Rebuild python3

python-3.7.4-2.build.sh

@@ -0,0 +1,224 @@
+#! /bin/bash
+
+PKG=python
+VERSION=3.7.4
+BUILD=2
+PYTHONVER=${VERSION%.*}
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
+
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
+
+set -xe
+umask 022
+
+BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
+test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; 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=$PREFIX/bin:\$PATH
+	PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
+	export PKG_CONFIG_PATH
+	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi
+EOF
+. $PREFIX/profile
+
+export MAKEFLAGS="-j $(nproc)"
+
+BUILDDIR=$PREFIX/build
+
+mkdir -p $BUILDDIR
+cd $BUILDDIR
+
+test -e Python-$VERSION.tar.xz || wget https://www.python.org/ftp/python/$VERSION/Python-$VERSION.tar.xz
+test -d Python-$VERSION        || tar xvf Python-$VERSION.tar.xz
+cd Python-$VERSION
+
+LDFLAGS="-Wl,-rpath=$PREFIX/lib" \
+./configure \
+        --prefix=$PREFIX \
+        --enable-shared
+
+make -j $(nproc)
+# make test || true # 'test_socket' seems to run for ever
+make install
+
+( # sip: tool to create Python bindings for C and C++ libraries.
+  cd $PREFIX/build
+  SIP_VERSION=4.19.18
+  SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz
+  test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
+  test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz
+
+  cd sip-$SIP_VERSION
+
+  python3 configure.py \
+      -b $PREFIX/bin \
+      -d $PREFIX/lib/python$PYTHONVER/site-packages \
+      -e $PREFIX/include/python${PYTHONVER}m \
+      -v $PREFIX/share/sip \
+      --sip-module=sip
+
+  # well, right here share/sip is spoilage, but maybe some packages will use the decent sip later on ...
+  mkdir -p $PREFIX/share/sip
+  make -j $(nproc);
+  make install
+)
+
+
+( # now for the private (sic!) version required by newer PyQt
+  cd $PREFIX/build
+  mkdir -p private_sip
+  cd private_sip
+  SIP_VERSION=4.19.18
+  SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz
+  test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
+  test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz
+
+  cd sip-$SIP_VERSION
+
+  # note $PREFIX/share/sip/PyQt5 is mandatory
+  python3 configure.py \
+      -d $PREFIX/lib/python$PYTHONVER/site-packages \
+      -v $PREFIX/share/sip/PyQt5 \
+      --no-tools \
+      --sip-module=PyQt5.sip
+
+  mkdir -p $PREFIX/share/sip/PyQt5
+  make -j $(nproc)
+  # The resulting sip.so in site-packages/PyQt5 differs indeed a bit (grep for PyQt5)
+  make install
+)
+
+(
+  PYQT_VERSION=5.13.0
+  PYQT_SRC=https://www.riverbankcomputing.com/static/Downloads/PyQt5/$PYQT_VERSION/PyQt5_gpl-$PYQT_VERSION.tar.gz
+
+  cd $BUILDDIR
+  test -e PyQt5_gpl-$PYQT_VERSION.tar.gz || wget $PYQT_SRC
+  test -d PyQt5_gpl-$PYQT_VERSION || tar -xf PyQt5_gpl-$PYQT_VERSION.tar.gz
+
+  cd PyQt5_gpl-$PYQT_VERSION
+
+  # export QTDIR=/usr/local/qt5
+  python3 configure.py \
+    -b $PREFIX/bin \
+    -d $PREFIX/lib/python$PYTHONVER/site-packages \
+    -n $PREFIX/share/qsci \
+    -q /usr/local/qt5/bin/qmake \
+    -v $PREFIX/share/sip/PyQt5 \
+    --sip-incdir=$PREFIX/include/python${PYTHONVER}m \
+    --confirm-license \
+    --no-qml-plugin \
+    --no-designer-plugin \
+    --no-dist-info \
+    --verbose
+
+  make -j $(nproc)
+
+  # Did I miss something in the docs ???
+  # w/o the *.so files inplace a clean 'make install' fails with file not found ...
+  # -> FileNotFoundError: [Errno 2] No such file or directory:
+  #         '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/QtCore.so'
+  mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
+  for F in `find | grep '\.so$' | grep -v '/lib'` ; do
+    cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5/
+  done
+  make install
+)
+
+(
+  QSCINTILLA_VERSION=2.11.2
+  QSCINTILLA_SRC=https://www.riverbankcomputing.com/static/Downloads/QScintilla/$QSCINTILLA_VERSION/QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
+
+  cd $BUILDDIR
+  test -e QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz || wget $QSCINTILLA_SRC
+  test -d QScintilla_gpl-$QSCINTILLA_VERSION || tar -xf QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
+  cd QScintilla_gpl-$QSCINTILLA_VERSION
+
+  cd Python
+
+  # apidir follows PyQt, not Qt (default is: QT_INSTALL_DATA/qsci)
+  # creation of PEP 376 .dist-info fails in $PREFIX/share
+  python3 configure.py \
+    --pyqt=PyQt5 \
+    --qmake=/usr/local/qt5/bin/qmake \
+    --apidir=$PREFIX/share/qsci \
+    --no-dist-info
+
+  make -j $(nproc)
+
+  # Call it a deja-vu, nerve ...
+  # -> FileNotFoundError: [Errno 2] No such file or directory: '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/Qsci.so'
+  mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
+  for F in `find | grep '\.so$' | grep -v '/lib'` ; do
+    cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
+  done
+  make install
+)
+
+python3 -m ensurepip
+pip3 install -I pip
+
+pip3 install ipython[all]
+
+pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels
+# clean up some dirt that statsmodels placed also into $PREFIX
+rm -vf $PREFIX/LICENSE.txt
+rm -vf $PREFIX/setup.cfg
+
+pip3 install Cython
+
+pip3 install pysam
+pip3 install seaborn
+pip3 install scikit-learn
+# pip3 install metaseq      # fails (Latest commit fa875d1 on Jan 10, 2017)
+pip3 install Mako
+pip3 install meson          # required in mariux
+
+pip3 install cutadapt       # Helpdesk 01/24/18 16:19, Sabrina Krakau
+pip3 install pygobject      # Helpdesk 03/26/18 14:19, Virginie Stanisla
+pip3 install blink1         # Blink1-lib 07/04/18 12:00, Niclas Hofmann
+
+pip3 install umi-tools
+pip3 install sphinx
+pip3 install recommonmark
+pip3 install fastcluster
+pip3 install pydot
+pip3 install pygraphviz
+pip3 install deeptools
+pip3 install HTSeq
+pip3 install keras
+pip3 install MotifScan      # Alena 30.8.2018
+pip3 install MAmotif
+pip3 install hic2cool       # Helpdesk Robert Schoepflin 17.09.2018
+# pip3 install hifive       # only python 2.7+
+pip3 install snakemake
+pip3 install virtualenv     # Donald
+pip3 install odfpy          # Donald
+pip3 install Dumper         # Thomas
+pip3 install igraph
+pip3 install louvain        # monocle3 prep for Helene
+pip3 install selenium       # 19.7.19 Kreitler  -> https://webxray.org/
+pip3 install cooltools      # Maria Valieva 17.7.2019
+pip3 install gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
+
+# pip3 install HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
+pip3 install HiCMatrix
+pip3 install pyGenomeTracks
+
+pip3 install python-bioformats
+
+pip3 install jupyterlab      # request Peter Arndt
+pip3 install libxml2-python3 # required by several bee packages after swich to python3
+pip3 install scour           # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98
+pip3 install jupyterlab-git  # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/96
+
+exit