python-3.10.12-0.build.sh

#!/bin/bash

# ------------------------------------------------------------------- Debug

 COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh
 #TESTING=1
 #SKIPTENSORFLOW=1

# ---------------------------------------------------------------- Preamble

#set -x

PKG=python
VERSION=3.10.12
BUILD=0
PYTHONVER=${VERSION%.*}

CUDADIR=/pkg/cuda-11.8.0-0

PREFIX=/pkg/$PKG-$VERSION-$BUILD
if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi

PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin

# set -xe
set -e
umask 022

BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp

test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR )
mkdir -p $BUILD_TMPDIR/home/.cache/pip
mkdir -p $BUILD_TMPDIR/home/.local
# copy script to an accessible location
cp $0 $BUILD_TMPDIR; ME="$BUILD_TMPDIR/$(basename $0)"
export TMPDIR=$BUILD_TMPDIR
export HOME=$BUILD_TMPDIR/home

exec </dev/null

mkdir -p $PREFIX
cat >$PREFIX/profile <<-EOF
	. $CUDADIR/profile
	PATH=$PREFIX/bin:\$PATH
	export 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
	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
EOF
. $PREFIX/profile

NPROC=$(( $(nproc) * 4 / 5 + 1 ))
export MAKEFLAGS="-j $NPROC"

BUILDDIR=$PREFIX/build

mkdir -p $BUILDDIR
cd $BUILDDIR

# -------------------------------------- Use git to track package evolution

test -d .git && rm -rf .git
git init -q; echo -e '[user]\n name = none\n email = of_your_business...' >> .git/config
echo '*' > .gitignore

function piplist() {
  pip3 list | awk '{ printf("%-36s %s\n", $1,$2) }' | grep -v '\----' > GameOfVersions
}

function track() {
  if [ -d .git ]; then
    if git add -f GameOfVersions; then
      git commit -q -n -m "Package: '$*'" || /bin/true
    fi
  fi
}

function install() {
  # no-color is nice, but doesn't work when dependencies are installed, so (mis-)use a pipe
  pip3 install --no-color --compile --cache-dir=$HOME/.cache/pip --prefix=$PREFIX "${@+$@}" | cat
  piplist
  track $*
}

# ---------------------------------------- Build Python & support libraries

(
  # orig: https://www.python.org/ftp/python/3.10.10/Python-3.10.10.tar.xz
  BEEHIVE="https://beehive.molgen.mpg.de/49b0342476b984e106d308c25d657f12/Python-3.10.12.tar.xz"

  test -e Python-$VERSION.tar.xz || wget -nv $BEEHIVE
  test -d Python-$VERSION || tar -xf Python-$VERSION.tar.xz
  cd Python-$VERSION

  # BerkeleyDB, the undead ...
  # Newer libgdbm_compat.so versions pull libgdbm.so on their own, our libgdbm_compat.so is older ...
  # So, let setup.py create '-lgdbm -lgdbm_compat' instead of a sole '-lgdbm_compat'
  # verbatim: ndbm_libs = ['gdbm_compat'] => ndbm_libs = ['gdbm','gdbm_compat']
  sed -i -e "/ndbm_libs = / s/_compat'/','gdbm_compat'/" setup.py

  # leave further hints in the log
  sed -i -e  '/db_setup_debug = False/ s/False/True/' \
         -e '/dbm_setup_debug = False/ s/False/True/' setup.py

  # These may come handy if the Python build needs exclusive stuff from $PREFIX
  # INCLUDEDIR=$PREFIX/include \
  # LIBDIR=$PREFIX/lib \
  LDFLAGS="-Wl,-rpath=$PREFIX/lib" \
  ./configure \
          --prefix=$PREFIX \
          --enable-shared

  make -j $NPROC
  make install

  # it might come to happen that something down the line may just call 'python', defuse ...
  test -e $PREFIX/bin/python || ln -s python3 $PREFIX/bin/python

  python3 -m ensurepip
  pip3 install --prefix=$PREFIX -I pip
  ( # fix 'please update' noise from pip
    cd $PREFIX/lib/python*/site-packages
    sed -ne '/^#Epatch:pip/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
  )
)
install setuptools==65.3.0 # see numba below
piplist; track START


# build various pythonbindings 'by hand', because pip installs do not deliver
# header files and the like.
# BTW: builds need meson

install meson

(
  DBUS_PYTHON_VERSION=1.3.2

	#PyPi
	# https://files.pythonhosted.org/packages/c1/d3/6be85a9c772d6ebba0cc3ab37390dd6620006dcced758667e0217fb13307/dbus-python-1.3.2.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/33be8a4a766e1c7c9a377b8f934ce21a/dbus-python-1.3.2.tar.gz
  test -e dbus-python-$DBUS_PYTHON_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d dbus-python-$DBUS_PYTHON_VERSION || tar -xf dbus-python-$DBUS_PYTHON_VERSION.tar.gz

  cd dbus-python-$DBUS_PYTHON_VERSION
  ./configure --prefix=$PREFIX

  make -j $NPROC
  make install

)

# ------------------------------------------------ build tool fuer Thomas
(
  set -x
  GYP_VERSION=20230301_c6d8b9f7
  # orig: https://mirror.netcologne.de/slackware/slackware64-current/source/d/gyp/
  BEEHIVE=https://beehive.molgen.mpg.de/ba0357be23ca55555714261afccc7aab/gyp-20230301_c6d8b9f7.tar.xz
  test -e gyp-${GYP_VERSION}.tar.xz || wget -nv $BEEHIVE
  test -d gyp-${GYP_VERSION} || tar -xf gyp-${GYP_VERSION}.tar.xz
  cd gyp-${GYP_VERSION}
  sed -ne '/^#Epatch:gyp1/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
  sed -ne '/^#Epatch:gyp2/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)
piplist; track gyp

(
  PYCAIRO_VERSION=1.23.0

	#PyPi
  # https://files.pythonhosted.org/packages/69/ca/9e9fa2e8be0876a9bbf046a1be7ee33e61d4fdfbd1fd25c76c1bdfddf8c4/pycairo-1.23.0.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/7a3729d21659098e1b9a411b62e88966/pycairo-1.23.0.tar.gz
  test -e pycairo-$PYCAIRO_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d pycairo-$PYCAIRO_VERSION || tar -xf pycairo-$PYCAIRO_VERSION.tar.gz

  cd pycairo-$PYCAIRO_VERSION

  mkdir -p meson-build
  cd meson-build

  meson setup \
    --prefix=$PREFIX \
    --buildtype=release \
    -Dpython=$PREFIX/bin/python \
    -Dtests=false \
    ..

  ninja -j $NPROC
  ninja install

)

(
  PYGOBJECT3_VERSION=3.44.1

  # https://files.pythonhosted.org/packages/07/73/a034fc1bcd6d402d6f72ff618c093f91ac6921f968cc19806b6a1b1b19c8/PyGObject-3.44.0.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/959259478566b24316edaa18da6e0eaa/PyGObject-3.44.1.tar.gz
  test -e PyGObject-$PYGOBJECT3_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d PyGObject-$PYGOBJECT3_VERSION || tar -xf PyGObject-$PYGOBJECT3_VERSION.tar.gz

  cd PyGObject-$PYGOBJECT3_VERSION

  mkdir -p meson-build
  cd meson-build
  meson setup \
    --prefix=$PREFIX \
    --buildtype=release \
    -Dpython=$PREFIX/bin/python \
    -Dtests=false \
    ..

  ninja -j $NPROC
  ninja install

)
piplist; track various pythonbindings

# build support to use QT from python -- see www.riverbankcomputing.com

( # sip: tool to create Python bindings for C and C++ libraries.
  SIP_VERSION=6.7.7

  # https://files.pythonhosted.org/packages/5b/cb/c27c925ae07bd03a2597fa1db17bfc2a4ac57da61aeb90f8ec98ffbb975b/sip-6.6.2.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/a131efd79649d31ee11601b19d1e3784/sip-6.7.7.tar.gz
  test -e sip-$SIP_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz

  cd sip-$SIP_VERSION

  python3 setup.py build
  python3 setup.py install --skip-build --optimize=1

)

# QT bindings need some python modules to build

install PyQt5-sip
install PyQt-builder

(
  PYQT_VERSION=5.15.9

	#PyPi
  # orig: https://files.pythonhosted.org/packages/5c/46/b4b6eae1e24d9432905ef1d4e7c28b6610e28252527cdc38f2a75997d8b5/PyQt5-5.15.9.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/9d97fc06b7ae75e654e946c49e07ff12/PyQt5-5.15.9.tar.gz
  test -e PyQt5-$PYQT_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d PyQt5-$PYQT_VERSION || tar -xf PyQt5-$PYQT_VERSION.tar.gz

  cd PyQt5-$PYQT_VERSION

  sip-build \
    --confirm-license \
    --no-make \
    --api-dir $PREFIX/share/qsci/api/python \
    --dbus $PREFIX/include/dbus-1.0 \
    --no-designer-plugin \
    --no-qml-plugin \
    --jobs $NPROC \

  cd build
  make -j $NPROC
  make install

  # Remove unused py2 version of uic modules
  rm -r $PREFIX/lib/python*/site-packages/PyQt5/uic/port_v2

)

(
  QSCINTILLA_VERSION=2.13.4 # no 2.14 in sight ...

  # orig: https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.13.4/QScintilla_src-2.13.4.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/4f83a4a4ad7da40eae80ad23f9fb18f2/QScintilla_src-2.13.4.tar.gz
  test -e QScintilla_src-$QSCINTILLA_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d QScintilla_src-$QSCINTILLA_VERSION || tar -xf QScintilla_src-$QSCINTILLA_VERSION.tar.gz

  cd QScintilla_src-$QSCINTILLA_VERSION
  cd Python

  cp -vp pyproject-qt5.toml pyproject.toml
  sip-build \
    --no-make \
    --qsci-features-dir ../src/features \
    --qsci-include-dir ../src \
    --qsci-library-dir ../src \
    --api-dir $PREFIX/share/qsci/api/python \
    --jobs $NPROC

  cd build
  make -j $NPROC
  make install

)

(
  set -x
  PYQTWEBENGINE_VERSION=5.15.6

  #orpg: https://pypi.org/project/PyQtWebEngine/#files
  BEEHIVE="https://beehive.molgen.mpg.de/d1e548617de149ba8142a32c1eb9f994/PyQtWebEngine-5.15.6.tar.gz"
  test -e PyQtWebEngine-${PYQTWEBENGINE_VERSION}.tar.gz || wget -nv $BEEHIVE
  test -d PyQtWebEngine-${PYQTWEBENGINE_VERSION} || tar -xf PyQtWebEngine-${PYQTWEBENGINE_VERSION}.tar.gz

  cd PyQtWebEngine-${PYQTWEBENGINE_VERSION}
  sip-build \
    --no-make \
    --api-dir ${PREFIX}/share/qsci/api/python \
    --jobs $NPROC

    cd build
    make -j $NPROC
    make install
)
piplist; track qt-support-riverbankcomputing

# -------------------------------------------------------- Install packages

# Install the psychotic diva first
install numpy==1.23.4

install Cython~=0.29 #last stable release, version 3 ganz frisch unlogische versionierung

# libxml2-python from pypi isn't up to date, cause lxml seems to be the favored binding
# do this early, not that some dependency tries it on its own.
# (btw. libxslt-python isn't ported to python3)
(
  LIBXML2_VERSION=2.9.12

  # orig: http://xmlsoft.org/sources/libxml2-${PKGVERSION}.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/f433a39be087a9f0b197eb2307ad9f75/libxml2-2.9.12.tar.gz
  test -e libxml2-$LIBXML2_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d libxml2-$LIBXML2_VERSION || tar -xf libxml2-$LIBXML2_VERSION.tar.gz libxml2-$LIBXML2_VERSION/python
  cd libxml2-$LIBXML2_VERSION/python
  python3 setup.py build
  python3 setup.py install
)
piplist; track legacy-libxml2


# 'numba' the cuda enabled numpy
(
  NUMBA_VERSION=0.56.3

  # orig: https://files.pythonhosted.org/packages/a3/95/7df08647e773a2417e24de8fea9087606b37074f63830a3f2dbabd97f01b/numba-0.56.3.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/ae0a008447f2f246523af143b1488e88/numba-0.56.3.tar.gz
  test -e numba-$NUMBA_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d numba-$NUMBA_VERSION || tar -xf numba-$NUMBA_VERSION.tar.gz
  cd numba-$NUMBA_VERSION

  # numba assumes that libcudart.so and friends reside in 'CUDA_HOME/lib64'
  sed -ne '/^#Epatch:numba1/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
  sed -ne '/^#Epatch:numba2/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
  install .
  # useful to see if numba works
  cp -p numba/misc/numba_sysinfo.py $PREFIX/bin
  chmod 0755 $PREFIX/bin/numba_sysinfo.py
)
piplist; track numba

PACKAGES=$(sed -e s/#.*$// <<- __PKGLIST__
	protobuf==3.19.4     # tensorflow likes to have an slightly older one [< 3.20], no conflicts with this
	onnx==1.12.0         # newer onnx (dep helen) needs newer protobuf
  Pillow<10.0.0        # pyimagej 1.4.1 downgrade to latest 9
	keras==2.11.0        # tensorflow 2.11.1 requires keras<2.12,>=2.11.0
  urllib3<2.0.0        # oauth brauch wird von tensorflow gebraucht
  Sphinx==4.5.0        # hic2cool(0.8.3) moecht gern was aelteres
  jedi<0.19.0          # spyder dwowngrade spyder 5.4.4
  black[d]             #onnx want but not install it
  flask
	ipython[all]

	SciPy
	pandas
	SymPy
	nose
	statsmodels
	pysam
	seaborn
	scikit-learn
	Mako
  pyimagej            # Mikroscop
	cutadapt            # Helpdesk 01/24/18 16:19, Sabrina Krakau
	pygobject           # Helpdesk 03/26/18 14:19, Virginie Stanisla
	blink1              # Blink1-lib 07/04/18 12:00, Niclas Hofmann
  hvplot              #ont/nextflow pipelines
  pyarrow             #ont/nextflow pipelines
	umi-tools
	recommonmark
	fastcluster
	pydot
	pygraphviz
	deeptools
	HTSeq
	keras_preprocessing # tensorflow ...
	MotifScan           # Alena 30.8.2018
	MAmotif
	hic2cool            # Helpdesk Robert Schoepflin 17.09.2018
	snakemake
	virtualenv          # Donald
	odfpy               # Donald
	Dumper              # Thomas
	igraph
	louvain             # monocle3 prep for Helene
	selenium            # 19.7.19 Kreitler  -> https://webxray.org/
	gmpy                # From viper context, Helpdesk Laura Glaser 9.8.2019
	plotly
	pyOpenCL
	docopt
	distro
	ply
	threadpoolctl
	HiCMatrix
	pybedtools
	gffutils
	python-bioformats
  jupyter
	jupyterlab
	jupyterlab-git      # request Peter Arndt
	igv_jupyterlab      # Matthias Lienhard HD 01-04-2020
  igv-notebook
	scour               # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98
	multiqc
	pybind11
	svgwrite
	pyomo
	bioservices
	SharedArray
	pyabc               # dependency for stochkit, HD 20.07.20 Gemma Noviello
	petab
	tadtool             # HD 26.01.21 Michael Robson
	pyperf              # Paul sep-20
	umap                # HD, used by Matthias Lienhard
	MACS3
 	biopython           # HD 2021-07-23 Magalhaes/Hnisz alphafold related -- cool that we have missed biopython so far, LOL
	dm-tree
	dm-haiku
	flatbuffers
	contextlib2
	ml_collections
  spyder
  spyder-kernels


	# additions/fixups since 3.9
	papermill           # turns jupyter notebooks into scripts [sic!] used by P.A. [who else, *grin*]
	opencv-python
	scikit-image
	git-cola
	cffi-glpk           # uses /usr/lib/libglpk.so.40, see if I can get it linked statically - kreitler
	czifile
	napari[pyqt5]
	napari-czifile2
	CrossMap
	scanpy
	asciidoc

	__PKGLIST__
)

for PKG in $PACKAGES; do
  install $PKG
done

(
  #install from git to get .so
  pip3 install git+https://github.com/open2c/pairtools.git@v1.0.2
)
piplist; track 'pairtools'

(
  TRITON_VERSION=2.0.0
  #triton 2.0.0 hat cmake als install dep, ist in 2.1.0 gefixt

  # orig: https://github.com/openai/triton/archive/refs/tags/v2.0.0.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/56b46016609039fac839f8297c88454c/triton-2.0.0.tar.gz
  test -e triton-${TRITON_VERSION}.tar.gz || wget -nv $BEEHIVE
  test -d triton-${TRITON_VERSION} || tar -xf triton-${TRITON_VERSION}.tar.gz
  cd triton-${TRITON_VERSION}/python
  sed -ne '/^#Epatch:triton/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
  pip install . --prefix=$PREFIX

  piplist; track triton==${TRITON_VERSION}
)

# torch bundled with a recent CUDA-Toolkit
install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu118

install pyopengl # Tk binding creates an error, so remove it (Expects Tk Togl installation...)
rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk

# install helen after our torch, otherwise we might catch the default torch from pip ...
install helen             # HD, a dependency from a request by helene

mkdir -vp $PREFIX/share/jupyter/lab/settings  # try to defeat a silly error in jupyter labextension install

# --------------------------------------------------- Install misc packages

(
  BOOST_VERSION=(1.80.0 1_80_0)
  PKGCFLAGS="-O2 -fPIC"

  # orig: https://boostorg.jfrog.io/artifactory/main/release/1.80.0/source/boost_1_80_0.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/077f074743ea7b0cb49c6ed43953ae95/boost_1_80_0.tar.gz
  test -e boost_${BOOST_VERSION[1]}.tar.gz || wget -nv $BEEHIVE
  test -d boost-${BOOST_VERSION[0]} || mkdir boost-${BOOST_VERSION[0]} && tar -xf boost_${BOOST_VERSION[1]}.tar.gz -C boost-${BOOST_VERSION[0]} --strip-components=1

  cd boost-${BOOST_VERSION[0]}
  sed -e "/using python/ s|;|: ${PREFIX}/include/python${PYTHONVER} ;|" \
      -i bootstrap.sh

  ./bootstrap.sh \
    --with-toolset=gcc \
    --with-icu \
    --with-python=$PREFIX/bin/python3 \
    --with-libraries=python,thread || exit 1

  ./b2 \
    -j $NPROC \
    --layout=system \
    --build-dir=build-python3 \
    --prefix=$PREFIX \
    --libdir=$PREFIX/lib \
    --build-type=minimal \
    toolset=gcc \
    variant=release \
    debug-symbols=off \
    link=shared \
    threading=multi \
    runtime-link=shared \
    python=$PYTHONVER \
    cflags="$PKGCFLAGS" \
    cxxflags="$PKGCFLAGS" \
    install || exit 1
)

(
  PYCUDAVERS=2022.1
  PYTHON_LIBNAME=boost_python${PYTHONVER/./}

  # orig: https://files.pythonhosted.org/packages/2d/1f/48a3a5b2c715345e7af1e09361100bd98c3d72b4025371692ab233f523d3/pycuda-2022.1.tar.gz # maybe those very long URLs compensate for other (shorter) things ...
  BEEHIVE="https://beehive.molgen.mpg.de/2fad5a15db4153d825822eba7cb25f25/pycuda-2022.1.tar.gz"
  test -e pycuda-${PYCUDAVERS}.tar.gz || wget -nv $BEEHIVE
  test -d pycuda-${PYCUDAVERS} || tar -xf pycuda-${PYCUDAVERS}.tar.gz

  cd pycuda-${PYCUDAVERS}
  test -e siteconf.py && rm siteconf.py
  python3 configure.py \
    --cuda-enable-gl \
    --cuda-root=$CUDADIR \
    --no-use-shipped-boost \
    --boost-python-libname=$PYTHON_LIBNAME \
    --boost-inc-dir=$PREFIX/include \
    --boost-lib-dir=$PREFIX/lib \
    --cudadrv-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \
    --cudart-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \
    --curand-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \
    --ldflags=-L$PREFIX/lib

  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)

(
  IDR_VERSION=2.0.3
  # orig: https://github.com/nboley/idr/archive/2.0.3/idr-2.0.3.tar.gz # HD: Tobias Zehnder, 18.3.21
  BEEHIVE=https://beehive.molgen.mpg.de/1bec61b526bb1dcf92a5ab99c27852d0/idr-2.0.3.tar.gz
  test -e idr-${IDR_VERSION}.tar.gz || wget -nv $BEEHIVE
  test -d idr-${IDR_VERSION} || tar -xf idr-${IDR_VERSION}.tar.gz
  cd idr-${IDR_VERSION}
  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)

(
  STGIT_VERSSION=1.0
  # orig: https://github.com/stacked-git/stgit/archive/v1.0/stgit-1.0.tar.gz # Paul mariux64/pkg-scripts/issues/152
  BEEHIVE=https://beehive.molgen.mpg.de/b20ab5a197fc3a141f4b00c5859c0a3b/stgit-1.0.tar.gz
  test -e stgit-${STGIT_VERSSION}.tar.gz || wget -nv $BEEHIVE
  test -d stgit-${STGIT_VERSSION} || tar -xf stgit-${STGIT_VERSSION}.tar.gz
  cd stgit-${STGIT_VERSSION}
  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)

(
  METH_VERSION=0.2.5
  # https://github.com/brentp/bwa-meth/archive/refs/tags/v0.2.5.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/33a4c416760dd67e77f17e07791527e2/bwa-meth-0.2.5.tar.gz
  test -e bwa-meth-${METH_VERSION}.tar.gz || wget -nv $BEEHIVE
  test -d bwa-meth-${METH_VERSION} || tar -xf bwa-meth-${METH_VERSION}.tar.gz
  cd bwa-meth-${METH_VERSION}
  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)
piplist; track misc packages

# ------------------------------------------------ finally build tensorflaw

install wheel # to build our tf-wheel (i.e. zip archive)

(
  test -n "$SKIPTENSORFLOW" && exit

  TFVERSION=2.11.1
  NCCLSHORTVERSION=$(pkg-config nccl --modversion | grep -Po '\d+\.\d+')

  . /pkg/bazel-5.4.1-0/profile

  # orig: https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.11.1.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/e1b60c6e074f8b4c83f184e2c298774f/tensorflow-2.11.1.tar.gz

  test -e tensorflow-${TFVERSION}.tar.gz || wget -nv $BEEHIVE
  test -d tensorflow-${TFVERSION} || tar -xf tensorflow-${TFVERSION}.tar.gz

  cd tensorflow-${TFVERSION}

  #vars for config
  export PYTHON_BIN_PATH=${PREFIX}/bin/python3
  export USE_DEFAULT_PYTHON_LIB_PATH=1
  export TF_NEED_JEMALLOC=1
  export TF_NEED_KAFKA=0
  export TF_NEED_OPENCL_SYCL=0
  export TF_NEED_AWS=0
  export TF_NEED_GCP=0
  export TF_NEED_HDFS=0
  export TF_NEED_S3=0
  export TF_ENABLE_XLA=1
  export TF_NEED_GDR=0
  export TF_NEED_VERBS=0
  export TF_NEED_OPENCL=0
  export TF_NEED_MPI=0
  export TF_NEED_TENSORRT=0
  export TF_NEED_NGRAPH=0
  export TF_NEED_IGNITE=0
  export TF_NEED_ROCM=0
  export TF_SET_ANDROID_WORKSPACE=0
  export TF_DOWNLOAD_CLANG=0
  export TF_NCCL_VERSION=${NCCLSHORTVERSION}
  export TF_IGNORE_MAX_BAZEL_VERSION=1
  export NCCL_INSTALL_PATH=${CUDADIR}
  export CC=gcc
  export CXX=g++
  export GCC_HOST_COMPILER_PATH=/usr/bin/${CC}
  export HOST_C_COMPILER=/usr/bin/${CC}
  export HOST_CXX_COMPILER=/usr/bin/${CXX}
  export TF_CUDA_CLANG=0
  export CLANG_CUDA_COMPILER_PATH=/usr/bin/clang
  export TF_CUDA_PATHS=${CUDADIR},${CUDADIR}/extras/CUPTI,${CUDADIR}/nvvm
  export TF_CUDA_VERSION=$(${CUDADIR}/bin/nvcc --version | sed -n 's/^.*release \(.*\),.*/\1/p') # 11.5
  export TF_CUDNN_VERSION=$(sed -n 's/^#define CUDNN_MAJOR\s*\(.*\).*/\1/p' ${CUDADIR}/include/cudnn_version.h)
  # hardware older than sm_52 is said to be unsupported, compute_86 denotes an emulation
  export TF_CUDA_COMPUTE_CAPABILITIES=sm_52,sm_53,sm_60,sm_61,sm_62,sm_70,sm_72,sm_75,sm_80,sm_86,compute_86

  # stay compatible with the cluster machines
  export CC_OPT_FLAGS="-march=nehalem"
  export TF_NEED_CUDA=1
  export BAZEL_ARGS="--config=mkl -c opt"

  ./configure

  bazel build \
    --cxxopt="-march=nehalem" \
    --copt="-march=nehalem" \
    --noshow_loading_progress \
    --noshow_progress \
    --color="no" \
    //tensorflow:libtensorflow.so \
    //tensorflow:libtensorflow_cc.so \
    //tensorflow:install_headers \
    //tensorflow/tools/pip_package:build_pip_package

  bazel shutdown # otherwise it hogs in cwd

  # create a _clean/decent_ python package from so far created debris
  test -d tensorflow-pip && rm -r tensorflow-pip
  mkdir tensorflow-pip
  ./bazel-bin/tensorflow/tools/pip_package/build_pip_package --src ${BUILDDIR}/tensorflow-pip
  cd ${BUILDDIR}
  # ... cope with the ??? symlink-structure placed in bazels' build-TMPDIR (-h) (tell me why ?)
  test -e tensorflow-pip.tar && rm tensorflow-pip.tar
  tar -chf tensorflow-pip.tar tensorflow-pip

  # and perform a regular install
  test -d tensorflow-pip && rm -r tensorflow-pip
  tar -xf tensorflow-pip.tar
  cd ${BUILDDIR}/tensorflow-pip

  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)
piplist; track tensorflow

# tidy up a bit
if [ -d  $PREFIX/man/man1 ]; then
  mv -v  $PREFIX/man/man1/* $PREFIX/share/man/man1 || true
  rm -rf $PREFIX/man
fi

# ------------------------------------------------------------ Sanity check

# load all packages, see warnings and spot installation errors
# But don't care about r2py, a further dependence into R is not wanted!
echo "# START load test."
python3 -c 'help("modules")' > /dev/null
echo "# END load test (passed)."

echo "# running pip check"
pip3 check

# I guess it makes sense that files can be read by all users ...
echo "# check for unreadable files"
cd $PREFIX
find \! -perm -004 -exec chmod -c a+r {} +

echo "For Deeper checks:"
echo "cd ${BUILDDIR} ;  git log --patch "


exit
# -------------------------------------------------------- Included patches

#Epatch:pip # Operation 'Forever young', disable version-check per default.
#Epatch:pip # The option needs to be kept, because some tools make use of
#Epatch:pip # it and would cause pip to fail.
#Epatch:pip --- a/pip/_internal/cli/cmdoptions.py  2022-08-09 17:29:15.853442948 +0200
#Epatch:pip +++ b/pip/_internal/cli/cmdoptions.py  2022-08-10 10:31:35.124945154 +0200
#Epatch:pip @@ -892,7 +892,6 @@
#Epatch:pip      dest="disable_pip_version_check",
#Epatch:pip      action="store_true",
#Epatch:pip -    default=False,
#Epatch:pip -    help="Don't periodically check PyPI to determine whether a new version "
#Epatch:pip -    "of pip is available for download. Implied with --no-index.",
#Epatch:pip +    default=True,
#Epatch:pip +    help="Ignore this option, the version check IS disabled.",
#Epatch:pip  )

#Epatch:numba1 # Fix lib location, turn numba_sysinfo.py into a common diag tool
#Epatch:numba1 --- a/numba/cuda/cuda_paths.py 2022-10-14 09:57:25.616827200 +0200
#Epatch:numba1 +++ b/numba/cuda/cuda_paths.py 2022-10-20 11:20:15.106019523 +0200
#Epatch:numba1 @@ -68,3 +68,3 @@
#Epatch:numba1      else:
#Epatch:numba1 -        return 'lib64'
#Epatch:numba1 +        return 'lib'

#Epatch:numba2 --- a/numba/misc/numba_sysinfo.py 2022-10-14 09:57:25.628827000 +0200
#Epatch:numba2 +++ b/numba/misc/numba_sysinfo.py 2022-10-20 11:02:54.056767540 +0200
#Epatch:numba2 @@ -1 +1,2 @@
#Epatch:numba2 +#! /usr/bin/env python3
#Epatch:numba2  import json
#Epatch:numba2 @@ -367,3 +368,3 @@
#Epatch:numba2              with redirect_stdout(output):
#Epatch:numba2 -                cudadrv.libs.test(sys.platform, print_paths=False)
#Epatch:numba2 +                cudadrv.libs.test(sys.platform, print_paths=True)
#Epatch:numba2              sys_info[_cu_lib_test] = output.getvalue()
#Epatch:numba2 @@ -626,9 +627,2 @@
#Epatch:numba2          ("",),
#Epatch:numba2 -        ("__Conda Information__",),
#Epatch:numba2 -        (DisplayMap({k: v for k, v in info.items()
#Epatch:numba2 -                     if k.startswith('Conda')}) or ("Conda not available.",)),
#Epatch:numba2 -        ("",),
#Epatch:numba2 -        ("__Installed Packages__",),
#Epatch:numba2 -        DisplaySeq(info.get(_inst_pkg, ("Couldn't retrieve packages info.",))),
#Epatch:numba2 -        ("",),
#Epatch:numba2          ("__Error log__" if info.get(_errors, [])

#Epatch:gyp1 --- a/pylib/gyp/generator/cmake.py
#Epatch:gyp1 +++ b/pylib/gyp/generator/cmake.py
#Epatch:gyp1 @@ -41,7 +41,7 @@
#Epatch:gyp1  try:
#Epatch:gyp1    # maketrans moved to str in python3.
#Epatch:gyp1 +  _maketrans = str.maketrans
#Epatch:gyp1 +except NameError:
#Epatch:gyp1    _maketrans = string.maketrans
#Epatch:gyp1 -except NameError:
#Epatch:gyp1 -  _maketrans = str.maketrans
#Epatch:gyp1  generator_default_variables = {
#Epatch:gyp1 	'EXECUTABLE_PREFIX': '',
#Epatch:gyp1  @@ -283,2 +283,2 @@
#Epatch:gyp1 	  if int(action.get('process_outputs_as_sources', False)):
#Epatch:gyp1 -      extra_sources.extend(zip(cmake_outputs, outputs))
#Epatch:gyp1 +      extra_sources.extend(list(zip(cmake_outputs, outputs)))
#Epatch:gyp1  @@ -988,6 +988,6 @@
#Epatch:gyp1 	  # XCode settings
#Epatch:gyp1 	  xcode_settings = config.get('xcode_settings', {})
#Epatch:gyp1   -    for xcode_setting, xcode_value in xcode_settings.viewitems():
#Epatch:gyp1   +    for xcode_setting, xcode_value in xcode_settings.items():
#Epatch:gyp1 	     SetTargetProperty(output, cmake_target_name,
#Epatch:gyp1 			       "XCODE_ATTRIBUTE_%s" % xcode_setting, xcode_value,
#Epatch:gyp1 			       '' if isinstance(xcode_value, str) else ' ')

#Epatch:gyp2 diff --git a/pylib/gyp/input.py b/pylib/gyp/input.py
#Epatch:gyp2 index 4c12891..2bea334 100644
#Epatch:gyp2 --- a/pylib/gyp/input.py
#Epatch:gyp2 +++ b/pylib/gyp/input.py
#Epatch:gyp2 @@ -1183,7 +1183,7 @@
#Epatch:gyp2        if variable_name in variables:
#Epatch:gyp2          # If the variable is already set, don't set it.
#Epatch:gyp2          continue
#Epatch:gyp2 -      if the_dict_key is 'variables' and variable_name in the_dict:
#Epatch:gyp2 +      if the_dict_key == 'variables' and variable_name in the_dict:
#Epatch:gyp2          # If the variable is set without a % in the_dict, and the_dict is a
#Epatch:gyp2          # variables dict (making |variables| a varaibles sub-dict of a
#Epatch:gyp2          # variables dict), use the_dict's definition.

#Epatch:triton diff --git a/setup.py b/setup.py
#Epatch:triton index 2ac3accd2..e7357be58 100644
#Epatch:triton --- a/setup.py
#Epatch:triton +++ b/setup.py
#Epatch:triton @@ -211,10 +211,7 @@ setup(
#Epatch:triton      long_description="",
#Epatch:triton      packages=["triton", "triton/_C", "triton/language", "triton/tools", "triton/impl", "triton/ops", "triton/runtime", "triton/ops/blocksparse"],
#Epatch:triton      install_requires=[
#Epatch:triton -        "cmake",
#Epatch:triton          "filelock",
#Epatch:triton -        "torch",
#Epatch:triton -        "lit",
#Epatch:triton      ],
#Epatch:triton      package_data={"triton": ["third_party/**/*"]},
#Epatch:triton      include_package_data=True,
#Epatch:triton @@ -233,6 +231,10 @@ setup(
#Epatch:triton      ],
#Epatch:triton      test_suite="tests",
#Epatch:triton      extras_require={
#Epatch:triton +        "build": [
#Epatch:triton +            "cmake>=3.18",
#Epatch:triton +            "lit",
#Epatch:triton +        ],
#Epatch:triton          "tests": [
#Epatch:triton              "autopep8",
#Epatch:triton              "flake8",

# -------------------------------------------------------- This is the end.