bottleneck: initial integration (#8303)

* bottleneck: initial integration

* bottleneck: refine setup

projects/bottleneck/Dockerfile

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+# Copyright 2022 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+################################################################################
+
+FROM gcr.io/oss-fuzz-base/base-builder-python
+RUN apt-get update && apt-get install -y make autoconf automake libtool
+RUN pip3 install cython
+RUN git clone https://github.com/numpy/numpy && cd numpy && git submodule update --init
+RUN cd $SRC/numpy && \
+    pip3 install . && \
+    python3 setup.py install
+RUN git clone --depth 1 https://github.com/pydata/bottleneck
+WORKDIR bottleneck
+COPY build.sh *.py $SRC/

projects/bottleneck/build.sh

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+#!/bin/bash -eu
+# Copyright 2022 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+################################################################################
+
+
+cd $SRC/bottleneck
+pip3 install .
+python3 setup.py install
+
+# Build fuzzers and put them in $OUT/
+for fuzzer in $(find $SRC -name 'fuzz_*.py'); do
+  compile_python_fuzzer $fuzzer
+done

projects/bottleneck/fuzz_bn.py

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+#!/usr/bin/python3
+# Copyright 2022 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Scalar equivalene checker"""
+
+import os
+import sys
+import atheris
+
+import numpy as np
+from numpy.testing import assert_array_almost_equal
+import bottleneck as bn
+
+
+def gen_random_array(data, fdp = None):
+  if fdp is None:
+    fdp = atheris.FuzzedDataProvider(data)
+  l1 = list()
+  for i in range(fdp.ConsumeIntInRange(5, 3000)):
+    l1.append(fdp.ConsumeIntInRange(1,10000))
+  a = np.array(l1)
+  return a
+
+def TestOneInput(data):
+  """Tests scalar equivalence and also move operations"""
+  fdp = atheris.FuzzedDataProvider(data)
+  a = gen_random_array(data, fdp)
+
+  func_pairs = [
+    (bn.nansum, bn.slow.nansum),
+    (bn.nanmean, bn.slow.nanmean),
+    (bn.nanstd, bn.slow.nanstd),
+    (bn.nanvar, bn.slow.nanvar),
+    (bn.nanmin, bn.slow.nanmin),
+    (bn.median, bn.slow.median),
+    (bn.nanmedian, bn.slow.nanmedian),
+    (bn.ss, bn.slow.ss),
+    (bn.nanargmin, bn.slow.nanargmin),
+    (bn.nanargmax, bn.slow.nanargmax),
+    (bn.anynan, bn.slow.anynan),
+    (bn.allnan, bn.slow.allnan),
+  ]
+
+  idx = 0
+  for func0, func1 in func_pairs:
+    idx = idx + 1
+    actual = func0(a)
+    desired = func1(a)
+    assert_array_almost_equal(
+      actual,
+      desired,
+      err_msg="Failed scalar equivalence"
+    )
+
+
+  # Test move operations
+  window = fdp.ConsumeIntInRange(2, 50)
+  min_count = fdp.ConsumeIntInRange(1, window)
+  actual = bn.move_median(
+    a,
+    window=window,
+    min_count = fdp.ConsumeIntInRange(1,100)
+  )
+  desired = bn.slow.move_median(
+    a,
+    window=window,
+    min_count=fdp.ConsumeIntInRange(1, 100)
+  )
+  assert_array_almost_equal(
+    actual,
+    desired,
+    err_msg="Failed move operation"
+  )
+
+
+def main():
+  atheris.instrument_all()
+  atheris.Setup(sys.argv, TestOneInput, enable_python_coverage=True)
+  atheris.Fuzz()
+
+if __name__ == "__main__":
+  main()

projects/bottleneck/project.yaml

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+homepage: "https://github.com/pydata/bottleneck"
+language: python
+main_repo: "https://github.com/pydata/bottleneck"
+fuzzing_engines:
+  - libfuzzer
+sanitizers:
+  - address
+  - undefined
+vendor_ccs:
+  - david@adalogics.com