + 1, color_cut(2) - 1,
                      color_cut(0.6) - 1]
 
-        H, xedges, yedges = np.histogram2d(b_minus_v, M_V, bins=1000)
+        H, xedges, yedges = np.histogram2d(b_minus_v[abs(b_minus_v) > 1e-3],
+                                           M_V[abs(b_minus_v) > 1e-3], bins=1000)
 
         extent = [xedges.min(), xedges.max(), yedges.max(), yedges.min()]
         ax.imshow(np.log10(H.T), extent=extent, cmap=plt.cm.Greys, aspect=0.2)

setup.cfg

@@ -0,0 +1,57 @@
+[build_sphinx]
+source-dir = docs
+build-dir = docs/_build
+all_files = 1
+
+[build_docs]
+source-dir = docs
+build-dir = docs/_build
+all_files = 1
+
+[upload_docs]
+upload-dir = docs/_build/html
+show-response = 1
+
+[tool:pytest]
+minversion = 3.0
+norecursedirs = build docs/_build
+doctest_plus = enabled
+addopts = -p no:warnings
+
+[ah_bootstrap]
+auto_use = True
+
+[pycodestyle]
+# E101 - mix of tabs and spaces
+# W191 - use of tabs
+# W291 - trailing whitespace
+# W292 - no newline at end of file
+# W293 - trailing whitespace
+# W391 - blank line at end of file
+# E111 - 4 spaces per indentation level
+# E112 - 4 spaces per indentation level
+# E113 - 4 spaces per indentation level
+# E901 - SyntaxError or IndentationError
+# E902 - IOError
+select = E101,W191,W291,W292,W293,W391,E111,E112,E113,E901,E902
+exclude = extern,sphinx,*parsetab.py
+
+[metadata]
+package_name = mrspoc
+description = mrspoc
+long_description = 'M-dwarf Rotational Stellar Photocenter Offset Calculator'
+author = Brett Morris
+author_email = bmmorris@uw.edu
+license = MIT License
+url = https://github.com/bmorris3/mrspoc
+edit_on_github = True
+github_project = bmorris3/mrspoc
+# install_requires should be formatted as a comma-separated list, e.g.:
+# install_requires = astropy, scipy, matplotlib
+install_requires = numpy, astropy, matplotlib, scipy, sphinx-automodapi
+# version should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386)
+version = 0.0.dev0
+
+[entry_points]
+
+