From ac9cd54e4cf488626ca23f996551acda89fa9324 Mon Sep 17 00:00:00 2001
From: Nalini Ganapati <35076948+nalinigans@users.noreply.github.com>
Date: Mon, 9 Oct 2023 13:39:42 -0700
Subject: [PATCH] Changes to get the GenomicsDB Python bindings packaged and
 published (#32)

---
 package/Dockerfile                    |  13 ++-
 package/docker-compose.yml            |  28 ++++++-
 package/publish_package.sh            |  45 +++++++++--
 package/publish_package_local.sh      |  75 ++++++++++++++----
 package/requirements_pkg.txt          |  40 +++++++++-
 package/scripts/create_package.sh     |  47 ++++++++---
 package/scripts/install_genomicsdb.sh | 110 +++++++++++---------------
 package/scripts/install_python.sh     |  19 ++---
 requirements.txt                      |  31 +++++++-
 requirements_dev.txt                  |  30 ++++++-
 requirements_pkg.txt                  |   3 -
 setup.py                              |  33 +++++++-
 12 files changed, 349 insertions(+), 125 deletions(-)
 delete mode 100644 requirements_pkg.txt

diff --git a/package/Dockerfile b/package/Dockerfile
index 92a50ab..d808a38 100644
--- a/package/Dockerfile
+++ b/package/Dockerfile
@@ -1,5 +1,10 @@
+#
+# Dockerfile
+#
 # The MIT License (MIT)
+#
 # Copyright (c) 2020 Omics Data Automation, Inc.
+# Copyright (c) 2023 dātma, inc™
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy of
 # this software and associated documentation files (the "Software"), to deal in
@@ -19,8 +24,9 @@
 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 #
 # Description: Base Docker file for creating PyPi Packages
+#
 
-FROM ghcr.io/genomicsdb/genomicsdb:centos_6_prereqs
+FROM centos:7
 
 ARG user=genomicsdb
 ARG user_id=0
@@ -29,12 +35,13 @@ ARG group_id=0
 ARG genomicsdb_branch=develop
 
 COPY scripts /build
-WORKDIR /build
-RUN ./install_python.sh $user $user_id $group_id
 
 WORKDIR /build
 RUN ./install_genomicsdb.sh $user $genomicsdb_branch
 
+WORKDIR /build
+RUN ./install_python.sh $user $user_id $group_id
+
 USER ${user}
 WORKDIR /home/${user}
 ENTRYPOINT ["/bin/bash", "--login"]
diff --git a/package/docker-compose.yml b/package/docker-compose.yml
index c4eb853..d1975a0 100644
--- a/package/docker-compose.yml
+++ b/package/docker-compose.yml
@@ -1,8 +1,34 @@
+#
+# docker-compose.yml
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: Base Docker file for creating PyPi Packages
+
 version: "3"
 services:
   package:
     image: genomicsdb:python
-    user: ${CURRENT_UID}
+    user: ${USER}
     volumes: 
       - ..:/home/${USER}/GenomicsDB-Python:delegated
     command: "/home/${USER}/GenomicsDB-Python/package/scripts/create_package.sh"
diff --git a/package/publish_package.sh b/package/publish_package.sh
index f058c5f..b6a91a9 100755
--- a/package/publish_package.sh
+++ b/package/publish_package.sh
@@ -1,3 +1,30 @@
+#
+# publish_package.sh
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: Bash script to help with packaging and releasing to PyPi
+#
+
 #!/bin/bash
 
 USAGE="Usage: publish_package.sh release|test-release macos|linux" 
@@ -43,9 +70,13 @@ docker create -it --name genomicsdb genomicsdb:python bash &&
   mv genomicsdb/protobuf/python/* genomicsdb/protobuf &&
   rmdir genomicsdb/protobuf/python &&
   mkdir -p genomicsdb/lib &&
-  docker cp genomicsdb:/usr/local/lib/libtiledbgenomicsdb.so genomicsdb/lib &&
+  docker cp -L genomicsdb:/usr/local/lib/libtiledbgenomicsdb.so genomicsdb/lib &&
   docker rm -fv genomicsdb &&
-  sed -i 's/import genomicsdb_/from . import genomicsdb_/g' genomicsdb/protobuf/*.py &&
+  if [[ $(uname) == "Darwin" ]]; then
+    sed -i '' 's/import genomicsdb_/from . import genomicsdb_/g' genomicsdb/protobuf/*.py
+  else
+    sed -i 's/import genomicsdb_/from . import genomicsdb_/g' genomicsdb/protobuf/*.py
+  fi &&
   echo "Docker copy from genomicsdb:python successful"
 
 RC=$?
@@ -59,19 +90,19 @@ python setup.py sdist
 
 popd
 
-# Use centos6 based genomicsdb:all_python Docker image to create packages for 3.9/3.10/1.11
-echo "Building packages for Linux on CentOS 6..."
-export CURRENT_UID="$(id -u):$(id -g)"
+# Use centos6 based genomicsdb:all_python Docker image to create packages for 3.9/3.10/3.11
+echo "Building packages for Linux on CentOS 7..."
 docker-compose run -e PYTHON_VERSION="3.9" package
 docker-compose run -e PYTHON_VERSION="3.10" package
 docker-compose run -e PYTHON_VERSION="3.11" package
-echo "Building packages for Linux on CentOS 6 DONE"
+echo "Building packages for Linux on CentOS 7 DONE"
 
 pushd ../
 
 # Repair linux wheel names
 for linux_wheel in dist/*-linux_*.whl; do
-  mv $linux_wheel ${linux_wheel//-linux_/-manylinux1_};
+  echo "Moving $linux_wheel to ${linux_wheel//-linux_/-manylinux_2_17_x86_64.manylinux2014_}"
+  mv $linux_wheel ${linux_wheel//-linux_/-manylinux_2_17_x86_64.manylinux2014_}
 done
 
 # Publish
diff --git a/package/publish_package_local.sh b/package/publish_package_local.sh
index b583b27..4629adc 100755
--- a/package/publish_package_local.sh
+++ b/package/publish_package_local.sh
@@ -1,13 +1,40 @@
+#
+# publish_package_local.sh
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: Bash script to publish locally on MacOS
+#
+
 #!/bin/bash
 
-PREFIX_DIR=$HOME/python
+PREFIX_DIR=${PREFIX_DIR:-$(mktemp -d)}
 GENOMICSDB_DIR=$PREFIX_DIR/GenomicsDB
 GENOMICSDB_HOME=$GENOMICSDB_DIR/release
-GENOMICSDB_BRANCH=master
+GENOMICSDB_BRANCH=${GENOMICSDB_BRANCH:-master}
 
 GENOMICSDB_PYTHON_DIR=$(readlink -f `pwd`/..)
 
-#MACOSX_DEPLOYMENT_TARGET=11.0
+MACOSX_DEPLOYMENT_TARGET=12.1
 HOMEBREW_NO_AUTO_UPDATE=1
 
 die() {
@@ -25,9 +52,15 @@ check_rc() {
   fi
 }
 
-install_openssl() {
-  check_rc $(brew list openssl@1.1 &> /dev/null || brew install openssl@1.1)
-  OPENSSL_ROOT_DIR=$(readlink -f /usr/local/opt/openssl@1.1)
+install_prereqs() {
+  HOMEBREW_NO_AUTO_UPDATE=1
+  HOMEBREW_NO_INSTALL_CLEANUP=1
+  check_rc $(brew list openssl@3 &> /dev/null || brew install openssl@3)
+  OPENSSL_ROOT_DIR=$(brew --prefix openssl@3)
+  brew list libcsv &> /dev/null && brew uninstall libcsv
+  # Use the uuid from framework
+  brew list ossp-uuid &> /dev/null && brew uninstall ossp-uuid
+
 }
 
 install_python_version() {
@@ -43,11 +76,9 @@ publish_package() {
 		source try$PYTHON_VERSION/bin/activate &&
 		pip install --upgrade pip &&
     pushd $GENOMICSDB_PYTHON_DIR &&
-	  pip install -r requirements.txt &&
-    cp $GENOMICSDB_HOME/genomicsdb/protobuf/python/* genomicsdb/protobuf &&
-    sed -i '' 's/import genomicsdb_/from . import genomicsdb_/g' genomicsdb/protobuf/*.py &&  
+    pip install -r package/requirements_pkg.txt &&
     python setup.py sdist --with-genomicsdb=$GENOMICSDB_HOME &&
-	  python setup.py bdist_wheel --with-genomicsdb=$GENOMICSDB_HOME --with-libs &&
+	  python setup.py bdist_wheel --with-genomicsdb=$GENOMICSDB_HOME --with-libs --with-protobuf &&
     popd &&
 		deactivate
 	RC=$?
@@ -59,19 +90,27 @@ publish_package() {
 
 publish() {
   echo "Installing Python" &&
-#  publish_package 3.7 &&
-#	publish_package 3.8 &&
-  publish_package 3.9
+  publish_package 3.9 &&
+  publish_package 3.10 &&
+  publish_package 3.11
 }
 
 install_genomicsdb() {
+  echo "Building GenomicsDB in $GENOMICSDB_DIR..."
   rm -fr $GENOMICSDB_DIR
   git clone https://github.com/GenomicsDB/GenomicsDB.git -b $GENOMICSDB_BRANCH $GENOMICSDB_DIR
   pushd $GENOMICSDB_DIR
   mkdir build
   cd build
-  cmake -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_HOME -DCMAKE_PREFIX_PATH=$OPENSSL_ROOT_DIR -DBUILD_EXAMPLES=False -DDISABLE_MPI=True -DBUILD_DISTRIBUTABLE_LIBRARY=1 -DBUILD_FOR_PYTHON=1 .. &&
-    make -j4 && make install
+  cmake -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_HOME -DCMAKE_PREFIX_PATH=$OPENSSL_ROOT_DIR -DPROTOBUF_ROOT_DIR=./protobuf-install -DAWSSDK_ROOT_DIR=./aws-install -DGCSSDK_ROOT_DIR=./gcs-install -DBUILD_EXAMPLES=False -DDISABLE_MPI=True -DBUILD_DISTRIBUTABLE_LIBRARY=1 -DBUILD_FOR_PYTHON=1 .. &&
+    make && make install
+  popd
+  if [[ -f $GENOMICSDB_HOME/lib/libtiledbgenomicsdb.dylib ]]; then
+    echo "Building GenomicsDB in $GENOMICSDB_DIR DONE"
+  else
+    echo "Something wrong with building GenomicsDB ar $GENOMICSDB_HOME"
+    exit 1
+  fi
 }
 
 if [[ `uname` != "Darwin" ]]; then
@@ -79,6 +118,8 @@ if [[ `uname` != "Darwin" ]]; then
   exit 1
 fi
 
-install_openssl &&
-  install_genomicsdb &&
+install_prereqs
+install_genomicsdb &&
   publish
+
+rm -fr $GENOMICSDB_DIR
diff --git a/package/requirements_pkg.txt b/package/requirements_pkg.txt
index f35b779..7a653aa 100644
--- a/package/requirements_pkg.txt
+++ b/package/requirements_pkg.txt
@@ -1 +1,39 @@
--r ../requirements_pkg.txt
+#
+# requirements_pkg.txt
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: Dependencies for packaging up the bindings
+#
+
+-r ../requirements.txt
+
+# C/C++ bindings
+cython>=0.29.31
+
+# Building
+setuptools>=18.0.1
+setuptools-scm>=1.5.4
+wheel>=0.37.0
+
+# Publishing
+twine
diff --git a/package/scripts/create_package.sh b/package/scripts/create_package.sh
index c003b0c..4bdd9dd 100755
--- a/package/scripts/create_package.sh
+++ b/package/scripts/create_package.sh
@@ -1,3 +1,31 @@
+#
+# create_package.sh
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: Bash script to be used with docker compose for creating a python
+#              package ready for publishing
+#
+
 #!/bin/bash
 
 set -e
@@ -13,24 +41,18 @@ if [ ! -d GenomicsDB-Python ]; then
   exit 1
 fi
 
-if [ -d /usr/local/ssl/lib ]; then
-	export LD_LIBRARY_PATH="/usr/local/ssl/lib:$LD_LIBRARY_PATH"
-else
-	echo "/usr/local/ssl/lib not found. Cannot continue."
-	exit 1
-fi
+source /opt/rh/devtoolset-11/enable
+export LD_LIBRARY_PATH="/usr/local/lib:/usr/local/lib64::$LD_LIBRARY_PATH"
 
+cd GenomicsDB-Python
+echo "PWD=$(pwd)"
 echo "Packaging genomicsdb for Python Version=$PYTHON_VERSION..."
 
 python$PYTHON_VERSION -m venv env-dist-$PYTHON_VERSION &&
   source env-dist-$PYTHON_VERSION/bin/activate &&
   echo "Installing required dependencies for $PYTHON_VERSION..." &&
   pip install --upgrade pip &&
-  echo "Installing wheel..." && pip install wheel && echo "Installing wheel DONE" &&
-  echo "Installing setuptools..." && pip install setuptools && echo "Installing setuptools DONE" &&
-  echo "Installing setuptools-scm..." && pip install setuptools-scm && echo "Installing setuptools-scm DONE" &&
-  echo "Installing numpy..." && pip install numpy && echo "Installing numpy DONE" &&
-  echo "Installing cython..." && pip install cython && echo "Installing cython DONE" &&
+  pip install -r package/requirements_pkg.txt &&
   echo "Installing required dependencies for $PYTHON_VERSION DONE"
 
 if [[ $? -ne 0 ]]; then
@@ -38,8 +60,7 @@ if [[ $? -ne 0 ]]; then
   exit 1
 fi
 
-cd GenomicsDB-Python &&
-  python setup.py bdist_wheel --python-tag=cp${PYTHON_VERSION//./} &&
+python setup.py bdist_wheel --python-tag=cp${PYTHON_VERSION//./} &&
   echo "Packaging genomicsdb for Python Version=$PYTHON_VERSION DONE" &&
   exit 0
 
diff --git a/package/scripts/install_genomicsdb.sh b/package/scripts/install_genomicsdb.sh
index baf9c35..caaf2c5 100755
--- a/package/scripts/install_genomicsdb.sh
+++ b/package/scripts/install_genomicsdb.sh
@@ -1,5 +1,9 @@
+#
+# install_genomicsdb.sh
+#
 # The MIT License (MIT)
 # Copyright (c) 2022 Omics Data Automation, Inc.
+# Copyright (c) 2023 dātma, inc™
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy of
 # this software and associated documentation files (the "Software"), to deal in
@@ -19,86 +23,68 @@
 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 #
 # Description: Script to build GenomicsDB
+#
 
 #!/bin/bash
 
-USER=$1
-BRANCH=$2
-
 set -e
 
 . /etc/profile
 
+USER=$1
+BRANCH=$2
+
 INSTALL_PREFIX=/usr/local
-OPENSSL_VERSION=1.1.1o
-CURL_VERSION=7.83.1
 
-WGET_NO_CERTIFICATE=" --no-check-certificate"
-OPENSSL_PREFIX=$INSTALL_PREFIX/ssl
-install_openssl() {
-  if [[ ! -d $OPENSSL_PREFIX ]]; then
-    echo "Installing OpenSSL"
-    pushd /tmp
-    wget $WGET_NO_CERTIFICATE -nv https://www.openssl.org/source/openssl-$OPENSSL_VERSION.tar.gz &&
-      tar -xvzf openssl-$OPENSSL_VERSION.tar.gz &&
-      cd openssl-$OPENSSL_VERSION &&
-      if [[ `uname` == "Linux" ]]; then
-	  CFLAGS=-fPIC ./config shared --prefix=$OPENSSL_PREFIX --openssldir=$OPENSSL_PREFIX
-      else
-	  ./Configure darwin64-x86_64-cc shared -fPIC --prefix=$OPENSSL_PREFIX
-      fi
-      make && make install && echo "Installing OpenSSL DONE"
-    rm -fr /tmp/openssl*
-    popd
-  fi
-}
+OPENSSL_VERSION=${OPENSSL_VERSION:-3.0.11}
 
-CURL_PREFIX=$INSTALL_PREFIX
-install_curl() {
-  if [[ `uname` == "Darwin" ]]; then
-    # curl is supported natively in macOS
-    return 0
-  fi
-  if [[ ! -f $CURL_PREFIX/libcurl.a ]]; then
-    echo "Installing CURL into $CURL_PREFIX"
-    pushd /tmp
-    CURL_VERSION_=$(echo $CURL_VERSION | sed -r 's/\./_/g')
-    wget -nv https://github.com/curl/curl/releases/download/curl-$CURL_VERSION_/curl-$CURL_VERSION.tar.gz &&
-    tar xzf curl-$CURL_VERSION.tar.gz &&
-    cd curl-$CURL_VERSION &&
-      ./configure --with-pic -without-zstd --with-ssl=$OPENSSL_PREFIX --prefix $CURL_PREFIX &&
-      make && make install && echo "Installing CURL DONE"
-    rm -fr /tmp/curl
-    popd
-  fi
-}
+echo "Installing minimal dependencies..."
+yum install -y centos-release-scl && yum install -y devtoolset-11 &&
+  yum install -y -q deltarpm &&
+  yum update -y -q &&
+  yum install -y -q epel-release &&
+  yum install -y -q which wget git &&
+  yum install -y -q autoconf automake libtool unzip &&
+  yum install -y -q cmake3 patch &&
+  yum install -y -q perl perl-IPC-Cmd
+  yum install -y -q libuuid libuuid-devel &&
+  yum install -y -q curl libcurl-devel &&
+  echo "Installing minimal dependencies DONE"
 
-#echo "Cleanup existing static libraries"
-#rm -fr $INSTALL_PREFIX/lib/libcurl*
-#rm -fr $INSTALL_PREFIX/lib/libuuid*
-#rm -fr $INSTALL_PREFIX/include/curl
-#rm -fr $INSTALL_PREFIX/include/uuid
-#rm -fr $INSTALL_PREFIX/ssl
+source /opt/rh/devtoolset-11/enable
 
-echo "Rebuilding openssl for shared libraries"
-install_openssl
-if [[ ! -f $OPENSSL_PREFIX/lib/libcrypto.a ]]; then
-   echo "Something wrong with OpenSSL installation"
-   exit 1
-fi
-echo "Rebuilding curl for shared libraries"
-install_curl
-if [[ ! -f $CURL_PREFIX/lib/libcurl.a ]]; then
-   echo "Something wrong with CURL installation"
-   exit 1
+echo "Building openssl..."
+OPENSSL_PREFIX=$INSTALL_PREFIX
+if [[ ! -d $OPENSSL_PREFIX/ssl ]]; then
+  pushd /tmp
+  wget $WGET_NO_CERTIFICATE https://www.openssl.org/source/openssl-$OPENSSL_VERSION.tar.gz &&
+    tar -xvzf openssl-$OPENSSL_VERSION.tar.gz &&
+    cd openssl-$OPENSSL_VERSION &&
+    CFLAGS=-fPIC ./config no-tests -fPIC --prefix=$OPENSSL_PREFIX --openssldir=$OPENSSL_PREFIX &&
+    make && make install && echo "Installing OpenSSL DONE"
+  rm -fr /tmp/openssl*
+  popd
 fi
+export OPENSSL_ROOT_DIR=$OPENSSL_PREFIX
+export LD_LIBRARY_PATH=$OPENSSL_PREFIX/lib64:$OPENSSL_PREFIX/lib:$LD_LIBRARY_PATH
 
 echo "git clone https://github.com/GenomicsDB/GenomicsDB.git --recursive -b $BRANCH GenomicsDB"
 git clone https://github.com/GenomicsDB/GenomicsDB.git --recursive -b $BRANCH GenomicsDB
 
+adduser $USER
+groupadd genomicsdb
+usermod -aG genomicsdb $USER
+
 pushd GenomicsDB
 echo "Starting GenomicsDB build"
-DOCKER_BUILD=true ./scripts/install_genomicsdb.sh $USER /usr/local true python false
+mkdir build && cd build &&
+  cmake3 -DCMAKE_INSTALL_PREFIX=$INSTALL_PREFIX -DUSE_HDFS=0 -DBUILD_EXAMPLES=False -DDISABLE_TESTING=1 -DBUILD_FOR_PYTHON=1 .. &&
+  make && make install
 popd
 
-echo "GenomicsDB for Python installed successfully"
+if [[ -f $INSTALL_PREFIX/lib/libtiledbgenomicsdb.so ]]; then
+  echo "GenomicsDB for Python installed successfully"
+else
+  echo "GenomicsDB does not seem to have installed properly"
+  exit 1
+fi
diff --git a/package/scripts/install_python.sh b/package/scripts/install_python.sh
index 7d1292a..3b0cea1 100755
--- a/package/scripts/install_python.sh
+++ b/package/scripts/install_python.sh
@@ -1,5 +1,9 @@
+#
+# install_python.sh
+#
 # The MIT License (MIT)
 # Copyright (c) 2022 Omics Data Automation, Inc.
+# Copyright (c) 2023 dātma, inc™
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy of
 # this software and associated documentation files (the "Software"), to deal in
@@ -19,6 +23,7 @@
 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 #
 # Description: Script to install python versions of interest
+#
 
 #!/bin/bash
 
@@ -28,7 +33,6 @@ PYTHON_USER_ID=$2
 PYTHON_GROUP_ID=$3
 
 PYTHON_MAJOR=3
-OPENSSL_VERSION=1.1.1o
 
 die() {
   if [[ $# -eq 1 ]]; then
@@ -52,7 +56,7 @@ install_python_version() {
     tar -xvzf Python-$VERSION.tgz
   check_rc $?
   pushd Python-$VERSION
-  ./configure --prefix=/usr/local --with-openssl=$OPENSSL_ROOT_DIR --enable-shared LDFLAGS="-Wl,-rpath /usr/local/lib" &&
+  ./configure --prefix=/usr/local --with-openssl=/usr/local --enable-shared LDFLAGS="-Wl,-rpath /usr/local/lib" &&
     make &&
     make altinstall
   RC=$?
@@ -77,15 +81,8 @@ sanity_test_python() {
   check_rc $RC
 }
 
-if [[ ! -f /etc/profile.d/genomicsdb_prereqs.sh ]]; then
-    echo "Missing genomicsdb_prereqs.sh. Start with a GenomicsDB prerequistes docker image"
-    exit 1
-fi
-source /etc/profile.d/genomicsdb_prereqs.sh
-if [[ -z ${OPENSSL_ROOT_DIR} ]]; then
-    echo "Point to a prerequistes docker image that has openssl installed and env OPENSSL_ROOT_DIR set"
-    exit 1
-fi
+source /opt/rh/devtoolset-11/enable
+export LD_LIBRARY_PATH=/usr/local/lib64:$LD_LIBRARY_PATH
 
 # Workaround for Centos 6 being EOL'ed
 WGET_NO_CERTIFICATE="--no-check-certificate"
diff --git a/requirements.txt b/requirements.txt
index 37664ad..8621ae1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,30 @@
-numpy>=1.19.3
-pandas>=1.5.0
+#
+# requirements.txt
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: Minimum Package Dependencies
+#
+
+numpy>=1.19.5
+pandas
 protobuf>=4.21.1
diff --git a/requirements_dev.txt b/requirements_dev.txt
index fc7ad83..f55e641 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -1,7 +1,34 @@
+#
+# requirements_dev.txt 
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: Developer Package Dependencies
+#
+
 -r requirements.txt
 
 # C/C++ bindings
-cython>=0.29.4
+cython>=0.29.31
 
 # Building
 setuptools>=18.0.1
@@ -14,4 +41,3 @@ bandit~=1.7.0
 
 # Testing
 pytest>==6.2.5
-pandas
diff --git a/requirements_pkg.txt b/requirements_pkg.txt
deleted file mode 100644
index c4794ac..0000000
--- a/requirements_pkg.txt
+++ /dev/null
@@ -1,3 +0,0 @@
--r requirements_dev.txt
-
-twine
diff --git a/setup.py b/setup.py
index 27da484..112af91 100644
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,30 @@
+#
+# setup.py
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2023 dātma, inc™
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Description: setup script to build the GenomicsDB python package
+#
+
 from setuptools import setup, Extension, find_packages
 
 import os
@@ -99,7 +126,7 @@ def run_cythonize(src):
     library_dirs=[GENOMICSDB_LIB_DIR],
     runtime_library_dirs=rpath,
     extra_link_args=link_args,
-    extra_compile_args=["-std=c++11"],
+    extra_compile_args=["-std=c++17"],
 )
 
 with open("README.md") as f:
@@ -118,13 +145,13 @@ def run_cythonize(src):
     ext_modules=[genomicsdb_extension],
     zip_safe=False,
     setup_requires=["cython>=0.27"],
-    install_requires=["numpy>=1.19.3", "pandas>=1.5.0"],
+    install_requires=["numpy>=1.19.5", "pandas"],
     extras_require = {"protobuf": ["protobuf>=4.21.1"]},
     python_requires=">=3.9",
     packages=find_packages(exclude=["package", "test"]),
     keywords=["genomics", "genomicsdb", "variant", "vcf", "variant calls"],
     include_package_data=True,
-    version="0.0.8.18",
+    version="0.0.9.1",
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Developers",