Merge branch 'docs_fix_duplicates' into 'master'

Removed duplicates of files and unused reference

See merge request !146

docs/Makefile

-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-
-.PHONY: help
-help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  dirhtml    to make HTML files named index.html in directories"
-	@echo "  singlehtml to make a single large HTML file"
-	@echo "  pickle     to make pickle files"
-	@echo "  json       to make JSON files"
-	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
-	@echo "  applehelp  to make an Apple Help Book"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
-	@echo "  epub       to make an epub"
-	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
-	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
-	@echo "  text       to make text files"
-	@echo "  man        to make manual pages"
-	@echo "  texinfo    to make Texinfo files"
-	@echo "  info       to make Texinfo files and run them through makeinfo"
-	@echo "  gettext    to make PO message catalogs"
-	@echo "  changes    to make an overview of all changed/added/deprecated items"
-	@echo "  xml        to make Docutils-native XML files"
-	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
-	@echo "  linkcheck  to check all external links for integrity"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-	@echo "  coverage   to run coverage check of the documentation (if enabled)"
-
-.PHONY: clean
-clean:
-	rm -rf $(BUILDDIR)/*
-
-.PHONY: html
-html:
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-.PHONY: dirhtml
-dirhtml:
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-.PHONY: singlehtml
-singlehtml:
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-.PHONY: pickle
-pickle:
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-.PHONY: json
-json:
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-.PHONY: htmlhelp
-htmlhelp:
-	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
-	@echo
-	@echo "Build finished; now you can run HTML Help Workshop with the" \
-	      ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-.PHONY: qthelp
-qthelp:
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/NIFTY.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/NIFTY.qhc"
-
-.PHONY: applehelp
-applehelp:
-	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
-	@echo
-	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
-	@echo "N.B. You won't be able to view it unless you put it in" \
-	      "~/Library/Documentation/Help or install it in your application" \
-	      "bundle."
-
-.PHONY: devhelp
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/NIFTY"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/NIFTY"
-	@echo "# devhelp"
-
-.PHONY: epub
-epub:
-	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
-	@echo
-	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-.PHONY: latex
-latex:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo
-	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
-	@echo "Run \`make' in that directory to run these through (pdf)latex" \
-	      "(use \`make latexpdf' here to do that automatically)."
-
-.PHONY: latexpdf
-latexpdf:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through pdflatex..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-.PHONY: latexpdfja
-latexpdfja:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through platex and dvipdfmx..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-.PHONY: text
-text:
-	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
-	@echo
-	@echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-.PHONY: man
-man:
-	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
-	@echo
-	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-.PHONY: texinfo
-texinfo:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo
-	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
-	@echo "Run \`make' in that directory to run these through makeinfo" \
-	      "(use \`make info' here to do that automatically)."
-
-.PHONY: info
-info:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo "Running Texinfo files through makeinfo..."
-	make -C $(BUILDDIR)/texinfo info
-	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-.PHONY: gettext
-gettext:
-	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
-	@echo
-	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-.PHONY: changes
-changes:
-	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
-	@echo
-	@echo "The overview file is in $(BUILDDIR)/changes."
-
-.PHONY: linkcheck
-linkcheck:
-	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
-	@echo
-	@echo "Link check complete; look for any errors in the above output " \
-	      "or in $(BUILDDIR)/linkcheck/output.txt."
-
-.PHONY: doctest
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
-
-.PHONY: coverage
-coverage:
-	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
-	@echo "Testing of coverage in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/coverage/python.txt."
-
-.PHONY: xml
-xml:
-	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
-	@echo
-	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
-
-.PHONY: pseudoxml
-pseudoxml:
-	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
-	@echo
-	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/source/composed_operator.rst

-.. currentmodule:: nifty
-
-The ``ComposedOperator`` class -- A possibility to combine several operators
-............................................................................
-
-.. autoclass:: ComposedOperator
-    :show-inheritance:
-    :members:

docs/source/conjugate_gradient.rst

-.. currentmodule:: nifty
-
-The ``ConjugateGradient`` class -- Minimization routine
-.......................................................
-
-.. autoclass:: ConjugateGradient
-    :show-inheritance:
-    :members:

docs/source/descent_minimizer.rst

-.. currentmodule:: nifty
-
-The ``DescentMinimizer`` class -- The Base class for minimizers
-...............................................................
-
-.. autoclass:: DescentMinimizer
-    :show-inheritance:
-    :members:

docs/source/diagonal_operator.rst

-.. currentmodule:: nifty
-
-The ``DiagonalOperator`` class -- ...
-.....................................
-
-.. autoclass:: DiagonalOperator
-    :show-inheritance:
-    :members:

docs/source/endomorphic_operator.rst

-.. currentmodule:: nifty
-
-The ``EndomorphicOperator`` class -- ...
-........................................
-
-.. autoclass:: EndomorphicOperator
-    :show-inheritance:
-    :members:

docs/source/fft_operator.rst

-.. currentmodule:: nifty
-
-The ``FFTOperator`` class -- Fourier Transformations
-....................................................
-
-.. autoclass:: FFTOperator
-    :show-inheritance:
-    :members:

docs/source/gl_space.rst

-.. currentmodule:: nifty
-
-The ``GLSpace`` class -- Gauss-Legendre pixelization of the sphere
-..................................................................
-
-.. autoclass:: GLSpace
-    :show-inheritance:
-    :members:

docs/source/gllm_transformation.rst

-.. currentmodule:: nifty
-
-The ``GLLMTransformation`` class -- A transformation routine
-............................................................
-
-
-.. autoclass:: GLLMTransformation
-    :show-inheritance:
-    :members:

docs/source/hp_space.rst

-.. currentmodule:: nifty
-
-The ``HPSpace`` class -- HEALPix discretization of the sphere
-.............................................................
-
-
-.. autoclass:: HPSpace
-    :show-inheritance:
-    :members:

docs/source/hplm_transformation.rst

-.. currentmodule:: nifty
-
-The ``HPLMTransformation`` class -- A transformation routine
-............................................................
-
-
-.. autoclass:: HPLMTransformation
-    :show-inheritance:
-    :members:

docs/source/invertible_operator_mixin.rst

-.. currentmodule:: nifty
-
-The ``InvertibleOperatorMixin`` class -- ...
-............................................
-
-.. autoclass:: InvertibleOperatorMixin
-    :show-inheritance:
-    :members:

docs/source/lm_space.rst

-.. currentmodule:: nifty
-
-The ``LMSpace`` class -- Spherical Harmonics components
-.......................................................
-
-.. autoclass:: LMSpace
-    :show-inheritance:
-    :members:

docs/source/lmgl_transformation.rst

-.. currentmodule:: nifty
-
-The ``LMGLTransformation`` class -- A transformation routine
-............................................................
-
-
-.. autoclass:: LMGLTransformation
-    :show-inheritance:
-    :members:

docs/source/lmhp_transformation.rst

-.. currentmodule:: nifty
-
-The ``LMHPTransformation`` class -- A transformation routine
-............................................................
-
-.. autoclass:: LMHPTransformation
-    :show-inheritance:
-    :members:

docs/source/minimization.rst

-Minimization
-------------
-NIFTY provides several minimization routines.
-
-
-.. toctree:: 
-    :maxdepth: 1
-
-    conjugate_gradient
-    descent_minimizer
-

docs/source/operator.rst

-Operators
-=========
-Operators perform some operation on a given field. In practice an operator can 
-take the form of an explicit matrix (e.g. stored in a Numpy array) or it may be 
-implicitly defined as a function (e.g. an FFT operation would not be encoded in
-a matrix, but performed using an FFT routine). NIFTY includes a framework for 
-handling arbitrary operators, and basic methods for manipulating these 
-operators. Common functions like taking traces and extracting diagonals are 
-provided.
-
-In order to have a blueprint for operators capable of handling fields, any 
-application of operators is split into a general and a concrete part. The 
-general part comprises the correct involvement of normalizations and 
-transformations, necessary for any operator type, while the concrete part is 
-unique for each operator subclass. In analogy to the field class, any operator 
-instance has a set of properties that specify its domain and target as well as 
-some additional flags.
-
-Operator classes
-----------------
-NIFTY provides a base class for defining operators, as well as several pre-implemented operator types that are very often needed for signal inference
-algorithms.
-
-.. toctree:: 
-    :maxdepth: 1
-
-    diagonal_operator
-    fft_operator
-    composed_operator
-    response_operator
-    smoothing_operator
-    projection_operator
-    propagator_operator
-    endomorphic_operator
-    invertible_operator_mixin
-    transformations
-
-.. currentmodule:: nifty
-
-The ``LinearOperator`` class -- The base Operator Object
---------------------------------------------------------
-
-.. autoclass:: LinearOperator
-    :show-inheritance:
-    :members:

docs/source/operators/operator.rst

@@ -33,7 +33,6 @@ algorithms.
     propagator_operator
     endomorphic_operator
     invertible_operator_mixin
-    transformations
 
 .. currentmodule:: nifty
 

docs/source/power_space.rst

-.. currentmodule:: nifty
-
-The ``PowerSpace`` class --  The natural space underlying power-spectra
-.......................................................................
-
-.. autoclass:: PowerSpace
-    :show-inheritance:
-    :members:

docs/source/projection_operator.rst

-.. currentmodule:: nifty
-
-The ``ProjectionOperator`` class -- ...
-.......................................
-
-.. autoclass:: ProjectionOperator
-    :show-inheritance:
-    :members: