Major documentation upgrade

spacetelescope · Jun 2, 2016 · e2a43de · e2a43de
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diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,7 @@ dist
 refstis.egg-info/
 refstis/anneal_info.db
 pipeline_data/config.yaml
+
+docs/_build/
+
+.DS_Store
diff --git a/README.md b/README.md
@@ -1,8 +1,22 @@
-Replacement pipeline for the STIS superdarks and superbiases
----
+STIS superdark and superbiase reference file creation routines
+--------------------------------------------------------------
 
-Build Status
-============
-[![Build Status](https://travis-ci.org/spacetelescope/refstis.svg?branch=master)](https://travis-ci.org/spacetelescope/refstis)
+Contribute
+----------
 
-[![Documentation Status](https://readthedocs.org/projects/refstis/badge/?version=latest)](http://refstis.readthedocs.io/en/latest/?badge=latest)
+This library primarily serves the internal needs of the STIS instrument team at
+STScI, and as such not all requested changes will be able to be accommodated.  
+Still, we'd love to know what issues and modifications are out there, so please
+don't be shy!
+
+For bugs, issues, suggestions, please use the github issue tracker.
+For code, please *fork* the repo, make your changes, and issue a pull request.
+
+Build Status and things
+-----------------------
+
+Travis-ci: [![Build Status](https://travis-ci.org/spacetelescope/refstis.svg?branch=master)](https://travis-ci.org/spacetelescope/refstis)
+
+Documentation: [![Documentation Status](https://readthedocs.org/projects/refstis/badge/?version=latest)](http://refstis.readthedocs.io/en/latest/?badge=latest)
+
+Conda install: [![Anaconda-Server Badge](https://anaconda.org/justincely/refstis/badges/installer/conda.svg)](https://conda.anaconda.org/justincely)
diff --git a/docs/STIS_logo.png b/docs/STIS_logo.png
diff --git a/docs/basedark.rst → docs/api/basedark.rst b/docs/basedark.rst → docs/api/basedark.rst
diff --git a/docs/basejoint.rst → docs/api/basejoint.rst b/docs/basejoint.rst → docs/api/basejoint.rst
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -0,0 +1,12 @@
+Api
+---
+
+.. toctree::
+  :maxdepth: 2
+
+  weekdark
+  basedark
+  weekbias
+  refbias
+  basejoint
+  pipeline
diff --git a/docs/pipeline.rst → docs/api/pipeline.rst b/docs/pipeline.rst → docs/api/pipeline.rst
diff --git a/docs/refbias.rst → docs/api/refbias.rst b/docs/refbias.rst → docs/api/refbias.rst
diff --git a/docs/weekbias.rst → docs/api/weekbias.rst b/docs/weekbias.rst → docs/api/weekbias.rst
diff --git a/docs/weekdark.rst → docs/api/weekdark.rst b/docs/weekdark.rst → docs/api/weekdark.rst
diff --git a/docs/command_line.rst b/docs/command_line.rst
@@ -0,0 +1,4 @@
+Command-line usage
+==================
+
+comming soon to documentation near you!
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,26 +3,53 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to refstis's documentation!
-===================================
 
-Contents:
+Refstis: Superdarks and Superbiases for STIS
+============================================
+
+Refstis is a collection of tasks and pipeline processes to create the superdark
+and superbias reference files for the Space Telescope Imaging Spectrograph (STIS)
+on board the Hubble Space Telescope (HST).
+
+.. image:: STIS_logo.png
+  :scale: 50 %
+  :alt: alternate text
+  :align: center
+
+.. note::
+
+  These routines, and particularly the pipeline, are designed to regularly create
+  and deliver the reference files that are applied in the MAST archive.  As such,
+  everything is geared particularly to the needs of the STIS instrument team at
+  STScI.
+
+Installation
+------------
+
+.. toctree::
+  :maxdepth: 2
+
+  installation
+
+Usage
+-----
 
 .. toctree::
    :maxdepth: 2
 
-  basedark
-  basejoint
-  refbias
-  weekbias
-  weekdark
-  pipeline
+   command_line
+   scripting
 
+Api
+---
+
+.. toctree::
+   :maxdepth: 2
+
+   api/index
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
-
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -0,0 +1,36 @@
+Installation Instructions
+=========================
+
+.. warning::
+
+  This package has a lingering dependency on an IRAF task that is accessed
+  through PyRAF.  IRAF/PyRAF can be obtained through
+  `Astroconda <http://astroconda.readthedocs.io/en/latest/>`_.  Though many
+  tasks will work without IRAF installed, some will fail under certain
+  circumstances.  This depencency will be removed in a future release as
+  resources permit.
+
+Install via Anaconda
+--------------------
+
+.. note::
+  If you do not have Anaconda, please follow the `instructions here
+  <https://www.continuum.io/downloads>`_ to install it, or scroll down for
+  manual installation of SpecViz.
+
+After you have anaconda setup, then you can install refstis by
+specifying the channel in your install command::
+
+    $ conda install --channel justincely refstis
+
+If you do not yet have IRAF or PyRAF installed, you can install them via the
+STScI supplied `AstroConda channel. <http://astroconda.readthedocs.io/>`_
+
+Install from source
+-------------------
+
+Refstis can also be installed manually using the source code::
+
+    $ git clone https://github.com/spacetelescope/refstis.git
+    $ cd refstis
+    $ python setup.py install
diff --git a/docs/scripting.rst b/docs/scripting.rst
@@ -0,0 +1,4 @@
+Examples in code
+================
+
+comming soon to documentation near you!
diff --git a/refstis/weekbias.py b/refstis/weekbias.py
@@ -30,7 +30,7 @@ def make_weekbias(input_list, refbias_name, basebias):
       Update ERR extension of new superbias by assigning the ERR values of the
       baseline superbias except for the new hot pixels that are updated from
       the weekly superbias, for which the error extension of the weekly
-      ssuperbias is taken. Put the result in temporary ERR image.
+      superbias is taken. Put the result in temporary ERR image.
 
     Parameters:
     -----------

diff --git a/setup.py b/setup.py
@@ -19,8 +19,7 @@
                    'Topic :: Scientific/Engineering :: Physics',
                    'Topic :: Software Development :: Libraries :: Python Modules'],
     scripts = glob.glob('scripts/*'),
-    install_requires = ['setuptools',
-                        'pyyaml',
+    install_requires = ['pyyaml',
                         'numpy>=1.10',
                         'astropy>=1.0.1',
                         'stistools>=1.0.2'],