From 0c739c2861e8044732795ce90be5104e23fd7e21 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Fri, 3 Feb 2023 20:33:12 -0500
Subject: [PATCH 01/28] Add Cygwin CI run

This probably uses setuptools instead of meson, but let's try this anyway.
---
 .github/workflows/cygwin.yml | 69 ++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 .github/workflows/cygwin.yml

diff --git a/.github/workflows/cygwin.yml b/.github/workflows/cygwin.yml
new file mode 100644
index 000000000000..7fab969c2de5
--- /dev/null
+++ b/.github/workflows/cygwin.yml
@@ -0,0 +1,69 @@
+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 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}"
+        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

From 6cb5d2d2a8da583b00990c8dabb6e1450da56636 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Fri, 3 Feb 2023 22:23:39 -0500
Subject: [PATCH 02/28] CI,FIX: Don't pip install scipy

I don't know how to tell SciPy to link to netlib blas and lapack.
---
 .github/workflows/cygwin.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cygwin.yml b/.github/workflows/cygwin.yml
index 7fab969c2de5..cd30b8290322 100644
--- a/.github/workflows/cygwin.yml
+++ b/.github/workflows/cygwin.yml
@@ -59,6 +59,7 @@ jobs:
         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 .

From 43b1341ad19ef5db7363c58c6163f0b084841391 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 08:00:03 -0500
Subject: [PATCH 03/28] CI,FIX: Install pytest-timeout before using.

---
 .github/workflows/cygwin.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin.yml b/.github/workflows/cygwin.yml
index cd30b8290322..a8a294985fb6 100644
--- a/.github/workflows/cygwin.yml
+++ b/.github/workflows/cygwin.yml
@@ -45,7 +45,7 @@ jobs:
           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 pybind11
+          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 ..

From 18d1958d4b6eb0885a536195cbf628fe8cd0f7c5 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 08:23:26 -0500
Subject: [PATCH 04/28] CI: Add Cygwin-Meson workflow

Actually test the build that people are complaining about.
---
 .github/workflows/cygwin_meson.yml | 174 +++++++++++++++++++++++++++++
 1 file changed, 174 insertions(+)
 create mode 100644 .github/workflows/cygwin_meson.yml

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
new file mode 100644
index 000000000000..647742583588
--- /dev/null
+++ b/.github/workflows/cygwin_meson.yml
@@ -0,0 +1,174 @@
+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/**
+
+permissions:
+   contents: read  # to fetch code (actions/checkout)
+
+env:
+  CCACHE_DIR: "${{ github.workspace }}/.ccache"
+  INSTALLDIR: "build-install"
+  CPPFLAGS: "-D_XOPEN_SOURCE=600"
+  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
+    # If using act to run CI locally the github object does not exist and the usual skipping should not be enforced
+    if: "github.repository == 'scipy/scipy' || github.repository == '' || github.repository == 'DWesl/scipy'"
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-minor-version: ['9']
+        maintenance-branch:
+          - ${{ contains(github.ref, 'maintenance/') || contains(github.base_ref, 'maintenance/') }}
+        exclude:
+          - maintenance-branch: true
+            python-version: '3.11-dev'
+    env:
+      PYTHONPATH: "/usr/local/lib/python3.${{ 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${{ matrix.python-minor-version }}-pytest
+            meson ninja cmake make git
+    - name: Fix git config
+        shell: bash.exe -eo pipefail -o igncr "{0}"
+        run: /usr/bin/git config --system --add safe.directory /cygdrive/d/a/*/scipy
+
+    - name: Install Python packages
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        python -m pip install numpy cython pytest pytest-xdist pytest-timeout pybind11 mpmath gmpy2 pythran ninja meson click rich-click doit pydevtool pooch
+    
+    - name:  Prepare compiler cache
+      id:    prep-ccache
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        mkdir -p "${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: |
+        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: |
+        pushd tools
+        python check_installation.py ${{ env.INSTALLDIR }}
+        ./check_pyext_symbol_hiding.sh ../build
+        popd
+    - name: Mypy
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        # Packages that are only needed for their annotations
+        python -m pip install -r mypy_requirements.txt
+        python -m pip install types-psutil pybind11 sphinx
+        python -u dev.py mypy
+    - name: Test SciPy
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: |
+        export OMP_NUM_THREADS=2
+        export SCIPY_USE_PROPACK=1
+        python dev.py --no-build test -j 2 -- --durations 10 --timeout=60
+
+  test_venv_install:
+    name: Pip install into venv
+    if: "github.repository == 'scipy/scipy' || github.repository == '' || github.repository == 'DWesl/scipy'"
+    runs-on: windows-latest
+    steps:
+    - run: git config --global core.autocrlf input
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: cygwin/cygwin-install-action@v3
+        with:
+          packages: >-
+            gcc-g++ gcc-fortran liblapack-devel libopenblas libmpfr-devel ccache swig libmpc-devel
+            libumfpack-devel libsliplu-devel libldl-devel libklu-devel libcxsparse-devel libcholmod-devel libamd-devel
+            python3${{ 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: Create venv, install SciPy
+      run: |
+        python -m venv ../venvs/scipy-venv
+        source ../venvs/scipy-venv/bin/activate
+        # Note that this uses build isolation. That's why we don't need build
+        # dependencies to be installed in the venv itself.
+        meson setup build -Dblas=blas -Dlapack=lapack --prefix=$(pwd)/${INSTALLDIR}
+        python -m pip install . -vv
+    - name: Basic imports and tests
+      run: |
+        source ../venvs/scipy-venv/bin/activate
+        cd ..
+        python -c "import scipy"
+        python -c "import scipy.linalg"
+        python -m pip install pytest
+        python -c "from scipy import cluster; cluster.test()"

From b792cf9a421111a01b9f130e363bd2de1d802297 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 08:41:51 -0500
Subject: [PATCH 05/28] CI,FIX: Fix syntax of Meson workflow file

---
 .github/workflows/cygwin_meson.yml | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 647742583588..5ae2933db41d 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -54,18 +54,19 @@ jobs:
         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${{ matrix.python-minor-version }}-pytest
-            meson ninja cmake make git
+      with:
+        packages: >-
+          gcc-g++ gcc-fortran liblapack-devel libopenblas libmpfr-devel ccache swig libmpc-devel
+          libumfpack-devel libsliplu-devel libldl-devel libklu-devel libcxsparse-devel libcholmod-devel libamd-devel
+          python3${{ 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

From 25bc80f06393efc55f00646c074d349b0e668a54 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 08:44:09 -0500
Subject: [PATCH 06/28] CI,FIX: Fix Cygwin-Meson workflow file syntax.

---
 .github/workflows/cygwin_meson.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 5ae2933db41d..bdd5d05ecce3 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -68,8 +68,8 @@ jobs:
           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
+      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}"

From bf020683ab021d56a419341b0c3997eca91dc692 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 08:46:04 -0500
Subject: [PATCH 07/28] CI,FIX: Fix syntax in Cygwin-Meson workflow file

---
 .github/workflows/cygwin_meson.yml | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index bdd5d05ecce3..bd03563c6089 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -140,22 +140,22 @@ jobs:
         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${{ matrix.python-minor-version }}-pytest
-            meson ninja cmake make git
+      with:
+        packages: >-
+          gcc-g++ gcc-fortran liblapack-devel libopenblas libmpfr-devel ccache swig libmpc-devel
+          libumfpack-devel libsliplu-devel libldl-devel libklu-devel libcxsparse-devel libcholmod-devel libamd-devel
+          python3${{ 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
+      shell: bash.exe -eo pipefail -o igncr "{0}"
+      run: /usr/bin/git config --system --add safe.directory /cygdrive/d/a/*/scipy
 
     - name: Create venv, install SciPy
       run: |

From 4a08a7f49f3ecb9dd81ac28724bebefaf8b55023 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 08:56:57 -0500
Subject: [PATCH 08/28] CI,FIX: Run venv tests in Cygwin shell.

---
 .github/workflows/cygwin_meson.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index bd03563c6089..ba22ca18f514 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -158,6 +158,7 @@ jobs:
       run: /usr/bin/git config --system --add safe.directory /cygdrive/d/a/*/scipy
 
     - name: Create venv, install SciPy
+      shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |
         python -m venv ../venvs/scipy-venv
         source ../venvs/scipy-venv/bin/activate
@@ -165,7 +166,9 @@ jobs:
         # dependencies to be installed in the venv itself.
         meson setup build -Dblas=blas -Dlapack=lapack --prefix=$(pwd)/${INSTALLDIR}
         python -m pip install . -vv
+
     - name: Basic imports and tests
+      shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |
         source ../venvs/scipy-venv/bin/activate
         cd ..

From d303abe22549d71e809e0eb1d09d5342e1901384 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 09:18:21 -0500
Subject: [PATCH 09/28] CI,DBG: Try to find failing command

It doesn't give me details.
---
 .github/workflows/cygwin_meson.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index ba22ca18f514..56ab5fb81fef 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -160,11 +160,15 @@ jobs:
     - name: Create venv, install SciPy
       shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |
+        echo Creating venv
         python -m venv ../venvs/scipy-venv
+        echo Activating venv
         source ../venvs/scipy-venv/bin/activate
+        echo Configuring blas and lapack
+        meson setup build -Dblas=blas -Dlapack=lapack --prefix=$(pwd)/${INSTALLDIR}
         # Note that this uses build isolation. That's why we don't need build
         # dependencies to be installed in the venv itself.
-        meson setup build -Dblas=blas -Dlapack=lapack --prefix=$(pwd)/${INSTALLDIR}
+        echo Installing SciPy
         python -m pip install . -vv
 
     - name: Basic imports and tests

From 5a2dfddcd5455302deee71dcbcaef4471cc9900a Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 09:44:22 -0500
Subject: [PATCH 10/28] CI,DBG: Try printing more debug info.

There's a consistent failure for no reason I can find.
---
 .github/workflows/cygwin_meson.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 56ab5fb81fef..aed68e762a28 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -160,8 +160,9 @@ jobs:
     - name: Create venv, install SciPy
       shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |
+        python -V
         echo Creating venv
-        python -m venv ../venvs/scipy-venv
+        python -v -m venv ../venvs/scipy-venv
         echo Activating venv
         source ../venvs/scipy-venv/bin/activate
         echo Configuring blas and lapack

From b7f8b4d360ba06f84dbc049b85f2e09e8b20f475 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 15:58:03 -0500
Subject: [PATCH 11/28] CI: Remove the Cygwin pip/venv tests

It wasn't actually running, just crashing during venv creation for no discernible reason.
---
 .github/workflows/cygwin_meson.yml | 53 ------------------------------
 1 file changed, 53 deletions(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index aed68e762a28..d7f3e61bbcb4 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -128,56 +128,3 @@ jobs:
         export OMP_NUM_THREADS=2
         export SCIPY_USE_PROPACK=1
         python dev.py --no-build test -j 2 -- --durations 10 --timeout=60
-
-  test_venv_install:
-    name: Pip install into venv
-    if: "github.repository == 'scipy/scipy' || github.repository == '' || github.repository == 'DWesl/scipy'"
-    runs-on: windows-latest
-    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${{ matrix.python-minor-version }}-pytest
-          meson ninja cmake make git
-
-    - name: Fix git config
-      shell: bash.exe -eo pipefail -o igncr "{0}"
-      run: /usr/bin/git config --system --add safe.directory /cygdrive/d/a/*/scipy
-
-    - name: Create venv, install SciPy
-      shell: bash.exe -eo pipefail -o igncr "{0}"
-      run: |
-        python -V
-        echo Creating venv
-        python -v -m venv ../venvs/scipy-venv
-        echo Activating venv
-        source ../venvs/scipy-venv/bin/activate
-        echo Configuring blas and lapack
-        meson setup build -Dblas=blas -Dlapack=lapack --prefix=$(pwd)/${INSTALLDIR}
-        # Note that this uses build isolation. That's why we don't need build
-        # dependencies to be installed in the venv itself.
-        echo Installing SciPy
-        python -m pip install . -vv
-
-    - name: Basic imports and tests
-      shell: bash.exe -eo pipefail -o igncr "{0}"
-      run: |
-        source ../venvs/scipy-venv/bin/activate
-        cd ..
-        python -c "import scipy"
-        python -c "import scipy.linalg"
-        python -m pip install pytest
-        python -c "from scipy import cluster; cluster.test()"

From 57cb6225bc4c475fa5de17bb3950aba2d1eb40a0 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 16:01:36 -0500
Subject: [PATCH 12/28] CI: Simplify the Cygwin-Meson build conditions

---
 .github/workflows/cygwin_meson.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index d7f3e61bbcb4..9e13836e592b 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -32,17 +32,10 @@ concurrency:
 jobs:
   test_meson:
     name: Cygwin Meson build
-    # If using act to run CI locally the github object does not exist and the usual skipping should not be enforced
-    if: "github.repository == 'scipy/scipy' || github.repository == '' || github.repository == 'DWesl/scipy'"
     runs-on: windows-latest
     strategy:
       matrix:
         python-minor-version: ['9']
-        maintenance-branch:
-          - ${{ contains(github.ref, 'maintenance/') || contains(github.base_ref, 'maintenance/') }}
-        exclude:
-          - maintenance-branch: true
-            python-version: '3.11-dev'
     env:
       PYTHONPATH: "/usr/local/lib/python3.${{ matrix.python-minor-version }}/site-packages"
 

From f8805d3b65bd6c736e4f9b5ec1d58a4363af104d Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 16:16:07 -0500
Subject: [PATCH 13/28] CI,FIX: Update meson

---
 .github/workflows/cygwin_meson.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 9e13836e592b..6b89c4373577 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -67,7 +67,8 @@ jobs:
     - 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 ninja meson click rich-click doit pydevtool pooch
+        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
     
     - name:  Prepare compiler cache
       id:    prep-ccache

From 6070d1f45c5a42294e2203299b02ba2e080e46d3 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 16:34:58 -0500
Subject: [PATCH 14/28] CI,FIX: Add /usr/local/bin to path

Still not sure why python defaults to /usr/local over /usr here, nor how best to change it.
---
 .github/workflows/cygwin_meson.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 6b89c4373577..89687ccd7374 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -96,6 +96,7 @@ jobs:
     - 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
@@ -105,6 +106,7 @@ jobs:
     - 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
@@ -112,6 +114,7 @@ jobs:
     - name: Mypy
       shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |
+        export PATH="/usr/local/bin:/usr/bin:/bin:/usr/lib/lapack"
         # Packages that are only needed for their annotations
         python -m pip install -r mypy_requirements.txt
         python -m pip install types-psutil pybind11 sphinx
@@ -119,6 +122,7 @@ jobs:
     - 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

From 2c1661f8ef9cd45b8701f909c8a81ec6eafa409d Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sat, 4 Feb 2023 16:53:21 -0500
Subject: [PATCH 15/28] CI,FIX: Update _XOPEN_SOURCE to 700 to match pyconfig.h

---
 .github/workflows/cygwin_meson.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 89687ccd7374..2b00aff2e76c 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -20,7 +20,7 @@ permissions:
 env:
   CCACHE_DIR: "${{ github.workspace }}/.ccache"
   INSTALLDIR: "build-install"
-  CPPFLAGS: "-D_XOPEN_SOURCE=600"
+  CPPFLAGS: "-D_XOPEN_SOURCE=700"
   SHELLOPTS: igncr
   CHERE_INVOKING: 1
   CYGWIN_NOWINPATH: 1

From 92c62a95a11c9dfa01a144fac044c3bd5307c43d Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sun, 5 Feb 2023 07:58:52 -0500
Subject: [PATCH 16/28] CI: Install tomli.

---
 .github/workflows/cygwin_meson.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 2b00aff2e76c..22bdb5d808f0 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -68,7 +68,7 @@ jobs:
       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
+        python -m pip install meson'>=0.64.0' ninja tomli
     
     - name:  Prepare compiler cache
       id:    prep-ccache

From 9610d10aeb0e3140164891999533ba89752cf6cc Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sun, 5 Feb 2023 12:05:50 -0500
Subject: [PATCH 17/28] BLD,BUG: Link flapack against blas.

Apparently there are blas symbols in the object.
Not entirely sure how they got there since the Windows build succeeds.
---
 scipy/linalg/meson.build | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scipy/linalg/meson.build b/scipy/linalg/meson.build
index ce383e5d51cb..c0f446e092fd 100644
--- a/scipy/linalg/meson.build
+++ b/scipy/linalg/meson.build
@@ -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'

From d221d44b5f4549b6af20717cb4fa6034cf57c68c Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sun, 5 Feb 2023 12:07:09 -0500
Subject: [PATCH 18/28] BUG: Include pyconfig.h before standard headers.

We need the visibility macros set before using them to define things.
---
 scipy/special/_faddeeva.cxx | 1 +
 scipy/special/_faddeeva.h   | 1 +
 scipy/special/wright.hh     | 1 +
 3 files changed, 3 insertions(+)

diff --git a/scipy/special/_faddeeva.cxx b/scipy/special/_faddeeva.cxx
index 6b619fb70bc5..7378b2770078 100644
--- 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
index d4ec3a755e2c..4def793ec61d 100644
--- 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
index ef168cba00ec..749f5f67af31 100644
--- 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 {

From b91928f3ea826f21a854813a1de3211f25771a01 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sun, 5 Feb 2023 17:42:04 -0500
Subject: [PATCH 19/28] BLD,BUG: Link more libraries against BLAS.

They call BLAS functions but do not link against BLAS, only Lapack.
---
 scipy/integrate/meson.build                   | 2 +-
 scipy/optimize/_trlib/meson.build             | 2 +-
 scipy/optimize/meson.build                    | 2 +-
 scipy/sparse/linalg/_eigen/arpack/meson.build | 2 +-
 scipy/sparse/linalg/_isolve/meson.build       | 2 +-
 scipy/sparse/linalg/_propack/meson.build      | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/scipy/integrate/meson.build b/scipy/integrate/meson.build
index 97c85b99dcf4..1b38a9ed9f46 100644
--- 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/optimize/_trlib/meson.build b/scipy/optimize/_trlib/meson.build
index 66fa0a39205c..c2cabb6c9796 100644
--- 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
index 05db6a680404..595febb1d896 100644
--- 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/_eigen/arpack/meson.build b/scipy/sparse/linalg/_eigen/arpack/meson.build
index bc77d411aabb..5b469a37914f 100644
--- 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
index 3009201862af..9af9fa146e6e 100644
--- 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
index 745d010ceb0a..898ecfb6b9be 100644
--- 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,

From e851779c273bec474bf06bf2586e8e6614f50ecd Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sun, 5 Feb 2023 18:50:15 -0500
Subject: [PATCH 20/28] CI: Don't run Mypy with Cygwin Meson

Linux-Meson already runs MyPy and should catch all errors.
I don't think that would catch many errors that Linux wouldn't.
Also, there's 17 errors in scipy.stats I don't feel like dealing with.
---
 .github/workflows/cygwin_meson.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 22bdb5d808f0..bd7e4f8542b1 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -111,14 +111,6 @@ jobs:
         python check_installation.py ${{ env.INSTALLDIR }}
         ./check_pyext_symbol_hiding.sh ../build
         popd
-    - name: Mypy
-      shell: bash.exe -eo pipefail -o igncr "{0}"
-      run: |
-        export PATH="/usr/local/bin:/usr/bin:/bin:/usr/lib/lapack"
-        # Packages that are only needed for their annotations
-        python -m pip install -r mypy_requirements.txt
-        python -m pip install types-psutil pybind11 sphinx
-        python -u dev.py mypy
     - name: Test SciPy
       shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |

From 19058034e676759079a8135c1f93ee5c33805480 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Sun, 5 Feb 2023 20:18:04 -0500
Subject: [PATCH 21/28] CI: Cygwin: Add an explicit "Does this import" test.

---
 .github/workflows/cygwin_meson.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index bd7e4f8542b1..009db368fd71 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -111,6 +111,13 @@ jobs:
         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
+        python -vvv -d "import scipy"
+        popd
     - name: Test SciPy
       shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |

From caa3b747c142a4b1cccab8ac1328b2aa82901f47 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Mon, 6 Feb 2023 10:31:42 -0500
Subject: [PATCH 22/28] CI: Properly set PYTHONPATH for import test.

---
 .github/workflows/cygwin_meson.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 009db368fd71..defff1bddd73 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -115,9 +115,12 @@ jobs:
       shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |
         export PATH="/usr/local/bin:/usr/bin:/bin:/usr/lib/lapack"
-        pushd build
+        pushd build-install
+        export PYTHONPATH="$(pwd)/lib/python3.${{ matrix.python-minor-version }}/site-packages/"
+        ls ${PYTHONPATH} ${PYTHONPATH}/scipy/*
         python -vvv -d "import scipy"
         popd
+
     - name: Test SciPy
       shell: bash.exe -eo pipefail -o igncr "{0}"
       run: |

From cbb27c8bf8110e323e8db524831728ef1e951db5 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Mon, 6 Feb 2023 16:11:49 -0500
Subject: [PATCH 23/28] CI,FIX: Fix scipy import check.

I forgot the -c to say the args were code, not a file.
---
 .github/workflows/cygwin_meson.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index defff1bddd73..177f484d8c51 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -118,7 +118,7 @@ jobs:
         pushd build-install
         export PYTHONPATH="$(pwd)/lib/python3.${{ matrix.python-minor-version }}/site-packages/"
         ls ${PYTHONPATH} ${PYTHONPATH}/scipy/*
-        python -vvv -d "import scipy"
+        python -vvv -d -c "import scipy"
         popd
 
     - name: Test SciPy

From 29778dcd5c222887552040cc888056c8bc51af2e Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Mon, 6 Feb 2023 18:51:13 -0500
Subject: [PATCH 24/28] BLD: Cygwin: Set Netlib reference as default
 BLAS/LAPACK.

There are no prebuilt development files for OpenBLAS, but linking
against the Netlib reference BLAS/LAPack files will usually pull in
the OpenBLAS BLAS at runtime.

I feel making people build and install OpenBLAS before they can
successfully run "pip install scipy" is the kind of thing SciPy is
trying to move away from.
---
 dev.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/dev.py b/dev.py
index 1594931996e0..c5659cedb4d5 100644
--- 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():

From ea3536db7172fbd0d50557e78c0d36ba6b02f68b Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Tue, 7 Feb 2023 00:10:29 -0500
Subject: [PATCH 25/28] BLD: Cygwin: Rebase libraries after dev.py install.

---
 dev.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/dev.py b/dev.py
index c5659cedb4d5..26f46274ec4c 100644
--- a/dev.py
+++ b/dev.py
@@ -554,6 +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
 

From 0091be6c2caf04d2720b5901528efc52c5eabf4f Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Tue, 7 Feb 2023 10:06:40 -0500
Subject: [PATCH 26/28] CI,FIX: Cygwin: Include failing imports in import test

It skipped this, before.
---
 .github/workflows/cygwin_meson.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 177f484d8c51..7fb22a587a87 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -118,7 +118,7 @@ jobs:
         pushd build-install
         export PYTHONPATH="$(pwd)/lib/python3.${{ matrix.python-minor-version }}/site-packages/"
         ls ${PYTHONPATH} ${PYTHONPATH}/scipy/*
-        python -vvv -d -c "import scipy"
+        python -vvv -d -c "import scipy.linalg"
         popd
 
     - name: Test SciPy

From db9ae7ce865362da73e42432f8a84a1971dd61c0 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Tue, 7 Feb 2023 12:53:10 -0500
Subject: [PATCH 27/28] CI,DBG: Allow manual trigger of Cygwin-Meson workflow

---
 .github/workflows/cygwin_meson.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cygwin_meson.yml b/.github/workflows/cygwin_meson.yml
index 7fb22a587a87..a24db6c56941 100644
--- a/.github/workflows/cygwin_meson.yml
+++ b/.github/workflows/cygwin_meson.yml
@@ -13,6 +13,7 @@ on:
     branches:
       - main
       - maintenance/**
+  workflow_dispatch:
 
 permissions:
    contents: read  # to fetch code (actions/checkout)

From 6d9ea8d981ff99ba966b51fcea91e8a0dbf02292 Mon Sep 17 00:00:00 2001
From: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Fri, 17 Feb 2023 10:03:29 -0500
Subject: [PATCH 28/28] BLD,BUG: Ensure proper dependency order for
 Lapack/BLAS.

Lapack depends on BLAS, so BLAS should be later in the dependency list.
---
 scipy/linalg/meson.build                | 6 +++---
 scipy/sparse/linalg/_dsolve/meson.build | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/scipy/linalg/meson.build b/scipy/linalg/meson.build
index c0f446e092fd..241a80272be2 100644
--- 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'
@@ -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/sparse/linalg/_dsolve/meson.build b/scipy/sparse/linalg/_dsolve/meson.build
index bf16643fe94c..4634cae247f8 100644
--- 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'
 )