python-3.9.12-0.build.sh

#! /bin/bash

# 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

PKG=python
VERSION=3.9.12
BUILD=0
PYTHONVER=${VERSION%.*}

CUDADIR=/pkg/cuda-11.1.1-0

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
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"

# bookkeeping, spots package downgrades
PIPMETADIR=$PREFIX/share/pipmeta
mkdir -p $PIPMETADIR

BUILDDIR=$PREFIX/build

mkdir -p $BUILDDIR
cd $BUILDDIR

# if false; then ######### DEBUG_BASE DEBUG_TF

#URL=https://www.python.org/ftp/python/$VERSION/Python-$VERSION.tar.xz
URL="https://beehive.molgen.mpg.de/4b5fda03e3fbfceca833c997d501bcca/Python-3.9.12.tar.xz"
test -e Python-$VERSION.tar.xz || wget -nv $URL
test -d Python-$VERSION || tar -xf 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
# 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

( # sip: tool to create Python bindings for C and C++ libraries., v6 is out, but not so popular at the moment
  cd $BUILDDIR
  SIP_VERSION=4.19.24

  # orig: https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/595e9ad6bb0a4b3a6ea92c163a05d19c/sip-4.19.24.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

  #### ATTN!
  #### python meanders between /python${PYTHONVER} and /python${PYTHONVER}m

  python3 configure.py \
      -b $PREFIX/bin \
      -d $PREFIX/lib/python$PYTHONVER/site-packages \
      -e $PREFIX/include/python${PYTHONVER} \
      -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 $BUILDDIR
  SIP_VERSION=4.19.24
  mkdir -p private_sip
  cd private_sip

  # orig: https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/595e9ad6bb0a4b3a6ea92c163a05d19c/sip-4.19.24.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

  # 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
)

(
  cd $BUILDDIR
  PYQT_VERSION=5.15.2

  # orig: https://files.pythonhosted.org/packages/28/6c/640e3f5c734c296a7193079a86842a789edb7988dca39eab44579088a1d1/PyQt5-5.15.2.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/b94576e9e013210dc5aba061913e4bd4/PyQt5-5.15.2.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

  #### ATTN!
  #### python meanders between /python${PYTHONVER} and /python${PYTHONVER}m

  # 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} \
    --confirm-license \
    --no-qml-plugin \
    --no-designer-plugin \
    --no-dist-info \
    --verbose

  make -j $NPROC
  make install
)

(
  cd $BUILDDIR
  QSCINTILLA_VERSION=2.11.6

  # orig: https://www.riverbankcomputing.com/static/Downloads/QScintilla/$QSCINTILLA_VERSION/QScintilla-$QSCINTILLA_VERSION.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/343cd0c2c8b425518df2e51eb994fbc6/QScintilla-2.11.6.tar.gz
  test -e QScintilla-$QSCINTILLA_VERSION.tar.gz || wget -nv $BEEHIVE
  test -d QScintilla-$QSCINTILLA_VERSION || tar -xf QScintilla-$QSCINTILLA_VERSION.tar.gz

  cd QScintilla-$QSCINTILLA_VERSION
  cd Python

  # apidir follows PyQt, not Qt (default is: QT_INSTALL_DATA/qsci)
  python3 configure.py \
    --pyqt=PyQt5 \
    --qmake=/usr/local/qt5/bin/qmake \
    --apidir=$PREFIX/share/qsci \
    --no-dist-info

  make -j $NPROC
  make install
)

# fi ######### DEBUG_BASE (1)
# cd $BUILDDIR

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

pip3 list > $PIPMETADIR/pip3list_initial

# ATTN: numpy=1.21.x is out but not everybody like it already (e.g. SciPy ...)
pip3 install --prefix=$PREFIX numpy==1.20.3
pip3 install --prefix=$PREFIX ipython[all]

# install the basic ballpark ...
# numpy holds no ref to *_MAX_THREADS, albeit it's an issue, fix via profile?
# still persisting: NUMEXPR_MAX_THREADS issue caused by numexpr.utils (braindead defaults from this dependency)
pip3 install --prefix=$PREFIX SciPy 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 --prefix=$PREFIX Cython

# 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. (btw. libxslt-python isn't ported to python3)
(
  . ${PREFIX}/profile
  LIBXML2_VERSION=2.9.12
  # orig: http://xmlsoft.org/sources/libxml2-${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
)

pip3 install --prefix=$PREFIX pysam
pip3 install --prefix=$PREFIX seaborn
pip3 install --prefix=$PREFIX scikit-learn
#pip3 install --prefix=$PREFIX metaseq        # fails (Latest commit fa875d1 on Jan 10, 2017)
pip3 install --prefix=$PREFIX Mako
pip3 install --prefix=$PREFIX meson          # required in mariux

pip3 install --prefix=$PREFIX cutadapt       # Helpdesk 01/24/18 16:19, Sabrina Krakau
pip3 install --prefix=$PREFIX pygobject      # Helpdesk 03/26/18 14:19, Virginie Stanisla
pip3 install --prefix=$PREFIX blink1         # Blink1-lib 07/04/18 12:00, Niclas Hofmann

pip3 install --prefix=$PREFIX umi-tools
pip3 install --prefix=$PREFIX sphinx
pip3 install --prefix=$PREFIX recommonmark
pip3 install --prefix=$PREFIX fastcluster
pip3 install --prefix=$PREFIX pydot
pip3 install --prefix=$PREFIX pygraphviz
pip3 install --prefix=$PREFIX deeptools
pip3 install --prefix=$PREFIX HTSeq
pip3 install --prefix=$PREFIX keras
pip3 install --prefix=$PREFIX keras_preprocessing # tensorflow ...
pip3 install --prefix=$PREFIX MotifScan      # Alena 30.8.2018
pip3 install --prefix=$PREFIX MAmotif
pip3 install --prefix=$PREFIX hic2cool       # Helpdesk Robert Schoepflin 17.09.2018
#pip3 install --prefix=$PREFIX hifive         # only python 2.7+
pip3 install --prefix=$PREFIX snakemake
pip3 install --prefix=$PREFIX virtualenv     # Donald
pip3 install --prefix=$PREFIX odfpy          # Donald
pip3 install --prefix=$PREFIX Dumper         # Thomas
pip3 install --prefix=$PREFIX igraph
pip3 install --prefix=$PREFIX louvain        # monocle3 prep for Helene
pip3 install --prefix=$PREFIX selenium       # 19.7.19 Kreitler  -> https://webxray.org/
pip3 install --prefix=$PREFIX cooltools      # Maria Valieva 17.7.2019
pip3 install --prefix=$PREFIX gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
pip3 install --prefix=$PREFIX torch
pip3 install --prefix=$PREFIX torchvision
pip3 install --prefix=$PREFIX plotly
pip3 install --prefix=$PREFIX pyOpenCL
pip3 install --prefix=$PREFIX docopt
pip3 install --prefix=$PREFIX dbus-python
pip3 install --prefix=$PREFIX distro
pip3 install --prefix=$PREFIX ply
pip3 install --prefix=$PREFIX threadpoolctl

pip3 install --prefix=$PREFIX pyopengl
# creates error, so remove it
rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk

# pip3 install --prefix=$PREFIX HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
pip3 install --prefix=$PREFIX HiCMatrix
pip3 install --prefix=$PREFIX pybedtools
pip3 install --prefix=$PREFIX gffutils
pip3 install --prefix=$PREFIX --no-deps "pyGenomeTracks" # example produces plots, so give it a chance, otherwise it's just a dumbfucked downgrader
pip3 install --prefix=$PREFIX python-bioformats

pip3 install --prefix=$PREFIX jupyterlab      # request Peter Arndt
pip3 install --prefix=$PREFIX jupyterlab-git
pip3 install --prefix=$PREFIX igv_jupyterlab  # Matthias Lienhard HD 01-04-2020
pip3 install --prefix=$PREFIX igv-jupyter
mkdir -vp $PREFIX/share/jupyter/lab/settings  # try to defeat a silly error in jupyter labextension install

pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98
pip3 install --prefix=$PREFIX multiqc

pip3 install --prefix=$PREFIX thonny          # nice little ide, kreitler
pip3 install --prefix=$PREFIX pybind11
pip3 install --prefix=$PREFIX svgwrite
pip3 install --prefix=$PREFIX pyomo
pip3 install --prefix=$PREFIX jsbsim          # kreitler, hobby

pip3 install --prefix=$PREFIX bioservices
pip3 install --prefix=$PREFIX pairtools
pip3 install --prefix=$PREFIX SharedArray
pip3 install --prefix=$PREFIX pyabc           # dependency for stochkit, HD 20.07.20 Gemma Noviello
pip3 install --prefix=$PREFIX petab
pip3 install --prefix=$PREFIX tadtool         # HD 26.01.21 Michael Robson
# pip3 install --prefix=$PREFIX perf          # fails, issue from Paul sep-20, no clue...
# pip3 install --prefix=$PREFIX glpk-py       # kreitler, fails, wants setuptools_scm, do I want setuptools_scm?
pip3 install --prefix=$PREFIX helen           # HD, a dependency from a request by helene :)
pip3 install --prefix=$PREFIX umap            # HD, used by Matthias Lienhard

pip3 install --prefix=$PREFIX macs2           # HD, Alessa Ringel, Tobias Zehnder, old python2 version broke after glibc update
pip3 install --prefix=$PREFIX macs3

pip3 install --prefix=$PREFIX biopython       # HD 2021-07-23 Magalhaes/Hnisz alphafold related (cool that we have missed biopython so far, LOL)
pip3 install --prefix=$PREFIX dm-tree
pip3 install --prefix=$PREFIX dm-haiku
# pip3 install --prefix=$PREFIX jaxlib        # these should be build from source, otherwise it will have trouble finding the right cuda
# pip3 install --prefix=$PREFIX jax
pip3 install --prefix=$PREFIX flatbuffers
pip3 install --prefix=$PREFIX contextlib2
pip3 install --prefix=$PREFIX ml_collections

pip3 install --prefix=$PREFIX wheel           # wheel is evil, but jaxlib needs it, and tf would pull it anyway


# fi ######### DEBUG_BASE (2)
# cd $BUILDDIR

# jax/jaxlib
(
  . ${PREFIX}/profile
  . /pkg/bazel-4.1.0-0/profile
  cd $BUILDDIR

  # orig: https://github.com/google/jax/archive/refs/tags/jaxlib-v0.1.71.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/10b3082f32e4088a139b8a5b9591ea9f/jax-jaxlib-v0.1.71.tar.gz
  test -e jax-jaxlib-v0.1.71.tar.gz || wget -nv $BEEHIVE
  test -d jax-jaxlib-v0.1.71 || tar -xf jax-jaxlib-v0.1.71.tar.gz

  cd jax-jaxlib-v0.1.71
  test -d dist && rm -f dist/*

  export JAX_CUDA_VERSION=11.1 # just to give a '+cuda111' in the wheel name

  python3 build/build.py \
    --target_cpu_features native \
    --enable_cuda \
    --cuda_path /pkg/cuda-11.1.1-0 \
    --cuda_version 11.1 \
    --cudnn_path /pkg/cuda-11.1.1-0 \
    --cudnn_version 8.0.4 \
    --noenable_tpu

  # result looks like dist/jaxlib-0.1.71-cp39-none-manylinux2010_x86_64.whl
  pip3 install --prefix=$PREFIX ./dist/*.whl
  # this brings the jax package
  pip3 install --prefix=$PREFIX .
)

# boost for pycuda
(
  . ${PREFIX}/profile
  BOOST_VERSION=(1.75.0 1_75_0)
  PKGCFLAGS="-O2 -fPIC"

  cd $BUILDDIR
  # orig: https://dl.bintray.com/boostorg/release/1.75.0/source/boost_1_75_0.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de//38813f6feb40387dfe90160debd71251/boost_1_75_0.tar.gz
  test -e boost_${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

  #### ATTN!
  #### python meanders between /python${PYTHONVER} and /python${PYTHONVER}m

  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
)

# use pycuda git version to get GL support
(
  PYCUDAVERS=2020.1
  PYTHON_LIBNAME=boost_python${PYTHONVER/./}

  . ${PREFIX}/profile
  cd $BUILDDIR

  # future build might try this one
  # https://github.com/inducer/pycuda/archive/refs/tags/v2021.1.tar.gz

  # orig: https://github.com/inducer/pycuda/archive/v2020.1.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/580562d7af4d3249c5b42a1df8d428a0/pycuda-2020.1.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 install --prefix $PREFIX
)

(
  # 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-2.0.3.tar.gz || wget -nv $BEEHIVE
  test -d idr-2.0.3 || tar -xf idr-2.0.3.tar.gz
  cd idr-2.0.3
  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)

(
  # 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-1.0.tar.gz || wget -nv $BEEHIVE
  test -d stgit-1.0 || tar -xf stgit-1.0.tar.gz
  cd stgit-1.0
  python3 setup.py build
  python3 setup.py install --prefix $PREFIX
)

(
  # orig: https://github.com/openmm/openmm/archive/refs/tags/7.5.1.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/12fefb6ca030d1f4aace78ac1a8b94c3/openmm-7.5.1.tar.gz
  test -e openmm-7.5.1.tar.gz || wget -nv $BEEHIVE
  test -d openmm-7.5.1 || tar -xf openmm-7.5.1.tar.gz
  cd openmm-7.5.1

  # replace hardcoded "/usr/local/cuda/bin/nvcc" in libOpenMMCUDA.so (crying four trouble dude?)
  # Otherwise OPENMM_CUDA_COMPILER needs to be used
  sed -i -e "/bin\/nvcc/ s,/usr/local/cuda/bin/nvcc,/$CUDADIR/bin/nvcc," \
    platforms/cuda/src/CudaPlatform.cpp

  # apply 'DeepMind modification' to openmm, hopefully it will leave openmm usable :)
  sed -ne '/^#Epatch:openmmtopo/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose

  mkdir -p build
  cd build

  cmake \
   -DCMAKE_INSTALL_PREFIX=$PREFIX \
   -DCUDA_TOOLKIT_ROOT_DIR=$CUDADIR \
   -DBUILD_TESTING=OFF \
   ..

  make -j $NPROC
  make install
  # make PythonInstall # this one sucks! (ignoring all locations cleanly found by cmake before...)

  echo "# openmm library part done, now python-binding."

  cd python
  OPENMM_INCLUDE_PATH=$PREFIX/include OPENMM_LIB_PATH=$PREFIX/lib python3 setup.py build
  OPENMM_INCLUDE_PATH=$PREFIX/include OPENMM_LIB_PATH=$PREFIX/lib python3 setup.py install

  # place symlinks from plugins to lib, saving a LD_LIBRARY_PATH entry
  cd $PREFIX/lib
  for SO in plugins/*.so; do
    ln -sv $SO
  done
)

(
  # orig:https://github.com/openmm/pdbfixer/archive/refs/tags/v1.7.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/dd383722fcf5213537656f691f4c2053/pdbfixer-1.7.tar.gz
  test -e pdbfixer-1.7.tar.gz || wget -nv $BEEHIVE
  test -d pdbfixer-1.7 || tar -xf pdbfixer-1.7.tar.gz
  cd pdbfixer-1.7
  python3 setup.py build
  python3 setup.py install
)

(
  # orig:https://github.com/brentp/bwa-meth/archive/refs/tags/v0.2.2.tar.gz # HD: Sven Klages 2021-09-02
  BEEHIVE=https://beehive.molgen.mpg.de/85e77f8c2d832af13f31d5b612ab27eb/bwa-meth-0.2.2.tar.gz
  test -e bwa-meth-0.2.2.tar.gz || wget -nv $BEEHIVE
  test -d bwa-meth-0.2.2 || tar -xf bwa-meth-0.2.2.tar.gz
  cd bwa-meth-0.2.2
  python3 setup.py build
  python3 setup.py install
)

pip3 list > $PIPMETADIR/pip3list_ballpark

# fi ######### DEBUG_TF
# cd $BUILDDIR

# finaly tensorflaw
(
  TFVERSION=2.5.0
  NCCLSHORTVERSION=2.7

  . ${PREFIX}/profile
  . /pkg/bazel-4.1.0-0/profile
  cd $BUILDDIR

  # https://github.com/tensorflow/tensorflow/archive/v2.5.0.tar.gz
  BEEHIVE=https://beehive.molgen.mpg.de/b152ebdc7f72c4d32f7a9e58aa41b80d/tensorflow-2.5.0.tar.gz

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

  cd tensorflow-${TFVERSION}

  # https://bugs.archlinux.org/task/65953

  #vars for config
  export PYTHON_BIN_PATH=${PREFIX}/bin/python3
  export USE_DEFAULT_PYTHON_LIB_PATH=1
  export TF_NEED_JEMALLOC=1
  export TF_NEED_KAFKA=0
  export TF_NEED_OPENCL_SYCL=0
  export TF_NEED_AWS=0
  export TF_NEED_GCP=0
  export TF_NEED_HDFS=0
  export TF_NEED_S3=0
  export TF_ENABLE_XLA=1
  export TF_NEED_GDR=0
  export TF_NEED_VERBS=0
  export TF_NEED_OPENCL=0
  export TF_NEED_MPI=0
  export TF_NEED_TENSORRT=1
  export TF_NEED_NGRAPH=0
  export TF_NEED_IGNITE=0
  export TF_NEED_ROCM=0
  export TF_SET_ANDROID_WORKSPACE=0
  export TF_DOWNLOAD_CLANG=0
  export TF_NCCL_VERSION=${NCCLSHORTVERSION}
  export TF_IGNORE_MAX_BAZEL_VERSION=1
  export NCCL_INSTALL_PATH=${CUDADIR}
  export GCC_HOST_COMPILER_PATH=/usr/bin/gcc
  export TF_CUDA_CLANG=0
  export CLANG_CUDA_COMPILER_PATH=/usr/bin/clang
  export TF_CUDA_PATHS=${CUDADIR},${CUDADIR}/extras/CUPTI,${CUDADIR}/nvvm
  export TF_CUDA_VERSION=$(${CUDADIR}/bin/nvcc --version | sed -n 's/^.*release \(.*\),.*/\1/p')
  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

  ./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

  # inhibit downgrading of packages installed
  sed -ne '/^#Epatch:tfdep/ s/^#Epatch:\S* // p' $ME | patch -p2 --verbose

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

pip3 list > $PIPMETADIR/pip3list_after_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


# 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."

exit

### PATCHES

# the code to cope with '--disable-pip-version-check' is spread over the module, so
# just quieten the enervating/misleading update reminder for at least 3 minors ...

#Epatch:pip *** a/pip/_internal/self_outdated_check.py  Mon May 16 13:16:30 2022
#Epatch:pip --- b/pip/_internal/self_outdated_check.py  Mon May 16 15:57:31 2022
#Epatch:pip ***************
#Epatch:pip *** 206,211 ****
#Epatch:pip --- 206,212 ----
#Epatch:pip       local_version_is_older = (
#Epatch:pip           local_version < remote_version
#Epatch:pip           and local_version.base_version != remote_version.base_version
#Epatch:pip +         and ( local_version.release[0] < remote_version.release[0] or local_version.release[1] < remote_version.release[1] - 3 )
#Epatch:pip       )
#Epatch:pip       if local_version_is_older:
#Epatch:pip           return UpgradePrompt(old=str(local_version), new=remote_version_str)

# BTW: numpy is installed ...

#Epatch:tfdep --- a/tensorflow-pip/setup.py.orig       2021-07-29 21:21:33.000000000 +0200
#Epatch:tfdep +++ b/tensorflow-pip/setup.py    2021-08-05 18:14:26.011647329 +0200
#Epatch:tfdep @@ -77,6 +77,2 @@
#Epatch:tfdep  REQUIRED_PACKAGES = [
#Epatch:tfdep -    # NOTE: As numpy has releases that break semver guarantees and several other
#Epatch:tfdep -    # deps depend on numpy without an upper bound, we must install numpy before
#Epatch:tfdep -    # everything else.
#Epatch:tfdep -    'numpy ~= 1.19.2',
#Epatch:tfdep      # Install other dependencies


# This is found in the docker image preparation for AlphaFold.
# I'm not completely happy patching existing libraries ...

#Epatch:openmmtopo --- a/wrappers/python/simtk/openmm/app/topology.py.orig   2021-04-07 22:09:01.000000000 +0200
#Epatch:openmmtopo +++ b/wrappers/python/simtk/openmm/app/topology.py        2021-08-05 16:49:10.191954117 +0200
#Epatch:openmmtopo @@ -355,2 +355,11 @@
#Epatch:openmmtopo              return 'SG' in names and 'HG' not in names
#Epatch:openmmtopo +        # This function is used to prevent multiple di-sulfide bonds from being
#Epatch:openmmtopo +        # assigned to a given atom. This is a DeepMind modification.
#Epatch:openmmtopo +        def isDisulfideBonded(atom):
#Epatch:openmmtopo +            for b in self._bonds:
#Epatch:openmmtopo +                if (atom in b and b[0].name == 'SG' and
#Epatch:openmmtopo +                    b[1].name == 'SG'):
#Epatch:openmmtopo +                    return True
#Epatch:openmmtopo +
#Epatch:openmmtopo +            return False
#Epatch:openmmtopo  
#Epatch:openmmtopo @@ -361,2 +370,3 @@
#Epatch:openmmtopo              pos1 = positions[sg1.index]
#Epatch:openmmtopo +            candidate_distance, candidate_atom = 0.3*nanometers, None
#Epatch:openmmtopo              for j in range(i):
#Epatch:openmmtopo @@ -366,4 +376,10 @@
#Epatch:openmmtopo                  distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2])
#Epatch:openmmtopo -                if distance < 0.3*nanometers:
#Epatch:openmmtopo -                    self.addBond(sg1, sg2)
#Epatch:openmmtopo +                if distance < candidate_distance and not isDisulfideBonded(sg2):
#Epatch:openmmtopo +                    candidate_distance = distance
#Epatch:openmmtopo +                    candidate_atom = sg2
#Epatch:openmmtopo +            # Assign bond to closest pair.
#Epatch:openmmtopo +            if candidate_atom:
#Epatch:openmmtopo +                self.addBond(sg1, candidate_atom)
#Epatch:openmmtopo +
#Epatch:openmmtopo +