Merge pull request #617 from mperrin/minor_fixes

misc minor fixes

docs/conf.py

@@ -60,13 +60,13 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    "sphinx.ext.mathjax",
     "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx.ext.todo",
     "sphinx.ext.inheritance_diagram",
     "sphinx.ext.viewcode",
     "sphinx.ext.autosummary",
-    "sphinx.ext.mathjax",
     "sphinx_automodapi.automodapi",
     "sphinx_issues",
     "nbsphinx",
@@ -76,10 +76,7 @@
 # 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']
+# The suffix of source filenames.
 source_suffix = ".rst"
 
 # The master toctree document.
@@ -90,7 +87,7 @@
 #
 # 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
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -104,20 +101,47 @@
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "sphinx"
+pygments_style = "default"
 
 
 # -- 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 = "stsci_rtd_theme"
-html_theme_path = [stsci_rtd_theme.get_html_theme_path()]
+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 = {}
+html_theme_options = {
+    "collapse_navigation": True,
+    "sticky_navigation": False,
+    # "nosidebar": "false",
+    # "sidebarbgcolor": "#4db8ff",
+    # "sidebartextcolor": "black",
+    # "sidebarlinkcolor": "black",
+    # "headbgcolor": "white",
+}
+
+html_logo = '_static/stsci_pri_combo_mark_white.png'
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+# html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = None
 
 # 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,
@@ -164,24 +188,17 @@
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
+# (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    (
-        master_doc,
-        "poppy.tex",
-        "poppy Documentation",
-        "Space Telescope Science Institute",
-        "manual",
-    ),
+    ("index", project + ".tex", project + " Documentation", author, "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, "poppy", "poppy Documentation", [author], 1)]
+man_pages = [("index", project.lower(), project + " Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------

poppy/instrument.py

@@ -324,6 +324,9 @@ def calc_datacube(self, wavelengths, progressbar=False, *args, **kwargs):
         else:
             raise ValueError("Maximum number of wavelengths exceeded. "
                              "Cannot be more than 10,000.")
+        # Handle astropy Quantities, if needed
+        if isinstance(wavelengths, units.Quantity):
+            wavelengths = wavelengths.to_value(units.meter)
 
         def wavelength_as_meters(wavelength):
             """helper function to avoid trying to put a Quantity into a FITS header """

poppy/poppy_core.py

@@ -225,7 +225,7 @@ def as_fits(self, what='intensity', includepadding=False, **kwargs):
         """ Return a wavefront as a pyFITS HDUList object
 
         Parameters
-        -----------
+        ----------
         what : string
             what kind of data to write. Must be one of 'all', 'parts', 'intensity',
             'phase' or 'complex'.  The default is to write intensity.
@@ -310,7 +310,7 @@ def writeto(self, filename, overwrite=True, **kwargs):
         """Write a wavefront to a FITS file.
 
         Parameters
-        -----------
+        ----------
         filename : string
             filename to use
         what : string
@@ -927,7 +927,7 @@ def invert(self, axis='both'):
         passes through a focus.
 
         Parameters
-        ------------
+        ----------
         axis : string
             either 'both', 'x', or 'y', for which axes to invert
 
@@ -1020,7 +1020,7 @@ def propagate_to(self, optic):
         wavefront accordingly.
 
         Parameters
-        -----------
+        ----------
         optic : OpticalElement
             The optic to propagate to. Used for determining the appropriate optical plane.
         """
@@ -1066,7 +1066,7 @@ def _propagate_fft(self, optic):
         """ Propagate from pupil to image or vice versa using a padded FFT
 
         Parameters
-        -----------
+        ----------
         optic : OpticalElement
             The optic to propagate to. Used for determining the appropriate optical plane.
 
@@ -1132,7 +1132,7 @@ def _propagate_mft(self, det):
         """ Compute from pupil to an image using the Soummer et al. 2007 MFT algorithm
 
         Parameters
-        -----------
+        ----------
         det : OpticalElement, must be of type DETECTOR
             The target optical plane to propagate to."""
 
@@ -1484,7 +1484,7 @@ def add_rotation(self, angle=0.0, index=None, *args, **kwargs):
         Add a clockwise or counterclockwise rotation around the optical axis
 
         Parameters
-        -----------
+        ----------
         angle : float
             Rotation angle, counterclockwise. By default in degrees.
         index : int
@@ -1505,7 +1505,7 @@ def add_inversion(self, index=None, *args, **kwargs):
         a flip in the sign of the X and Y axes due to passage through a focus.
 
         Parameters
-        -----------
+        ----------
         index : int
             Index into the optical system's planes for where to add the new optic. Defaults to
             appending the optic to the end of the plane list.
@@ -3324,7 +3324,7 @@ class CoordinateInversion(CoordinateTransform):
     The actual inversion happens in Wavefront.propagate_to
 
     Parameters
-    ------------
+    ----------
     axes : string
         either 'both', 'x', or 'y', for which axes to invert
     hide : bool

poppy/utils.py

@@ -586,7 +586,7 @@ def radial_profile(hdulist_or_filename=None, ext=0, ee=False, center=None, stdde
         the minimum in each radial bin.
 
     Returns
-    --------
+    -------
     results : tuple
         Tuple containing (radius, profile) or (radius, profile, EE) depending on what is requested.
         The radius gives the center radius of each bin, while the EE is given inside the whole bin
@@ -754,7 +754,7 @@ def measure_ee(hdulist_or_filename=None, ext=0, center=None, binsize=None, norma
         Default is no normalization (i.e. retain whatever normalization was used in computing the PSF itself)
 
     Returns
-    --------
+    -------
     encircled_energy: function
         A function which will return the encircled energy interpolated to any desired radius.
 
@@ -800,7 +800,7 @@ def measure_radius_at_ee(hdulist_or_filename=None, ext=0, center=None, binsize=N
         Default is no normalization (i.e. retain whatever normalization was used in computing the PSF itself)
 
     Returns
-    --------
+    -------
     radius: function
         A function which will return the radius of a desired encircled energy.
 
@@ -841,7 +841,7 @@ def measure_radial(hdulist_or_filename=None, ext=0, center=None, binsize=None):
         size of step for profile. Default is pixel size.
 
     Returns
-    --------
+    -------
     radial_profile: function
         A function which will return the mean PSF value at any desired radius.
 
@@ -1175,7 +1175,7 @@ def pad_to_size(array, padded_shape):
 
 
     See Also
-    ---------
+    --------
     pad_to_oversample, pad_or_crop_to_shape
     """
     if len(padded_shape) < 2:
@@ -1496,7 +1496,7 @@ def spectrum_from_spectral_type(sptype, return_list=False, catalog=None):
     convenient access function.
 
     Parameters
-    -----------
+    ----------
     sptype : str
         Spectral type, like "G0V"
     catalog : str