<commit_before>#!/bin/bash
# These are all of the packages that need to be installed before bootstrap
# is run
# 
# Note that all apache modules should have already been installed
# in the bootstrap image.  Otherwise you will have the system attempt
# to reload httpd which causes the httpd connection to go down
#
# dokuwiki also needs to be in bootstrap for the same reasons
set -e -v

cat <<EOF >> $rootfsDir/etc/dnf/dnf.conf
fastestmirror=true
max_parallel_downloads=15
EOF
if [ -e $rootfsDir/tmp/proxy.sh ]; then
    source $rootfsDir/tmp/proxy.sh
fi

dnf makecache $rootfsArg
dnf upgrade --best --nodocs --allowerasing --refresh -y \
    --setopt=install_weak_deps=False $rootfsArg

# workaround bug RHEL #1765718
dnf autoremove python3-dnf-plugins-core -y $rootfsArg

# Refresh locale and glibc for missing latin items
# needed for R to build packages
dnf reinstall -v -y --setopt=install_weak_deps=False --best --nodocs --allowerasing \
    locales locales-en glibc $rootfsArg

#texlive needs to be run because it is not relocatable
if [ ! -z $container ] ; then
    if [ -z $releasever ]; then
	releasever="cauldron"
    fi
buildah run $container -- dnf --setopt=install_weak_deps=False --best \
	--allowerasing install -v -y --nodocs --releasever="$releasever" texlive 
fi
#repeat packages in setup
dnf --setopt=install_weak_deps=False --best --allowerasing install -v -y --nodocs $rootfsArg \
      apache \
      apache-mod_proxy \
      php-fpm \
      apache-mod_authnz_external \
      apache-mod_ssl \
      dokuwiki \
      dokuwiki-plugin-auth \
      dokuwiki-plugin-dokufreaks \
      dokuwiki-plugin-s5  \
      python3-flask \
      python3-pexpect \
      python3-matplotlib \
      webmin \
      sudo \
      git \
      R-base \
      nodejs \
      npm \
      octave \
      redis \
      unzip \
      mongodb-server \
      mongodb \
      mongo-tools \
      java \
      texlive \
      vim-minimal \
      ruby-sass \
      zeromq-utils \
      python3-pip \
      python3-cffi \
      python3-cython \
      python3-pexpect \
      R-Rcpp-devel \
      root \
      python3-jupyroot \
      root-r \
      libglu-devel \
      rclone \
      root-physics \
      root-geom \
      root-fftw \
      root-hist \
      root-foam \
      root-vecops \
      root-graf \
      root-graf-asimage \
      root-graf-gpad \
      root-graf-gpadv7 \
      root-graf-gviz \
      root-graf-postscript \
      root-graf-primitives \
      root-graf3d \
      root-geom \
      root-gui \
      root-hist \
      root-mathcore \
      root-mathmore \
      root-matrix \
      root-minuit \
      root-multiproc \
      root-graf-postscript \
      root-graf-asimage \
      fuse \
      parallel \
      gcc-c++ \
      make \
      r-quantlib \
      pkgconfig\(libczmq\) \
      zeromq-devel \
      giflib-devel \
      cmake \
      python3-tornado \
      python3-mglob \
      python3-pytz \
      python3-devel \
      readline-devel \
      lapack-devel \
      python3-pandas \
      python3-pandas-datareader \
      python3-numpy \
      python3-numpy-devel \
      python3-tables \
      python3-fs \
      python3-scipy \
      python3-qstk \
      python3-scikits-learn \
      python3-rpy2 \
      python3-xlwt \
      python3-xlrd \
      python3-gevent \
      python3-sqlalchemy \
      python3-sympy \
      python3-pillow \
      python3-lxml \
      python3-mistune \
      python3-cryptography \
      python3-pyasn1 \
      python3-pyglet \
      python3-py4j \
      python3-mysql \
      python3-wheel \
      python3-quantlib \
      curl-devel \
      icu-devel \
      libpcre-devel \
      liblzma-devel \
      libbzip2-devel \
      zeromq-devel \
      ta-lib-devel \
      libxml2-devel \
      make \
      python3-cairo-devel \
      jpeg-devel \
      java-devel \
      openmpi-devel \
      libssh2-devel \
      ruby-devel \
      libtool \
      automake \
      autoconf \
      swig \
      protobuf-devel \
      unwind-devel \
      graphviz-devel \
      glpk-devel \
      glpk \
      llvm-devel \
      llvm \
      librdkafka-devel \
      libumfpack-devel \
      hdf5-devel \
      libxt-devel \
      libmagick-devel \
      cargo \
      lib64git2-devel \
      pybind11-devel \
      gzip \
      ncurses \
      nss \
      nspr \
      passwd \
      tar \
      xeus-devel \
      xtl-devel \
      'pkgconfig(Magick++)' \
      spack \
      spack-repos \
      distcc \
      julia \
      curl \
      conda

# install curl for julia

# xeus-devel for r juniper

# nss/nspr to prevent poppler from pulling in firefox
# cargo for gifski<commit_msg>add xeus-sqlite<commit_after>#!/bin/bash
# These are all of the packages that need to be installed before bootstrap
# is run
# 
# Note that all apache modules should have already been installed
# in the bootstrap image.  Otherwise you will have the system attempt
# to reload httpd which causes the httpd connection to go down
#
# dokuwiki also needs to be in bootstrap for the same reasons
set -e -v

cat <<EOF >> $rootfsDir/etc/dnf/dnf.conf
fastestmirror=true
max_parallel_downloads=15
EOF
if [ -e $rootfsDir/tmp/proxy.sh ]; then
    source $rootfsDir/tmp/proxy.sh
fi

dnf makecache $rootfsArg
dnf upgrade --best --nodocs --allowerasing --refresh -y \
    --setopt=install_weak_deps=False $rootfsArg

# workaround bug RHEL #1765718
dnf autoremove python3-dnf-plugins-core -y $rootfsArg

# Refresh locale and glibc for missing latin items
# needed for R to build packages
dnf reinstall -v -y --setopt=install_weak_deps=False --best --nodocs --allowerasing \
    locales locales-en glibc $rootfsArg

#texlive needs to be run because it is not relocatable
if [ ! -z $container ] ; then
    if [ -z $releasever ]; then
	releasever="cauldron"
    fi
buildah run $container -- dnf --setopt=install_weak_deps=False --best \
	--allowerasing install -v -y --nodocs --releasever="$releasever" texlive 
fi
#repeat packages in setup
dnf --setopt=install_weak_deps=False --best --allowerasing install -v -y --nodocs $rootfsArg \
      apache \
      apache-mod_proxy \
      php-fpm \
      apache-mod_authnz_external \
      apache-mod_ssl \
      dokuwiki \
      dokuwiki-plugin-auth \
      dokuwiki-plugin-dokufreaks \
      dokuwiki-plugin-s5  \
      python3-flask \
      python3-pexpect \
      python3-matplotlib \
      webmin \
      sudo \
      git \
      R-base \
      nodejs \
      npm \
      octave \
      redis \
      unzip \
      mongodb-server \
      mongodb \
      mongo-tools \
      java \
      texlive \
      vim-minimal \
      ruby-sass \
      zeromq-utils \
      python3-pip \
      python3-cffi \
      python3-cython \
      python3-pexpect \
      R-Rcpp-devel \
      root \
      python3-jupyroot \
      root-r \
      libglu-devel \
      rclone \
      root-physics \
      root-geom \
      root-fftw \
      root-hist \
      root-foam \
      root-vecops \
      root-graf \
      root-graf-asimage \
      root-graf-gpad \
      root-graf-gpadv7 \
      root-graf-gviz \
      root-graf-postscript \
      root-graf-primitives \
      root-graf3d \
      root-geom \
      root-gui \
      root-hist \
      root-mathcore \
      root-mathmore \
      root-matrix \
      root-minuit \
      root-multiproc \
      root-graf-postscript \
      root-graf-asimage \
      fuse \
      parallel \
      gcc-c++ \
      make \
      r-quantlib \
      pkgconfig\(libczmq\) \
      zeromq-devel \
      giflib-devel \
      cmake \
      python3-tornado \
      python3-mglob \
      python3-pytz \
      python3-devel \
      readline-devel \
      lapack-devel \
      python3-pandas \
      python3-pandas-datareader \
      python3-numpy \
      python3-numpy-devel \
      python3-tables \
      python3-fs \
      python3-scipy \
      python3-qstk \
      python3-scikits-learn \
      python3-rpy2 \
      python3-xlwt \
      python3-xlrd \
      python3-gevent \
      python3-sqlalchemy \
      python3-sympy \
      python3-pillow \
      python3-lxml \
      python3-mistune \
      python3-cryptography \
      python3-pyasn1 \
      python3-pyglet \
      python3-py4j \
      python3-mysql \
      python3-wheel \
      python3-quantlib \
      curl-devel \
      icu-devel \
      libpcre-devel \
      liblzma-devel \
      libbzip2-devel \
      zeromq-devel \
      ta-lib-devel \
      libxml2-devel \
      make \
      python3-cairo-devel \
      jpeg-devel \
      java-devel \
      openmpi-devel \
      libssh2-devel \
      ruby-devel \
      libtool \
      automake \
      autoconf \
      swig \
      protobuf-devel \
      unwind-devel \
      graphviz-devel \
      glpk-devel \
      glpk \
      llvm-devel \
      llvm \
      librdkafka-devel \
      libumfpack-devel \
      hdf5-devel \
      libxt-devel \
      libmagick-devel \
      cargo \
      lib64git2-devel \
      pybind11-devel \
      gzip \
      ncurses \
      nss \
      nspr \
      passwd \
      tar \
      xeus-devel \
      xtl-devel \
      'pkgconfig(Magick++)' \
      spack \
      spack-repos \
      distcc \
      julia \
      curl \
      conda \
      xeus-sqlite

# install curl for julia

# xeus-devel for r juniper

# nss/nspr to prevent poppler from pulling in firefox
# cargo for gifski
{'fraction_non_alphanumeric': 0.09319112260288731, 'fraction_numerical': 0.013574660633484163, 'mean_word_length': 1.5398084815321478, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '352094', 'n_tokens_mistral': 3408, 'n_tokens_neox': 3229, 'n_words': 681}