CellProfiler-2.2.0-0.build.sh

#! /bin/bash

PKG=CellProfiler
VERSION=2.2.0
BUILD=0
SRC=https://github.com/CellProfiler/CellProfiler/archive/$VERSION.tar.gz

PREFIX=/pkg/$PKG-$VERSION-$BUILD
# PREFIX=/dev/shm/pkg/$PKG-$VERSION-$BUILD

# we need /usr/local/package/bin for pip
PATH=/bin:/usr/bin:/usr/sbin:/usr/local/package/bin:/usr/local/bin
export PATH

set -xe
umask 022

BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR
mkdir -p $BUILD_TMPDIR/home
export TMPDIR=$BUILD_TMPDIR
export HOME=$BUILD_TMPDIR/home

exec </dev/null

mkdir -p $PREFIX
cat >$PREFIX/profile <<-EOF
	PATH=$PREFIX/bin:\$PATH
	PYTHONPATH=$PREFIX/lib/python2.7/site-packages
	LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH}
	PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
	export PKG_CONFIG_PATH LD_LIBRARY_PATH PYTHONPATH
EOF
. $PREFIX/profile

BUILDDIR=$PREFIX/build

mkdir -p $BUILDDIR
cd $BUILDDIR

function at_plaininstall() {
  local dir=$1
  local tar=$2
  local url=$3
  (
    cd $BUILDDIR
    test -e $tar || wget $url
    test -n 'XWIPE' && rm -rf ./$dir
    test -d $dir || tar xvf $tar
    cd $dir
    ./configure --prefix=$PREFIX
    make -j $(nproc)
    make install
  )
}

function cm_plaininstall() {
  local dir=$1
  local tar=$2
  local url=$3
  local extra=$4
  (
    cd $BUILDDIR
    test -e $tar || wget $url
    test -n 'XWIPE' && rm -rf ./$dir
    test -d $dir || tar xvf $tar
    mkdir -p $dir/build
    cd $dir/build
    echo "# extra args: '$extra'"
    cmake .. \
      -DCMAKE_INSTALL_PREFIX=$PREFIX \
      -DCMAKE_COLOR_MAKEFILE=OFF \
      -DCMAKE_VERBOSE_MAKEFILE=ON \
      $extra
    make -j $(nproc)
    make install
  )
}

# start with PyQt4, sip
(
  # version 4.19.13 is not working with pyqt-version 4.11.4, version 4.18.1 wasn't tested
  SIP_VERSION=4.16.9
  SIP_SRC=https://sourceforge.net/projects/pyqt/files/sip/sip-$SIP_VERSION/sip-$SIP_VERSION.tar.gz

  test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
  test -n 'XWIPE' && rm -rf sip-$SIP_VERSION
  test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz

  cd sip-$SIP_VERSION

  python configure.py \
      -b $PREFIX/bin \
      -d $PYTHONPATH \
      -e $PREFIX/include/python2.7 \
      -v $PREFIX/share/sip

  mkdir -p $PREFIX/share/sip
  make; make install
)

(
  # version 4.12.3 fails
  # PYQT_SRC=http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-$PYQT_VERSION/PyQt4_gpl_x11-$PYQT_VERSION.tar.gz

  PYQT_VERSION=4.11.4
  PYQT_SRC=http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-$PYQT_VERSION/PyQt-x11-gpl-$PYQT_VERSION.tar.gz

  test -e PyQt-x11-gpl-$PYQT_VERSION.tar.gz || wget $PYQT_SRC
  test -n 'XWIPE' && rm -rf PyQt-x11-gpl-$PYQT_VERSION
  test -d PyQt-x11-gpl-$PYQT_VERSION || tar -xf PyQt-x11-gpl-$PYQT_VERSION.tar.gz

  cd PyQt-x11-gpl-$PYQT_VERSION

  export QTDIR=/usr/local/qt4

  python configure.py \
    -b $PREFIX/bin \
    -d $PYTHONPATH \
    -q /usr/local/qt4/bin/qmake \
    -v $PREFIX/share/sip \
    --confirm-license \
    --no-designer-plugin \
    --verbose

  # missing include path for *our* phonon
  sed -i -e '/^CPPFLAGS/ s,/usr/X11R6/include,/usr/include/phonon,' phonon/Makefile

  make -j $(( 2 * $(nproc) - 1 ))
  make install
)


at_plaininstall \
  zeromq-4.2.2 \
  zeromq-4.2.2.tar.gz \
  https://github.com/zeromq/libzmq/releases/download/v4.2.2/zeromq-4.2.2.tar.gz

cm_plaininstall \
  vigra-1.11.1 \
  vigra-1.11.1-src.tar.gz \
  https://github.com/ukoethe/vigra/releases/download/Version-1-11-1/vigra-1.11.1-src.tar.gz \
  "-DVIGRANUMPY_INSTALL_DIR=$PYTHONPATH"

at_plaininstall \
  wxPython-src-3.0.2.0 \
  wxPython-src-3.0.2.0.tar.bz2 \
  https://sourceforge.net/projects/wxpython/files/wxPython/3.0.2.0/wxPython-src-3.0.2.0.tar.bz2

(
  cd $BUILDDIR/wxPython-src-3.0.2.0/wxPython
  python2.7 setup.py build
  python2.7 setup.py install --prefix $PREFIX
  # build leaves 2gig rubbish
  cd ..
  make clean
)


# NOTE: I'm going to install downgraded versions of matplotlib and
#       h5py, thus PYTHONPATH has to be exported, when using parts
#       from this package interactively. And/or sys.path has to be
#       adjusted in the main app (see MANGLE_SYS_PATH_PATCH)

# yields to matplotlib-1.5.3
pip install --ignore-installed --prefix $PREFIX 'matplotlib<1.9'

# try 2.0.2, resume don't use !
# pip install --prefix $PREFIX 'matplotlib<2.1'

pip install --ignore-installed --prefix $PREFIX 'h5py<2.8'

# needed by ilastik
pip install --prefix $PREFIX 'yapsy'

# 'the' CellProfiler
(
  test -e $VERSION.tar.gz || wget $SRC
  test -d CellProfiler-$VERSION || tar -xf $VERSION.tar.gz

  cd CellProfiler-$VERSION
  python2.7 setup.py build
  python2.7 setup.py install --prefix $PREFIX

  # Message: Plugin directory doesn't point to valid folder: /dev/shm/pkg/CellProfiler-2.2.0-0/plugins
  # create it, it will be r/o ...
  mkdir $PREFIX/plugins
)


# now an ancient ilastik
(
  test -e v0.5.12.tar.gz || wget https://github.com/ilastik/ilastik-0.5/archive/v0.5.12.tar.gz
  test -d ilastik-0.5-0.5.12 || tar -xf v0.5.12.tar.gz
  cd ilastik-0.5-0.5.12
  python2.7 setup.py build
  python2.7 setup.py install --prefix $PREFIX
)


# and a more recent ilastik

# this brings trouble with the lazyflow and volumina modules
# (
#   test -e 1.1.5.tar.gz || https://github.com/ilastik/ilastik/archive/1.1.5.tar.gz
#   test -d ilastik-1.1.5 || tar -xf 1.1.5.tar.gz
# )

# ... thus slaughter an older linux release, caus this one contains also an usable source tree
(
  ILASTIKVERSION=1.1.5
  test -e ilastik-$ILASTIKVERSION-Linux.tar.gz || wget http://files.ilastik.org/ilastik-$ILASTIKVERSION-Linux.tar.gz
  test -d ilastik-$ILASTIKVERSION-Linux || tar -xf ilastik-$ILASTIKVERSION-Linux.tar.gz --exclude='*.pyc' ilastik-$ILASTIKVERSION-Linux/src
  cd ilastik-$ILASTIKVERSION-Linux/src/ilastik
  for MODULE in ilastik lazyflow volumina; do 
    echo "# -- -- -- -- -- -- -- ILASTIK: $MODULE -- -- -- -- -- -- --"
    cd $MODULE
    python setup.py build
    python setup.py install --prefix $PREFIX
    cd ..
  done
  # 'install' this one, 'caus cellprofiler references it
  cp ilastik/ilastik_main.py $PYTHONPATH

  # mingle the old version with the newer, caus that's obviously the
  # setup as of ver 2.2.0, what to say ...
  (
    cd $PYTHONPATH/ilastik-$ILASTIKVERSION-py2.7.egg/ilastik
    for DIR in core gui modules; do
      ln -vs ../../ilastik-0.5-py2.7.egg/ilastik/$DIR
    done
  )
)

# Time to patch ...
# Note, we should be still in $BUILDDIR.
cd $PREFIX

NAVTOOLBAR_MIN_HEIGHT_PATCH='
--- CellProfiler-2.2.0-0/lib/python2.7/site-packages/CellProfiler-2.2.0-py2.7.egg/cellprofiler/gui/cpfigure.py.dist	2018-10-22 16:24:35.161104708 +0200
+++ CellProfiler-2.2.0-0/lib/python2.7/site-packages/CellProfiler-2.2.0-py2.7.egg/cellprofiler/gui/cpfigure.py	2018-10-23 13:26:01.855642371 +0200
@@ -474,4 +474,6 @@
         available_width, available_height = self.GetClientSize()
         nbheight = self.navtoolbar.GetSize()[1]
+        if nbheight < 40:
+            nbheight = 40
         self.navtoolbar.SetPosition((0, 0))
         self.navtoolbar.SetSize((available_width, nbheight))
'

NO_CHECK_NEW_VERSION_PATCH="
--- CellProfiler-2.2.0-0/lib/python2.7/site-packages/CellProfiler-2.2.0-py2.7.egg/cellprofiler/cellprofilerapp.py.dist	2018-10-22 16:24:35.146104724 +0200
+++ CellProfiler-2.2.0-0/lib/python2.7/site-packages/CellProfiler-2.2.0-py2.7.egg/cellprofiler/cellprofilerapp.py	2018-10-23 08:41:53.601299559 +0200
@@ -20,2 +20,3 @@
         self.check_for_new_version = kwargs.pop('check_for_new_version', False)
+        self.check_for_new_version = False
         self.workspace_path = kwargs.pop('workspace_path', None)
"

MANGLE_SYS_PATH_PATCH="
--- CellProfiler-2.2.0-0/lib/python2.7/site-packages/CellProfiler-2.2.0-py2.7.egg/cellprofiler/__main__.py.dist	2018-10-23 13:15:18.843495001 +0200
+++ CellProfiler-2.2.0-0/lib/python2.7/site-packages/CellProfiler-2.2.0-py2.7.egg/cellprofiler/__main__.py	2018-10-23 13:23:04.150877887 +0200
@@ -1,7 +1,12 @@
+import sys
+# put our site-packages *before* the ones from /pkg/python-2.7.15-1, otherwise 
+# we'll get the bad h5py v2.8 again
+if sys.path.count('$PREFIX/lib/python2.7/site-packages'):
+  sys.path.remove('$PREFIX/lib/python2.7/site-packages')
+sys.path.insert(1,'$PREFIX/lib/python2.7/site-packages')
 import h5py
 import logging
 import logging.config
 import re
-import sys
 import os
 import numpy as np
"

# apply PR https://github.com/CellProfiler/CellProfiler/pull/3445
# or with less fuzz https://github.com/CellProfiler/CellProfiler/issues/2679#issuecomment-355004994
echo "$NAVTOOLBAR_MIN_HEIGHT_PATCH" | patch -p1 --verbose --read-only=ignore

# slap the update check
# "Exception fetching new version information from http://cellprofiler.org/CPupdate.html: HTTP Error 404: Not Found"
echo "$NO_CHECK_NEW_VERSION_PATCH" | patch -p1 --verbose --read-only=ignore

# not shure, why PYTHONPATH isn't preferred.
echo "$MANGLE_SYS_PATH_PATCH" | patch -p1 --verbose --read-only=ignore

# exit 1 # don't close ...
exit