merge NIFTy_5

.gitlab-ci.yml

@@ -34,32 +34,24 @@ build_docker_from_cache:
     - docker build -t $CONTAINER_TEST_IMAGE .
     - docker push $CONTAINER_TEST_IMAGE
 
-test_python2_with_coverage:
+test:
   stage: test
   variables:
     OMPI_MCA_btl_vader_single_copy_mechanism: none
   script:
-    - mpiexec -n 2 --bind-to none pytest -q test
-    - pytest -q --cov=nifty5 test
+    - mpiexec -n 2 --bind-to none pytest-3 -q test
+    - pytest-3 -q --cov=nifty5 test
     - >
-      python -m coverage report --omit "*plotting*,*distributed_do*"
+      python3 -m coverage report --omit "*plotting*,*distributed_do*"
     - >
-      python -m coverage report --omit "*plotting*,*distributed_do*" | grep TOTAL | awk '{ print "TOTAL: "$4; }'
-
-test_python3:
-  stage: test
-  variables:
-    OMPI_MCA_btl_vader_single_copy_mechanism: none
-  script:
-    - pytest-3 -q
-    - mpiexec -n 2 --bind-to none pytest-3 -q
+      python3 -m coverage report --omit "*plotting*,*distributed_do*" | grep TOTAL | awk '{ print "TOTAL: "$4; }'
 
 pages:
   stage: release
   before_script:
     - ls
   script:
-    - python setup.py install --user -f
+    - python3 setup.py install --user -f
     - sh docs/generate.sh
     - mv docs/build/ public/
   artifacts:
@@ -69,7 +61,6 @@ pages:
   - NIFTy_4
 
 before_script:
-  - python setup.py install --user -f
   - python3 setup.py install --user -f
 
 run_ipynb:
@@ -80,7 +71,6 @@ run_ipynb:
 run_getting_started_1:
   stage: demo_runs
   script:
-    - python demos/getting_started_1.py
     - python3 demos/getting_started_1.py
     - mpiexec -n 2 --bind-to none python3 demos/getting_started_1.py 2> /dev/null
   artifacts:
@@ -90,7 +80,6 @@ run_getting_started_1:
 run_getting_started_2:
   stage: demo_runs
   script:
-    - python demos/getting_started_2.py
     - python3 demos/getting_started_2.py
     - mpiexec -n 2 --bind-to none python3 demos/getting_started_2.py 2> /dev/null
   artifacts:
@@ -100,7 +89,6 @@ run_getting_started_2:
 run_getting_started_3:
   stage: demo_runs
   script:
-    - python demos/getting_started_3.py
     - python3 demos/getting_started_3.py
   artifacts:
     paths:
@@ -109,7 +97,6 @@ run_getting_started_3:
 run_bernoulli:
   stage: demo_runs
   script:
-    - python demos/bernoulli_demo.py
     - python3 demos/bernoulli_demo.py
   artifacts:
     paths:
@@ -118,7 +105,6 @@ run_bernoulli:
 run_curve_fitting:
   stage: demo_runs
   script:
-    - python demos/polynomial_fit.py
     - python3 demos/polynomial_fit.py
   artifacts:
     paths:

Dockerfile

@@ -5,27 +5,23 @@ RUN apt-get update && apt-get install -y \
     git \
     # Packages needed for NIFTy
     libfftw3-dev \
-    python python-pip python-dev python-future python-scipy cython \
     python3 python3-pip python3-dev python3-future python3-scipy cython3 \
     # Documentation build dependencies
-    python-sphinx python-sphinx-rtd-theme python-numpydoc \
+    python3-sphinx python3-sphinx-rtd-theme python3-numpydoc \
     # Testing dependencies
-    python-nose python-coverage python-parameterized python-pytest python-pytest-cov \
-    python3-nose python3-coverage python3-parameterized python3-pytest python3-pytest-cov \
+    python3-coverage python3-parameterized python3-pytest python3-pytest-cov \
     # Optional NIFTy dependencies
-    openmpi-bin libopenmpi-dev python-mpi4py python3-mpi4py \
+    openmpi-bin libopenmpi-dev python3-mpi4py \
     # Packages needed for NIFTy
-  && pip install pyfftw \
   && pip3 install pyfftw \
   # Optional NIFTy dependencies
-  && pip install git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git \
   && pip3 install git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git \
   # Testing dependencies
   && rm -rf /var/lib/apt/lists/*
 
 # Needed for demos to be running
-RUN apt-get update && apt-get install -y python-matplotlib python3-matplotlib \
-  && python3 -m pip install --upgrade pip && python3 -m pip install jupyter && python -m pip install --upgrade pip && python -m pip install jupyter \
+RUN apt-get update && apt-get install -y python3-matplotlib \
+  && python3 -m pip install --upgrade pip && python3 -m pip install jupyter \
   && rm -rf /var/lib/apt/lists/*
 
 # Set matplotlib backend

README.md

@@ -37,7 +37,7 @@ Installation
 
 ### Requirements
 
-- [Python](https://www.python.org/) (v2.7.x or 3.5.x)
+- [Python 3](https://www.python.org/) (3.5.x or later)
 - [SciPy](https://www.scipy.org/)
 - [pyFFTW](https://pypi.python.org/pypi/pyFFTW)
 
@@ -61,8 +61,8 @@ distributions, the "apt" lines will need slight changes.
 
 NIFTy5 and its mandatory dependencies can be installed via:
 
-    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_5
+    sudo apt-get install git libfftw3-dev python3 python3-pip python3-dev
+    pip3 install --user git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@NIFTy_5
 
 (Note: If you encounter problems related to `pyFFTW`, make sure that you are
 using a pip-installed `pyFFTW` package. Unfortunately, some distributions are
@@ -71,35 +71,26 @@ with the installed `FFTW3` libraries.)
 
 Plotting support is added via:
 
-    pip install --user matplotlib
+    pip3 install --user matplotlib
 
 Support for spherical harmonic transforms is added via:
 
-    pip install --user git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
+    pip3 install --user git+https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
 
 MPI support is added via:
 
     sudo apt-get install openmpi-bin libopenmpi-dev
-    pip install --user mpi4py
-
-### Installation for Python 3
-
-If you want to run NIFTy with Python 3, you need to make the following changes
-to the instructions above:
-
-- in all `apt-get` commands, replace `python-*` by `python3-*`
-- in all `pip` commands, replace `pip` by `pip3`
+    pip3 install --user mpi4py
 
 ### Running the tests
 
 In oder to run the tests one needs two additional packages:
-
-    pip install --user nose parameterized coverage
+    sudo apt-get install python3-coverage python3-parameterized python3-pytest python3-pytest-cov
 
 Afterwards the tests (including a coverage report) can be run using the
 following command in the repository root:
 
-    nosetests -x --with-coverage --cover-html --cover-package=nifty5
+    pytest-3 --cov=nifty5 test
 
 
 ### First Steps
@@ -108,7 +99,7 @@ For a quick start, you can browse through the [informal
 introduction](http://ift.pages.mpcdf.de/NIFTy/code.html) or
 dive into NIFTy by running one of the demonstrations, e.g.:
 
-    python demos/getting_started_1.py
+    python3 demos/getting_started_1.py
 
 
 ### Acknowledgement

demos/bernoulli_demo.py

@@ -11,10 +11,9 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright(C) 2013-2018 Max-Planck-Society
+# Copyright(C) 2013-2019 Max-Planck-Society
 #
-# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
-# and financially supported by the Studienstiftung des deutschen Volkes.
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
 
 import nifty5 as ift
 import numpy as np

demos/getting_started_1.py

@@ -11,10 +11,9 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright(C) 2013-2018 Max-Planck-Society
+# Copyright(C) 2013-2019 Max-Planck-Society
 #
-# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
-# and financially supported by the Studienstiftung des deutschen Volkes.
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
 
 import nifty5 as ift
 import numpy as np
@@ -78,7 +77,10 @@ if __name__ == '__main__':
     GR = ift.GeometryRemover(position_space)
     mask = ift.Field.from_global_data(position_space, mask)
     Mask = ift.DiagonalOperator(mask)
+    # Operators can be composed either with paranthesis
     R = GR(Mask(HT))
+    # or with @
+    R = GR @ Mask @ HT
 
     data_space = GR.target
 
@@ -93,7 +95,7 @@ if __name__ == '__main__':
 
     # Build propagator D and information source j
     j = R.adjoint_times(N.inverse_times(data))
-    D_inv = R.adjoint(N.inverse(R)) + S.inverse
+    D_inv = R.adjoint @ N.inverse @ R + S.inverse
     # Make it invertible
     IC = ift.GradientNormController(iteration_limit=500, tol_abs_gradnorm=1e-3)
     D = ift.InversionEnabler(D_inv, IC, approximation=S.inverse).inverse
@@ -105,15 +107,16 @@ if __name__ == '__main__':
     rg = isinstance(position_space, ift.RGSpace)
     plot = ift.Plot()
     if rg and len(position_space.shape) == 1:
-        plot.add([HT(MOCK_SIGNAL), GR.adjoint(data), HT(m)],
-                 label=['Mock signal', 'Data', 'Reconstruction'],
-                 alpha=[1, .3, 1])
-        plot.add(mask_to_nan(mask, HT(m-MOCK_SIGNAL)), title='Residuals')
+        plot.add(
+            [HT(MOCK_SIGNAL), GR.adjoint(data),
+             HT(m)],
+            label=['Mock signal', 'Data', 'Reconstruction'],
+            alpha=[1, .3, 1])
+        plot.add(mask_to_nan(mask, HT(m - MOCK_SIGNAL)), title='Residuals')
         plot.output(nx=2, ny=1, xsize=10, ysize=4, title="getting_started_1")
     else:
         plot.add(HT(MOCK_SIGNAL), title='Mock Signal')
-        plot.add(mask_to_nan(mask, (GR(Mask)).adjoint(data)),
-                 title='Data')
+        plot.add(mask_to_nan(mask, (GR(Mask)).adjoint(data)), title='Data')
         plot.add(HT(m), title='Reconstruction')
         plot.add(mask_to_nan(mask, HT(m-MOCK_SIGNAL)), title='Residuals')
         plot.output(nx=2, ny=2, xsize=10, ysize=10, title="getting_started_1")

demos/getting_started_2.py

@@ -11,10 +11,9 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright(C) 2013-2018 Max-Planck-Society
+# Copyright(C) 2013-2019 Max-Planck-Society
 #
-# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
-# and financially supported by the Studienstiftung des deutschen Volkes.
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
 
 import nifty5 as ift
 import numpy as np

demos/getting_started_3.py

@@ -11,10 +11,9 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright(C) 2013-2018 Max-Planck-Society
+# Copyright(C) 2013-2019 Max-Planck-Society
 #
-# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
-# and financially supported by the Studienstiftung des deutschen Volkes.
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
 
 import nifty5 as ift
 import numpy as np

demos/plot_test.py

+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright(C) 2013-2019 Max-Planck-Society
+#
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
+
 import nifty5 as ift
 import numpy as np
 

demos/polynomial_fit.py

+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright(C) 2013-2019 Max-Planck-Society
+#
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
+
 import matplotlib.pyplot as plt
 import numpy as np
 

docs/source/conf.py

@@ -52,9 +52,6 @@ extensions = [
     'numpydoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
- #   'sphinx.ext.coverage',
- #   'sphinx.ext.todo',
- #   'sphinx.ext.mathjax',
     'sphinx.ext.imgmath',
     'sphinx.ext.viewcode'
 ]
@@ -75,7 +72,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'NIFTy5'
-copyright = u'2013-2018, Max-Planck-Society'
+copyright = u'2013-2019, Max-Planck-Society'
 author = u'Theo Steininger / Martin Reinecke'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -94,20 +91,10 @@ release = u'5.0.0'
 # Usually you set "language" from the command line for these cases.
 language = None
 
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = []
 
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-#default_role = None
-
 # If true, '()' will be appended to :func: etc. cross-reference text.
 #add_function_parentheses = True
 
@@ -122,12 +109,6 @@ add_module_names = False
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
-
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
@@ -149,175 +130,27 @@ html_theme_options = {
 
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents.  If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
-
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 html_logo = 'nifty_logo_black.png'
 
-# The name of an image file (relative to this directory) to use as a favicon of
-# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = []
 
-# Add any extra paths that contain custom files (such as robots.txt or
-# .htaccess) here, relative to this directory. These files are copied
-# directly to the root of the documentation.
-#html_extra_path = []
-
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
 html_last_updated_fmt = '%b %d, %Y'
 
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
 # If false, no module index is generated.
 html_domain_indices = False
 
 # If false, no index is generated.
 html_use_index = False
 
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
 
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it.  The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Language to be used for generating the HTML full-text search index.
-# Sphinx supports the following languages:
-#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
-#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
-#html_search_language = 'en'
-
-# A dictionary with options for the search language support, empty by default.
-# Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
-
-# The name of a javascript file (relative to the configuration directory) that
-# implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
-
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'NIFTydoc'
-
-# -- Options for LaTeX output ---------------------------------------------
-
-#latex_elements = {