gen-website

#!/bin/bash

cd /opt/biogears/core/build

# Build BioGears
echo "Building BioGears ..."
cmake -DCMAKE_INSTALL_PREFIX=/opt/biogears/usr -DBiogears_BUILD_WEBSITE=ON -DBiogears_BUILD_JAVATOOLS=ON -DBiogears_BUILD_HOWTOS=OFF -DBiogears_BUILD_TEST=OFF -DCMAKE_BUILD_TYPE=Release .. && make -j2

cd runtime

echo "Finished building BioGears"

if [ "${GENSTATES}" == "true" ]; then
    echo "Running cmd_bio GENSTATES ..."
    ../outputs/Release/bin/cmd_bio GENSTATES
fi

echo "Passed GENSTATES"

if [ "${VALIDATE}" == "true" ]; then
    echo "Running cmd_bio VALIDATE all ..."
    ../outputs/Release/bin/cmd_bio VALIDATE all
fi

echo "Passed VALIDATE"

# Only run if starting from a clean build of BioGears... running and validating everything from scratch

# Always run this
echo "Running cmd_bio GENTABLES ..."
../outputs/Release/bin/cmd_bio GENTABLES all

echo "Passed GENTABLES"

# Copy non-regenerated files from share/website into runtime and reorganizes files in runtime+
python3 ../../share/website/WebsiteGenerationPreProcess.py /opt/biogears/core/share/website /opt/biogears/core/build/runtime

echo "Passed WebGenPreProcess"

# Preprocess MD files for website generation and create graphs
cmake --build .. --target docs-prepare

echo "Passed docs-prepare"

# Run Doxygen
cmake --build .. --target docs-doxygen

echo "Passed docs-doxygen"

# Copy files into documentation folder
cmake --build .. --target docs-stage