DOC: Fix readthedocs build (#419)

readthedocs was broken by directory restructuring and because the
environment spec was deleted. Also moving renaming the bibtex
files so the citations are picked up on the first try.

doc/source/conf.py

@@ -19,7 +19,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath('../../source'))
 
 # -- General configuration ------------------------------------------------
 
@@ -77,9 +77,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = open(os.path.join('..', '..', 'VERSION')).read().strip()
+# version = open(os.path.join('..', '..', 'VERSION')).read().strip()
 # The full version, including alpha/beta/rc tags.
-release = version
+# release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -301,4 +301,3 @@
 
 # http://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autodoc_mock_imports
 autodoc_mock_imports = "numpy scipy matplotlib tifffile pywt skimage DM3lib pyfftw numexpr concurrent libtomopy".split()
-

doc/source/credits.rst

@@ -4,25 +4,25 @@ Credits
 
 We kindly request that you cite the following article(s) :cite:`Gursoy:14a` if
 you use TomoPy (and also cite :cite:`Pelt:16a` if you use ASTRA or
-:cite:`Vogelgesang:12` if you use UFO). For vector reconstructions please 
+:cite:`Vogelgesang:12` if you use UFO). For vector reconstructions please
 additionally cite :cite:`Hierro-Rodriguez:18`.
 
-.. bibliography:: bibtex/cite.bib
+.. bibliography:: bibtex/zcite.bib
    :style: unsrt
    :labelprefix: A
 
 Applications
 ============
 
-.. bibliography:: bibtex/app.bib
+.. bibliography:: bibtex/zapp.bib
    :style: plain
    :labelprefix: B
    :all:
 
 References
 ==========
 
-.. bibliography:: bibtex/ref.bib
+.. bibliography:: bibtex/zref.bib
    :style: plain
    :labelprefix: C
    :all:

doc/source/gpu.rst

@@ -39,7 +39,7 @@ a factor of 90 degrees:
 
 .. code-block:: python
 
-        obj = tomopy.misc.phantom("shepp2d")
+        obj = tomopy.shepp2d()
         obj = tomopy.misc.morph.pad(obj, axis=1, mode='constant')
         obj = tomopy.misc.morph.pad(obj, axis=2, mode='constant')
 

envs/requirements-doc.txt

@@ -0,0 +1,6 @@
+sphinx
+sphinx_rtd_theme
+sphinxcontrib-bibtex
+nbsphinx
+pandoc
+jupyter

source/tomopy/misc/morph.py

@@ -85,10 +85,10 @@ def pad(arr, axis, npad=None, mode='constant', ncore=None, **kwargs):
     ----------
     arr : ndarray
         Input array.
+    axis : int
+        Axis along which padding will be performed.
     npad : int, optional
         New dimension after padding.
-    axis : int, optional
-        Axis along which padding will be performed.
     mode : str or function
         One of the following string values or a user supplied function.