Commit 58d4b593 authored by Philipp Arras's avatar Philipp Arras
Browse files

Rename nifty4 -> nifty5

parent 02f153a5
Pipeline #31301 passed with stages
in 8 minutes and 24 seconds
...@@ -34,7 +34,7 @@ test_python2_with_coverage: ...@@ -34,7 +34,7 @@ test_python2_with_coverage:
script: script:
- python setup.py install --user -f - python setup.py install --user -f
- mpiexec -n 2 --bind-to none nosetests -q 2> /dev/null - mpiexec -n 2 --bind-to none nosetests -q 2> /dev/null
- nosetests -q --with-coverage --cover-package=nifty4 --cover-erase - nosetests -q --with-coverage --cover-package=nifty5 --cover-erase
- > - >
coverage report --omit "*plotting*,*distributed_do*" coverage report --omit "*plotting*,*distributed_do*"
- > - >
......
...@@ -49,8 +49,8 @@ Optional dependencies: ...@@ -49,8 +49,8 @@ Optional dependencies:
### Sources ### Sources
The current version of Nifty4 can be obtained by cloning the repository and The current version of Nifty5 can be obtained by cloning the repository and
switching to the NIFTy_4 branch: switching to the NIFTy_5 branch:
git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git
...@@ -59,7 +59,7 @@ switching to the NIFTy_4 branch: ...@@ -59,7 +59,7 @@ switching to the NIFTy_4 branch:
In the following, we assume a Debian-based distribution. For other In the following, we assume a Debian-based distribution. For other
distributions, the "apt" lines will need slight changes. distributions, the "apt" lines will need slight changes.
NIFTy4 and its mandatory dependencies can be installed via: NIFTy5 and its mandatory dependencies can be installed via:
sudo apt-get install git libfftw3-dev python python-pip python-dev sudo apt-get install git libfftw3-dev python python-pip python-dev
pip install --user git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@NIFTy_4 pip install --user git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@NIFTy_4
...@@ -99,7 +99,7 @@ In oder to run the tests one needs two additional packages: ...@@ -99,7 +99,7 @@ In oder to run the tests one needs two additional packages:
Afterwards the tests (including a coverage report) can be run using the Afterwards the tests (including a coverage report) can be run using the
following command in the repository root: following command in the repository root:
nosetests -x --with-coverage --cover-html --cover-package=nifty4 nosetests -x --with-coverage --cover-html --cover-package=nifty5
### First Steps ### First Steps
......
...@@ -140,7 +140,7 @@ ...@@ -140,7 +140,7 @@
"source": [ "source": [
"import numpy as np\n", "import numpy as np\n",
"np.random.seed(40)\n", "np.random.seed(40)\n",
"import nifty4 as ift\n", "import nifty5 as ift\n",
"import matplotlib.pyplot as plt\n", "import matplotlib.pyplot as plt\n",
"%matplotlib inline" "%matplotlib inline"
] ]
......
import nifty4 as ift import nifty5 as ift
from nifty4.library.nonlinearities import Linear, Tanh, Exponential from nifty5.library.nonlinearities import Linear, Tanh, Exponential
import numpy as np import numpy as np
np.random.seed(42) np.random.seed(42)
......
import nifty4 as ift import nifty5 as ift
from nifty4.library.nonlinearities import Exponential from nifty5.library.nonlinearities import Exponential
import numpy as np import numpy as np
np.random.seed(42) np.random.seed(42)
......
import nifty4 as ift import nifty5 as ift
from nifty4.library.nonlinearities import Linear, Exponential, Tanh from nifty5.library.nonlinearities import Linear, Exponential, Tanh
import numpy as np import numpy as np
np.random.seed(20) np.random.seed(20)
......
import numpy as np import numpy as np
import nifty4 as ift import nifty5 as ift
if __name__ == "__main__": if __name__ == "__main__":
signal_to_noise = 0.5 # The signal to noise ratio signal_to_noise = 0.5 # The signal to noise ratio
......
import nifty4 as ift import nifty5 as ift
import numpy as np import numpy as np
......
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
# to get exact figure of paper comment out lines marked by "COMMENT OUT" # to get exact figure of paper comment out lines marked by "COMMENT OUT"
import numpy as np import numpy as np
import nifty4 as ift import nifty5 as ift
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
......
import nifty4 as ift import nifty5 as ift
import numpy as np import numpy as np
......
import nifty4 as ift import nifty5 as ift
import numpy as np import numpy as np
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from nifty4.sugar import create_power_operator from nifty5.sugar import create_power_operator
np.random.seed(42) np.random.seed(42)
......
import nifty4 as ift import nifty5 as ift
import numpy as np import numpy as np
......
import numpy as np import numpy as np
import nifty4 as ift import nifty5 as ift
# TODO: MAKE RESPONSE MPI COMPATIBLE OR USE LOS RESPONSE INSTEAD # TODO: MAKE RESPONSE MPI COMPATIBLE OR USE LOS RESPONSE INSTEAD
......
import numpy as np import numpy as np
import nifty4 as ift import nifty5 as ift
if __name__ == "__main__": if __name__ == "__main__":
......
import numpy as np import numpy as np
import nifty4 as ift import nifty5 as ift
import numericalunits as nu import numericalunits as nu
......
import nifty4 as ift import nifty5 as ift
import numpy as np import numpy as np
np.random.seed(42) np.random.seed(42)
......
rm -rf docs/build docs/source/mod rm -rf docs/build docs/source/mod
sphinx-apidoc -l -e -d 2 -o docs/source/mod nifty4 sphinx-apidoc -l -e -d 2 -o docs/source/mod nifty5
sphinx-build -b html docs/source/ docs/build/ sphinx-build -b html docs/source/ docs/build/
...@@ -7,7 +7,7 @@ NIFTy-related publications ...@@ -7,7 +7,7 @@ NIFTy-related publications
author = {{Martin Reinecke, Theo Steininger, Marco Selig}}, author = {{Martin Reinecke, Theo Steininger, Marco Selig}},
title = {NIFTy -- Numerical Information Field TheorY}, title = {NIFTy -- Numerical Information Field TheorY},
url = {https://gitlab.mpcdf.mpg.de/ift/NIFTy}, url = {https://gitlab.mpcdf.mpg.de/ift/NIFTy},
version = {nifty4}, version = {nifty5},
date = {2018-04-05}, date = {2018-04-05},
} }
......
.. currentmodule:: nifty4 .. currentmodule:: nifty5
============= =============
Code Overview Code Overview
...@@ -35,7 +35,7 @@ Domains ...@@ -35,7 +35,7 @@ Domains
Abstract base class Abstract base class
------------------- -------------------
One of the fundamental building blocks of the NIFTy4 framework is the *domain*. One of the fundamental building blocks of the NIFTy5 framework is the *domain*.
Its required capabilities are expressed by the abstract :class:`Domain` class. Its required capabilities are expressed by the abstract :class:`Domain` class.
A domain must be able to answer the following queries: A domain must be able to answer the following queries:
...@@ -151,7 +151,7 @@ performance benefits. ...@@ -151,7 +151,7 @@ performance benefits.
Linear Operators Linear Operators
================ ================
A linear operator (represented by NIFTy4's abstract :class:`LinearOperator` A linear operator (represented by NIFTy5's abstract :class:`LinearOperator`
class) can be interpreted as an (implicitly defined) matrix. class) can be interpreted as an (implicitly defined) matrix.
It can be applied to :class:`Field` instances, resulting in other :class:`Field` It can be applied to :class:`Field` instances, resulting in other :class:`Field`
instances that potentially live on other domains. instances that potentially live on other domains.
...@@ -245,7 +245,7 @@ high-dimensional functions, which are often nonlinear. ...@@ -245,7 +245,7 @@ high-dimensional functions, which are often nonlinear.
Energy functionals Energy functionals
------------------ ------------------
In NIFTy4 such functions are represented by objects of type :class:`Energy`. In NIFTy5 such functions are represented by objects of type :class:`Energy`.
These hold the prescription how to calculate the function's These hold the prescription how to calculate the function's
:attr:`~Energy.value`, :attr:`~Energy.gradient` and :attr:`~Energy.value`, :attr:`~Energy.gradient` and
(optionally) :attr:`~Energy.curvature` at any given :attr:`~Energy.position` (optionally) :attr:`~Energy.curvature` at any given :attr:`~Energy.position`
...@@ -256,9 +256,9 @@ linear operator objects. ...@@ -256,9 +256,9 @@ linear operator objects.
Energies are classes that typically have to be provided by the user when Energies are classes that typically have to be provided by the user when
tackling new IFT problems. tackling new IFT problems.
Some examples of concrete energy classes delivered with NIFTy4 are Some examples of concrete energy classes delivered with NIFTy5 are
:class:`QuadraticEnergy` (with position-independent curvature, mainly used with :class:`QuadraticEnergy` (with position-independent curvature, mainly used with
conjugate gradient minimization) and :class:`~nifty4.library.WienerFilterEnergy`. conjugate gradient minimization) and :class:`~nifty5.library.WienerFilterEnergy`.
Iteration control Iteration control
...@@ -269,7 +269,7 @@ checking the quality of the current solution estimate and stopping once ...@@ -269,7 +269,7 @@ checking the quality of the current solution estimate and stopping once
it is sufficiently accurate. In case of numerical problems, the iteration needs it is sufficiently accurate. In case of numerical problems, the iteration needs
to be terminated as well, returning a suitable error description. to be terminated as well, returning a suitable error description.
In NIFTy4, this functionality is encapsulated in the abstract In NIFTy5, this functionality is encapsulated in the abstract
:class:`IterationController` class, which is provided with the initial energy :class:`IterationController` class, which is provided with the initial energy
object before starting the minimization, and is updated with the improved object before starting the minimization, and is updated with the improved
energy after every iteration. Based on this information, it can either continue energy after every iteration. Based on this information, it can either continue
......
...@@ -73,7 +73,7 @@ source_suffix = '.rst' ...@@ -73,7 +73,7 @@ source_suffix = '.rst'
master_doc = 'index' master_doc = 'index'
# General information about the project. # General information about the project.
project = u'NIFTy4' project = u'NIFTy5'
copyright = u'2013-2018, Max-Planck-Society' copyright = u'2013-2018, Max-Planck-Society'
author = u'Theo Steininger / Martin Reinecke' author = u'Theo Steininger / Martin Reinecke'
......
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