Merge branch 'master' into 'sphinx_docs'

# Conflicts:
#   docs/source/conf.py
#   docs/source/field.rst
#   docs/source/index.rst

README.md

@@ -11,7 +11,7 @@ Summary
 
 ### Description
 
-**NIFTY**, "**N**umerical **I**nformation **F**ield **T**heor**y**", is
+**NIFTY**, "**N**umerical **I**nformation **F**ield **T**heor<strong>y</strong>", is
 a versatile library designed to enable the development of signal
 inference algorithms that operate regardless of the underlying spatial
 grid and its resolution. Its object-oriented framework is written in
@@ -87,21 +87,17 @@ Starting with a fresh Ubuntu installation move to a folder like
 
 -   Install basic packages like python, python-dev, gsl and others:
 
-        sudo apt-get install curl git autoconf python-dev python-pip python-numpy
+        sudo apt-get install curl git autoconf libtool python-dev python-pip python-numpy
 
 -   Install pyHealpix:
 
         git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
-        cd pyHealpix
-        autoreconf -i && ./configure --prefix=$HOME/.local --enable-openmp --enable-native-optimizations && make -j4 && make install
-        cd ..
+        (cd pyHealpix && autoreconf -i && ./configure --prefix=$HOME/.local --enable-openmp --enable-native-optimizations && make -j4 install)
 
 -   Finally, NIFTy:
 
         git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git
-        cd NIFTy
-        python setup.py install --user
-        cd ..
+        (cd NIFTy && python setup.py install --user)
 
 ### Installation on Linux systems in general
 
@@ -139,16 +135,13 @@ may cause trouble.
 -   Install NIFTy:
 
         git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git
-        cd NIFTy
-        python setup.py install --user
-        cd ..
+        (cd NIFTy && python setup.py install --user)
 
 ### Running the tests
 
 In oder to run the tests one needs two additional packages:
 
-    pip install nose
-    pip install parameterized
+    pip install nose parameterized
 
 Afterwards the tests (including a coverage report) are run using the following
 command in the repository root:

ci/install_basics.sh

 #!/bin/bash
 
-apt-get install -y build-essential python python-pip python-dev git autoconf gsl-bin libgsl-dev wget 
+apt-get install -y build-essential python python-pip python-dev git autoconf libtool gsl-bin libgsl-dev wget

ci/install_h5py.sh

 #!/bin/bash
 
 apt-get install -y libhdf5-10 libhdf5-dev libhdf5-openmpi-10 libhdf5-openmpi-dev hdf5-tools
-
-export CC=mpicc
-export HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-export HDF5_MPI="ON"
-
-pip install --no-binary=h5py h5py
+CC=mpicc HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi HDF5_MPI="ON" pip install --no-binary=h5py h5py

ci/install_mpi4py.sh

 #!/bin/bash
 
 apt-get install -y openmpi-bin libopenmpi-dev
-pip install mpi4py
\ No newline at end of file
+pip install mpi4py

ci/install_pyHealpix.sh

 #!/bin/bash
 
 git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
-cd pyHealpix
-autoreconf -i && ./configure && make -j4 install
-cd ..
+(cd pyHealpix && autoreconf -i && ./configure --enable-openmp --enable-native-optimizations && make -j4 install)
 rm -rf pyHealpix

ci/install_pyfftw.sh

@@ -3,7 +3,5 @@
 apt-get install -y libatlas-base-dev libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3 libfftw3-quad3 libfftw3-single3
 
 git clone -b mpi https://github.com/fredros/pyFFTW.git
-cd pyFFTW/
-CC=mpicc python setup.py build_ext install
-cd ..
-rm -r pyFFTW
+(cd pyFFTW && CC=mpicc python setup.py build_ext install)
+rm -rf pyFFTW

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/conf.py

@@ -325,4 +325,4 @@ texinfo_documents = [
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-#intersphinx_mapping = {'https://docs.python.org/': None}
+#intersphinx_mapping = {'https://docs.python.org/': None}
\ No newline at end of file

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/field.rst

@@ -10,4 +10,3 @@ In NIFTY, Fields are used to store data arrays and carry all the needed metainfo
 .. autoclass:: Field
     :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/index.rst

@@ -38,4 +38,3 @@ Indices and tables
 * :ref:`genindex`
 * :any:`Module Index <mod/modules>`
 * :ref:`search`
-