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ENH: add support for nan-like null strings in string replace #3477

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ENH: add support for nan-like null strings in string replace

ENH: add support for nan-like null strings in string replace #3477

Workflow file for this run

.github/workflows/linux_blas.yml at 0905dd8
name: BLAS tests (Linux)
# This file is meant for testing different BLAS/LAPACK flavors and build
# options on Linux. All other yml files for Linux will only test without BLAS
# (mostly because that's easier and faster to build) or with the same 64-bit
# OpenBLAS build that is used in the wheel jobs.
#
# Jobs and their purpose:
#
# - openblas32_stable_nightly:
# Uses the 32-bit OpenBLAS builds, both the latest stable release
# and a nightly build.
# - openblas_no_pkgconfig_fedora:
# Test OpenBLAS on Fedora. Fedora doesn't ship .pc files for OpenBLAS,
# hence this exercises the "system dependency" detection method.
# - flexiblas_fedora:
# Tests FlexiBLAS (the default on Fedora for its own packages), via
# pkg-config. FlexiBLAS allows runtime switching of BLAS/LAPACK
# libraries, which is a useful capability (not tested in this job).
# - openblas_cmake:
# Tests whether OpenBLAS LP64 is detected correctly when only CMake
# and not pkg-config is installed.
# - netlib-debian:
# Installs libblas/liblapack, which in Debian contains libcblas within
# libblas.
# - netlib-split:
# Installs vanilla Netlib blas/lapack with separate libcblas, which is
# the last option tried in auto-detection.
# - mkl:
# Tests MKL installed from PyPI (because easiest/fastest, if broken) in
# 3 ways: both LP64 and ILP64 via pkg-config, and then using the
# Single Dynamic Library (SDL, or `libmkl_rt`).
# - blis:
# Simple test for LP64 via pkg-config
# - atlas:
# Simple test for LP64 via pkg-config
on:
pull_request:
branches:
- main
- maintenance/**
defaults:
run:
shell: bash
concurrency:
group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
cancel-in-progress: true
permissions:
contents: read # to fetch code (actions/checkout)
jobs:
openblas32_stable_nightly:
# To enable this workflow on a fork, comment out:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
USE_NIGHTLY_OPENBLAS: [false, true]
env:
USE_NIGHTLY_OPENBLAS: ${{ matrix.USE_NIGHTLY_OPENBLAS }}
name: "Test Linux (${{ matrix.USE_NIGHTLY_OPENBLAS && 'nightly' || 'stable' }} OpenBLAS)"
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
with:
python-version: '3.11'
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
# Install OpenBLAS
if [[ $USE_NIGHTLY_OPENBLAS == "true" ]]; then
python -m pip install -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy-openblas32
else
python -m pip install -r requirements/ci32_requirements.txt
fi
mkdir -p ./.openblas
python -c"import scipy_openblas32 as ob32; print(ob32.get_pkg_config())" > ./.openblas/scipy-openblas.pc
echo "PKG_CONFIG_PATH=${{ github.workspace }}/.openblas" >> $GITHUB_ENV
ld_library_path=$(python -c"import scipy_openblas32 as ob32; print(ob32.get_lib_dir())")
echo "LD_LIBRARY_PATH=$ld_library_path" >> $GITHUB_ENV
- name: Build
shell: 'script -q -e -c "bash --noprofile --norc -eo pipefail {0}"'
env:
TERM: xterm-256color
run:
spin build -- --werror -Dallow-noblas=false
- name: Check build-internal dependencies
run:
ninja -C build -t missingdeps
- name: Check installed test and stub files
run:
python tools/check_installed_files.py $(find ./build-install -path '*/site-packages/numpy')
- name: Ensure scipy-openblas
run: |
set -ex
spin python tools/check_openblas_version.py 0.3.26
- name: Test
shell: 'script -q -e -c "bash --noprofile --norc -eo pipefail {0}"'
env:
TERM: xterm-256color
run: |
pip install pytest pytest-xdist hypothesis typing_extensions
spin test -j auto
openblas_no_pkgconfig_fedora:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
container: fedora:39
name: "OpenBLAS (Fedora, no pkg-config, LP64/ILP64)"
steps:
- name: Install system dependencies
run: |
dnf install git gcc-gfortran g++ python3-devel openblas-devel -y
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
pip install pytest hypothesis typing_extensions
- name: Build (LP64)
run: spin build -- -Dblas=openblas -Dlapack=openblas -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg
- name: Build (ILP64)
run: |
rm -rf build
spin build -- -Duse-ilp64=true -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg
flexiblas_fedora:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
container: fedora:39
name: "FlexiBLAS (LP64, ILP64 on Fedora)"
steps:
- name: Install system dependencies
run: |
dnf install git gcc-gfortran g++ python3-devel flexiblas-devel -y
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
pip install pytest hypothesis typing_extensions
- name: Build
run: spin build -- -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg
- name: Build (ILP64)
run: |
rm -rf build
spin build -- -Ddisable-optimization=true -Duse-ilp64=true -Dallow-noblas=false
- name: Test (ILP64)
run: spin test -- numpy/linalg
openblas_cmake:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
name: "OpenBLAS with CMake"
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
with:
python-version: '3.11'
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
pip install pytest pytest-xdist hypothesis typing_extensions
sudo apt-get update
sudo apt-get install libopenblas-dev cmake
sudo apt-get remove pkg-config
- name: Build
run: spin build -- -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -j auto -- numpy/linalg
netlib-debian:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
name: "Debian libblas/liblapack"
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
with:
python-version: '3.11'
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
sudo apt-get update
sudo apt-get install liblapack-dev pkg-config
- name: Build
run: |
spin build -- -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: |
pip install pytest pytest-xdist hypothesis typing_extensions
spin test -j auto -- numpy/linalg
netlib-split:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
container: opensuse/tumbleweed
name: "OpenSUSE Netlib BLAS/LAPACK"
steps:
- name: Install system dependencies
run: |
# No blas.pc on OpenSUSE as of Nov 2023, so no need to install pkg-config.
# If it is needed in the future, use install name `pkgconf-pkg-config`
zypper install -y git gcc-c++ python3-pip python3-devel blas cblas lapack
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- name: Install PyPI dependencies
run: |
pip install --break-system-packages -r requirements/build_requirements.txt
- name: Build
run: |
spin build -- -Dblas=blas -Dlapack=lapack -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: |
pip install --break-system-packages pytest pytest-xdist hypothesis typing_extensions
spin test -j auto -- numpy/linalg
mkl:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
name: "MKL (LP64, ILP64, SDL)"
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
with:
python-version: '3.11'
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
pip install pytest pytest-xdist hypothesis typing_extensions
pip install mkl mkl-devel
- name: Repair MKL pkg-config files and symlinks
run: |
# MKL 2023.2 works when installed from conda-forge (except for `-iomp`
# and `-tbb` pkg-config files), Spack, or with the standalone Intel
# installer. The standalone installer is the worst option, since it's
# large and clumsy to install and requires running a setvars.sh script
# before things work. The PyPI MKL packages are broken and need the
# fixes in this step. For details, see
# https://github.com/conda-forge/intel_repack-feedstock/issues/34
cd $Python3_ROOT_DIR/lib/pkgconfig
sed -i 's/\/intel64//g' mkl*.pc
# add the expected .so -> .so.2 symlinks to fix linking
cd ..
for i in $( ls libmkl*.so.2 ); do ln -s $i ${i%.*}; done
- name: Build with defaults (LP64)
run: |
pkg-config --libs mkl-dynamic-lp64-seq # check link flags
spin build -- -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg
- name: Build with ILP64
run: |
git clean -xdf > /dev/null
pkg-config --libs mkl-dynamic-ilp64-seq
spin build -- -Duse-ilp64=true -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg
- name: Build without pkg-config (default options, SDL)
run: |
git clean -xdf > /dev/null
pushd $Python3_ROOT_DIR/lib/pkgconfig
rm mkl*.pc
popd
export MKLROOT=$Python3_ROOT_DIR
spin build -- -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg
blis:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
name: "BLIS"
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
with:
python-version: '3.11'
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
pip install pytest pytest-xdist hypothesis typing_extensions
sudo apt-get update
sudo apt-get install libblis-dev libopenblas-dev pkg-config
- name: Add BLIS pkg-config file
run: |
# Needed because blis.pc missing in Debian:
# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=989076
# The alternative here would be to use another distro or Miniforge
sudo cp tools/ci/_blis_debian.pc /usr/lib/x86_64-linux-gnu/pkgconfig/blis.pc
# Check if the patch works:
pkg-config --libs blis
pkg-config --cflags blis
- name: Build
run: spin build -- -Dblas=blis -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg
atlas:
if: github.repository == 'numpy/numpy'
runs-on: ubuntu-latest
name: "ATLAS"
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
submodules: recursive
fetch-tags: true
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
with:
python-version: '3.11'
- name: Install dependencies
run: |
pip install -r requirements/build_requirements.txt
pip install pytest pytest-xdist hypothesis typing_extensions
sudo apt-get update
sudo apt-get install libatlas-base-dev pkg-config
- name: Build
run: spin build -- -Dblas=blas-atlas -Dlapack=lapack-atlas -Ddisable-optimization=true -Dallow-noblas=false
- name: Test
run: spin test -- numpy/linalg