tweak the build process to get more up-to-date packages

.gitlab-ci.yml

@@ -14,7 +14,7 @@ before_script:
   - >
     apt-get install -y build-essential python python-pip python-dev git
     autoconf gsl-bin libgsl-dev wget python-numpy cython
-  - pip install -r ci/requirements_base.txt
+  - pip install --upgrade -r ci/requirements_base.txt
   - chmod +x ci/*.sh
 
 test_min:
@@ -26,7 +26,8 @@ test_min:
 test_mpi:
   stage: test
   script:
-    - apt-get install -y openmpi-bin libopenmpi-dev python-mpi4py
+    - apt-get install -y openmpi-bin libopenmpi-dev
+    - pip install mpi4py
     - ci/install_pyHealpix.sh
     - python setup.py build_ext --inplace
     - nosetests -vv
@@ -38,8 +39,10 @@ test_mpi_fftw:
     - >
       apt-get install -y libatlas-base-dev libfftw3-bin libfftw3-dev
       libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3
-      libfftw3-quad3 libfftw3-single3 python-mpi4py python-pyfftw
+      libfftw3-quad3 libfftw3-single3
+    - pip install mpi4py
     - ci/install_pyHealpix.sh
+    - ci/install_pyfftw.sh
     - python setup.py build_ext --inplace
     - nosetests -vv
 
@@ -53,8 +56,11 @@ test_mpi_fftw_hdf5:
       libfftw3-quad3 libfftw3-single3
     - >
       apt-get install -y libhdf5-10 libhdf5-dev libhdf5-openmpi-10
-      libhdf5-openmpi-dev hdf5-tools python-mpi4py python-pyfftw python-h5py
+      libhdf5-openmpi-dev hdf5-tools
+    - pip install mpi4py
     - ci/install_pyHealpix.sh
+    - ci/install_h5py.sh
+    - ci/install_pyfftw.sh
     - python setup.py build_ext --inplace
     - nosetests -vv --with-coverage --cover-package=nifty --cover-branches
     - >

Dockerfile

@@ -4,19 +4,24 @@ FROM ubuntu:latest
 RUN \
     apt-get update && \
     apt-get install -y build-essential python python-pip python-dev git \
-    gfortran autoconf gsl-bin libgsl-dev python-matplotlib openmpi-bin \
+    autoconf gsl-bin libgsl-dev python-matplotlib openmpi-bin \
     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-h5py python-pyfftw
+    libhdf5-openmpi-10 libhdf5-openmpi-dev hdf5-tools
 
 # python dependencies
 ADD ci/requirements.txt /tmp/requirements.txt
-RUN pip install -r /tmp/requirements.txt
+RUN pip install --upgrade -r /tmp/requirements.txt
+RUN pip install mpi4py
 
-# install pyHealpix
+# 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_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

ci/install_h5py.sh

+#!/bin/bash
+
+wget https://api.github.com/repos/h5py/h5py/tags -O - | grep tarball_url | grep -v rc | head -n 1 | cut -d '"' -f 4 | wget -i - -O h5py.tar.gz
+tar xzf h5py.tar.gz
+cd h5py-h5py*
+export CC=mpicc
+export HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+python setup.py configure --mpi
+python setup.py build
+python setup.py install
+cd ..
+rm -r h5py-h5py*
+rm h5py.tar.gz

ci/install_pyfftw.sh

+#!/bin/bash
+
+git clone -b mpi https://github.com/fredRos/pyFFTW.git
+cd pyFFTW/
+CC=mpicc python setup.py build_ext install
+cd ..
+rm -r pyFFTW

ci/requirements.txt

+numpy
 nose
 parameterized
 coverage

ci/requirements_base.txt

+numpy
 nose
 parameterized
 coverage