From 5daf4bf9ffe7254cc5f936c08ba692ab65f1ea22 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Thu, 25 Feb 2016 14:15:42 +0100 Subject: [PATCH 01/19] petsc: fix when building with standard blas and lapack --- pkgs/petsc/petsc.py | 4 ++-- pkgs/petsc/petsc.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/petsc/petsc.py b/pkgs/petsc/petsc.py index ba0d5bdae..acd5c8e7a 100644 --- a/pkgs/petsc/petsc.py +++ b/pkgs/petsc/petsc.py @@ -117,8 +117,8 @@ def configure(ctx, stage_args): # Special case, no meaningful BLAS/LAPACK directories when using Accelerate if ctx.parameters['platform'] != 'Darwin': - conf_lines.append('--with-blas-dir=$BLAS_DIR') - conf_lines.append('--with-lapack-dir=$LAPACK_DIR') + conf_lines.append('--with-blas-lib=$BLAS_DIR/lib/libblas.so') + conf_lines.append('--with-lapack-lib=$LAPACK_DIR/lib/liblapack.so') # Special case, ParMETIS also provides METIS if 'PARMETIS' in ctx.dependency_dir_vars: diff --git a/pkgs/petsc/petsc.yaml b/pkgs/petsc/petsc.yaml index 45fe482ad..00ffd46e6 100644 --- a/pkgs/petsc/petsc.yaml +++ b/pkgs/petsc/petsc.yaml @@ -1,6 +1,6 @@ extends: [autotools_package] dependencies: - build: [blas, mpi, python, {{build_with}}] + build: [blas, lapack, mpi, python, {{build_with}}] when version == '3.6.1': sources: From a43a7958cd078fb364efaa7e135bc2dd0baf6f9e Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Thu, 25 Feb 2016 14:17:50 +0100 Subject: [PATCH 02/19] OS X fixes --- base/cmake_package.py | 3 +++ base/cmake_package.yaml | 2 ++ pkgs/dolfin/dolfin.yaml | 5 ++++- pkgs/parmetis/parmetis.yaml | 5 ++++- 4 files changed, 13 insertions(+), 2 deletions(-) diff --git a/base/cmake_package.py b/base/cmake_package.py index f045b1660..fcf6f2f29 100644 --- a/base/cmake_package.py +++ b/base/cmake_package.py @@ -38,6 +38,9 @@ def configure(ctx, stage_args): if stage_args.get('empty_osx_deployment_target', False): conf_lines.append('-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=""') + if stage_args.get('cmake_osx_sysroot', False): + conf_lines.append('-DCMAKE_OSX_SYSROOT:STRING=%s' % stage_args['cmake_osx_sysroot']) + #cmake needs to be given all the dependency dirs as prefix paths #so that we search the hashdist directories before the system directories #CMake doesn't use the CPPFLAGS implicitly to find libraries diff --git a/base/cmake_package.yaml b/base/cmake_package.yaml index 3cd08dea1..ee6f7cbc2 100644 --- a/base/cmake_package.yaml +++ b/base/cmake_package.yaml @@ -15,6 +15,8 @@ build_stages: - name: configure after: setup_builddir debug: {{debug}} + empty_osx_deployment_target: {{empty_osx_deployment_target}} + cmake_osx_sysroot: {{cmake_osx_sysroot}} - name: make after: configure diff --git a/pkgs/dolfin/dolfin.yaml b/pkgs/dolfin/dolfin.yaml index 21cedc748..3935fb990 100644 --- a/pkgs/dolfin/dolfin.yaml +++ b/pkgs/dolfin/dolfin.yaml @@ -49,7 +49,10 @@ build_stages: after: install handler: bash bash: | - # FIXME: use install_name_tool to fix rpath + for lib in ${ARTIFACT}/lib/python{{pyver}}/site-packages/dolfin/cpp/_*.so; do + install_name_tool -add_rpath ${BOOST_DIR}/lib ${lib} + install_name_tool -add_rpath ${VTK_DIR}/lib/vtk-5.10 ${lib} + done - when: platform == 'Cygwin' name: dll_fix diff --git a/pkgs/parmetis/parmetis.yaml b/pkgs/parmetis/parmetis.yaml index 1511db4d7..5f63d8140 100644 --- a/pkgs/parmetis/parmetis.yaml +++ b/pkgs/parmetis/parmetis.yaml @@ -59,7 +59,10 @@ build_stages: before: configure handler: bash bash: | - CMAKE_FLAGS="${CMAKE_FLAGS} -DCMAKE_MACOSX_RPATH:BOOL=ON" + CMAKE_FLAGS=" + ${CMAKE_FLAGS} + -DCMAKE_MACOSX_RPATH:BOOL=ON + -DCMAKE_OSX_SYSROOT:STRING=/" - name: configure after: cmake-flags From 4ffc7dce51d5aba440f0af3a456873bddab07a68 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Thu, 25 Feb 2016 14:27:55 +0100 Subject: [PATCH 03/19] scipy: add parameter to build with openblas --- pkgs/scipy/scipy.yaml | 31 ++++++++++++++++++++++++++++--- 1 file changed, 28 insertions(+), 3 deletions(-) diff --git a/pkgs/scipy/scipy.yaml b/pkgs/scipy/scipy.yaml index 395626deb..65c520474 100644 --- a/pkgs/scipy/scipy.yaml +++ b/pkgs/scipy/scipy.yaml @@ -3,15 +3,19 @@ when platform != 'linux': when platform == 'linux': extends: [distutils_package, libflags] dependencies: - build: [lapack, numpy] - run: [lapack, numpy] + build: [blas, lapack, numpy] + run: [blas, lapack, numpy] sources: - url: http://downloads.sourceforge.net/scipy/scipy-0.13.3.tar.gz key: tar.gz:vhrty7xamdbvzvog5y5mtzpjxo4zegox +defaults: + # Build with OpenBLAS + with_openblas: false + build_stages: - - when: platform == 'linux' + - when: platform == 'linux' and not with_openblas name: set-lapack-paths after: libflags before: install @@ -21,3 +25,24 @@ build_stages: export ATLAS=$LAPACK_DIR export BLAS=$LAPACK_DIR export LAPACK=$LAPACK_DIR + + - when: platform == 'linux' and with_openblas + name: set-lapack-paths + after: libflags + before: install + handler: bash + bash: | + export LDFLAGS="-shared -Wl,-rpath=${PYTHON_DIR}/lib -Wl,-rpath=${BLAS_DIR}/lib $(${PYTHON_DIR}/bin/python-config --ldflags)" + #export ATLAS=None + export LAPACK=${BLAS_DIR}/lib/libopenblas.so + export BLAS=${BLAS_DIR}/lib/libopenblas.so + +# Make sure that the fortran objects are compiled with -fPIC + - when: platform == 'linux' + name: compile-fc-with-fPIC + after: setup_dirs + before: install + handler: bash + bash: | + export FFLAGS="$FFLAGS -fPIC" + export FCFLAGS="$FCFLAGS -fPIC" From 484a699ff5530536e94e5fa895f9b22592e73c04 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 26 Feb 2016 11:43:26 +0100 Subject: [PATCH 04/19] Add host packages for pip and py --- pkgs/host-pip.yaml | 10 ++++++++++ pkgs/host-py.yaml | 10 ++++++++++ 2 files changed, 20 insertions(+) create mode 100644 pkgs/host-pip.yaml create mode 100644 pkgs/host-py.yaml diff --git a/pkgs/host-pip.yaml b/pkgs/host-pip.yaml new file mode 100644 index 000000000..1ec10d085 --- /dev/null +++ b/pkgs/host-pip.yaml @@ -0,0 +1,10 @@ +build_stages: +- handler: bash + bash: | + mkdir -p ${ARTIFACT}/{{python_site_packages_rel}} + ln -s {{python_host_packages}}/pip ${ARTIFACT}/{{python_site_packages_rel}} + +profile_links: +- name: python_packages + link: '{{python_site_packages_rel}}/*' + dirs: true diff --git a/pkgs/host-py.yaml b/pkgs/host-py.yaml new file mode 100644 index 000000000..2ebdcf535 --- /dev/null +++ b/pkgs/host-py.yaml @@ -0,0 +1,10 @@ +build_stages: +- handler: bash + bash: | + mkdir -p ${ARTIFACT}/{{python_site_packages_rel}} + ln -s {{python_host_packages}}/py ${ARTIFACT}/{{python_site_packages_rel}} + +profile_links: +- name: python_packages + link: '{{python_site_packages_rel}}/*' + dirs: true From 4cb8ec1e1169a548d00a39b3fd9bb8525f6a0d8e Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 26 Feb 2016 11:45:03 +0100 Subject: [PATCH 05/19] pip: update to version 8.0.3 --- pkgs/pip.yaml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/pkgs/pip.yaml b/pkgs/pip.yaml index 6f82388b3..7c3e0d927 100644 --- a/pkgs/pip.yaml +++ b/pkgs/pip.yaml @@ -1,9 +1,5 @@ extends: [setuptools_package] -dependencies: - build: [] - run: [] - sources: -- key: tar.gz:zichtbxqkkgpvf22ct5z67yqmjy5jygd - url: https://pypi.python.org/packages/source/p/pip/pip-7.1.2.tar.gz +- key: tar.gz:gd4ywzxt7yigtrjjusivs7juuhbcjjug + url: https://pypi.python.org/packages/source/p/pip/pip-8.0.3.tar.gz From a0437679dcdafe7fe5e15463c220da714c2b3c7e Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 26 Feb 2016 11:45:52 +0100 Subject: [PATCH 06/19] setuptools: update to version 20.1.1 --- pkgs/setuptools.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/setuptools.yaml b/pkgs/setuptools.yaml index 4a5beb306..0acb52b0b 100644 --- a/pkgs/setuptools.yaml +++ b/pkgs/setuptools.yaml @@ -18,8 +18,8 @@ build_stages: ${PYTHON} setup.py install --prefix=. --root=${ARTIFACT}/Python.framework/Versions/{{pyver}} --single-version-externally-managed sources: - - url: https://pypi.python.org/packages/source/s/setuptools/setuptools-3.4.3.tar.gz - key: tar.gz:yfr3o4jkjyuvq7cmwfn52gmjt7xmiopn +- key: tar.gz:ezr44cyooqxoe7b2a2znufcwhzhw64j6 + url: https://pypi.python.org/packages/source/s/setuptools/setuptools-20.1.1.tar.gz when_build_dependency: - when: not python_framework From 96d8ff575421b8f75cf720c6cc81958a2226ec5e Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 26 Feb 2016 11:46:17 +0100 Subject: [PATCH 07/19] py: update to version 1.4.31 --- pkgs/py.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/py.yaml b/pkgs/py.yaml index 5523c68a9..d2cad85dc 100644 --- a/pkgs/py.yaml +++ b/pkgs/py.yaml @@ -1,5 +1,5 @@ extends: [setuptools_package] sources: - - url: https://pypi.python.org/packages/source/p/py/py-1.4.20.tar.gz - key: tar.gz:epez3gplwkta5nychn2xpp6jrcwlacja +- key: tar.gz:uzibsy6hex6ckvg2x7worlu2r626csoa + url: https://pypi.python.org/packages/source/p/py/py-1.4.31.tar.gz From bbf2f77ec152dd6b3d10cec019fc38e84c653dda Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 26 Feb 2016 14:26:41 +0100 Subject: [PATCH 08/19] vtk: add parameter vtk_wrap_python that build vtk without python if set to false (default is true) --- pkgs/vtk/vtk.yaml | 36 +++++++++++++++++++++++++----------- 1 file changed, 25 insertions(+), 11 deletions(-) diff --git a/pkgs/vtk/vtk.yaml b/pkgs/vtk/vtk.yaml index 79d8f02ee..aebf775b2 100644 --- a/pkgs/vtk/vtk.yaml +++ b/pkgs/vtk/vtk.yaml @@ -1,8 +1,9 @@ extends: [cmake_package] dependencies: build: - - python - - setuptools + - when vtk_wrap_python: + - python + - setuptools - libtiff - when platform == 'linux': - patchelf @@ -17,10 +18,11 @@ defaults: # lib/vtk-5.10/libvtkHybrid.so.5.10.1 contains hard-coded path relocatable: false vtk_use_tk: false + vtk_wrap_python: true build_stages: - -- name: setup_dirs +- when: vtk_wrap_python + name: setup_dirs after: prologue before: setup_builddir handler: bash @@ -56,12 +58,9 @@ build_stages: - '-D BUILD_TESTING:BOOL=OFF' - '-D BUILD_EXAMPLES:BOOL=OFF' - '-D BUILD_SHARED_LIBS:BOOL=ON' - - '-D VTK_WRAP_PYTHON:BOOL=ON' - '-D VTK_WRAP_TCL:BOOL=OFF' - '-D VTK_USE_GL2PS:BOOL=ON' - - '-D VTK_PYTHON_SETUP_ARGS:STRING="--prefix=. --root=${ARTIFACT} --single-version-externally-managed"' - '-D CMAKE_INSTALL_RPATH:STRING="${ARTIFACT}/lib/vtk-5.10"' - - '-D PYTHON_EXECUTABLE:FILEPATH="${PYTHON}"' - '-D VTK_USE_SYSTEM_TIFF:BOOL=ON' - when: vtk_use_tk @@ -74,7 +73,19 @@ build_stages: mode: update extra: ['-D VTK_USE_TK:BOOL=OFF'] -- when: platform == 'linux' +- when: vtk_wrap_python + name: configure + mode: update + extra: ['-D VTK_WRAP_PYTHON:BOOL=ON', + '-D VTK_PYTHON_SETUP_ARGS:STRING="--prefix=. --root=${ARTIFACT} --single-version-externally-managed"', + '-D PYTHON_EXECUTABLE:FILEPATH="${PYTHON}"'] + +- when: not vtk_wrap_python + name: configure + mode: update + extra: ['-D VTK_WRAP_PYTHON:BOOL=OFF'] + +- when: platform == 'linux' and vtk_wrap_python name: rpath_fix after: install handler: bash @@ -103,15 +114,18 @@ build_stages: done profile_links: -- name: python_packages +- when: vtk_wrap_python + name: python_packages link: 'lib/python{{pyver}}/site-packages/*' dirs: true -- name: python_exclude +- when: vtk_wrap_python + name: python_exclude after: python_packages before: everything exclude: 'lib/python{{pyver}}/site-packages/**/*' when_build_dependency: -- prepend_path: PYTHONPATH +- when: vtk_wrap_python + prepend_path: PYTHONPATH value: '${ARTIFACT}/lib/python{{pyver}}/site-packages' From 3d6f80310174bad03f2910712544f5f3b6ca480b Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 4 Mar 2016 19:13:02 +0100 Subject: [PATCH 09/19] Switch to setuptools for fenics python packages and update their dependencies --- pkgs/ffc.yaml | 6 +++--- pkgs/fiat.yaml | 2 +- pkgs/instant.yaml | 3 ++- pkgs/ufl.yaml | 4 ++-- pkgs/uflacs.yaml | 6 +++--- 5 files changed, 11 insertions(+), 10 deletions(-) diff --git a/pkgs/ffc.yaml b/pkgs/ffc.yaml index 8d269c472..125fa7244 100644 --- a/pkgs/ffc.yaml +++ b/pkgs/ffc.yaml @@ -1,7 +1,7 @@ -extends: [distutils_package] +extends: [setuptools_package] dependencies: - build: [numpy, swig] - run: [fiat, instant, numpy, six, ufl] + build: [fiat, instant, numpy, six, ufl, swig] + run: [fiat, instant, numpy, six, ufl, swig] sources: - key: tar.gz:haxhoe76owljjzpqoudlcrho5llidylj diff --git a/pkgs/fiat.yaml b/pkgs/fiat.yaml index ea893d751..882b135a5 100644 --- a/pkgs/fiat.yaml +++ b/pkgs/fiat.yaml @@ -1,6 +1,6 @@ extends: [setuptools_package] dependencies: - build: [] + build: [numpy, sympy] run: [numpy, sympy] sources: diff --git a/pkgs/instant.yaml b/pkgs/instant.yaml index c73c41bf4..ed4b3e9be 100644 --- a/pkgs/instant.yaml +++ b/pkgs/instant.yaml @@ -1,5 +1,6 @@ -extends: [distutils_package] +extends: [setuptools_package] dependencies: + build: [numpy] run: [cmake, flufl_lock, numpy, swig] sources: diff --git a/pkgs/ufl.yaml b/pkgs/ufl.yaml index ebd4ead97..a3f58fc84 100644 --- a/pkgs/ufl.yaml +++ b/pkgs/ufl.yaml @@ -1,6 +1,6 @@ -extends: [distutils_package] +extends: [setuptools_package] dependencies: - build: [] + build: [numpy, six] run: [numpy, six] sources: diff --git a/pkgs/uflacs.yaml b/pkgs/uflacs.yaml index ed76d9532..0b5778749 100644 --- a/pkgs/uflacs.yaml +++ b/pkgs/uflacs.yaml @@ -1,7 +1,7 @@ -extends: [distutils_package] +extends: [setuptools_package] dependencies: - build: [] - run: [ffc, numpy, six, ufl] + build: [numpy, six, ufl] + run: [numpy, six, ufl] sources: - key: tar.gz:x2ybjis6ms5zjw3hodnelft2gsq32t4x From 7aa51011288b3cccdeed54af1440095f386ef244 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Mon, 7 Mar 2016 13:54:59 +0100 Subject: [PATCH 10/19] pip: add 'bin' dir to PATH when build dependency --- pkgs/pip.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/pip.yaml b/pkgs/pip.yaml index 7c3e0d927..ce2b5977f 100644 --- a/pkgs/pip.yaml +++ b/pkgs/pip.yaml @@ -3,3 +3,7 @@ extends: [setuptools_package] sources: - key: tar.gz:gd4ywzxt7yigtrjjusivs7juuhbcjjug url: https://pypi.python.org/packages/source/p/pip/pip-8.0.3.tar.gz + +when_build_dependency: +- prepend_path: PATH + value: '${ARTIFACT}/bin' From 88716eac86fbe1cf0ccc3724ff49d0b26cfbff82 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Mon, 7 Mar 2016 13:56:18 +0100 Subject: [PATCH 11/19] Add base package for installing Python packages using pip --- base/pip_package.yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 base/pip_package.yaml diff --git a/base/pip_package.yaml b/base/pip_package.yaml new file mode 100644 index 000000000..f7f65517d --- /dev/null +++ b/base/pip_package.yaml @@ -0,0 +1,29 @@ +# pip_package.yaml +# Use for installing Python packages using pip. + +extends: [base_package] + +dependencies: + build: [python, pip, setuptools] + run: [python, pip, setuptools] + +build_stages: + +- name: install + handler: bash + bash: | + pip install --verbose --no-deps --upgrade --prefix=${ARTIFACT} . + +profile_links: +- name: python_packages + link: 'lib/python{{pyver}}/site-packages/*' + dirs: true + +- name: python_exclude + after: python_packages + before: everything + exclude: 'lib/python{{pyver}}/site-packages/**/*' + +when_build_dependency: +- prepend_path: PYTHONPATH + value: '${ARTIFACT}/lib/python{{pyver}}/site-packages' From 1d385d49eef90a3fed5610c6110d841f09381496 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Mon, 7 Mar 2016 13:57:42 +0100 Subject: [PATCH 12/19] ffc: switch to pip_package and set UFC_DIR when build dependency --- pkgs/ffc.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pkgs/ffc.yaml b/pkgs/ffc.yaml index 125fa7244..80db9bfc9 100644 --- a/pkgs/ffc.yaml +++ b/pkgs/ffc.yaml @@ -1,4 +1,4 @@ -extends: [setuptools_package] +extends: [pip_package] dependencies: build: [fiat, instant, numpy, six, ufl, swig] run: [fiat, instant, numpy, six, ufl, swig] @@ -14,3 +14,5 @@ defaults: when_build_dependency: - prepend_path: PATH value: '${ARTIFACT}/bin' +- set: UFC_DIR + value: '${ARTIFACT}' From cdc31f1d35e723052daf69cf189c2053ded49730 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Tue, 8 Mar 2016 11:23:24 +0100 Subject: [PATCH 13/19] Switch to pip_package for fiat, instant and ufl --- pkgs/fiat.yaml | 2 +- pkgs/instant.yaml | 2 +- pkgs/ufl.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/fiat.yaml b/pkgs/fiat.yaml index 882b135a5..78a27a68e 100644 --- a/pkgs/fiat.yaml +++ b/pkgs/fiat.yaml @@ -1,4 +1,4 @@ -extends: [setuptools_package] +extends: [pip_package] dependencies: build: [numpy, sympy] run: [numpy, sympy] diff --git a/pkgs/instant.yaml b/pkgs/instant.yaml index ed4b3e9be..9bd7d12c0 100644 --- a/pkgs/instant.yaml +++ b/pkgs/instant.yaml @@ -1,4 +1,4 @@ -extends: [setuptools_package] +extends: [pip_package] dependencies: build: [numpy] run: [cmake, flufl_lock, numpy, swig] diff --git a/pkgs/ufl.yaml b/pkgs/ufl.yaml index a3f58fc84..28b7a3c29 100644 --- a/pkgs/ufl.yaml +++ b/pkgs/ufl.yaml @@ -1,4 +1,4 @@ -extends: [setuptools_package] +extends: [pip_package] dependencies: build: [numpy, six] run: [numpy, six] From 246ffc6f5710f0ed71e402e9cf1842654e5cad51 Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 29 Apr 2016 13:25:27 +0200 Subject: [PATCH 14/19] patch for MAX_JBUFS in parmetis on OS X clang 7.3 requires MAX_JBUFS < 25 --- pkgs/parmetis/clang_max_jbufs.patch | 12 ++++++++++++ pkgs/parmetis/parmetis.yaml | 5 ++++- 2 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 pkgs/parmetis/clang_max_jbufs.patch diff --git a/pkgs/parmetis/clang_max_jbufs.patch b/pkgs/parmetis/clang_max_jbufs.patch new file mode 100644 index 000000000..670ca2759 --- /dev/null +++ b/pkgs/parmetis/clang_max_jbufs.patch @@ -0,0 +1,12 @@ +--- parmetis-4.0.3/metis/GKlib/error.c 2016-04-29 13:21:02.000000000 +0200 ++++ parmetis-4.0.3/metis/GKlib/error.c 2016-04-29 13:21:06.000000000 +0200 +@@ -18,7 +18,7 @@ + + /* These are the jmp_buf for the graceful exit in case of severe errors. + Multiple buffers are defined to allow for recursive invokation. */ +-#define MAX_JBUFS 128 ++#define MAX_JBUFS 24 + __thread int gk_cur_jbufs=-1; + __thread jmp_buf gk_jbufs[MAX_JBUFS]; + __thread jmp_buf gk_jbuf; + \ No newline at end of file diff --git a/pkgs/parmetis/parmetis.yaml b/pkgs/parmetis/parmetis.yaml index 5f63d8140..989fbe9c7 100644 --- a/pkgs/parmetis/parmetis.yaml +++ b/pkgs/parmetis/parmetis.yaml @@ -23,11 +23,14 @@ build_stages: - when: platform == 'Darwin' name: no_unused_but_set_variable - files: [no_unused_but_set_variable.patch] + files: + - no_unused_but_set_variable.patch + - clang_max_jbufs.patch before: configure handler: bash bash: | patch -p1 < _hashdist/no_unused_but_set_variable.patch + patch -p1 < _hashdist/clang_max_jbufs.patch - when: platform == 'Cygwin' name: fix___cdecl_redefined From a7d2246aef0edd37c2d2c456932fb67e40752cf6 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 17 Jun 2016 11:31:38 +0200 Subject: [PATCH 15/19] cython: use tarball from github --- pkgs/cython.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/cython.yaml b/pkgs/cython.yaml index 46489c9c5..7e2d86db9 100644 --- a/pkgs/cython.yaml +++ b/pkgs/cython.yaml @@ -1,8 +1,8 @@ extends: [distutils_package] sources: -- key: tar.gz:lebhjlenxupgftdz3fhlfyxuvzqm5ki2 - url: http://cython.org/release/Cython-0.23.3.tar.gz +- key: tar.gz:iqajqxtqrijqcfgww7vbkl7dxpgmj333 + url: https://github.com/cython/cython/archive/0.23.3.tar.gz when_build_dependency: - prepend_path: PATH From e92f0a4598fc9afc5ec6bd9d8b2486ee6d4bb319 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Thu, 23 Jun 2016 19:20:01 +0200 Subject: [PATCH 16/19] Update FEniCS packages for 2016.1.0 release --- pkgs/dijitso.yaml | 8 ++++++++ pkgs/dolfin/dolfin.yaml | 4 ++-- pkgs/ffc.yaml | 4 ++-- pkgs/fiat.yaml | 4 ++-- pkgs/instant.yaml | 4 ++-- pkgs/mshr.yaml | 4 ++-- pkgs/ufl.yaml | 4 ++-- 7 files changed, 20 insertions(+), 12 deletions(-) create mode 100644 pkgs/dijitso.yaml diff --git a/pkgs/dijitso.yaml b/pkgs/dijitso.yaml new file mode 100644 index 000000000..29101e62c --- /dev/null +++ b/pkgs/dijitso.yaml @@ -0,0 +1,8 @@ +extends: [pip_package] +dependencies: + build: [mpi4py, numpy, six] + run: [mpi4py, numpy, six] + +sources: +- key: tar.gz:amakzmnzx6kojxrgbznuf5jklopvcwsw + url: https://bitbucket.org/fenics-project/dijitso/downloads/dijitso-2016.1.0.tar.gz diff --git a/pkgs/dolfin/dolfin.yaml b/pkgs/dolfin/dolfin.yaml index a2377cd5a..9ad33a4ae 100644 --- a/pkgs/dolfin/dolfin.yaml +++ b/pkgs/dolfin/dolfin.yaml @@ -15,8 +15,8 @@ dependencies: run: [ply] sources: -- key: tar.gz:m7vkyx7m43tr3icvtngkqqrrk346tguv - url: https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.6.0.tar.gz +- key: tar.gz:miuljvsbqknezuzbig742il2cwlke7kz + url: https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-2016.1.0.tar.gz defaults: # share/dolfin/DOLFINConfig.cmake contains hard-coded path diff --git a/pkgs/ffc.yaml b/pkgs/ffc.yaml index 80db9bfc9..a5eca4a5b 100644 --- a/pkgs/ffc.yaml +++ b/pkgs/ffc.yaml @@ -4,8 +4,8 @@ dependencies: run: [fiat, instant, numpy, six, ufl, swig] sources: -- key: tar.gz:haxhoe76owljjzpqoudlcrho5llidylj - url: https://bitbucket.org/fenics-project/ffc/downloads/ffc-1.6.0.tar.gz +- key: tar.gz:kjbqzzgh2v6odoa6wx5tasmser6jis6g + url: https://bitbucket.org/fenics-project/ffc/downloads/ffc-2016.1.0.tar.gz defaults: # share/ufc/UFCConfig.cmake contains hard-coded path diff --git a/pkgs/fiat.yaml b/pkgs/fiat.yaml index 78a27a68e..5195fa99e 100644 --- a/pkgs/fiat.yaml +++ b/pkgs/fiat.yaml @@ -4,5 +4,5 @@ dependencies: run: [numpy, sympy] sources: -- key: tar.gz:qwhkh2jwvu5tkwfuot74zlukpoo53ovp - url: https://bitbucket.org/fenics-project/fiat/downloads/fiat-1.6.0.tar.gz +- key: tar.gz:qulsgetkog6bvyw4jllosmyl3g2u2uw3 + url: https://bitbucket.org/fenics-project/fiat/downloads/fiat-2016.1.0.tar.gz diff --git a/pkgs/instant.yaml b/pkgs/instant.yaml index 9bd7d12c0..baec60f83 100644 --- a/pkgs/instant.yaml +++ b/pkgs/instant.yaml @@ -4,5 +4,5 @@ dependencies: run: [cmake, flufl_lock, numpy, swig] sources: -- key: tar.gz:end6aiuvggljbfmrd7nr3yyl2555274b - url: https://bitbucket.org/fenics-project/instant/downloads/instant-1.6.0.tar.gz +- key: tar.gz:ppydzct3mh6r4qzlr45aibkbbltirexl + url: https://bitbucket.org/fenics-project/instant/downloads/instant-2016.1.0.tar.gz diff --git a/pkgs/mshr.yaml b/pkgs/mshr.yaml index 06c4da327..1fdf8fd6a 100644 --- a/pkgs/mshr.yaml +++ b/pkgs/mshr.yaml @@ -4,8 +4,8 @@ dependencies: build: [python, boost, dolfin, gmp, mpfr, mpi, swig, {{build_with}}] sources: -- key: tar.gz:afm2l4z7m53oxkxxf4dsfxmth4jnxmsg - url: https://bitbucket.org/fenics-project/mshr/downloads/mshr-1.6.0.tar.gz +- key: tar.gz:5ehq6cmiyeclibycpkxslq2h7jxjtrf7 + url: https://bitbucket.org/fenics-project/mshr/downloads/mshr-2016.1.0.tar.gz defaults: # lib/CMake/mshr/mshr-config.cmake contains hard-coded path diff --git a/pkgs/ufl.yaml b/pkgs/ufl.yaml index 28b7a3c29..0f223ea75 100644 --- a/pkgs/ufl.yaml +++ b/pkgs/ufl.yaml @@ -4,5 +4,5 @@ dependencies: run: [numpy, six] sources: -- key: tar.gz:y5oepapfcbcqj4kyznbm3b5m575jauxi - url: https://bitbucket.org/fenics-project/ufl/downloads/ufl-1.6.0.tar.gz +- key: tar.gz:rxgp4egreun2jcsniosmnse2xydwhebc + url: https://bitbucket.org/fenics-project/ufl/downloads/ufl-2016.1.0.tar.gz From 2b3175daaa1159f5f885011ade5282d3c83cecac Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Wed, 29 Jun 2016 14:43:29 +0200 Subject: [PATCH 17/19] Respect prologue in pip_package --- base/pip_package.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base/pip_package.yaml b/base/pip_package.yaml index f7f65517d..35edd2b6a 100644 --- a/base/pip_package.yaml +++ b/base/pip_package.yaml @@ -8,8 +8,8 @@ dependencies: run: [python, pip, setuptools] build_stages: - - name: install + after: prologue handler: bash bash: | pip install --verbose --no-deps --upgrade --prefix=${ARTIFACT} . From 910f04e7fa6c8c7cac55c1298481cff07550e4b2 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Tue, 12 Jul 2016 14:18:13 +0200 Subject: [PATCH 18/19] Try to use trusty for travis and use libboost-all-dev for dolfin tests --- .travis.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 849c50d74..6dd1ff2ac 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,6 +17,8 @@ env: - TEST_PROFILE="test.dolfin.yaml" python: - 2.7 +sudo: required +dist: trusty before_install: - sudo apt-get update -qq - sudo apt-get install gfortran pv @@ -45,7 +47,7 @@ before_install: sudo apt-get install python-scipy; fi - if [[ "${TEST_PROFILE}" == "test.dolfin.yaml" ]]; then - sudo apt-get install cmake libopenmpi-dev python-dev libblas-dev liblapack-dev wget libboost-program-options1.48-dev libboost-filesystem1.48-dev libboost-serialization1.48-dev libboost-thread1.48-dev libboost-iostreams1.48-dev libboost-math1.48-dev libboost-timer1.48-dev libboost-chrono1.48-dev; + sudo apt-get install cmake libopenmpi-dev python-dev libblas-dev liblapack-dev wget libboost-all-dev; fi install: - git clone https://github.com/hashdist/hashdist From ac4e52afe35f648aca96d4e08862e4372acbdf29 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Tue, 12 Jul 2016 14:33:02 +0200 Subject: [PATCH 19/19] Automatic yes to prompts for apt-get --- .travis.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.travis.yml b/.travis.yml index 6dd1ff2ac..aed27ea34 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,33 +21,33 @@ sudo: required dist: trusty before_install: - sudo apt-get update -qq - - sudo apt-get install gfortran pv + - sudo apt-get -y install gfortran pv - if [[ "${TEST_PROFILE}" == "test.packages1.yaml" ]]; then - sudo apt-get install liblapack-dev; + sudo apt-get -y install liblapack-dev; fi - if [[ "${TEST_PROFILE}" == "test.packages2.yaml" ]]; then - sudo apt-get install mpich2 liblapack-dev; + sudo apt-get -y install mpich2 liblapack-dev; fi - if [[ "${TEST_PROFILE}" == "test.packages3.yaml" ]]; then - sudo apt-get install mpich2 liblapack-dev; + sudo apt-get -y install mpich2 liblapack-dev; fi - if [[ "${TEST_PROFILE}" == "test.cmake.yaml" ]]; then - sudo apt-get install mpich2; + sudo apt-get -y install mpich2; fi - if [[ "${TEST_PROFILE}" == "test.boost.yaml" ]]; then - sudo apt-get install mpich2; + sudo apt-get -y install mpich2; fi - if [[ "${TEST_PROFILE}" == "test.clawpack.gitsubmodules.yaml" ]]; then - sudo apt-get install liblapack-dev; + sudo apt-get -y install liblapack-dev; fi - if [[ "${TEST_PROFILE}" == "test.netcdf4.yaml" ]]; then - sudo apt-get install mpich2; + sudo apt-get -y install mpich2; fi - if [[ "${TEST_PROFILE}" == "test.host-scipy.yaml" ]]; then - sudo apt-get install python-scipy; + sudo apt-get -y install python-scipy; fi - if [[ "${TEST_PROFILE}" == "test.dolfin.yaml" ]]; then - sudo apt-get install cmake libopenmpi-dev python-dev libblas-dev liblapack-dev wget libboost-all-dev; + sudo apt-get -y install cmake libopenmpi-dev python-dev libblas-dev liblapack-dev wget libboost-all-dev; fi install: - git clone https://github.com/hashdist/hashdist