restructured and deduplicated ci components

.gitlab-ci.yml

@@ -11,10 +11,8 @@ 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
+  - ci/install_basics.sh
+  - pip install --upgrade -r ci/requirements.txt
   - chmod +x ci/*.sh
 
 test_min:
@@ -26,22 +24,16 @@ 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 +41,10 @@ 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_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