Merge pull request #231 from migueldvb/docs

Updating documentation

README.rst

@@ -4,10 +4,10 @@
     :alt: sbpy	     
 
 
-sbpy is an `Astropy <http://www.astropy.org/>`_ affiliated package for small-body
+sbpy is an `Astropy <https://www.astropy.org/>`_ affiliated package for small-body
 planetary astronomy.
 
-.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
+.. image:: https://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
     :target: http://www.astropy.org
     :alt: Powered by Astropy Badge
 
@@ -16,10 +16,10 @@ planetary astronomy.
     :alt: Travis-CI status
 
 .. image:: https://readthedocs.org/projects/sbpy/badge/?version=latest
-    :target: http://sbpy.readthedocs.io/en/latest/?badge=latest
+    :target: https://sbpy.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation status
 
-.. image:: http://joss.theoj.org/papers/10.21105/joss.01426/status.svg
+.. image:: https://joss.theoj.org/papers/10.21105/joss.01426/status.svg
     :target: https://doi.org/10.21105/joss.01426
     :alt: JOSS documentation
 
@@ -51,7 +51,7 @@ For details on the installation process, please refer to the `detailed installat
 Documentation
 -------------
 
-The official documentation and API reference is available `here <http://sbpy.readthedocs.io/en/latest/>`_.
+The official documentation and API reference is available `here <https://sbpy.readthedocs.io/en/latest/>`_.
 
 Status
 ------
@@ -66,4 +66,4 @@ Acknowledgements
 
 If you use `sbpy` in your work, please acknowledge it by citing
 
-    `Mommert, Kelley, de-Val Borro, Li et al., (2019). sbpy: A Python module for small-body planetary astronomy. Journal of Open Source Software, 4(38), 1426 <http://joss.theoj.org/papers/8b8e7bb15fb4a14f80f2afd06b6ce060>`_
+    `Mommert, Kelley, de-Val Borro, Li et al., (2019). sbpy: A Python module for small-body planetary astronomy. Journal of Open Source Software, 4(38), 1426 <https://joss.theoj.org/papers/8b8e7bb15fb4a14f80f2afd06b6ce060>`_

ah_bootstrap.py

@@ -150,7 +150,7 @@
 
 
 # What follows are several import statements meant to deal with install-time
-# issues with either missing or misbehaving pacakges (including making sure
+# issues with either missing or misbehaving packages (including making sure
 # setuptools itself is installed):
 
 # Check that setuptools 30.3 or later is present

docs/about.rst

@@ -151,7 +151,7 @@ derived with methods in `~sbpy.shape`. We also include the most
 commonly used 5-parameter version of the Hapke scattering
 model. Empirical cometary dust phase functions are implemented, too
 (Marcus 2007; Schleicher & Bair 2011,
-http://asteroid.lowell.edu/comet/dustphase.html).  Some
+https://asteroid.lowell.edu/comet/dustphase.html).  Some
 single-scattering phase functions such as the Henyey-Greenstein
 function will also be implemented.
 
@@ -395,18 +395,18 @@ methods.
 
 
 
-.. _JPL Horizons: http://ssd.jpl.nasa.gov/horizons.cgi
-.. _Minor Planet Center: http://minorplanetcenter.net/
-.. _IMCCE: http://vo.imcce.fr/webservices/miriade
-.. _Lowell Observatory: http://asteroid.lowell.edu
-.. _PyEphem: http://rhodesmill.org/pyephem
-.. _REBOUND: http://github.com/hannorein/rebound
-.. _OpenOrb: http://github.com/oorb/oorb
-.. _SpiceyPy: http://github.com/AndrewAnnex/SpiceyPy
-.. _web-API: http://minorplanetcenter.net/search_db
+.. _JPL Horizons: https://ssd.jpl.nasa.gov/horizons.cgi
+.. _Minor Planet Center: https://minorplanetcenter.net/
+.. _IMCCE: http://vo.imcce.fr/webservices/miriade/
+.. _Lowell Observatory: https://asteroid.lowell.edu
+.. _PyEphem: https://rhodesmill.org/pyephem
+.. _REBOUND: https://github.com/hannorein/rebound
+.. _OpenOrb: https://github.com/oorb/oorb
+.. _SpiceyPy: https://github.com/AndrewAnnex/SpiceyPy
+.. _web-API: https://minorplanetcenter.net/search_db
 .. _Solar System Object Image Search function of the Canadian Astronomy Data Centre: http://goo.gl/2aGYsW
-.. _skybot: http://vo.imcce.fr/webservices/skybot
-.. _small bodies data ferret: http://sbntools.psi.edu/ferret
-.. _github wiki: http://github.com/mommermi/sbpy/wiki
-.. _Ginga Image Viewer: http://ejeschke.github.io/ginga/
+.. _skybot: http://vo.imcce.fr/webservices/skybot/
+.. _small bodies data ferret: https://sbnapps.psi.edu/ferret
+.. _github wiki: https://github.com/mommermi/sbpy/wiki
+.. _Ginga Image Viewer: https://ejeschke.github.io/ginga/
 .. _photutils: https://github.com/astropy/photutils

docs/index.rst

@@ -24,19 +24,19 @@ in 2021.
 Current Status
 **************
 
-.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
-    :target: http://www.astropy.org
+.. image:: https://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
+    :target: https://www.astropy.org
     :alt: Powered by Astropy Badge
 
 .. image:: https://readthedocs.org/projects/sbpy/badge/?version=latest
-    :target: http://sbpy.readthedocs.io/en/latest/?badge=latest
+    :target: https://sbpy.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation status
 
-.. image:: http://joss.theoj.org/papers/10.21105/joss.01426/status.svg
+.. image:: https://joss.theoj.org/papers/10.21105/joss.01426/status.svg
     :target: https://doi.org/10.21105/joss.01426
     :alt: JOSS documentation
 
-.. image:: https://travis-ci.org/NASA-Planetary-Science/sbpy.svg?branch=master
+.. image:: https://api.travis-ci.org/NASA-Planetary-Science/sbpy.svg?branch=master
     :target: https://travis-ci.org/NASA-Planetary-Science/sbpy
     :alt: Travis-CI status
 
@@ -138,7 +138,7 @@ Acknowledgments
 
 If you use `sbpy` in your work, please acknowledge it by citing
 
-    `Mommert, Kelley, de-Val Borro, Li et al., (2019). sbpy: A Python module for small-body planetary astronomy. Journal of Open Source Software, 4(38), 1426 <http://joss.theoj.org/papers/8b8e7bb15fb4a14f80f2afd06b6ce060>`_
+    `Mommert, Kelley, de-Val Borro, Li et al., (2019). sbpy: A Python module for small-body planetary astronomy. Journal of Open Source Software, 4(38), 1426 <https://joss.theoj.org/papers/8b8e7bb15fb4a14f80f2afd06b6ce060>`_
 
 and also please consider using the `~sbpy.bib` reference tracking
 system to properly acknowledge and reference the methods you used in

docs/sbpy/activity/gas.rst

@@ -91,12 +91,12 @@ The gas coma models work with sbpy's apertures:
 Production Rate calculations
 ----------------------------
 
-`~sbpy.activity.gas.productionrate` offers various functions that aid in the calculation
-of production rates. `~sbpy.data.phys` has a function called `~sbpy.data.Phys.from_jplspec`
+Various functions that aid in the calculation of production rates are offered.
+`~sbpy.data.Phys` has a function called `~sbpy.data.Phys.from_jplspec`
 which takes care of querying the JPL Molecular Spectral Catalog through the use of
 `~astroquery.jplspec` and calculates all the necessary constants needed for
 production rate calculations in this module. Yet, the option for the user to
-provide their own molecular data is possible through the use of an `~sbpy.data.phys`
+provide their own molecular data is possible through the use of an `~sbpy.data.Phys`
 object, as long as it has the required information. It is imperative to read
 the documentation of the functions in this section to understand what is needed
 for each. If the user does not have the necessary data, they can build an object
@@ -132,8 +132,8 @@ at 300 K for a molecule. Yet, in order to calculate production rate, we need
 to know the integrated line intensity at a given temperature. This function
 takes care of converting the integrated line intensity at 300 K to its equivalent
 in the desired temperature using equations provided by the JPLSpec documentation.
-For more information on the needed parameters for this function follow the link
-for `~sbpy.activity.intensity_conversion` under Reference/API section.
+For more information on the needed parameters for this function see
+`~sbpy.activity.intensity_conversion`.
 
 .. doctest-skip::
 
@@ -161,8 +161,7 @@ allowed to provide their own Einstein Coefficient if they want. If the user
 does want to provide their own Einstein Coefficient, they may do so simply
 by appending their value with the unit 1/s to the `~sbpy.data.Phys` object, called
 `mol_data` in these examples. For more information on the needed parameters
-for this function follow the link for `~sbpy.activity.einstein_coeff`
-under Reference/API section.
+for this function see `~sbpy.activity.einstein_coeff`.
 
 .. doctest-skip::
 
@@ -178,17 +177,16 @@ Beta Factor Calculation
 ^^^^^^^^^^^^^^^^^^^^^^^
 
 Returns beta factor based on timescales from `~sbpy.activity.gas` and distance
-from the Sun using an `~sbpy.data.ephem` object. The calculation is
+from the Sun using an `~sbpy.data.Ephem` object. The calculation is
 parent photodissociation timescale * (distance from comet to Sun)**2
 and it accounts for certain photodissociation and geometric factors needed
-in the calculation of total number of molecules `~sbpy.activity.total_number_nocd`
+in the calculation of total number of molecules `~sbpy.activity.total_number`
 If you wish to provide your own beta factor, you can calculate the equation
 expressed in units of AU**2 * s , all that is needed is the timescale
 of the molecule and the distance of the comet from the Sun. Once you
-have the beta factor you can append it to your mol_data phys object
+have the beta factor you can append it to your `mol_data` phys object
 with the name 'beta' or any of its alternative names. For more information on
-the needed parameters for this function follow the link for
-`~sbpy.activity.beta_factor` under Reference/API section.
+the needed parameters for this function see `~sbpy.activity.beta_factor`.
 
 .. doctest-skip::
 
@@ -219,9 +217,8 @@ One of the models followed by this module is based on the following paper:
 The following example shows the usage of the function. This LTE model does not
 include photodissociation, but it does serve as way to obtain educated
 first guesses for other models within sbpy. For more information on the
-parameters that are needed for the function follow
-the link for the function `from_Drahus` in `~sbpy.activity.LTE`
-under Reference/API section.
+parameters that are needed for the function see
+`~sbpy.activity.LTE.from_Drahus`.
 
 .. doctest-skip::
 
@@ -238,7 +235,7 @@ LTE Column Density Calculation
 
 To calculate a column density with no previous column density information,
 we can use equation 10 from `Bockelee-Morvan et al. 2004
-<https://ui.adsabs.harvard.edu/#abs/2004come.book..391B>`. This function is
+<https://ui.adsabs.harvard.edu/abs/2004come.book..391B>`_. This function is
 very useful to obtain a column density with no previous guess for it,
 and also useful to provide a first guess for the more involved Non-LTE model
 for column density explained in the next section.
@@ -253,32 +250,31 @@ Non-LTE Column Density Calculation
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Once the user has a guess for their column density, the user can then
-implement the `sbpy.activity` NonLTE function `from_pyradex`. This function
-calculates the best fitting column density for the integrated flux data using
-the python wrapper pyradex of the Non-LTE iterative code RADEX.
+implement the `sbpy.activity` NonLTE function `sbpy.activity.NonLTE.from_pyradex`.
+This function calculates the best fitting column density for the integrated
+flux data using the python wrapper pyradex of the Non-LTE iterative code RADEX.
 The code utilizes the LAMDA catalog collection of molecular data files,
 presently this is the only functionality available, yet in the future a function
 will be provided by `sbpy` to build your own molecular data file from JPLSpec
 for use in this function. The code will look for a 'cdensity' column value
 within `mol_data` to use as its first guess. For a more detailed look at the
-input parameters and defaults, search for `from_pyradex` in
-`~sbpy.activity.NonLTE` under the Reference/API section.
+input parameters, please see `~sbpy.activity.NonLTE.from_pyradex`.
 
 .. doctest-skip::
 
-    >>> from sbpy.activty import NonLTE
+    >>> from sbpy.activity import NonLTE
     >>> nonlte = NonLTE()
     >>> cdensity = nonlte.from_pyradex(integrated_flux,  mol_data, iter=500)
     >>> mol_data.apply([cdensity.value] * cdensity.unit, name='cdensity')
 
 Note that for this calculation the installation of `pyradex` is needed. Pyradex
-is a python wrapper for the RADEX fortran code. See `here
-<https://github.com/keflavich/pyradex/blob/master/INSTALL.rstB>` and
-`here <https://github.com/keflavich/pyradex>` for installation instruction and
-tips as well as a briefing of how pyradex works and what common errors
-might arise. You need to make sure you have a fortran compiler installed
-in order for pyradex to work (gfortran works and can be installed with
-homebrew for easier management).
+is a python wrapper for the RADEX fortran code. See `pyradex installation
+<https://github.com/keflavich/pyradex/blob/master/INSTALL.rst>`_ and
+`README file <https://github.com/keflavich/pyradex/blob/master/README.rst>`_
+for installation instruction and tips as well as a briefing of how pyradex
+works and what common errors might arise. You need to make sure you have a
+fortran compiler installed in order for pyradex to work (gfortran works and can
+be installed with homebrew for easier management).
 
 Total Number
 ^^^^^^^^^^^^
@@ -291,10 +287,9 @@ in equation 1.3 from:
     | coma in comets. PhD Thesis, Georg-August-Universität Göttingen.
 
 If the user prefers to give the total number, they may do so by appending
-to the mol_data `~sbpy.data.phys` object with the name `total_number_nocd` or
+to the mol_data `~sbpy.data.Phys` object with the name `total_number` or
 any of its alternative names. For more information on the needed parameters
-for this function follow the link for `~sbpy.activity.total_number_nocd`
-under Reference/API section.
+for this function see `~sbpy.activity.total_number`.
 
 .. doctest-skip::
 
@@ -324,9 +319,8 @@ module found in `~sbpy.activity.gas` to find a ratio between the model
 total number of molecules and the number of molecules calculated from the data
 to scale the model Q and output the new production rate from the result. This
 LTE model does account for the effects of photolysis. For more information
-on the parameters that are needed for the function follow
-the link for the function `from_Haser` in `~sbpy.activity.LTE`
-under Reference/API section.
+on the parameters that are needed for the function see
+`~sbpy.activity.LTE.from_Haser`.
 
 .. doctest-skip::
 

docs/sbpy/activity/index.rst

@@ -4,7 +4,7 @@ Activity Module (`sbpy.activity`)
 Introduction
 ------------
 
-`sbpy.activity` models cometary dust and gas activity.  It is separated into two main sub-modules: :doc:`dust` and :doc:`gas`.  The base module itself defines photmetric apertures that may be useful for observations of comets.
+`sbpy.activity` models cometary dust and gas activity.  It is separated into two main sub-modules: :doc:`dust` and :doc:`gas`.  The base module itself defines photometric apertures that may be useful for observations of comets.
 
 .. toctree::
    :maxdepth: 2

docs/sbpy/bib.rst

@@ -100,7 +100,7 @@ BibTeX (`~sbpy.bib.to_bibtex`)
             month = Sep,
               eid = {25.04},
             pages = {25.04},
-           adsurl = {https://ui.adsabs.harvard.edu/#abs/1996DPS....28.2504G},
+           adsurl = {https://ui.adsabs.harvard.edu/abs/1996DPS....28.2504G},
           adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
 
@@ -140,7 +140,7 @@ journal rules, can be readily implemented.
 Filtering
 ---------
 
-The aformentioned output functions enable the filtering of references
+The aforementioned output functions enable the filtering of references
 based on their relevance. For instance, in the examples show above,
 the relevance is ``data source``. In order to properly use filter,
 only select keywords can be used a relevance: allowed is any string

docs/sbpy/calib.rst

@@ -224,8 +224,9 @@ Solar spectra in Sun objects can be plotted at the native resolution of the data
   >>> fluxd_binned = sun.observe(wave_binned, unit='W / (m2 um)')
   >>> # Plot
   >>> plt.plot(sun.wave.to('um'), sun.fluxd.to('W/(m2 um)'),
-  ...          ls='steps-mid', color='#1f77b4', label='Native resolution')
-  >>> plt.plot(wave_binned, fluxd_binned, ls='steps-mid',
+  ...          drawstyle='steps-mid', color='#1f77b4',
+  ...          label='Native resolution')
+  >>> plt.plot(wave_binned, fluxd_binned, drawstyle='steps-mid',
   ...          color='#ff7f0e', label='R~25')
   >>> plt.setp(plt.gca(), xlim=wrange, xlabel='Wavelength (μm)',
   ...          ylabel='Flux density (W/(m2 μm)')
@@ -244,8 +245,8 @@ Solar spectra in Sun objects can be plotted at the native resolution of the data
   wave_binned = wrange[0] * d**np.arange(n) * u.um
   sun = Sun.from_default()
   fluxd_binned = sun.observe(wave_binned, unit='W / (m2 um)')
-  plt.plot(sun.wave.to('um'), sun.fluxd.to('W/(m2 um)'), ls='steps-mid', color='#1f77b4', label='Native resolution')
-  plt.plot(wave_binned, fluxd_binned, ls='steps-mid', color='#ff7f0e', label='R~25')
+  plt.plot(sun.wave.to('um'), sun.fluxd.to('W/(m2 um)'), drawstyle='steps-mid', color='#1f77b4', label='Native resolution')
+  plt.plot(wave_binned, fluxd_binned, drawstyle='steps-mid', color='#ff7f0e', label='R~25')
   plt.setp(plt.gca(), xlim=wrange, xlabel='Wavelength (μm)', ylabel='Flux density (W/(m2 μm)')
   plt.legend()
   plt.tight_layout()

docs/sbpy/data/dataclass.rst

@@ -31,7 +31,7 @@ unstructured meta data.
 
 The user is free to add any fields they want to a
 `~sbpy.data.DataClass` object. However, in order to enable the
-seemless use of `sbpy` functions and methods, we require the user to
+seamless use of `sbpy` functions and methods, we require the user to
 pick among a few common field names for different properties as listed
 :ref:`here <field name list>`. `~sbpy.data.DataClass` objects
 are able to identify alternative field names as listed in this
@@ -428,7 +428,7 @@ The same result can be achieved using the following syntax:
     10.243452 -12.40435  2451523.8525      R       R
      10.25546  -12.3946 2451523.94653      i       i
 
-Similarly, exisiting columns can be modified using:
+Similarly, existing columns can be modified using:
 
     >>> obs['filter'] = ['g', 'i', 'R', 'V']  # doctest: +SKIP
 

docs/sbpy/data/ephem.rst

@@ -117,7 +117,7 @@ option should be less than a few hundred to prevent corruption of the
 query (see `~astroquery.jplhorizons.HorizonsClass.ephemerides` for
 details).
 
-Observer locations can be defined as strings using offical `IAU
+Observer locations can be defined as strings using official `IAU
 observatory codes
 <https://www.minorplanetcenter.net/iau/lists/ObsCodesF.html>`__ or
 using `~astropy.coordinates.EarthLocation` as shown in the following

docs/sbpy/spectroscopy/sources.rst

@@ -41,7 +41,7 @@ Observe the source through a low-resolution spectrometer:
   >>> wave = np.logspace(0.5, 1.5, 100) * u.um
   >>> fluxd = B.observe(wave, unit='MJy')
   >>>
-  >>> plt.plot(wave, fluxd, ls='steps-mid', label=str(B.T))
+  >>> plt.plot(wave, fluxd, drawstyle='steps-mid', label=str(B.T))
   ...     # doctest: +IGNORE_OUTPUT
   >>> plt.setp(plt.gca(), xlabel='Wavelength (μm)', ylabel='$F_ν$ (MJy)')
   ...     # doctest: +IGNORE_OUTPUT
@@ -57,7 +57,7 @@ Observe the source through a low-resolution spectrometer:
    wave = np.logspace(0.5, 1.5, 100) * u.um
    fluxd = B.observe(wave, unit='MJy')
 
-   plt.plot(wave, fluxd, ls='steps-mid', label=str(B.T))
+   plt.plot(wave, fluxd, drawstyle='steps-mid', label=str(B.T))
    plt.setp(plt.gca(), xlabel='Wavelength (μm)', ylabel='$F_ν$ (MJy)')