Revert "[ci] remove CI folder and update README"

This reverts commit 915986c.

README.md

@@ -30,8 +30,8 @@ A **wrapper script** is also available to enable easier usage to the end-user fo
 To install Racon run the following commands:
 
 ```bash
-git clone --recursive https://github.com/lbcb-sci/racon.git racon
-cd racon
+git clone --recursive https://github.com/clara-genomics/racon-gpu.git
+cd racon-gpu
 mkdir build
 cd build
 cmake -DCMAKE_BUILD_TYPE=Release ..

ci/checks/changelog.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+# Copyright (c) 2018, NVIDIA CORPORATION.
+#########################
+# cuDF CHANGELOG Tester #
+#########################
+
+# Checkout master for comparison
+git checkout --quiet master
+
+# Switch back to tip of PR branch
+git checkout --quiet current-pr-branch
+
+# Ignore errors during searching
+set +e
+
+# Get list of modified files between matster and PR branch
+CHANGELOG=`git diff --name-only master...current-pr-branch | grep CHANGELOG.md`
+RETVAL=0
+
+exit $RETVAL

ci/checks/style.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+# Copyright (c) 2018, NVIDIA CORPORATION.
+#####################
+# cuDF Style Tester #
+#####################
+
+# Ignore errors and set path
+set +e
+PATH=/conda/bin:$PATH
+
+# Activate common conda env
+source activate gdf
+
+# Run flake8 and get results/return code
+#FLAKE=`flake8 python`
+#RETVAL=$?
+RETVAL=0
+
+# Output results if failure otherwise show pass
+#if [ "$FLAKE" != "" ]; then
+#  echo -e "\n\n>>>> FAILED: flake8 style check; begin output\n\n"
+#  echo -e "$FLAKE"
+#  echo -e "\n\n>>>> FAILED: flake8 style check; end output\n\n"
+#else
+#  echo -e "\n\n>>>> PASSED: flake8 style check\n\n"
+#fi
+
+exit $RETVAL

ci/common/build.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+# Copyright (c) 2018, NVIDIA CORPORATION.
+######################################
+# racon-gpu CPU/GPU conda build script for CI #
+######################################
+set -e
+
+# Get commandline arguments
+LOCAL_BUILD_DIR=$1
+
+# Logger function for build status output
+function logger() {
+  echo -e "\n>>>> $@\n"
+}
+
+# Set path and build parallel level
+export PATH=/conda/bin:/usr/local/cuda/bin:$PATH
+export PARALLEL_LEVEL=4
+
+# Set home to the job's workspace
+export HOME=$WORKSPACE
+
+# Switch to project root; also root of repo checkout
+cd $WORKSPACE
+
+################################################################################
+# SETUP - Check environment
+################################################################################
+
+logger "Get env..."
+env
+
+logger "Check versions..."
+gcc --version
+g++ --version
+
+# FIX Added to deal with Anancoda SSL verification issues during conda builds
+conda config --set ssl_verify False
+
+CUDA_REL=${CUDA:0:3}
+if [ "${CUDA:0:2}" == '10' ]; then
+  # CUDA 10 release
+  CUDA_REL=${CUDA:0:4}
+fi
+
+git clean -xdf
+
+CMAKE_COMMON_VARIABLES="-DCMAKE_BUILD_TYPE=Release -Dracon_build_tests=ON"
+
+if [ "${BUILD_FOR_GPU}" == '1' ]; then
+  CMAKE_BUILD_GPU="-Dracon_enable_cuda=ON"
+else
+  CMAKE_BUILD_GPU="-Dracon_enable_cuda=OFF"
+fi
+
+# Use CMake-based build procedure
+mkdir --parents ${LOCAL_BUILD_DIR}
+cd ${LOCAL_BUILD_DIR}
+
+# configure
+cmake $CMAKE_COMMON_VARIABLES ${CMAKE_BUILD_GPU} ..
+# build
+make -j${PARALLEL_LEVEL} VERBOSE=1 all

ci/cpu/build.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+# Copyright (c) 2018, NVIDIA CORPORATION.
+######################################
+# cuDF CPU conda build script for CI #
+######################################
+set -e
+
+# Logger function for build status output
+function logger() {
+  echo -e "\n>>>> $@\n"
+}
+
+cd ${WORKSPACE}
+
+LOCAL_BUILD_DIR=${WORKSPACE}/build
+
+. ci/common/build.sh ${LOCAL_BUILD_DIR}
+
+if [ "${TEST_ON_CPU}" == '1' ]; then
+  logger "Running CPU-based test..."
+  cd ${LOCAL_BUILD_DIR}/bin
+
+  logger "Test results..."
+  ./racon_test
+fi
+

ci/cpu/prebuild.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+export BUILD_FOR_GPU=0
+export TEST_ON_CPU=1
+export TEST_ON_GPU=0

ci/gpu/build.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+# Copyright (c) 2018, NVIDIA CORPORATION.
+######################################
+# cuDF GPU conda build script for CI #
+######################################
+set -e
+
+# Logger function for build status output
+function logger() {
+  echo -e "\n>>>> $@\n"
+}
+
+cd ${WORKSPACE}
+
+LOCAL_BUILD_DIR=${WORKSPACE}/build
+
+. ci/common/build.sh ${LOCAL_BUILD_DIR}
+
+if [ "${TEST_ON_GPU}" == '1' ]; then
+  logger "GPU config..."
+  nvidia-smi
+
+  logger "Running GPU-based test..."
+
+  logger "Pulling GPU test data..."
+  cd ${WORKSPACE}
+  if [ ! -d "ont-racon-data" ]; then
+    if [ ! -f "${ont-racon-data.tar.gz}" ]; then
+      wget -q -L https://s3.us-east-2.amazonaws.com/racon-data/ont-racon-data.tar.gz
+    fi
+    tar xvzf ont-racon-data.tar.gz
+  fi
+  ci/gpu/cuda_test.sh
+
+  logger "Unit test results..."
+  cd ${LOCAL_BUILD_DIR}/bin
+  ./racon_test --gtest_filter=*CUDA*
+fi

ci/gpu/cuda_test.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+SCRIPT_DIRECTORY=`dirname $0`
+BIN_DIRECTORY="${SCRIPT_DIRECTORY}/../../build/bin"
+DATA="${HOME}/ont-racon-data/nvidia"
+RESULT_FILE="test-output.txt"
+GOLDEN_FILE="$SCRIPT_DIRECTORY/golden-output.txt"
+
+if [ $# -eq 0 ]; then
+    BATCHES=2
+else
+    BATCHES=$1
+fi
+
+if [ ! -d $BIN_DIRECTORY ]; then
+    echo "Could not find bin directory for racon binary"
+    exit 1
+fi
+
+if [ -f $RESULT_FILE ]; then
+    rm $RESULT_FILE
+fi
+
+if [ ! -f $GOLDEN_FILE ]; then
+    echo "Could not find golden value file at $GOLDEN_FILE"
+    exit 1
+fi
+
+CMD="$BIN_DIRECTORY/racon --cudaaligner-batches 0 -c ${BATCHES} -m 8 -x -6 -g -8  -w 500 -t 24 -q -1 $DATA/iterated_racon/reads.fa.gz $DATA/iterated_racon/reads2contigs_1_1.paf.gz $DATA/canu.contigs.fasta"
+echo "Running command:"
+echo $CMD
+$CMD > ${RESULT_FILE}
+diff ${RESULT_FILE} ${GOLDEN_FILE} >& /dev/null
+RES=$?
+
+if [ $RES -eq "0" ]; then
+    echo "Test passed."
+    rm $RESULT_FILE
+else
+    echo "Test failed."
+    echo "Result in ${RESULT_FILE}, golden vales in ${GOLDEN_FILE}"
+fi
+
+exit $RES

ci/gpu/prebuild.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+export BUILD_FOR_GPU=1
+export TEST_ON_GPU=1
+
+