build_and_test.sh

#!/bin/bash

# Copyright 2017 Google Inc.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
#    this list of conditions and the following disclaimer.
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# 2. Redistributions in binary form must reproduce the above copyright
#    notice, this list of conditions and the following disclaimer in the
#    documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
#    contributors may be used to endorse or promote products derived from this
#    software without specific prior written permission.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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# POSSIBILITY OF SUCH DAMAGE.

# NOLINT
set -eux -o pipefail

source settings.sh

# bazel should have been installed in build-prereq.sh, but the PATH might
# need to be added in this script.
if ! bazel; then
  PATH="$HOME/bin:$PATH"
fi

# Run all deepvariant tests.  Take bazel options from args, if any.
# Note: If running with GPU, tests must be executed serially due to a GPU
# contention issue.
if [[ "${DV_GPU_BUILD:-0}" = "1" ]]; then
  bazel test -c opt --local_test_jobs=1 ${DV_COPT_FLAGS} "$@" \
    deepvariant/...
  # Also run the GPU-specific tests.
  bazel test -c opt --local_test_jobs=1 ${DV_COPT_FLAGS} "$@" \
    deepvariant:gpu_tests
else
  # Running parallel tests on CPU.
  bazel test -c opt ${DV_COPT_FLAGS} "$@" deepvariant/...
fi

# Create some build artifacts (two ways), and execute one of them.
bazel build -c opt ${DV_COPT_FLAGS} "$@" deepvariant:binaries
echo 'Expect a usage message:'
(bazel-bin/deepvariant/call_variants --help || : ) | grep '/call_variants.py:'

bazel build -c opt ${DV_COPT_FLAGS} "$@" deepvariant:binaries --build_python_zip
echo 'Expect a usage message:'
(bazel-bin/deepvariant/call_variants --help || : ) | grep '/call_variants.py:'

# Bundle the licenses.
bazel build :licenses_zip