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pkg-scripts/python-3.13.2-0.build.sh
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| #!/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-$COOKIE.sh | |
| # TESTING=1 | |
| # ---------------------------------------------------------------- Preamble | |
| PKG=python | |
| VERSION=3.13.2 | |
| BUILD=0 | |
| PYTHONVER=${VERSION%.*} | |
| CUDADIR=/pkg/cuda-12.1.0-0 | |
| 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 -b root -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 $* | |
| } | |
| # ---------------------------------------- Build Python & support libraries | |
| ( | |
| # orig: https://www.python.org/ftp/python/3.13.2/Python-3.13.2.tgz | |
| BEEHIVE=https://beehive.molgen.mpg.de/6192ce4725d9c9fc0e8a1cd38410b417/Python-3.13.2.tgz | |
| test -e Python-$VERSION.tgz || wget -nv $BEEHIVE | |
| test -d Python-$VERSION || tar -xf Python-$VERSION.tgz | |
| cd Python-$VERSION | |
| # 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 $NPROC | |
| make install | |
| ) | |
| ( | |
| PYCAIRO_VERSION=1.27.0 | |
| # https://files.pythonhosted.org/packages/07/4a/42b26390181a7517718600fa7d98b951da20be982a50cd4afb3d46c2e603/pycairo-1.27.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/12097575a1bb683cab7dc425d9769a68/pycairo-1.27.0.tar.gz | |
| test -e pycairo-$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 $NPROC | |
| ninja install | |
| ) | |
| ( | |
| PYGOBJECT3_VERSION=3.50.0 | |
| # https://files.pythonhosted.org/packages/2b/58/d34e67a79631177e3c08e7d02b5165147f590171f2cae6769502af5f7f7e/pygobject-3.50.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/a6904c6f523b9f7ca2dec63d8c24de92/pygobject-3.50.0.tar.gz | |
| test -e pygobject-$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 $NPROC | |
| ninja install | |
| ) | |
| piplist; track various pythonbindings | |
| # build support to use QT from python -- see www.riverbankcomputing.com | |
| ( # sip: tool to create Python bindings for C and C++ libraries. | |
| SIP_VERSION=6.9.1 | |
| # orig: https://files.pythonhosted.org/packages/e2/83/b23f610ef99fa23aa3c8dcd2ff8536c37b943654405ff4f45f3230327a40/sip-6.9.1.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/a6f939e7c1e4d1c3feb39ed56e7b2297/sip-6.9.1.tar.gz | |
| test -e sip-$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=5.15.11 | |
| # orig: https://files.pythonhosted.org/packages/0e/07/c9ed0bd428df6f87183fca565a79fee19fa7c88c7f00a7f011ab4379e77a/PyQt5-5.15.11.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/51ff7c7ccec76a5de36db3ff88140eaf/PyQt5-5.15.11.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 \ | |
| --quiet \ | |
| --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 $PREFIX/lib/python*/site-packages/PyQt5/uic/port_v2 | |
| ) | |
| ( | |
| QSCINTILLA_VERSION=2.14.1 | |
| # orig: https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.14.1/QScintilla_src-2.14.1.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/9c9e3803e4371ebbb218682e8596af5d/QScintilla_src-2.14.1.tar.gz | |
| test -e QScintilla_src-$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 \ | |
| --quiet \ | |
| --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 $NPROC | |
| make install | |
| ) | |
| ( | |
| set -x | |
| PYQTWEBENGINE_VERSION=5.15.7 | |
| # see: https://pypi.org/project/PyQtWebEngine/#files | |
| # orig: https://files.pythonhosted.org/packages/18/e8/19a00646866e950307f8cd73841575cdb92800ae14837d5821bcbb91392c/PyQtWebEngine-5.15.7.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/a3394e93d8b5077e8355f57d79c2ed58/PyQtWebEngine-5.15.7.tar.gz | |
| test -e PyQtWebEngine-${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 \ | |
| --quiet \ | |
| --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<2' | |
| # install numba==0.60.0 | |
| # skip this here | |
| # install numpy==2.1.3 | |
| # install numba | |
| install numpy | |
| 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 | |
| rm -rf python-javabridge | |
| git clone https://github.com/CellProfiler/python-javabridge | |
| cd python-javabridge | |
| git checkout v4.0.3 | |
| sed -ne '/^#Epatch:javabridge/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| export JAVA_HOME=/pkg/openjdk-17.0.2.8-0 | |
| PATH=/pkg/openjdk-17.0.2.8-0/bin:$PATH | |
| pip install . | |
| ) | |
| PACKAGES=$(sed -e s/#.*$// <<- __PKGLIST__ | |
| igraph | |
| keras | |
| ipython[all] | |
| snakemake # December 2023 brought snakemake 8, it seems to be working again | |
| Pillow | |
| protobuf | |
| onnx | |
| Sphinx | |
| jedi | |
| black[d] # onnx wants it, but does not install it ... | |
| flask | |
| SciPy | |
| pandas | |
| SymPy # torch does not like 1.13.3, so may need to use 1.13.1 | |
| 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 | |
| MotifScan # A.B. 30.8.2018 | |
| MAmotif | |
| hic2cool # Helpdesk R. S. 17.09.2018 | |
| 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 G. N. | |
| petab | |
| tadtool # HD 26.01.21 M. R. | |
| pyperf # Paul sep-20 | |
| umap # HD, used by M. L. | |
| # MACS3 numpy downgrader! | |
| biopython # HD 2021-07-23 alphafold related -- cool that we have missed 'biopython' so far, GRIN | |
| flatbuffers | |
| contextlib2 | |
| ml_collections | |
| python-bioformats | |
| # additions/fixups since 3.9 | |
| # spyder # downgrader for ipython 8.34.0 vs. 9.0.2 | |
| # 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 | |
| triangle==20230923 | |
| # napari[pyqt5]==0.5.5 # always check ... | |
| # napari-czifile2 | |
| # napari-plugin-manager==0.1.3 | |
| bx-python | |
| leidenalg | |
| # scanpy downgrader for scikit-learn # this is a MESS, you might always get broken/ugly plots ... | |
| asciidoc | |
| html2text | |
| # additions/fixups since 3.10 | |
| aicspylibczi | |
| filetype | |
| gmpy2 | |
| # shap # uses numba !!! | |
| UpSetPlot | |
| hypothesis | |
| # nf-core / epi2me related | |
| dominate | |
| libsass | |
| sigfig | |
| whatshap | |
| Truvari | |
| nanopack | |
| # nlp related | |
| spacy | |
| paramiko | |
| scp | |
| psutil | |
| # pylibCZIrw - this brings cmake ... | |
| # appease some warnings from the load test | |
| siphash24 | |
| dask[dataframe] | |
| __PKGLIST__ | |
| ) | |
| for PKG in $PACKAGES; do | |
| install $PKG | |
| done | |
| # skip torch for this test build | |
| # # py-torch bundled with a recent CUDA-Toolkit from meta, | |
| # # and then the packages that would eventually interfere with torch | |
| # | |
| # install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121 | |
| # install xformers | |
| install xgboost | |
| install pyopengl | |
| # ----------------------------------------------------- Post install fixups | |
| mkdir -vp $PREFIX/share/jupyter/lab/settings # try to defeat a silly error in jupyter labextension 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 misc packages | |
| # these mostly bigger packages require either wheel, other treatments, | |
| # or java. | |
| # build CrossMap from git, https://github.com/liguowang/CrossMap/issues/67 | |
| ( | |
| git clone https://github.com/liguowang/CrossMap | |
| cd CrossMap | |
| git rm src/__init__.py | |
| git commit -a -m 'remove badly placed src/__init__.py' | |
| # pip install . --prefix=$PREFIX | |
| pip install . | |
| ) | |
| piplist; track CrossMap | |
| # GYP is a Meta-Build system: a build system that generates other build systems. https://gyp.gsrc.io/ | |
| ( | |
| set -x | |
| GYP_VERSION=20230301_c6d8b9f7 | |
| # orig: https://mirror.netcologne.de/slackware/slackware64-current/source/d/gyp/ | |
| BEEHIVE=https://beehive.molgen.mpg.de/ba0357be23ca55555714261afccc7aab/gyp-20230301_c6d8b9f7.tar.xz | |
| test -e gyp-${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' $ME | patch -p1 --verbose | |
| pip install . | |
| ) | |
| piplist; track gyp | |
| ( | |
| BOOSTVERSION=1.87.0 | |
| BOOSTVERSION_USCORED=${BOOSTVERSION//./_} | |
| PKGCFLAGS="-O2 -fPIC" | |
| # orig: https://archives.boost.io/release/1.87.0/source/boost_1_87_0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/f435e8ae57edb203a1165cdb99cfb2a3/boost_1_87_0.tar.gz | |
| test -e boost_$BOOSTVERSION_USCORED.tar.gz || wget -nv $BEEHIVE | |
| test -d boost_$BOOSTVERSION_USCORED || tar -xf boost_$BOOSTVERSION_USCORED.tar.gz | |
| cd boost_$BOOSTVERSION_USCORED | |
| ./bootstrap.sh \ | |
| --with-toolset=gcc \ | |
| --with-icu \ | |
| --with-python=$PREFIX/bin/python3 \ | |
| --with-libraries=python,thread,filesystem,stacktrace || exit 1 | |
| ./b2 \ | |
| $B2FLAGS \ | |
| -j $NPROC \ | |
| --prefix=$PREFIX \ | |
| --enable-shared \ | |
| --without-mpi \ | |
| install | |
| ) | |
| piplist; track boost | |
| ( | |
| PYCUDAVERS=2025.1 | |
| PYTHON_LIBNAME=boost_python${PYTHONVER/./} | |
| # orig: https://files.pythonhosted.org/packages/15/31/12640e87fcc6fc42468dfbeb38f9c0fd7b0a25bf9e6d9e0a7609f915dd18/pycuda-2025.1.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/27a054314adbb589e85efee2fa3b15be/pycuda-2025.1.tar.gz | |
| test -e pycuda-${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@v1.1.2 --prefix=$PREFIX # :xxx:tk: numpy 1.26.4 | |
| # pip install git+https://github.com/brentp/bwa-meth.git@v0.2.7 --prefix=$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_xxx bwa-meth_xxx stgit | |
| # 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 | |
| echo "# --------- *** SANITY CHECKS *** ---------" | |
| # I guess it makes sense that files can be read by all users ... | |
| echo "# 1) 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 | |
| # a cheap one :) | |
| echo "# 2) Running pip check" | |
| pip check | |
| # load all packages, see warnings and spot installation errors | |
| echo "# 3) Module load test." | |
| export NUMEXPR_MAX_THREADS=1 | |
| python -c 'help("modules")' | |
| echo "# Note: reached end of load test" | |
| echo "For Deeper checks:" | |
| echo "cd ${BUILDDIR} ; git log --patch | grep ^[\+\-][^\+\-]" | |
| 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. | |