DWesl · DWesl · Feb 4, 2023 · Feb 4, 2023 · Feb 4, 2023 · Feb 4, 2023
diff --git a/.github/workflows/cygwin.yml b/.github/workflows/cygwin.yml
@@ -0,0 +1,70 @@
+name: Cygwin Tests
+
+on:
+  push:
+    branches:
+      - main
+      - maintenance/**
+  pull_request:
+    branches:
+      - main
+      - maintenance/**
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  cygwin:
+    name: Cygwin tests
+    runs-on: windows-latest
+    env:
+      SHELLOPTS: igncr
+      CHERE_INVOKING: 1
+      CYGWIN_NOWINPATH: 1
+      PYTHONPATH: /usr/local/lib/python3.8/site-packages
+    steps:
+      - run: git config --global core.autocrlf input
+      - uses: actions/checkout@v3
+        with:
+          submodules: recursive
+      - uses: cygwin/cygwin-install-action@v2
+        with:
+          packages: >-
+            gcc-g++ gcc-fortran liblapack-devel libopenblas libmpfr-devel ccache swig libmpc-devel
+            libumfpack-devel libsliplu-devel libldl-devel libklu-devel libcxsparse-devel libcholmod-devel libamd-devel
+            python38-devel python38-pip python38-setuptools python38-wheel python38-numpy python38-cython
+            python38-pytest
+            meson ninja cmake make git
+      - name: Fix git config
+        shell: bash.exe -eo pipefail -o igncr "{0}"
+        run: /usr/bin/git config --system --add safe.directory /cygdrive/d/a/*/scipy
+      - name: Install Python dependencies
+        shell: bash.exe -eo pipefail -o igncr "{0}"
+        run: |
+          mkdir builds
+          cd builds
+          python3.8 -m pip install --upgrade pip 'setuptools<60' wheel
+          python3.8 -m pip install --upgrade numpy cython pytest pytest-xdist pytest-timeout pybind11
+          python3.8 -m pip install --upgrade mpmath gmpy2 pythran threadpoolctl pooch
+          python3.8 -m pip uninstall -y nose
+          cd ..
+      - name: Check NumPy import
+        shell: bash.exe -eo pipefail -o igncr "{0}"
+        run: /usr/bin/env PATH="/bin:/usr/bin:/usr/local/bin:/usr/lib/lapack" python3.8 -c "import numpy as np; print(np.__version__)"
+      - name: Building SciPy
+        shell: bash.exe -eo pipefail -o igncr "{0}"
+        env:
+          CPPFLAGS: -D_XOPEN_SOURCE=600
+        run: /usr/bin/env PATH="/bin:/usr/bin:/usr/local/bin:/usr/lib/lapack" python3.8 -u runtests.py -g -j2 --build-only
+      - name: Check SciPy installs
+        shell: bash.exe -eo pipefail -o igncr "{0}"
+        if: false
+        env:
+          CPPFLAGS: -D_XOPEN_SOURCE=600
+        run: /usr/bin/env PATH="/bin:/usr/bin:/usr/local/bin:/usr/lib/lapack" python3.8 -m pip install -e .
+      - name: Testing SciPy
+        shell: bash.exe -eo pipefail -o igncr "{0}"
+        run: |
+          /usr/bin/env PATH="/bin:/usr/bin:/usr/local/bin:/usr/lib/lapack" python3.8 -u runtests.py -n -g -j2 -m fast -- -rfEX --durations=10 --timeout=60 2>&1 | tee runtests.log
+          python3.8 tools/validate_runtests_log.py fast < runtests.log
diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
@@ -0,0 +1,131 @@
+name: Cygwin Meson tests
+
+# This is a single job: Python 3.9, building with Meson, using -Werror to
+# ensure we remain at zero build warnings. Other Meson CI jobs are running
+# on https://github.com/rgommers/scipy/tree/meson
+
+on:
+  push:
+    branches:
+      - main
+      - maintenance/**
+  pull_request:
+    branches:
+      - main
+      - maintenance/**
+  workflow_dispatch:
+
+permissions:
+   contents: read  # to fetch code (actions/checkout)
+
+env:
+  CCACHE_DIR: "${{ github.workspace }}/.ccache"
+  INSTALLDIR: "build-install"
+  CPPFLAGS: "-D_XOPEN_SOURCE=700"
+  SHELLOPTS: igncr
+  CHERE_INVOKING: 1
+  CYGWIN_NOWINPATH: 1
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  test_meson:
+    name: Cygwin Meson build
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-minor-version: ['9']
+    env:
+      PYTHONPATH: "/usr/local/lib/python3.${{ matrix.python-minor-version }}/site-packages"
+
+    steps:
+    - run: git config --global core.autocrlf input
+
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: cygwin/cygwin-install-action@v3
+      with:
+        packages: >-
+          gcc-g++ gcc-fortran liblapack-devel libopenblas libmpfr-devel ccache swig libmpc-devel
+          libumfpack-devel libsliplu-devel libldl-devel libklu-devel libcxsparse-devel libcholmod-devel libamd-devel
+          python3${{ matrix.python-minor-version }}-devel
+          python3${{ matrix.python-minor-version }}-pip
+          python3${{ matrix.python-minor-version }}-setuptools
+          python3${{ matrix.python-minor-version }}-wheel
+          python3${{ matrix.python-minor-version }}-numpy
+          python3${{ matrix.python-minor-version }}-cython
+          python3${{ matrix.python-minor-version }}-pytest
+          meson ninja cmake make git
+
+    - name: Fix git config
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: /usr/bin/git config --system --add safe.directory /cygdrive/d/a/*/scipy
+
+    - name: Install Python packages
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        python -m pip install numpy cython pytest pytest-xdist pytest-timeout pybind11 mpmath gmpy2 pythran click rich-click doit pydevtool pooch
+        python -m pip install meson'>=0.64.0' ninja tomli
+
+    - name:  Prepare compiler cache
+      id:    prep-ccache
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        mkdir -p "${CCACHE_DIR}"
+        echo "dir=$(cygpath -wa $CCACHE_DIR)" >> $GITHUB_OUTPUT
+        NOW=$(date -u +"%F-%T")
+        echo "timestamp=${NOW}" >> $GITHUB_OUTPUT
+    - name: Setup compiler cache
+      uses:  actions/cache@v3
+      id:    cache-ccache
+      # Reference: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key
+      # NOTE: The caching strategy is modeled in a way that it will always have a unique cache key for each workflow run
+      # (even if the same workflow is run multiple times). The restore keys are not unique and for a partial match, they will
+      # return the most recently created cache entry, according to the GitHub Action Docs.
+      with:
+        path: ${{ steps.prep-ccache.outputs.dir }}
+        # Restores ccache from either a previous build on this branch or on main
+        key:  ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-${{ steps.prep-ccache.outputs.timestamp }}
+        # This evaluates to `Linux Tests-3.9-ccache-linux-` which is not unique. As the CI matrix is expanded, this will
+        # need to be updated to be unique so that the cache is not restored from a different job altogether.
+        restore-keys: |
+          ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-
+    - name: Setup build and install scipy
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        export PATH="/usr/local/bin:/usr/bin:/bin:/usr/lib/lapack"
+        meson setup build -Dblas=blas -Dlapack=lapack --prefix=$(pwd)/${INSTALLDIR}
+        python dev.py build -j 2 --werror
+    - name: Ccache performance
+      shell: bash -l -eo pipefail -o igncr "{0}"
+      run: ccache -s
+
+    - name: Check installation
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        export PATH="/usr/local/bin:/usr/bin:/bin:/usr/lib/lapack"
+        pushd tools
+        python check_installation.py ${{ env.INSTALLDIR }}
+        ./check_pyext_symbol_hiding.sh ../build
+        popd
+    - name: Check import
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        export PATH="/usr/local/bin:/usr/bin:/bin:/usr/lib/lapack"
+        pushd build-install
+        export PYTHONPATH="$(pwd)/lib/python3.${{ matrix.python-minor-version }}/site-packages/"
+        ls ${PYTHONPATH} ${PYTHONPATH}/scipy/*
+        python -vvv -d -c "import scipy.linalg"
+        popd
+
+    - name: Test SciPy
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        export PATH="/usr/local/bin:/usr/bin:/bin:/usr/lib/lapack"
+        export OMP_NUM_THREADS=2
+        export SCIPY_USE_PROPACK=1
+        python dev.py --no-build test -j 2 -- --durations 10 --timeout=60
diff --git a/dev.py b/dev.py
@@ -436,6 +436,13 @@ def setup_build(cls, dirs, args):
                 raise RuntimeError("Can't build into non-empty directory "
                                    f"'{build_dir.absolute()}'")
 
+        if sys.platform == "cygwin":
+            # Cygwin only has netlib lapack, but can link against
+            # OpenBLAS rather than netlib blas at runtime.  There is
+            # no libopenblas-devel to enable linking against
+            # openblas-specific functions or OpenBLAS Lapack
+            cmd.extend(["-Dlapack=lapack", "-Dblas=blas"])
+
         build_options_file = (
             build_dir / "meson-info" / "intro-buildoptions.json")
         if build_options_file.exists():
@@ -547,6 +554,11 @@ def install_project(cls, dirs, args):
         with open(dirs.installed / ".gitignore", "w") as f:
             f.write("*")
 
+        if sys.platform == "cygwin":
+            rebase_cmd = ["/usr/bin/rebase", "--database", "--oblivious"]
+            rebase_cmd.extend(Path(dirs.installed).glob("**/*.dll"))
+            subprocess.check_call(rebase_cmd)
+
         print("Installation OK")
         return
 

diff --git a/scipy/integrate/meson.build b/scipy/integrate/meson.build
@@ -136,7 +136,7 @@ py3.extension_module('_vode',
   c_args: [numpy_nodepr_api, Wno_unused_variable],
   include_directories: [inc_np, inc_f2py],
   link_args: version_link_args,
-  dependencies: [lapack, fortranobject_dep],
+  dependencies: [lapack, blas, fortranobject_dep],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/integrate'

diff --git a/scipy/linalg/meson.build b/scipy/linalg/meson.build
@@ -55,7 +55,7 @@ py3.extension_module('_fblas',
   c_args: numpy_nodepr_api,
   include_directories: [inc_np, inc_f2py],
   link_args: version_link_args,
-  dependencies: [blas, lapack, fortranobject_dep],
+  dependencies: [lapack, blas, fortranobject_dep],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/linalg'
@@ -76,7 +76,7 @@ py3.extension_module('_flapack',
   c_args: [numpy_nodepr_api, Wno_empty_body],
   include_directories: [inc_np, inc_f2py],
   link_args: version_link_args,
-  dependencies: [lapack, fortranobject_dep],
+  dependencies: [lapack, blas, fortranobject_dep],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/linalg'
@@ -204,7 +204,7 @@ cython_blas = py3.extension_module('cython_blas',
   link_with: fwrappers,
   include_directories: inc_np,
   link_args: version_link_args,
-  dependencies: [blas, lapack],
+  dependencies: [lapack, blas],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/linalg'
@@ -220,7 +220,7 @@ cython_lapack = py3.extension_module('cython_lapack',
   link_with: fwrappers,
   include_directories: inc_np,
   link_args: version_link_args,
-  dependencies: [blas, lapack],
+  dependencies: [lapack, blas],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/linalg'

diff --git a/scipy/optimize/_trlib/meson.build b/scipy/optimize/_trlib/meson.build
@@ -8,7 +8,7 @@ _trlib = py3.extension_module('_trlib',
     'trlib_tri_factor.c'
   ],
   c_args: cython_c_args,
-  dependencies: [lapack],
+  dependencies: [lapack, blas],
   include_directories: [
     inc_np,
     '../../_lib',

diff --git a/scipy/optimize/meson.build b/scipy/optimize/meson.build
@@ -109,7 +109,7 @@ _lbfgsb = py3.extension_module('_lbfgsb',
   fortran_args: fortran_ignore_warnings,
   include_directories: [inc_np, inc_f2py],
   link_args: version_link_args,
-  dependencies: [lapack, fortranobject_dep],
+  dependencies: [lapack, blas, fortranobject_dep],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/optimize'

diff --git a/scipy/sparse/linalg/_dsolve/meson.build b/scipy/sparse/linalg/_dsolve/meson.build
@@ -199,7 +199,7 @@ _superlu = py3.extension_module('_superlu',
   link_with: [superlu_lib],
   include_directories: [incdir_numpy, 'SuperLU/SRC'],
   link_args: version_link_args,
-  dependencies: [blas, lapack],
+  dependencies: [lapack, blas],
   install: true,
   subdir: 'scipy/sparse/linalg/_dsolve'
 )

diff --git a/scipy/sparse/linalg/_eigen/arpack/meson.build b/scipy/sparse/linalg/_eigen/arpack/meson.build
@@ -103,7 +103,7 @@ _arpack = py3.extension_module('_arpack',
   link_with: [arpack_lib],
   include_directories: [incdir_numpy, incdir_f2py],
   link_args: version_link_args,
-  dependencies: [lapack, fortranobject_dep],
+  dependencies: [lapack, blas, fortranobject_dep],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/sparse/linalg/_eigen/arpack'

diff --git a/scipy/sparse/linalg/_isolve/meson.build b/scipy/sparse/linalg/_isolve/meson.build
@@ -74,7 +74,7 @@ _iterative = py3.extension_module('_iterative',
   fortran_args: fortran_ignore_warnings,
   include_directories: [inc_np, inc_f2py],
   link_args: version_link_args,
-  dependencies: [lapack, fortranobject_dep],
+  dependencies: [lapack, blas, fortranobject_dep],
   install: true,
   link_language: 'fortran',
   subdir: 'scipy/sparse/linalg/_isolve'

diff --git a/scipy/sparse/linalg/_propack/meson.build b/scipy/sparse/linalg/_propack/meson.build
@@ -109,7 +109,7 @@ foreach ele: elements
     link_with: propack_lib,
     c_args: ['-U_OPENMP', _cpp_Wno_cpp],
     fortran_args: _fflag_Wno_maybe_uninitialized,
-    dependencies: [lapack, fortranobject_dep],
+    dependencies: [lapack, blas, fortranobject_dep],
     include_directories: [inc_np, inc_f2py],
     link_args: version_link_args,
     install: true,

diff --git a/scipy/special/_faddeeva.cxx b/scipy/special/_faddeeva.cxx
@@ -1,3 +1,4 @@
+#include <pyconfig.h>
 #include <complex>
 #include <cmath>
 

diff --git a/scipy/special/_faddeeva.h b/scipy/special/_faddeeva.h
@@ -9,6 +9,7 @@
 #define EXTERN_C_END
 #endif
 
+#include <pyconfig.h>
 #include <complex>
 #include <Python.h>
 

diff --git a/scipy/special/wright.hh b/scipy/special/wright.hh
@@ -1,6 +1,7 @@
 #ifndef WRIGHT_HH
 #define WRIGHT_HH
 
+#include <pyconfig.h>
 #include <complex>
 
 namespace wright {