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Bump scipy from 1.5.4 to 1.10.0 in /MicroBenchmarks/libs/benchmark #18

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@dependabot dependabot bot commented on behalf of github Jul 6, 2023

Bumps scipy from 1.5.4 to 1.10.0.

Release notes

Sourced from scipy's releases.

SciPy 1.10.0 Release Notes

SciPy 1.10.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.10.x branch, and on adding new features on the main branch.

This release requires Python 3.8+ and NumPy 1.19.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

  • A new dedicated datasets submodule (scipy.datasets) has been added, and is now preferred over usage of scipy.misc for dataset retrieval.
  • A new scipy.interpolate.make_smoothing_spline function was added. This function constructs a smoothing cubic spline from noisy data, using the generalized cross-validation (GCV) criterion to find the tradeoff between smoothness and proximity to data points.
  • scipy.stats has three new distributions, two new hypothesis tests, three new sample statistics, a class for greater control over calculations involving covariance matrices, and many other enhancements.

New features

scipy.datasets introduction

  • A new dedicated datasets submodule has been added. The submodules is meant for datasets that are relevant to other SciPy submodules ands content (tutorials, examples, tests), as well as contain a curated set of datasets that are of wider interest. As of this release, all the datasets from scipy.misc have been added to scipy.datasets (and deprecated in scipy.misc).
  • The submodule is based on Pooch (a new optional dependency for SciPy), a Python package to simplify fetching data files. This move will, in a subsequent release, facilitate SciPy to trim down the sdist/wheel sizes, by decoupling the data files and moving them out of the SciPy repository, hosting them externally and

... (truncated)

Commits
  • dde5059 REL: 1.10.0 final [wheel build]
  • 7856f28 Merge pull request #17696 from tylerjereddy/treddy_110_final_prep
  • 205b624 DOC: add missing author
  • 1ab9f1b DOC: update 1.10.0 relnotes
  • ac2f45f MAINT: integrate._qmc_quad: mark as private with preceding underscore
  • 3e0ae1a REV: integrate.qmc_quad: delay release to SciPy 1.11.0
  • 34cdf05 MAINT: FFT pybind11 fixups
  • 843500a Merge pull request #17689 from mdhaber/gh17686
  • 089924b REL: integrate.qmc_quad: remove from release notes
  • 3e47110 REL: 1.10.0rc3 unreleased
  • Additional commits viewable in compare view

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Bumps [scipy](https://github.com/scipy/scipy) from 1.5.4 to 1.10.0.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.5.4...v1.10.0)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Jul 6, 2023
@MatzeB
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MatzeB commented Oct 5, 2023

"benchmark" is a copy of the third-party benchmark. So let's skip this update and instead wait till we update all of google benchmark.

@MatzeB MatzeB closed this Oct 5, 2023
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dependabot bot commented on behalf of github Oct 5, 2023

OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting @dependabot ignore this major version or @dependabot ignore this minor version.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.

@dependabot dependabot bot deleted the dependabot/pip/MicroBenchmarks/libs/benchmark/scipy-1.10.0 branch October 5, 2023 01:24
@sstamenova
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sstamenova commented Jun 20, 2024

@MatzeB This update was skipped last year, but benchmark hasn't been updated yet. Is there a plan to at any specific time? The vulnerabilities in scipy and numpy still exist.

ekilmer added a commit to trail-of-forks/instafix-llvm-test-suite that referenced this pull request Jun 10, 2025
Just one example, but others are likely similar (at least with same
stacktrace)

```
[1/7] : && /home/erickilmer/src/instafix/out/build/linux/bin/instafix-front/instafix-front --ld-path=instafix-lld-tool --for-linker=--fake-executable=/home/erickilmer/src/instafix/out/build/linux/bin/instafix-ld/instafix-ld    -O3 -DNDEB
UG  tools/CMakeFiles/not.dir/not.cpp.o -o tools/not   && :
FAILED: tools/not
: && /home/erickilmer/src/instafix/out/build/linux/bin/instafix-front/instafix-front --ld-path=instafix-lld-tool --for-linker=--fake-executable=/home/erickilmer/src/instafix/out/build/linux/bin/instafix-ld/instafix-ld    -O3 -DNDEBUG  tools/CMakeFiles/not.dir/not.cpp.o -o tools/not   && :
ClangLoc: /home/erickilmer/src/instafix-llvm/llvm/out/install/linux/bin/clang
Executing a non indexed phase: "/home/erickilmer/src/instafix/out/build/linux/instafix-lld/instafix-lld-tool" -z relro --hash-style=gnu --eh-frame-hdr -m elf_x86_64 -pie -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o tools/not /lib/x86_64-linux-gnu/Scrt1.o /lib/x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib64 -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/usr/lib64 -L/lib -L/usr/lib --fake-executable=/home/erickilmer/src/instafix/out/build/linux/bin/instafix-ld/instafix-ld tools/CMakeFiles/not.dir/not.cpp.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /lib/x86_64-linux-gnu/crtn.o
program_name: /home/erickilmer/src/instafix/out/build/linux/instafix-lld/instafix-lld-tool
input_file: /lib/x86_64-linux-gnu/Scrt1.o
input_file: /lib/x86_64-linux-gnu/crti.o
input_file: /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o
input_file: tools/CMakeFiles/not.dir/not.cpp.o
input_file: /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o
input_file: /lib/x86_64-linux-gnu/crtn.o
loc("/lib/x86_64-linux-gnu/libc.so":1:1): error: unexpected character
PLEASE submit a bug report to https://github.com/llvm/llvm-project/issues/ and include the crash backtrace.
Stack dump:
0.      Program arguments: /home/erickilmer/src/instafix/out/build/linux/bin/instafix-front/instafix-front --ld-path=instafix-lld-tool --for-linker=--fake-executable=/home/erickilmer/src/instafix/out/build/linux/bin/instafix-ld/instafix-ld -O3 -DNDEBUG tools/CMakeFiles/not.dir/not.cpp.o -o tools/not
 #0 0x000064b890eb6d41 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) /home/erickilmer/src/instafix-llvm/llvm/lib/Support/Unix/Signals.inc:804:11
 #1 0x000064b890eb723b PrintStackTraceSignalHandler(void*) /home/erickilmer/src/instafix-llvm/llvm/lib/Support/Unix/Signals.inc:880:1
 #2 0x000064b890eb49a6 llvm::sys::RunSignalHandlers() /home/erickilmer/src/instafix-llvm/llvm/lib/Support/Signals.cpp:105:5
 llvm#3 0x000064b890eb7a1d SignalHandler(int, siginfo_t*, void*) /home/erickilmer/src/instafix-llvm/llvm/lib/Support/Unix/Signals.inc:418:7
 llvm#4 0x00007c3845445330 (/lib/x86_64-linux-gnu/libc.so.6+0x45330)
 llvm#5 0x000064b883cd967c llvm::Value::getType() const /home/erickilmer/src/instafix-llvm/llvm/include/llvm/IR/Value.h:255:34
 llvm#6 0x000064b88fc554d2 llvm::CastInst::castIsValid(llvm::Instruction::CastOps, llvm::Value*, llvm::Type*) /home/erickilmer/src/instafix-llvm/llvm/include/llvm/IR/InstrTypes.h:623:31
 llvm#7 0x000064b890752419 llvm::ConstantExpr::getBitCast(llvm::Constant*, llvm::Type*, bool) /home/erickilmer/src/instafix-llvm/llvm/lib/IR/Constants.cpp:2325:3
 llvm#8 0x000064b887051e16 mlir::LLVM::detail::getLLVMConstant(llvm::Type*, mlir::Attribute, mlir::Location, mlir::LLVM::ModuleTranslation const&) /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:602:5
 llvm#9 0x000064b88705bb47 mlir::LLVM::ModuleTranslation::convertOneFunction(mlir::LLVM::LLVMFuncOp) /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:1465:25
llvm#10 0x000064b88705eea3 mlir::LLVM::ModuleTranslation::convertFunctions() /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:1804:16
llvm#11 0x000064b88706144d mlir::translateModuleToLLVMIR(mlir::Operation*, llvm::LLVMContext&, llvm::StringRef, bool) /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:2218:25
llvm#12 0x000064b883ba2fda instafix::Loader::LinkInstafixLLVM() /home/erickilmer/src/instafix/instafix/lib/instafix.cpp:837:7
llvm#13 0x000064b883bd9dc2 instafix::LLDLoader::NativeLinkAndJIT(int, llvm::ArrayRef<char const*>, bool) /home/erickilmer/src/instafix/instafix/lib/LLDLoader.cpp:42:27
llvm#14 0x000064b883b9d649 instafix::instafix_main(int, char**) /home/erickilmer/src/instafix/instafix/lib/instafix.cpp:264:32
llvm#15 0x000064b883b99992 main /home/erickilmer/src/instafix/bin/instafix-front/Main.cpp:25:3
llvm#16 0x00007c384542a1ca __libc_start_call_main ./csu/../sysdeps/nptl/libc_start_call_main.h:74:3
llvm#17 0x00007c384542a28b call_init ./csu/../csu/libc-start.c:128:20
llvm#18 0x00007c384542a28b __libc_start_main ./csu/../csu/libc-start.c:347:5
llvm#19 0x000064b883b998a5 _start (/home/erickilmer/src/instafix/out/build/linux/bin/instafix-front/instafix-front+0x688a8a5)
Segmentation fault (core dumped)
```

with gdb stacktrace:

```
$ cd build
$ gdb --args /home/erickilmer/src/instafix/out/build/linux/bin/instafix-front/instafix-front --ld-path=instafix-lld-tool --for-linker=--fake-executable=/home/erickilmer/src/instafix/out/build/linux/bin/instafix-ld/instafix-ld -O3 -DNDEBUG tools/CMakeFiles/not.dir/not.cpp.o -o tools/not
[...]
(gdb) r
[...]
Thread 1 "instafix-front" received signal SIGSEGV, Segmentation fault.
llvm::Value::getType (this=0x0) at /home/erickilmer/src/instafix-llvm/llvm/include/llvm/IR/Value.h:255
255	  Type *getType() const { return VTy; }
(gdb) bt
#0  llvm::Value::getType (this=0x0) at /home/erickilmer/src/instafix-llvm/llvm/include/llvm/IR/Value.h:255
#1  0x0000555567e9a4d2 in llvm::CastInst::castIsValid (op=llvm::Instruction::BitCast, S=0x0, DstTy=0x555569811470) at /home/erickilmer/src/instafix-llvm/llvm/include/llvm/IR/InstrTypes.h:623
#2  0x0000555568997419 in llvm::ConstantExpr::getBitCast (C=0x0, DstTy=0x555569811470, OnlyIfReduced=false) at /home/erickilmer/src/instafix-llvm/llvm/lib/IR/Constants.cpp:2325
llvm#3  0x000055555f296e16 in mlir::LLVM::detail::getLLVMConstant (llvmType=0x555569811470, attr=..., loc=..., moduleTranslation=...) at /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:602
llvm#4  0x000055555f2a0b47 in mlir::LLVM::ModuleTranslation::convertOneFunction (this=0x7fffffff3710, func=...) at /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:1465
llvm#5  0x000055555f2a3ea3 in mlir::LLVM::ModuleTranslation::convertFunctions (this=0x7fffffff3710) at /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:1804
llvm#6  0x000055555f2a644d in mlir::translateModuleToLLVMIR (module=0x5555697e32b0, llvmContext=..., name=..., disableVerification=false) at /home/erickilmer/src/instafix-llvm/mlir/lib/Target/LLVMIR/ModuleTranslation.cpp:2218
llvm#7  0x000055555bde7fda in instafix::Loader::LinkInstafixLLVM (this=0x55556979ea80) at /home/erickilmer/src/instafix/instafix/lib/instafix.cpp:837
llvm#8  0x000055555be1edc2 in instafix::LLDLoader::NativeLinkAndJIT (this=0x55556979ea80, argc=7, argv=..., exec=false) at /home/erickilmer/src/instafix/instafix/lib/LLDLoader.cpp:42
llvm#9  0x000055555bde2649 in instafix::instafix_main (argc=8, argv=0x7fffffffccc8) at /home/erickilmer/src/instafix/instafix/lib/instafix.cpp:264
llvm#10 0x000055555bdde992 in main (argc=8, argv=0x7fffffffccc8) at /home/erickilmer/src/instafix/bin/instafix-front/Main.cpp:25
```
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