Merge pull request #532 from robelgeda/docs

Doc Cleanup

docs/_static/specutils.css

@@ -0,0 +1,15 @@
+@import url("bootstrap-astropy.css");
+
+div.topbar a.brand {
+  background: transparent url("logo_icon.png") no-repeat 8px 3px;
+  background-image: url("logo_icon.png"), none;
+  background-size: 32px 32px;
+}
+
+#logotext1 {
+  color: #667C8A;
+}
+
+#logotext2 {
+  color: #F09156;
+}

docs/conf.py

@@ -117,7 +117,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes. To override the custom theme, set this to the
 # name of a builtin theme or the name of a custom theme in html_theme_path.
-#html_theme = None
+html_static_path = ['_static']
+html_style = 'specutils.css'
 
 # Please update these texts to match the name of your package.
 html_theme_options = {
@@ -133,12 +134,12 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = ''
+# html_logo = ''
 
 # 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 = ''
+html_favicon = 'img/logo_icon.svg'
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.

docs/nitpick-exceptions

@@ -1,4 +1,6 @@
 # Temporary exception of inherited astropy classes
 py:class astropy.nddata.mixins.ndio.NDIOMixin
 py:class astropy.nddata.mixins.ndslicing.NDSlicingMixin
-py:class astropy.nddata.mixins.ndarithmetic.NDArithmeticMixin
+py:class astropy.nddata.mixins.ndarithmetic.NDArithmeticMixin
+py:obj NDData
+py:obj NDUncertainty

docs/spectral_regions.rst

@@ -99,11 +99,9 @@ One can also delete a sub-region:
 
     >>> del sr[1]
     >>> sr #doctest:+SKIP
-    [(<Quantity 0.15 um>, <Quantity 0.2 um>),
-     (<Quantity 0.45 um>, <Quantity 0.6 um>),
-     (<Quantity 0.8 um>, <Quantity 0.9 um>),
-     (<Quantity 1. um>, <Quantity 1.2 um>),
-     (<Quantity 1.3 um>, <Quantity 1.5 um>)]
+    Spectral Region, 5 sub-regions:
+    (0.15 um, 0.2 um)   (0.45 um, 0.6 um)   (0.8 um, 0.9 um)
+    (1.0 um, 1.2 um)    (1.3 um, 1.5 um)
 
 There is also the ability to iterate:
 
@@ -118,12 +116,12 @@ There is also the ability to iterate:
 
     >>> for s in sr:
     ...     print(s.lower) #doctest:+SKIP
-    SpectralRegion: 0.15 um - 0.2 um
-    SpectralRegion: 0.3 um - 0.4 um
-    SpectralRegion: 0.45 um - 0.6 um
-    SpectralRegion: 0.8 um - 0.9 um
-    SpectralRegion: 1.0 um - 1.2 um
-    SpectralRegion: 1.3 um - 1.5 um
+    0.15 um
+    0.3 um
+    0.45 um
+    0.8 um
+    1.0 um
+    1.3 um
 
 
 And, lastly, there is the ability to invert a `~specutils.SpectralRegion` given a
@@ -142,8 +140,10 @@ defines the baseline/noise regions:
 
     >>> sr_inverted = sr.invert(0.05*u.um, 3*u.um)
     >>> sr_inverted #doctest:+SKIP
-    SpectralRegion: 0.05 um - 0.15 um, 0.2 um - 0.3 um, 0.4 um - 0.45 um, 0.6 um - 0.8 um, 0.9 um - 1.0 um, 1.2 um - 1 .3 um, 1.5 um - 3.0 um
-
+    Spectral Region, 7 sub-regions:
+    (0.05 um, 0.15 um)   (0.2 um, 0.3 um)     (0.4 um, 0.45 um)
+    (0.6 um, 0.8 um)     (0.9 um, 1.0 um)     (1.2 um, 1.3 um)
+    (1.5 um, 3.0 um)
 
 Region Extraction
 -----------------

docs/spectrum1d.rst

@@ -97,7 +97,7 @@ Providing a FITS-style WCS
     >>> import numpy as np
     >>> my_wcs = fitswcs.WCS(header={'CDELT1': 1, 'CRVAL1': 6562.8, 'CUNIT1': 'Angstrom', 'CTYPE1': 'WAVE', 'RESTFRQ': 1400000000, 'CRPIX1': 25})
     >>> spec = Spectrum1D(flux=[5,6,7] * u.Jy, wcs=my_wcs)
-    >>> spec.wavelength #doctest:+SKIP
+    >>> spec.spectral_axis #doctest:+SKIP
     <Quantity [ 6538.8, 6539.8, 6540.8] Angstrom>
     >>> spec.wcs.pixel_to_world(np.arange(3)) #doctest:+SKIP
     array([6.5388e-07, 6.5398e-07, 6.5408e-07])
@@ -126,8 +126,8 @@ common spectral axis.
 
     >>> spec = Spectrum1D(spectral_axis=np.arange(5000, 5010)*u.AA, flux=np.random.sample((5, 10))*u.Jy)
     >>> spec_slice = spec[0] #doctest:+SKIP
-    >>> spec_slice.wavelength #doctest:+SKIP
-    <Quantity [0., 1., 2., 3., 4., 5., 6., 7., 8., 9.] Angstrom>
+    >>> spec_slice.spectral_axis #doctest:+SKIP
+    <Quantity [5000., 5001., 5002., 5003., 5004., 5005., 5006., 5007., 5008., 5009.] Angstrom>
     >>> spec_slice.flux #doctest:+SKIP
     <Quantity [0.72722821, 0.32147784, 0.70256482, 0.04445197, 0.03390352,
            0.50835299, 0.87581725, 0.50270413, 0.08556376, 0.53713355] Jy>
@@ -143,6 +143,7 @@ Reference/API
 
 .. automodapi:: specutils
     :no-main-docstr:
+    :inherited-members:
     :no-heading:
     :headings: -~
 

docs/spectrum_collection.rst

@@ -36,9 +36,9 @@ solution.
     (5,)
     >>> spec_coll.flux.unit
     Unit("Jy")
-    >>> spec_coll.wavelength.shape
+    >>> spec_coll.spectral_axis.shape
     (5, 10)
-    >>> spec_coll.wavelength.unit
+    >>> spec_coll.spectral_axis.unit
     Unit("Angstrom")
 
 Collections from 1D spectra
@@ -65,9 +65,9 @@ a list of :class:`~specutils.Spectrum1D`:
     (2,)
     >>> spec_coll.flux.unit
     Unit("Jy")
-    >>> spec_coll.wavelength.shape
+    >>> spec_coll.spectral_axis.shape
     (2, 50)
-    >>> spec_coll.wavelength.unit
+    >>> spec_coll.spectral_axis.unit
     Unit("Angstrom")
 
 :class:`~specutils.SpectrumCollection` objects can be treated just like

specutils/spectra/spectrum_mixin.py

@@ -49,6 +49,9 @@ def _data_with_spectral_axis_first(self):
 
     @property
     def spectral_wcs(self):
+        """
+        Returns the spectral axes of the WCS
+        """
         return self.wcs.axes.spectral
 
     @lazyproperty
@@ -130,6 +133,9 @@ def new_flux_unit(self, unit, equivalencies=None, suppress_conversion=False):
 
     @property
     def velocity_convention(self):
+        """
+        Returns the velocity convention
+        """
         return self._velocity_convention
 
     def with_velocity_convention(self, velocity_convention):