From 7ac43a4c73b73d25774eb6b4d71f3765fa66f00b Mon Sep 17 00:00:00 2001
From: Chris Harris <cjh@lbl.gov>
Date: Fri, 13 Sep 2024 13:22:34 +0000
Subject: [PATCH 1/5] Add CIBW_BEFORE_ALL_MACOS to build HDF5

The brew installed version has a too new min os version
---
 .github/scripts/install.sh            |  2 +-
 .github/scripts/install_hdf5_macos.sh | 18 ++++++++++++++++++
 .github/workflows/build_wheels.yml    |  8 ++++++--
 3 files changed, 25 insertions(+), 3 deletions(-)
 create mode 100644 .github/scripts/install_hdf5_macos.sh

diff --git a/.github/scripts/install.sh b/.github/scripts/install.sh
index 1c2944b9..bed4f25a 100644
--- a/.github/scripts/install.sh
+++ b/.github/scripts/install.sh
@@ -6,5 +6,5 @@ pip install cibuildwheel
 if [[ $RUNNER_OS == "Windows" ]]; then
     git clone --recursive -b 3.3.9 --depth 1 https://gitlab.com/libeigen/eigen /c/eigen
 elif [[ $RUNNER_OS == "macOS" ]]; then
-    brew install eigen hdf5 ninja
+    brew install eigen ninja
 fi
diff --git a/.github/scripts/install_hdf5_macos.sh b/.github/scripts/install_hdf5_macos.sh
new file mode 100644
index 00000000..8e15ad93
--- /dev/null
+++ b/.github/scripts/install_hdf5_macos.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+set -ev
+
+VERSION="1.14.4"
+PATCH_LABEL="3"
+VERSION_PATH="hdf5_$VERSION.$PATCH_LABEL"
+NAME="hdf5-$VERSION-$PATCH_LABEL"
+TARBALL="$NAME.tar.gz"
+wget https://github.com/HDFGroup/hdf5/releases/download/$VERSION_PATH/$TARBALL
+tar -xzf $TARBALL
+mkdir build
+cd build
+cmake -GNinja ../$NAME -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF -DBUILD_TESTING:BOOL=OFF
+ninja
+sudo ninja install
+# We create a symlink to the install directory that doesn't include the version number, so
+# we can use it elsewhere without having to change the version number.
+sudo ln -s /usr/local/HDF_Group/HDF5/$VERSION /usr/local/HDF_Group/HDF5/current
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index dd6e66b0..6a5ecb9a 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -20,11 +20,13 @@ env:
 
   # Specify eigen location for windows, and force it to use python in the path...
   CIBW_ENVIRONMENT_WINDOWS: >
-    EXTRA_CMAKE_ARGS="-DEIGEN3_INCLUDE_DIR=C:\\eigen;-Dstempy_ENABLE_HDF5=OFF"
+    EXTRA_CMAKE_ARGS="-DEIGEN3_DIR=C:\\PROGRA~2\\Eigen3\\share\\eigen3\\cmake\\;-Dstempy_ENABLE_HDF5=OFF"
     USE_PYTHON_IN_PATH=1
 
   # Get cmake to use python in the path...
-  CIBW_ENVIRONMENT_MACOS: USE_PYTHON_IN_PATH=1
+  CIBW_ENVIRONMENT_MACOS: >
+    EXTRA_CMAKE_ARGS="-DHDF5_DIR=/usr/local/HDF_Group/HDF5/current/cmake"
+    USE_PYTHON_IN_PATH=1
 
   CIBW_BEFORE_TEST: pip install -r {project}/tests/requirements.txt
 
@@ -32,6 +34,8 @@ env:
 
   CIBW_ARCHS_MACOS: x86_64 arm64
 
+  CIBW_BEFORE_ALL_MACOS: . .github/scripts/install_hdf5_macos.sh
+
 # Use bash by default for the run command
 defaults:
   run:

From 02f864483a70b547bb928f187f2ca71b0a7c3154 Mon Sep 17 00:00:00 2001
From: Chris Harris <cjh@lbl.gov>
Date: Fri, 13 Sep 2024 16:35:12 +0000
Subject: [PATCH 2/5] Build Eigen on Windows

---
 .github/scripts/install.sh               | 2 +-
 .github/scripts/install_eigen_windows.sh | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)
 create mode 100644 .github/scripts/install_eigen_windows.sh

diff --git a/.github/scripts/install.sh b/.github/scripts/install.sh
index bed4f25a..fed93ab1 100644
--- a/.github/scripts/install.sh
+++ b/.github/scripts/install.sh
@@ -4,7 +4,7 @@ set -ev
 pip install cibuildwheel
 
 if [[ $RUNNER_OS == "Windows" ]]; then
-    git clone --recursive -b 3.3.9 --depth 1 https://gitlab.com/libeigen/eigen /c/eigen
+    .github/scripts/install_eigen_windows.sh
 elif [[ $RUNNER_OS == "macOS" ]]; then
     brew install eigen ninja
 fi
diff --git a/.github/scripts/install_eigen_windows.sh b/.github/scripts/install_eigen_windows.sh
new file mode 100644
index 00000000..b9c14b0b
--- /dev/null
+++ b/.github/scripts/install_eigen_windows.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -ev
+
+choco install ninja
+git clone --recursive -b 3.3.9 --depth 1 https://gitlab.com/libeigen/eigen /c/eigen
+mkdir /c/build
+cd /c/build
+cmake -GNinja /c/eigen
+ninja install

From 440464161c9b72fa5a2e3224ca4c3ed9dbbb9bf4 Mon Sep 17 00:00:00 2001
From: Chris Harris <cjh@lbl.gov>
Date: Fri, 13 Sep 2024 16:35:45 +0000
Subject: [PATCH 3/5] Use Eigen target

---
 CMakeLists.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e19343b3..2b00f851 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -30,7 +30,6 @@ include_directories(
 )
 
 find_package(Eigen3 REQUIRED)
-include_directories(SYSTEM ${EIGEN3_INCLUDE_DIR})
 
 find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module)
 add_subdirectory(${PROJECT_SOURCE_DIR}/thirdparty/pybind11)
@@ -39,7 +38,7 @@ set(PYBIND11_CPP_STANDARD "-std=c++14" CACHE STRING "")
 
 option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 
-set(_libs Threads::Threads)
+set(_libs Threads::Threads Eigen3::Eigen)
 
 option(stempy_ENABLE_MPI "Build with MPI" OFF)
 if (stempy_ENABLE_MPI)

From 28d2a73fdc113c9c35a9f86f61e037d91b5715de Mon Sep 17 00:00:00 2001
From: Chris Harris <cjh@lbl.gov>
Date: Fri, 13 Sep 2024 16:37:37 +0000
Subject: [PATCH 4/5] Relax pin on sckit-build

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8af79e3d..bcd2d41d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "scikit-build==0.14.1", "setuptools_scm[toml]"]
+requires = ["setuptools", "wheel", "scikit-build", "setuptools_scm[toml]"]

From deb307cb3161cc46831de1b79e077535cb8bb9e8 Mon Sep 17 00:00:00 2001
From: Chris Harris <cjh@lbl.gov>
Date: Fri, 13 Sep 2024 17:39:17 +0000
Subject: [PATCH 5/5] Bump actions versions

For depreciated Node.js version
---
 .github/workflows/build_wheels.yml | 2 +-
 .github/workflows/docker.yml       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 6a5ecb9a..d1362836 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -58,7 +58,7 @@ jobs:
           fetch-depth: 0
           submodules: recursive
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: '3.10'
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index f4a8dee6..1321c40f 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -25,7 +25,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           submodules: 'recursive'