Merge branch 'master' into spherical_plots

.gitlab-ci.yml

@@ -11,11 +11,10 @@ variables:
 
 before_script:
   - apt-get update
-  - >
-    apt-get install -y build-essential python python-pip python-dev git
-    autoconf gsl-bin libgsl-dev wget python-numpy cython
-  - pip install --upgrade -r ci/requirements_base.txt
   - chmod +x ci/*.sh
+  - ci/install_basics.sh
+  - pip install --upgrade -r ci/requirements.txt
+
 
 test_min:
   stage: test
@@ -26,22 +25,16 @@ test_min:
 test_mpi:
   stage: test
   script:
-    - apt-get install -y openmpi-bin libopenmpi-dev
-    - pip install mpi4py
     - ci/install_pyHealpix.sh
+    - ci/install_mpi4py.sh
     - python setup.py build_ext --inplace
     - nosetests -vv
 
 test_mpi_fftw:
   stage: test
   script:
-    - apt-get install -y openmpi-bin libopenmpi-dev
-    - >
-      apt-get install -y libatlas-base-dev libfftw3-bin libfftw3-dev
-      libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3
-      libfftw3-quad3 libfftw3-single3
-    - pip install mpi4py
     - ci/install_pyHealpix.sh
+    - ci/install_mpi4py.sh
     - ci/install_pyfftw.sh
     - python setup.py build_ext --inplace
     - nosetests -vv
@@ -49,18 +42,10 @@ test_mpi_fftw:
 test_mpi_fftw_hdf5:
   stage: test
   script:
-    - apt-get install -y openmpi-bin libopenmpi-dev
-    - >
-      apt-get install -y libatlas-base-dev libfftw3-bin libfftw3-dev
-      libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3
-      libfftw3-quad3 libfftw3-single3
-    - >
-      apt-get install -y libhdf5-10 libhdf5-dev libhdf5-openmpi-10
-      libhdf5-openmpi-dev hdf5-tools
-    - pip install mpi4py
     - ci/install_pyHealpix.sh
-    - ci/install_h5py.sh
+    - ci/install_mpi4py.sh
     - ci/install_pyfftw.sh
+    - ci/install_h5py.sh
     - python setup.py build_ext --inplace
     - nosetests -vv --with-coverage --cover-package=nifty --cover-branches
     - >

Dockerfile

 FROM ubuntu:latest
 
 # dependencies via apt
-RUN \
-    apt-get update && \
-    apt-get install -y build-essential python python-pip python-dev git \
-    autoconf gsl-bin libgsl-dev openmpi-bin wget \
-    libopenmpi-dev libatlas-base-dev libfftw3-bin libfftw3-dev \
-    libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3 \
-    libfftw3-quad3 libfftw3-single3 libhdf5-10 libhdf5-dev \
-    libhdf5-openmpi-10 libhdf5-openmpi-dev hdf5-tools \
-	python-tk
+RUN apt-get update 
+ADD ci/install_basics.sh /tmp/install_basics.sh
+RUN cd /tmp && chmod +x install_basics.sh && ./install_basics.sh
+
 
 # python dependencies
 ADD ci/requirements.txt /tmp/requirements.txt
 RUN pip install --upgrade -r /tmp/requirements.txt
 
+ADD ci/requirements_extras.txt /tmp/requirements_extras.txt
+RUN pip install --upgrade -r /tmp/requirements_extras.txt
+
+
 # install pyHealpix, pyfftw and h5py
 ADD ci/install_pyHealpix.sh /tmp/install_pyHealpix.sh
 RUN cd /tmp && chmod +x install_pyHealpix.sh && ./install_pyHealpix.sh
+
+ADD ci/install_mpi4py.sh /tmp/install_mpi4py.sh
+RUN cd /tmp && chmod +x install_mpi4py.sh && ./install_mpi4py.sh
+
 ADD ci/install_pyfftw.sh /tmp/install_pyfftw.sh
 RUN cd /tmp && chmod +x install_pyfftw.sh && ./install_pyfftw.sh
+
 ADD ci/install_h5py.sh /tmp/install_h5py.sh
 RUN cd /tmp && chmod +x install_h5py.sh && ./install_h5py.sh
 
+
 # copy sources and install nifty
 COPY . /tmp/NIFTy
 RUN pip install /tmp/NIFTy
 
+
 # Cleanup
 RUN rm -r /tmp/*

ci/install_basics.sh

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

ci/install_mpi4py.sh

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

ci/install_pyfftw.sh

 #!/bin/bash
 
+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

ci/requirements.txt

 numpy
 cython
-mpi4py
 matplotlib
 plotly
-ipython==5.3.0
 nose
 parameterized
 coverage

ci/requirements_base.txt

-numpy
-cython
-nose
-parameterized
-coverage
-git+https://gitlab.mpcdf.mpg.de/ift/mpi_dummy.git
-git+https://gitlab.mpcdf.mpg.de/ift/keepers.git
-git+https://gitlab.mpcdf.mpg.de/ift/D2O.git

ci/requirements_extras.txt

+ipython==5.3.0

nifty/energies/energy.py

@@ -30,7 +30,7 @@ class Energy(Loggable, object):
             position = position.copy()
         except AttributeError:
             pass
-        self.position = position
+        self._position = position
 
     def at(self, position):
         return self.__class__(position)

nifty/field_types/field_type.py

@@ -27,16 +27,3 @@ class FieldType(DomainObject):
         else:
             result = x.copy()
         return result
-
-    def process(self, method_name, array, inplace=True, **kwargs):
-        try:
-            result_array = self.__getattr__(method_name)(array,
-                                                         inplace,
-                                                         **kwargs)
-        except AttributeError:
-            if inplace:
-                result_array = array
-            else:
-                result_array = array.copy()
-
-        return result_array

nifty/plotting/plotter/plotter.py

@@ -2,6 +2,7 @@
 
 import abc
 import os
+import sys
 
 import numpy as np
 
@@ -19,10 +20,8 @@ from nifty.plotting.figures import MultiFigure
 
 plotly = gdi.get('plotly')
 
-try:
+if plotly is not None and 'IPython' in sys.modules:
     plotly.offline.init_notebook_mode()
-except AttributeError:
-    pass
 
 rank = d2o.config.dependency_injector[
         d2o.configuration['mpi_module']].COMM_WORLD.rank