diff --git a/python-3.11.7-0.build.sh b/python-3.11.7-0.build.sh
new file mode 100755
index 0000000..f989e50
--- /dev/null
+++ b/python-3.11.7-0.build.sh
@@ -0,0 +1,863 @@
+#!/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-$COOKIE.sh
+ # TESTING=1
+ # SKIPTENSORFLOW=1
+
+# ---------------------------------------------------------------- Preamble
+
+PKG=python
+VERSION=3.11.7
+BUILD=0
+PYTHONVER=${VERSION%.*}
+
+CUDADIR=/pkg/cuda-11.8.0-0
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi
+
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
+
+set -e
+umask 022
+
+BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp
+
+# keep pip's download cache when testing
+test -z "$TESTING" && 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() {
+ pip 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() {
+ echo "# ::INST:: # '${@+$@}'"
+ # no-color is nice, but doesn't work when dependencies are installed, so (mis-)use a pipe
+ pip install --no-color --compile --cache-dir=$HOME/.cache/pip --prefix=$PREFIX "${@+$@}" | cat
+ piplist
+ track $*
+}
+
+
+# ---------------------------------------- Build Python & support libraries
+
+(
+
+ # orig: https://www.python.org/ftp/python/3.11.7/Python-3.11.7.tgz
+ BEEHIVE=https://beehive.molgen.mpg.de/ef61f81ec82c490484219c7f0ec96783/Python-3.11.7.tgz
+ test -e Python-$VERSION.tar.xz || wget -nv $BEEHIVE
+ test -d Python-$VERSION || tar -xf Python-$VERSION.tgz
+ cd Python-$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 $PREFIX/bin/python
+
+ python -m ensurepip
+ pip3 install --prefix=$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
+ )
+ # libblosc2 installs in $PREFIX/lib64, I hate to do this ...
+ ln -s lib $PREFIX/lib64
+)
+install setuptools
+piplist; track START
+
+
+# build various pythonbindings 'by hand', because pip installs do not deliver
+# header files and the like.
+# BTW: builds need meson
+
+install meson
+
+(
+ DBUS_PYTHON_VERSION=1.3.2
+
+ # PyPi
+ # https://files.pythonhosted.org/packages/c1/d3/6be85a9c772d6ebba0cc3ab37390dd6620006dcced758667e0217fb13307/dbus-python-1.3.2.tar.gz
+ BEEHIVE=https://beehive.molgen.mpg.de/33be8a4a766e1c7c9a377b8f934ce21a/dbus-python-1.3.2.tar.gz
+ test -e dbus-python-$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 $NPROC
+ make install
+
+)
+
+(
+ PYCAIRO_VERSION=1.23.0
+
+ # PyPi
+ # https://files.pythonhosted.org/packages/69/ca/9e9fa2e8be0876a9bbf046a1be7ee33e61d4fdfbd1fd25c76c1bdfddf8c4/pycairo-1.23.0.tar.gz
+ BEEHIVE=https://beehive.molgen.mpg.de/7a3729d21659098e1b9a411b62e88966/pycairo-1.23.0.tar.gz
+ test -e pycairo-$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
+
+ pip install .
+
+)
+
+# QT bindings need some python modules to build
+
+install PyQt5-sip
+install PyQt-builder
+
+(
+ PYQT_VERSION=5.15.9
+
+ # 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 $NPROC
+ make install
+)
+piplist; track qt-support-riverbankcomputing
+
+
+# -------------------------------------------------------- Install packages
+
+
+install Cython
+
+
+# libxml2-python from pypi isn't up to date, cause lxml seems to be the favored binding
+# do this early, not that some dependency tries it on its own.
+# (btw. libxslt-python isn't ported to python3)
+(
+ LIBXML2_VERSION=2.9.12
+
+ # orig: http://xmlsoft.org/sources/libxml2-${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
+ pip install .
+)
+piplist; track legacy-libxml2
+
+# Install the most 'sensitive' packages first
+install numpy==1.25.2
+install numba==0.58.1
+
+install wheel
+
+# python-javabridge, problems with python 3.11 and recent cython, thus
+# regenerate C bindings from *pxd, *pyx -- so must use github, and wheel
+(
+ # use the fork from cellprofiler, as used in pypi
+ git clone https://github.com/CellProfiler/python-javabridge
+ cd python-javabridge
+ git checkout v4.0.3
+ sed -ne '/^#Epatch:javabridge/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
+ pip install .
+)
+
+PACKAGES=$(sed -e s/#.*$// <<- __PKGLIST__
+ igraph==0.10.8 # louvain
+ keras==2.14.0 # tensorflow 2.14.1
+ ml-dtypes==0.2.0 # tensorflow, dm-haiku, jax, tensorstore
+ seaborn==0.12.2 # scanpy
+ wrapt==1.14.1 # tensorflow vs. snakemake
+
+ pytest==6.2.5
+ pytest-asyncio==0.19.0 # to get rid of a deprecation warning in 0.20.3, -> 0.19.0
+
+ urllib3==2.0.7
+ ipython[all]
+
+ Pillow
+ protobuf
+ onnx
+ Sphinx
+ jedi
+ black[d] # onnx wants it, but does not install it ...
+ flask
+
+ SciPy
+ pandas
+ SymPy
+ nose
+ statsmodels
+ pysam
+ seaborn
+ scikit-learn
+ Mako
+ cutadapt # Helpdesk 01/24/18 16:19, S. K.
+ pygobject # Helpdesk 03/26/18 14:19, V. S.
+ blink1 # Blink1-lib 07/04/18 12:00, N. H.
+ hvplot # ont/nextflow pipelines
+ pyarrow # ont/nextflow pipelines
+ umi-tools
+ recommonmark
+ fastcluster
+ pydot
+ pygraphviz
+ deeptools
+ HTSeq
+ keras_preprocessing # tensorflow ...
+ MotifScan # A.B. 30.8.2018
+ MAmotif
+ hic2cool # Helpdesk R. S. 17.09.2018
+ snakemake
+ virtualenv # Donald
+ odfpy # Donald
+ Dumper # Thomas
+ louvain # monocle3 prep for H. K.
+ selenium # 19.7.19 T.K. -> https://webxray.org/
+ plotly
+ pyOpenCL
+ docopt
+ distro
+ ply
+ threadpoolctl
+ HiCMatrix # 17.1 -> https://github.com/deeptools/HiCMatrix/issues/47
+ pybedtools
+ gffutils
+ jupyter
+ jupyterlab
+ jupyterlab-git # request P. A.
+ igv_jupyterlab # M. L. 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 M. R.
+ pyperf # Paul sep-20
+ umap # HD, used by M. L.
+ MACS3
+ biopython # HD 2021-07-23 Magalhaes/Hnisz alphafold related -- cool that we have missed biopython so far, LOL
+ # prevent dm-haiku from fetching 'brand-new' stuff, thus avoiding further havoc
+ tensorstore==0.1.45 # tensorflow
+ orbax-checkpoint==0.4.4 # tensorflow
+ dm-tree
+ dm-haiku
+ flatbuffers
+ contextlib2
+ ml_collections
+ python-bioformats==4.0.6 # 4.0.7 would pull up too much other packages
+
+
+ # additions/fixups since 3.9
+ spyder
+ spyder-kernels
+ 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
+ # watch https://pypi.org/project/napari/#history
+ napari[pyqt5]==0.4.19rc2 # 0.4.18 would turn into a psychotic downgrader via numpydoc ...
+ napari-czifile2
+ CrossMap
+ scanpy
+ asciidoc
+ triton
+
+ # additions/fixups since 3.10
+ aicspylibczi
+ filetype
+ gmpy2
+
+ # nf-core / epi2me related
+ dominate
+ libsass
+ sigfig
+ whatshap
+ Truvari
+
+ __PKGLIST__
+)
+
+for PKG in $PACKAGES; do
+ install $PKG
+done
+
+
+# remove unneeded dependency, and save the current pillow, then go for pyimagej, nerve ...
+(
+ LABELING_VERSION=0.1.13
+ # https://files.pythonhosted.org/packages/71/b0/c3c3c6931850c05e548c0a8cfadb8e6d8c5bd5ad18dce90ad4c909db5867/labeling-0.1.13.tar.gz
+ BEEHIVE=https://beehive.molgen.mpg.de/6da91e43f9864e9f4d4acb252eb486eb/labeling-0.1.13.tar.gz
+ test -e labeling-${LABELING_VERSION}.tar.gz || wget -nv $BEEHIVE
+ test -d labeling-${LABELING_VERSION} || tar -xf labeling-${LABELING_VERSION}.tar.gz
+ cd labeling-${LABELING_VERSION}
+ # not needed (tests work...)
+ sed -i -e '/pillow/ s/<10//' ./setup.py
+ sed -i -e '/pillow/ s/<10//' ./labeling.egg-info/requires.txt
+ pip install . --prefix=$PREFIX
+
+ piplist; track labeling==${LABELING_VERSION}
+)
+
+install pyimagej # Microscopy
+
+
+# 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
+
+
+mkdir -vp $PREFIX/share/jupyter/lab/settings # try to defeat a silly error in jupyter labextension install
+
+
+# --------------------------------------------------- Install misc packages
+
+# these mostly bigger packages require either wheel, other treatments,
+# or java.
+
+# GYP is a Meta-Build system: a build system that generates other build systems. https://gyp.gsrc.io/
+(
+ set -x
+ GYP_VERSION=20230301_c6d8b9f7
+ # orig: https://mirror.netcologne.de/slackware/slackware64-current/source/d/gyp/
+ BEEHIVE=https://beehive.molgen.mpg.de/ba0357be23ca55555714261afccc7aab/gyp-20230301_c6d8b9f7.tar.xz
+ test -e gyp-${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:gyp/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
+ pip install .
+)
+piplist; track gyp
+
+(
+ BOOST_VERSION=(1.80.0 1_80_0)
+ PKGCFLAGS="-O2 -fPIC"
+
+ # orig: https://boostorg.jfrog.io/artifactory/main/release/1.80.0/source/boost_1_80_0.tar.gz
+ BEEHIVE=https://beehive.molgen.mpg.de/077f074743ea7b0cb49c6ed43953ae95/boost_1_80_0.tar.gz
+ test -e boost_${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=2023.1
+ PYTHON_LIBNAME=boost_python${PYTHONVER/./}
+
+ # orig: https://files.pythonhosted.org/packages/dd/b2/e30282f3286ddad05ef44548fa5c306a179ed3baceefa699af078e49ce6e/pycuda-2023.1.tar.gz
+ BEEHIVE="https://beehive.molgen.mpg.de/3193e66e54242ac634825b14944295ac/pycuda-2023.1.tar.gz"
+ test -e pycuda-${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
+ python 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$PREFIX/lib
+
+ pip install . --prefix=$PREFIX
+)
+piplist; track pycuda
+
+(
+ # install from git to get .so files in case
+ pip install git+https://github.com/open2c/pairtools.git@v1.0.2 --prefix=$PREFIX
+ pip install git+https://github.com/brentp/bwa-meth.git@v0.2.7 --prefix=$PREFIX
+
+ # versions > 1.5 will not work with pip install github
+ pip install git+https://github.com/stacked-git/stgit.git@v1.5 --prefix=$PREFIX
+)
+piplist; track pairtools bwa-meth stgit
+
+(
+ IDR_VERSION=2.0.3
+ # orig: https://github.com/nboley/idr/archive/2.0.3/idr-2.0.3.tar.gz # HD: T. Z., 18.3.21
+ BEEHIVE=https://beehive.molgen.mpg.de/1bec61b526bb1dcf92a5ab99c27852d0/idr-2.0.3.tar.gz
+ test -e idr-${IDR_VERSION}.tar.gz || wget -nv $BEEHIVE
+ test -d idr-${IDR_VERSION} || tar -xf idr-${IDR_VERSION}.tar.gz
+ cd idr-${IDR_VERSION}
+ pip install . --prefix=$PREFIX
+)
+piplist; track IDR
+
+
+# ------------------------------------------------ finally build tensorflaw
+
+(
+ test -n "$SKIPTENSORFLOW" && exit
+
+ TFVERSION=2.14.1
+ NCCLSHORTVERSION=$(pkg-config nccl --modversion | grep -Po '\d+\.\d+')
+
+ # need newer jre to handle --add-opens=java.base/java.lang=ALL-UNNAMED, and bazel >= 6.1
+ . /pkg/openjdk-21.0.0.35-0/profile
+ . /pkg/bazel-6.2.1-0/profile
+
+ # orig: https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.14.1.tar.gz
+ BEEHIVE=https://beehive.molgen.mpg.de/c7ba144a4b1b0a6d5fea5ecd274172d3/tensorflow-2.14.1.tar.gz
+
+ test -e tensorflow-${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=${PREFIX}/bin/python3
+ export USE_DEFAULT_PYTHON_LIB_PATH=1
+ export TF_PYTHON_VERSION=3.11
+ export TF_NEED_JEMALLOC=1
+ export TF_NEED_KAFKA=0
+ export TF_NEED_OPENCL_SYCL=0
+ export TF_NEED_AWS=0
+ export TF_NEED_GCP=0
+ export TF_NEED_HDFS=0
+ export TF_NEED_S3=0
+ export TF_ENABLE_XLA=1
+ export TF_NEED_GDR=0
+ export TF_NEED_VERBS=0
+ export TF_NEED_OPENCL=0
+ export TF_NEED_MPI=0
+ export TF_NEED_TENSORRT=0
+ export TF_NEED_NGRAPH=0
+ export TF_NEED_IGNITE=0
+ export TF_NEED_ROCM=0
+ export TF_SET_ANDROID_WORKSPACE=0
+ export TF_DOWNLOAD_CLANG=0
+ export TF_NCCL_VERSION=${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' ${CUDADIR}/include/cudnn_version.h)
+ # hardware older than sm_52 is said to be unsupported, compute_86 denotes an emulation
+ export TF_CUDA_COMPUTE_CAPABILITIES=sm_52,sm_53,sm_60,sm_61,sm_62,sm_70,sm_72,sm_75,sm_80,sm_86,sm_87,sm_89,sm_90,compute_90
+
+ # stay compatible with the cluster machines
+ # https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html
+ export CC_OPT_FLAGS="-march=broadwell" # or haswell to be safe ? no more nehalem
+ export TF_NEED_CUDA=1
+
+ export BAZEL_ARGS="--config=mkl -c opt"
+
+ # avoid: Auto-Configuration Warning: 'TMP' environment variable is not set, using 'C:\Windows\Temp' as default :/
+ export TMP=$BUILD_TMPDIR/tf_tmp
+ mkdir -p $TMP
+
+ ./configure
+
+ bazel build \
+ --cxxopt="-march=broadwell" \
+ --copt="-march=broadwell" \
+ --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 weird 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 ${BUILDDIR}/tensorflow-pip
+
+ pip install . --prefix=$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."
+python -c 'help("modules")' > /dev/null
+echo "# END load test (passed)."
+
+echo "# running pip check"
+pip check
+
+# I guess it makes sense that files can be read by all users ...
+echo "# check for unreadable files"
+cd $PREFIX
+for D in bin etc include lib share; do
+ find $D \! -perm -004 -exec chmod -c a+r {} +
+done
+
+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:gyp --- a/pylib/gyp/generator/cmake.py
+#Epatch:gyp +++ b/pylib/gyp/generator/cmake.py
+#Epatch:gyp @@ -41,7 +41,7 @@
+#Epatch:gyp try:
+#Epatch:gyp # maketrans moved to str in python3.
+#Epatch:gyp + _maketrans = str.maketrans
+#Epatch:gyp +except NameError:
+#Epatch:gyp _maketrans = string.maketrans
+#Epatch:gyp -except NameError:
+#Epatch:gyp - _maketrans = str.maketrans
+#Epatch:gyp generator_default_variables = {
+#Epatch:gyp 'EXECUTABLE_PREFIX': '',
+#Epatch:gyp @@ -283,2 +283,2 @@
+#Epatch:gyp if int(action.get('process_outputs_as_sources', False)):
+#Epatch:gyp - extra_sources.extend(zip(cmake_outputs, outputs))
+#Epatch:gyp + extra_sources.extend(list(zip(cmake_outputs, outputs)))
+#Epatch:gyp @@ -988,6 +988,6 @@
+#Epatch:gyp # XCode settings
+#Epatch:gyp xcode_settings = config.get('xcode_settings', {})
+#Epatch:gyp - for xcode_setting, xcode_value in xcode_settings.viewitems():
+#Epatch:gyp + for xcode_setting, xcode_value in xcode_settings.items():
+#Epatch:gyp SetTargetProperty(output, cmake_target_name,
+#Epatch:gyp "XCODE_ATTRIBUTE_%s" % xcode_setting, xcode_value,
+#Epatch:gyp '' if isinstance(xcode_value, str) else ' ')
+
+#Epatch:gyp diff --git a/pylib/gyp/input.py b/pylib/gyp/input.py
+#Epatch:gyp index 4c12891..2bea334 100644
+#Epatch:gyp --- a/pylib/gyp/input.py
+#Epatch:gyp +++ b/pylib/gyp/input.py
+#Epatch:gyp @@ -1183,7 +1183,7 @@
+#Epatch:gyp if variable_name in variables:
+#Epatch:gyp # If the variable is already set, don't set it.
+#Epatch:gyp continue
+#Epatch:gyp - if the_dict_key is 'variables' and variable_name in the_dict:
+#Epatch:gyp + if the_dict_key == 'variables' and variable_name in the_dict:
+#Epatch:gyp # If the variable is set without a % in the_dict, and the_dict is a
+#Epatch:gyp # variables dict (making |variables| a varaibles sub-dict of a
+#Epatch:gyp # variables dict), use the_dict's definition.
+
+
+#Epatch:javabridge diff --git a/_javabridge_nomac.pyx b/_javabridge_nomac.pyx
+#Epatch:javabridge index 9f28939..c437db0 100644
+#Epatch:javabridge --- a/_javabridge_nomac.pyx
+#Epatch:javabridge +++ b/_javabridge_nomac.pyx
+#Epatch:javabridge @@ -16,30 +16,30 @@ cdef extern from "jni.h":
+#Epatch:javabridge jint (*AttachCurrentThreadAsDaemon)(JavaVM *vm, void *penv, void *args) nogil
+#Epatch:javabridge jint JNI_CreateJavaVM(JavaVM **pvm, void **penv, void *args) nogil
+#Epatch:javabridge
+#Epatch:javabridge -cdef int MacStartVM(JavaVM **pvm, JavaVMInitArgs *pVMArgs, char *class_name) nogil:
+#Epatch:javabridge +cdef extern int MacStartVM(JavaVM **pvm, JavaVMInitArgs *pVMArgs, char *class_name) nogil:
+#Epatch:javabridge return -1
+#Epatch:javabridge
+#Epatch:javabridge -cdef void StopVM(JavaVM *vm) nogil:
+#Epatch:javabridge +cdef extern void StopVM(JavaVM *vm) nogil:
+#Epatch:javabridge vm[0].DestroyJavaVM(vm)
+#Epatch:javabridge
+#Epatch:javabridge -cdef void MacRunLoopInit() nogil:
+#Epatch:javabridge +cdef extern void MacRunLoopInit() nogil:
+#Epatch:javabridge pass
+#Epatch:javabridge
+#Epatch:javabridge -cdef void MacRunLoopRun() nogil:
+#Epatch:javabridge +cdef extern void MacRunLoopRun() nogil:
+#Epatch:javabridge pass
+#Epatch:javabridge
+#Epatch:javabridge -cdef void MacRunLoopStop() nogil:
+#Epatch:javabridge +cdef extern void MacRunLoopStop() nogil:
+#Epatch:javabridge pass
+#Epatch:javabridge
+#Epatch:javabridge -cdef void MacRunLoopReset() nogil:
+#Epatch:javabridge +cdef extern void MacRunLoopReset() nogil:
+#Epatch:javabridge pass
+#Epatch:javabridge
+#Epatch:javabridge -cdef int MacIsMainThread() nogil:
+#Epatch:javabridge +cdef extern int MacIsMainThread() nogil:
+#Epatch:javabridge return 0
+#Epatch:javabridge
+#Epatch:javabridge -cdef void MacRunLoopRunInMode(double timeout) nogil:
+#Epatch:javabridge +cdef extern void MacRunLoopRunInMode(double timeout) nogil:
+#Epatch:javabridge pass
+#Epatch:javabridge
+#Epatch:javabridge -cdef int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args) nogil:
+#Epatch:javabridge +cdef extern int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args) nogil:
+#Epatch:javabridge return JNI_CreateJavaVM(pvm, pEnv, args)
+#Epatch:javabridge
+
+#Epatch:javabridge diff --git a/_javabridge_mac.pyx b/_javabridge_mac.pyx
+#Epatch:javabridge index 2e3c524..daed790 100644
+#Epatch:javabridge --- a/_javabridge_mac.pyx
+#Epatch:javabridge +++ b/_javabridge_mac.pyx
+#Epatch:javabridge @@ -31,11 +31,11 @@ cdef extern from "mac_javabridge_utils.h":
+#Epatch:javabridge int MacIsMainThread() nogil
+#Epatch:javabridge void MacRunLoopRunInMode(double) nogil
+#Epatch:javabridge
+#Epatch:javabridge -cdef void StopVM(JavaVM *vm):
+#Epatch:javabridge +cdef extern void StopVM(JavaVM *vm):
+#Epatch:javabridge MacStopVM()
+#Epatch:javabridge
+#Epatch:javabridge #
+#Epatch:javabridge # Unused stub in Mac
+#Epatch:javabridge #
+#Epatch:javabridge -cdef int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args):
+#Epatch:javabridge +cdef extern int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args):
+#Epatch:javabridge return -1
+
+# -------------------------------------------------------- This is the end.
+