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Commit 550f3aa1 authored by Theo Steininger's avatar Theo Steininger
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Merge branch 'master' into fix_parameterized 

# Conflicts:
#	test/common.py
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ci/install_pyHealpix.sh
View file @ 550f3aa1
#!/bin/bash
git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
(cd pyHealpix && autoreconf -i && ./configure --enable-openmp --enable-native-optimizations && make -j4 install)
(cd pyHealpix && autoreconf -i && ./configure --enable-openmp && make -j4 install)
rm -rf pyHealpix
docs/Makefile deleted 100644 → 0
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# 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 deleted 100644 → 0
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.. currentmodule:: nifty
The ``ComposedOperator`` class -- A possibility to combine several operators
............................................................................
.. autoclass:: ComposedOperator
:show-inheritance:
:members:
docs/source/conjugate_gradient.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``ConjugateGradient`` class -- Minimization routine
.......................................................
.. autoclass:: ConjugateGradient
:show-inheritance:
:members:
docs/source/descent_minimizer.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``DescentMinimizer`` class -- The Base class for minimizers
...............................................................
.. autoclass:: DescentMinimizer
:show-inheritance:
:members:
docs/source/diagonal_operator.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``DiagonalOperator`` class -- ...
.....................................
.. autoclass:: DiagonalOperator
:show-inheritance:
:members:
docs/source/endomorphic_operator.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``EndomorphicOperator`` class -- ...
........................................
.. autoclass:: EndomorphicOperator
:show-inheritance:
:members:
docs/source/fft_operator.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``FFTOperator`` class -- Fourier Transformations
....................................................
.. autoclass:: FFTOperator
:show-inheritance:
:members:
docs/source/gl_space.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``GLSpace`` class -- Gauss-Legendre pixelization of the sphere
..................................................................
.. autoclass:: GLSpace
:show-inheritance:
:members:
docs/source/gllm_transformation.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``GLLMTransformation`` class -- A transformation routine
............................................................
.. autoclass:: GLLMTransformation
:show-inheritance:
:members:
docs/source/hp_space.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``HPSpace`` class -- HEALPix discretization of the sphere
.............................................................
.. autoclass:: HPSpace
:show-inheritance:
:members:
docs/source/hplm_transformation.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``HPLMTransformation`` class -- A transformation routine
............................................................
.. autoclass:: HPLMTransformation
:show-inheritance:
:members:
docs/source/invertible_operator_mixin.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``InvertibleOperatorMixin`` class -- ...
............................................
.. autoclass:: InvertibleOperatorMixin
:show-inheritance:
:members:
docs/source/lm_space.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``LMSpace`` class -- Spherical Harmonics components
.......................................................
.. autoclass:: LMSpace
:show-inheritance:
:members:
docs/source/lmgl_transformation.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``LMGLTransformation`` class -- A transformation routine
............................................................
.. autoclass:: LMGLTransformation
:show-inheritance:
:members:
docs/source/lmhp_transformation.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``LMHPTransformation`` class -- A transformation routine
............................................................
.. autoclass:: LMHPTransformation
:show-inheritance:
:members:
docs/source/minimization.rst deleted 100644 → 0
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Minimization
------------
NIFTY provides several minimization routines.
.. toctree::
:maxdepth: 1
conjugate_gradient
descent_minimizer
docs/source/operator.rst deleted 100644 → 0
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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
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......@@ -33,7 +33,6 @@ algorithms.
propagator_operator
endomorphic_operator
invertible_operator_mixin
transformations
.. currentmodule:: nifty
......
docs/source/power_space.rst deleted 100644 → 0
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.. currentmodule:: nifty
The ``PowerSpace`` class -- The natural space underlying power-spectra
.......................................................................
.. autoclass:: PowerSpace
:show-inheritance:
:members:
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