extracted numpy component

2584a608 · Marco Mariani · 90d74c37 · 2584a608 · 2584a608 · 2584a608
Commit 2584a608 authored Aug 05, 2014 by Marco Mariani
5 changed files
--- a/component/libatlas/buildout.cfg
+++ b/component/libatlas/buildout.cfg
@@ -11,22 +11,40 @@ filename = ${:_buildout_section_name_}
 download-only = true


+[atlas-download]
+recipe = hexagonit.recipe.download
+version = 3.10.1
+filename = atlas${:version}.tar.bz2
+url = http://downloads.sourceforge.net/project/math-atlas/Stable/${:version}/${:filename}
+md5sum = 78753e869231cc1417a92eebaa076718
+download-only = true
+mode = 0644
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+
+
+[lapack-download]
+recipe = hexagonit.recipe.download
+version = 3.5.0
+filename = lapack-${:version}.tgz
+url = http://www.netlib.org/lapack/${:filename}
+md5sum = b1d3e3e425b2e44a06760ff173104bdf
+download-only = true
+mode = 0644
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+
+
+
 [libatlas]
 recipe = cp.recipe.cmd
 location = ${buildout:parts-directory}/${:_buildout_section_name_}
-version = 3.10.1
 lapack_version = 3.5.0
-filename = atlas${:version}.tar.bz2
 install_cmd =
  set -e
  mkdir -p ${:location}__compile__
  cd ${:location}__compile__
  export SRCdir=`pwd`/ATLAS
  export BLDdir=`pwd`/build
-  wget -nc http://downloads.sourceforge.net/project/math-atlas/Stable/${:version}/${:filename}
-  wget -nc http://www.netlib.org/lapack/lapack-${:lapack_version}.tgz
-  echo "78753e869231cc1417a92eebaa076718  ${:filename}" | md5sum --check --strict --quiet -
-  tar xfj atlas${:version}.tar.bz2
+  tar xfj ${atlas-download:location}/${atlas-download:filename}
  cd $SRCdir
  # http://stackoverflow.com/questions/14592401/atlas-install-really-need-to-get-past-cpu-throttle-check
  # http://sourceforge.net/p/math-atlas/support-requests/886/
@@ -37,7 +55,7 @@ install_cmd =
  export LD_PRELOAD=$F77LIB
  $SRCdir/configure -b 64 \
        --prefix=${:location} \
-        --with-netlib-lapack-tarfile=${:location}__compile__/lapack-${:lapack_version}.tgz \
+        --with-netlib-lapack-tarfile=${lapack-download:location}/${lapack-download:filename} \
        -C acg ${gcc-fortran:location}/bin/gcc \
        -C if ${gcc-fortran:location}/bin/gfortran \
        --shared

--- a/component/numpy/buildout.cfg
+++ b/component/numpy/buildout.cfg
+[buildout]
+
+extends =
+  ../git/buildout.cfg
+  ../gcc/buildout.cfg
+  ../libatlas/buildout.cfg
+  ../libblas/buildout.cfg
+
+
+[scipy-repository.git]
+recipe = slapos.recipe.build:gitclone
+repository = https://github.com/mmariani/scipy.git
+branch = hardcoded-numpy-location
+git-executable = ${git:location}/bin/git
+
+[scikit-learn-repository.git]
+recipe = slapos.recipe.build:gitclone
+repository = https://github.com/scikit-learn/scikit-learn.git
+branch = master
+git-executable = ${git:location}/bin/git
+
+
+[build-venv]
+dependency = ${prerequired-eggs:recipe}
+recipe = cp.recipe.cmd
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+install_cmd =
+  if [ -d ${:location} ]; then
+    exit
+  fi
+  mkdir -p ${:location}
+  cd ${:location}
+  unset PYTHONPATH
+  export PATH="${gcc-fortran:location}/bin:$PATH"
+  export LD_PRELOAD="${gcc-fortran:location}/lib64/libgfortran.so.3 ${libblas:location}/libf77blas.so.3"
+  export ATLAS=${libatlas:location}/lib/libsatlas.so
+  export BLAS=${libblas:location}/lib/libfblas.a
+  export LAPACK=${libatlas:location}/lib/liblapack.a
+  ${python2.7-virtualenv:executable} ${:location}
+  . ${:location}/bin/activate
+  ${:location}/bin/pip install numpy
+  ${:location}/bin/pip install Tempita
+  export PYTHONPATH=${buildout:eggs-directory}/numpy-1.8.1-py2.7-linux-x86_64.egg
+  cd ${scipy-repository.git:location}
+  python setupegg.py bdist_egg
+  cd ${scikit-learn-repository.git:location}
+  python setup.py bdist_egg
+update_cmd = ${:install_cmd}
+
+
+[prerequired-eggs]
+recipe = zc.recipe.egg
+eggs =
+  slapos.cookbook
+  numpy
+
+
+[numpy-eggs]
+dependencies = ${build-venv:recipe}
+recipe = zc.recipe.egg
+find-links =
+    ${scipy-repository.git:location}/dist
+    ${scikit-learn-repository.git:location}/dist
+eggs =
+  numpy
+  scipy
+  scikit-learn
+interpreter = python-numpy
+
+
+[versions]
+cp.recipe.cmd = 0.5nxd001
+numpy = 1.8.1
+scipy = 0.13.3001
+scikit-learn = 0.16-git
+
--- a/software/numpy/erp5.cfg
+++ b/software/numpy/erp5.cfg
+[buildout]
+extends =
+  ../../stack/erp5/buildout.cfg
+  ../../component/numpy/buildout.cfg
+
+
+parts =
+  build-venv
+  numpy-eggs
+
+# erp5 stack
+  rdiff-backup
+  aspell
+  aspell-en-dictionary
+  apache
+  apache-antiloris
+  file
+  graphviz
+  haproxy
+  jsl
+  stunnel
+  varnish-3.0
+  w3m
+  poppler
+  libpng
+  ghostscript
+  mariadb
+  mroonga-mariadb
+  imagemagick
+  inkscape
+  libdmtx
+  dmtx-utils
+  kumo
+  libreoffice-bin
+  w3-validator
+  tesseract
+  hookbox
+  perl-DBD-mariadb
+  perl-DBI
+  percona-toolkit
+  zabbix-agent
+  dcron
+  dash
+  wget
+
+# Buildoutish
+  patched-eggs
+  eggs
+  testrunner
+  test_suite_runner
+
+# basic Xorg
+  libXdmcp
+  libXext
+  libXau
+  libSM
+  libXrender
+
+# fonts
+  liberation-fonts
+  ipaex-fonts
+  ipa-fonts
+  ocrb-fonts
+  android-fonts
+
+# Cloudooo specific part
+  cloudooo
+
+# get git repositories
+  erp5
+  genbt5list
+
+# fix products path (Zeo needs ERP5 Products to be available for
+# conflict resolution)
+  fix-products-paths
+# some additional utils
+  slapos-toolbox
+  zodbanalyze
+
+# Local development
+  slapos.cookbook-repository
+  check-recipe
+# Create instance template
+  template
+
+
+
+
+[networkcache]
+# signature certificates of the following uploaders.
+#   Romain Courteaud
+#   Sebastien Robin
+#   Kazuhiko Shiozaki
+#   Cedric de Saint Martin
+#   Yingjie Xu
+#   Gabriel Monnerat
+#   Łukasz Nowak
+#   Test Agent (Automatic update from tests)
+#   Aurélien Calonne
+signature-certificate-list =
+  -----BEGIN CERTIFICATE-----
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+  q7jdfWO18Zp/BG7tagz0jmmC4y/8akzHsVlruo2+2du2freE8dK746uoMlXlP93g
+  QUUGLQ==
+  -----END CERTIFICATE-----
+  -----BEGIN CERTIFICATE-----
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+  -----END CERTIFICATE-----
+  -----BEGIN CERTIFICATE-----
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+  -----END CERTIFICATE-----
+  -----BEGIN CERTIFICATE-----
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--- a/software/numpy/software.cfg
+++ b/software/numpy/software.cfg
@@ -6,26 +6,18 @@ extends =
  ../../component/gcc/buildout.cfg
  ../../component/libatlas/buildout.cfg
  ../../component/libblas/buildout.cfg
-  ../../component/r-language/buildout.cfg
+


 parts =
-  python2.7-virtualenv
  eggs
-  gcc-fortran
-  libatlas
-  libblas
-  r-language
-  sh-build-environment
  build-venv
  numpy-eggs

-#  dream-venv
-#  scipy-eggs
-
-
-
-
+#  python2.7-virtualenv
+#  gcc-fortran
+#  libatlas
+#  libblas



@@ -36,8 +28,7 @@ install_cmd =
  mkdir -p ${:location}
  cd ${:location}
  unset PYTHONPATH
-  export PATH="${r-language:location}/bin:${gcc-fortran:location}/bin:$PATH"
-  export LD_LIBRARY_PATH="`${r-language:location}/bin/R RHOME`/lib"
+  export PATH="${gcc-fortran:location}/bin:$PATH"
  export LD_PRELOAD="${gcc-fortran:location}/lib64/libgfortran.so.3 ${libblas:location}/libf77blas.so.3"
  export ATLAS=${libatlas:location}/lib/libsatlas.so
  export BLAS=${libblas:location}/lib/libfblas.a
@@ -49,61 +40,16 @@ install_cmd =
  pip install numpy
  pip install Tempita
  export PYTHONPATH=/opt/slapgrid/72198f37425e64dd3f28648ea523da1d/eggs/numpy-1.8.1-py2.7-linux-x86_64.egg
-  git clone https://github.com/mmariani/scipy.git -b hardcoded-numpy-location
+  ${git:location}/bin/git clone https://github.com/mmariani/scipy.git -b hardcoded-numpy-location
  cd scipy
  python setupegg.py bdist_egg
  cd ..
-  git clone https://github.com/scikit-learn/scikit-learn.git
+  ${git:location}/bin/git clone https://github.com/scikit-learn/scikit-learn.git
  cd scikit-learn
  python setup.py bdist_egg
 #update_cmd = ${:install_cmd}


-#[dream-venv]
-#recipe = cp.recipe.cmd
-#location = ${buildout:parts-directory}/${:_buildout_section_name_}
-#install_cmd =
-#  mkdir -p ${:location}
-#  cd ${:location}
-#  unset PYTHONPATH
-#  export PATH="${r-language:location}/bin:${gcc-fortran:location}/bin:$PATH"
-#  export LD_LIBRARY_PATH="`${r-language:location}/bin/R RHOME`/lib"
-#  export LD_PRELOAD="${gcc-fortran:location}/lib64/libgfortran.so.3 ${libblas:location}/libf77blas.so.3"
-#  export ATLAS=${libatlas:location}/lib/libsatlas.so
-#  export BLAS=${libblas:location}/lib/libfblas.a
-#  export LAPACK=${libatlas:location}/lib/liblapack.a
-#  ${python2.7-virtualenv:executable} ${:location}
-#  . ${:location}/bin/activate
-#  #pip install -U setuptools
-#  #pip install -U pip
-#  pip install numpy
-#  pip install simpy==2.3
-#  pip install scipy==0.13.3
-#  pip install scikit-learn
-#  pip install xlrd
-#  pip install xlwt
-#  pip install flask
-#  pip install pyparsing==1.5.7
-#  pip install pydot
-#  # export LDFLAGS="-lncurses"
-#  export PATH=${r-language:location}/bin:$PATH
-#  # pip install rpy2
-#  # clone repo for:
-#  #   bug fix - https://bitbucket.org/lgautier/rpy2/issue/183
-#  # (may switch to released egg later)
-#  pip install mercurial
-#  hg clone -b version_2.4.x_noreadline https://marco.mariani@bitbucket.org/marco.mariani/rpy2
-#  cd rpy2
-#  python setup.py install
-#  cd ..
-#  ${git:location}/bin/git clone http://git.erp5.org/repos/dream.git -b marco
-#  cd dream
-#  python setup.py install
-#update_cmd = ${:install_cmd}
-
-
-
-


 [eggs]
@@ -134,43 +80,9 @@ interpreter = python-numpy



-#[scipy-eggs]
-#recipe = zc.recipe.egg:custom
-#eggs =
-#  scipy
-#environment = build-environment
-
-
-#[base-environment]
-#recipe = collective.recipe.environment
-
-
-#[build-environment]
-#PYTHONPATH=
-#PATH="${r-language:location}/bin:${gcc-fortran:location}/bin:${base-environment:PATH}"
-#LD_LIBRARY_PATH="`${r-language:location}/bin/R RHOME`/lib"
-#LD_PRELOAD="${gcc-fortran:location}/lib64/libgfortran.so.3 ${libblas:location}/libf77blas.so.3"
-#ATLAS="${libatlas:location}/lib/libsatlas.so"
-#BLAS="${libblas:location}/lib/libfblas.a"
-#LAPACK="${libatlas:location}/lib/liblapack.a"
-
-
-[sh-build-environment]
-# environment needed for running/debugging the applications, exported to a shell script to be sourced.
-recipe = collective.recipe.template
-output = ${buildout:directory}/environment.sh
-input = inline:
-  unset PYTHONPATH
-  export PATH="${r-language:location}/bin:${gcc-fortran:location}/bin:$PATH"
-  export LD_LIBRARY_PATH="`${r-language:location}/bin/R RHOME`/lib"
-  export LD_PRELOAD="${gcc-fortran:location}/lib64/libgfortran.so.3 ${libblas:location}/libf77blas.so.3"
-  export ATLAS=${libatlas:location}/lib/libsatlas.so
-  export BLAS=${libblas:location}/lib/libfblas.a
-  export LAPACK=${libatlas:location}/lib/liblapack.a
-
-
-
 [versions]
 cp.recipe.cmd = 0.5nxd001
 scipy = 0.13.3001
-scikit-learn = 0.15-git
+scikit-learn = 0.16-git
+
+
--- a/stack/erp5/buildout.cfg
+++ b/stack/erp5/buildout.cfg
@@ -70,6 +70,7 @@ extends =
  ../../component/aspell/buildout.cfg
  ../../component/cloudooo/buildout.cfg
  ../../component/jsl/buildout.cfg
+  ../../component/numpy/buildout.cfg

 parts =
  rdiff-backup
@@ -434,6 +435,7 @@ ZODB3-patch-binary = ${patch:location}/bin/patch
 [eggs]
 recipe = zc.recipe.egg
 eggs =
+  ${numpy-eggs:eggs}
  ${mysql-python:egg}
  ${lxml-python:egg}
  ${pillow-python:egg}
@@ -583,7 +585,7 @@ setuptools = 2.2
 huBarcode = 0.63

 # Known version with works
-numpy = 1.6.2
+numpy = 1.8.1

 # test_UserManagerInterfaces in testERP5Security fails with 1.10.0.
 Products.PluggableAuthService = 1.9.0