Add cellprofiler 2.2.0 0 (#31)

CellProfiler2: Add version 2.2.0

Notes:
 - Build with python-2.7.15-1
 - Binary is installed as cellprofiler2
 - some packages from python-2.7.15-1 needed a downgrade
   - h5py -> h5py-2.7.1 (this was the meanest showstopper)
   - matplotlib -> matplotlib-1.5.3

CellProfiler-2.2.0-0.build.sh

@@ -0,0 +1,291 @@
+#! /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