Commit 3681524e authored by Theo Steininger's avatar Theo Steininger
Browse files

Merge branch 'master' into 'sphinx_docs'

# Conflicts:
#   docs/source/conf.py
#   docs/source/field.rst
#   docs/source/index.rst
parents 37034664 4efa0f58
Pipeline #13045 passed with stage
in 5 minutes and 42 seconds
......@@ -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:
......
#!/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
#!/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
#!/bin/bash
apt-get install -y openmpi-bin libopenmpi-dev
pip install mpi4py
\ No newline at end of file
pip install mpi4py
#!/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
......@@ -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
# 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."
.. currentmodule:: nifty
The ``ComposedOperator`` class -- A possibility to combine several operators
............................................................................
.. autoclass:: ComposedOperator
:show-inheritance:
:members:
......@@ -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
.. currentmodule:: nifty
The ``ConjugateGradient`` class -- Minimization routine
.......................................................
.. autoclass:: ConjugateGradient
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``DescentMinimizer`` class -- The Base class for minimizers
...............................................................
.. autoclass:: DescentMinimizer
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``DiagonalOperator`` class -- ...
.....................................
.. autoclass:: DiagonalOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``EndomorphicOperator`` class -- ...
........................................
.. autoclass:: EndomorphicOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``FFTOperator`` class -- Fourier Transformations
....................................................
.. autoclass:: FFTOperator
:show-inheritance:
:members:
......@@ -10,4 +10,3 @@ In NIFTY, Fields are used to store data arrays and carry all the needed metainfo
.. autoclass:: Field
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``GLSpace`` class -- Gauss-Legendre pixelization of the sphere
..................................................................
.. autoclass:: GLSpace
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``GLLMTransformation`` class -- A transformation routine
............................................................
.. autoclass:: GLLMTransformation
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``HPSpace`` class -- HEALPix discretization of the sphere
.............................................................
.. autoclass:: HPSpace
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``HPLMTransformation`` class -- A transformation routine
............................................................
.. autoclass:: HPLMTransformation
:show-inheritance:
:members:
......@@ -38,4 +38,3 @@ Indices and tables
* :ref:`genindex`
* :any:`Module Index <mod/modules>`
* :ref:`search`
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