From d0aa69bee4cd0c3412a99bc61ec5c242e5f7bfaa Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Wed, 15 May 2024 18:37:57 +0530
Subject: [PATCH 01/23] Set `MACOSX_DEPLOYMENT_TARGET` for prerequisites

---
 .github/workflows/publish_pypi.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index fb4a203e5d..fc233d9423 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -115,6 +115,9 @@ jobs:
       # sometimes gfortran cannot be found, so reinstall gcc just to be sure
       - name: Install SuiteSparse and SUNDIALS on macOS
         if: matrix.os == 'macos-12'
+        # cibuildwheel sets this, but not for prerequisite C++ deps
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 10.9
         run: |
           brew install graphviz libomp
           brew reinstall gcc
@@ -163,6 +166,9 @@ jobs:
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
       - name: Install SuiteSparse and SUNDIALS on macOS
+        # cibuildwheel sets this, but not for prerequisite C++ deps
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 11.0
         run: |
           brew install graphviz libomp
           brew reinstall gcc

From 9ea58f31439749500ac4d555fcaec94fa47d23db Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 00:42:09 +0530
Subject: [PATCH 02/23] Remove previously set environment variables

---
 .github/workflows/publish_pypi.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index fc233d9423..fb4a203e5d 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -115,9 +115,6 @@ jobs:
       # sometimes gfortran cannot be found, so reinstall gcc just to be sure
       - name: Install SuiteSparse and SUNDIALS on macOS
         if: matrix.os == 'macos-12'
-        # cibuildwheel sets this, but not for prerequisite C++ deps
-        env:
-          MACOSX_DEPLOYMENT_TARGET: 10.9
         run: |
           brew install graphviz libomp
           brew reinstall gcc
@@ -166,9 +163,6 @@ jobs:
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
       - name: Install SuiteSparse and SUNDIALS on macOS
-        # cibuildwheel sets this, but not for prerequisite C++ deps
-        env:
-          MACOSX_DEPLOYMENT_TARGET: 11.0
         run: |
           brew install graphviz libomp
           brew reinstall gcc

From 5c724f1f4a905c2dad1653d86459392db25a8303 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 00:43:47 +0530
Subject: [PATCH 03/23] Remove Homebrew libomp installations

---
 .github/workflows/publish_pypi.yml       | 4 ++--
 .github/workflows/run_periodic_tests.yml | 2 +-
 .github/workflows/test_on_push.yml       | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index fb4a203e5d..740c0766dd 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -116,7 +116,7 @@ jobs:
       - name: Install SuiteSparse and SUNDIALS on macOS
         if: matrix.os == 'macos-12'
         run: |
-          brew install graphviz libomp
+          brew install graphviz
           brew reinstall gcc
           python -m pip install cmake wget
           python scripts/install_KLU_Sundials.py
@@ -164,7 +164,7 @@ jobs:
 
       - name: Install SuiteSparse and SUNDIALS on macOS
         run: |
-          brew install graphviz libomp
+          brew install graphviz
           brew reinstall gcc
           python -m pip install cmake pipx
           python scripts/install_KLU_Sundials.py
diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
index 671d2b371d..848297241e 100644
--- a/.github/workflows/run_periodic_tests.yml
+++ b/.github/workflows/run_periodic_tests.yml
@@ -68,7 +68,7 @@ jobs:
         if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
         run: |
           brew analytics off
-          brew install graphviz libomp
+          brew install graphviz
           brew reinstall gcc
 
       - name: Install Windows system dependencies
diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index f79bc61ddf..2f56f501eb 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -74,7 +74,7 @@ jobs:
         # sometimes gfortran cannot be found, so reinstall gcc just to be sure
         run: |
           brew analytics off
-          brew install graphviz libomp
+          brew install graphviz
           brew reinstall gcc
 
       - name: Install Windows system dependencies
@@ -209,7 +209,7 @@ jobs:
         # sometimes gfortran cannot be found, so reinstall gcc just to be sure
         run: |
           brew analytics off
-          brew install graphviz libomp
+          brew install graphviz
           brew reinstall gcc
 
       - name: Install Windows system dependencies

From 580f5ad09a5d4e313e42ecd759b111d2cddb0601 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 00:44:14 +0530
Subject: [PATCH 04/23] Ignore `pybamm-requires` OpenMP downloads

---
 .gitignore | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.gitignore b/.gitignore
index 03750e18b2..6f1f201617 100644
--- a/.gitignore
+++ b/.gitignore
@@ -137,3 +137,7 @@ results/
 
 # tests
 test_callback.log
+
+# openmp downloads
+install_KLU_Sundials/openmp-*
+install_KLU_Sundials/usr/

From 4efd259e8102bb191a471f2d6106c845f119a11d Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 00:50:09 +0530
Subject: [PATCH 05/23] Rework docs to add OpenMP instructions

---
 .../installation/install-from-source.rst        | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/docs/source/user_guide/installation/install-from-source.rst b/docs/source/user_guide/installation/install-from-source.rst
index ea664b4a5b..a2a7637c9e 100644
--- a/docs/source/user_guide/installation/install-from-source.rst
+++ b/docs/source/user_guide/installation/install-from-source.rst
@@ -43,11 +43,11 @@ You can install the above with
 
 	Where ``X`` is the version sub-number.
 
-.. tab:: MacOS
+.. tab:: macOS
 
 	.. code:: bash
 
-		brew install python openblas gcc gfortran graphviz libomp cmake pandoc
+		brew install python openblas gcc gfortran graphviz cmake pandoc
 
 .. note::
 
@@ -82,8 +82,9 @@ If you are running windows, you can simply skip this section and jump to :ref:`p
 	  # in the PyBaMM/ directory
 	  nox -s pybamm-requires
 
-This will download, compile and install the SuiteSparse and SUNDIALS libraries.
-Both libraries are installed in ``~/.local``.
+This will download, compile and install the SuiteSparse and SUNDIALS (with OpenMP) libraries
+and the ``pybind11`` headers.
+SuiteSparse and SUNDIALS are installed in ``~/.local`` by default.
 
 For users requiring more control over the installation process, the ``pybamm-requires`` session supports additional command-line arguments:
 
@@ -110,7 +111,7 @@ If you'd rather do things yourself,
 
 1. Make sure you have CMake installed
 2. Compile and install SuiteSparse (PyBaMM only requires the ``KLU`` component).
-3. Compile and install SUNDIALS.
+3. Compile and install SUNDIALS with `OpenMP support <https://mac.r-project.org/openmp/>`_.
 4. Clone the pybind11 repository in the ``PyBaMM/`` directory (make sure the directory is named ``pybind11``).
 
 
@@ -315,12 +316,12 @@ source files to your current directory.
 ``ValueError: Integrator name ida does not exist``, or
 ``ValueError: Integrator name cvode does not exist``.
 
-**Solution:** This could mean that you have not installed
-``scikits.odes`` correctly, check the instructions given above and make
+**Solution:** This could mean that you have not linked to
+SUNDIALS correctly, check the instructions given above and make
 sure each command was successful.
 
 One possibility is that you have not set your ``LD_LIBRARY_PATH`` to
-point to the sundials library, type ``echo $LD_LIBRARY_PATH`` and make
+point to the SUNDIALS library, type ``echo $LD_LIBRARY_PATH`` and make
 sure one of the directories printed out corresponds to where the
 SUNDIALS libraries are located.
 

From 0c8a9293df2e726cf84ae6b0d834b9fc3c9441cc Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 00:51:26 +0530
Subject: [PATCH 06/23] Download LLVM-OpenMP on macOS

---
 scripts/install_KLU_Sundials.py | 110 ++++++++++++++++++++++++++------
 1 file changed, 90 insertions(+), 20 deletions(-)

diff --git a/scripts/install_KLU_Sundials.py b/scripts/install_KLU_Sundials.py
index 6224e40776..620ea54d1d 100755
--- a/scripts/install_KLU_Sundials.py
+++ b/scripts/install_KLU_Sundials.py
@@ -14,18 +14,35 @@
 
 SUITESPARSE_VERSION = "6.0.3"
 SUNDIALS_VERSION = "6.5.0"
+
 SUITESPARSE_URL = f"https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v{SUITESPARSE_VERSION}.tar.gz"
 SUNDIALS_URL = f"https://github.com/LLNL/sundials/releases/download/v{SUNDIALS_VERSION}/sundials-{SUNDIALS_VERSION}.tar.gz"
+
 SUITESPARSE_CHECKSUM = (
     "7111b505c1207f6f4bd0be9740d0b2897e1146b845d73787df07901b4f5c1fb7"
 )
 SUNDIALS_CHECKSUM = "4e0b998dff292a2617e179609b539b511eb80836f5faacf800e688a886288502"
+
+# universal binaries for macOS 11.0 and later; sourced from https://mac.r-project.org/openmp/
+OPENMP_VERSION = "16.0.4"
+OPENMP_URL = (
+    f"https://mac.r-project.org/openmp/openmp-{OPENMP_VERSION}-darwin20-Release.tar.gz"
+)
+OPENMP_CHECKSUM = "a763f0bdc9115c4f4933accc81f514f3087d56d6528778f38419c2a0d2231972"
+
+
 DEFAULT_INSTALL_DIR = os.path.join(os.getenv("HOME"), ".local")
 
 
 def safe_remove_dir(path):
-    if os.path.exists(path):
-        shutil.rmtree(path)
+    """Remove a directory or file if it exists."""
+    try:
+        if os.path.isfile(path):
+            os.remove(path)
+        elif os.path.isdir(path):
+            shutil.rmtree(path)
+    except Exception as e:
+        print(f"Error while removing {path}: {e}")
 
 
 def install_suitesparse(download_dir):
@@ -93,23 +110,13 @@ def install_sundials(download_dir, install_dir):
     # try to find OpenMP on mac
     if platform.system() == "Darwin":
         # flags to find OpenMP on mac
-        if platform.processor() == "arm":
-            OpenMP_C_FLAGS = (
-                "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include"
-            )
-            OpenMP_C_LIB_NAMES = "omp"
-            OpenMP_omp_LIBRARY = "/opt/homebrew/opt/libomp/lib/libomp.dylib"
-        elif platform.processor() == "i386":
-            OpenMP_C_FLAGS = "-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include"
-            OpenMP_C_LIB_NAMES = "omp"
-            OpenMP_omp_LIBRARY = "/usr/local/opt/libomp/lib/libomp.dylib"
-        else:
-            raise NotImplementedError(
-                f"Unsupported processor architecture: {platform.processor()}. Only 'arm' and 'i386' architectures are supported."
-            )
+        OpenMP_C_FLAGS = f"-Xpreprocessor -fopenmp -lomp -L{os.path.join(KLU_LIBRARY_DIR)} -I{os.path.join(KLU_INCLUDE_DIR)}"
+        OpenMP_C_LIB_NAMES = "omp"
+        OpenMP_omp_LIBRARY = os.path.join(KLU_LIBRARY_DIR, "libomp.dylib")
 
         cmake_args += [
             "-DOpenMP_C_FLAGS=" + OpenMP_C_FLAGS,
+            "-DOpenMP_CXX_FLAGS=" + OpenMP_C_FLAGS,
             "-DOpenMP_C_LIB_NAMES=" + OpenMP_C_LIB_NAMES,
             "-DOpenMP_omp_LIBRARY=" + OpenMP_omp_LIBRARY,
         ]
@@ -130,6 +137,36 @@ def install_sundials(download_dir, install_dir):
     subprocess.run(make_cmd, cwd=build_dir, check=True)
 
 
+# relevant for macOS only because recent Xcode Clang does not include OpenMP headers.
+# Other compilers (e.g. GCC) include OpenMP specification by default.
+def set_up_openmp(download_dir, install_dir):
+    print("-" * 10, "Extracting OpenMP archive", "-" * 40)
+
+    openmp_dir = f"openmp-{OPENMP_VERSION}"
+    openmp_src = os.path.join(download_dir, openmp_dir)
+
+    # extract OpenMP archive
+    with tarfile.open(
+        os.path.join(download_dir, f"{openmp_dir}-darwin20-Release.tar.gz")
+    ) as tar:
+        tar.extractall(openmp_src)
+
+    # create directories
+    os.makedirs(os.path.join(install_dir, "lib"), exist_ok=True)
+    os.makedirs(os.path.join(install_dir, "include"), exist_ok=True)
+
+    # copy files
+    shutil.copy(
+        os.path.join(openmp_src, "usr", "local", "lib", "libomp.dylib"),
+        os.path.join(install_dir, "lib"),
+    )
+    for file in os.listdir(os.path.join(openmp_src, "usr", "local", "include")):
+        shutil.copy(
+            os.path.join(openmp_src, "usr", "local", "include", file),
+            os.path.join(install_dir, "include"),
+        )
+
+
 def check_libraries_installed(install_dir):
     # Define the directories to check for SUNDIALS and SuiteSparse libraries
     lib_dirs = [install_dir]
@@ -177,7 +214,7 @@ def check_libraries_installed(install_dir):
         suitesparse_files = [file + ".dylib" for file in suitesparse_files]
     else:
         raise NotImplementedError(
-            f"Unsupported operating system: {platform.system()}. This script currently supports only Linux and macOS."
+            f"Unsupported operating system: {platform.system()}. This script supports only Linux and macOS."
         )
 
     suitesparse_lib_found = True
@@ -199,6 +236,16 @@ def check_libraries_installed(install_dir):
     return sundials_lib_found, suitesparse_lib_found
 
 
+def check_openmp_installed_on_macos(install_dir):
+    openmp_lib_found = isfile(join(install_dir, "lib", "libomp.dylib"))
+    openmp_headers_found = isfile(join(install_dir, "include", "omp.h"))
+    if not openmp_lib_found or not openmp_headers_found:
+        print("libomp.dylib or omp.h not found. Proceeding with OpenMP installation.")
+    else:
+        print(f"libomp.dylib and omp.h found in {install_dir}.")
+    return openmp_lib_found
+
+
 def calculate_sha256(file_path):
     sha256_hash = hashlib.sha256()
     with open(file_path, "rb") as f:
@@ -266,6 +313,9 @@ def parallel_download(urls, download_dir):
 # Build in parallel wherever possible
 os.environ["CMAKE_BUILD_PARALLEL_LEVEL"] = str(cpu_count())
 
+# Set macOS environment variables for compatibility
+os.environ["MACOSX_DEPLOYMENT_TARGET"] = "11.0"
+
 # Create download directory in PyBaMM dir
 pybamm_dir = os.path.split(os.path.abspath(os.path.dirname(__file__)))[0]
 download_dir = os.path.join(pybamm_dir, "install_KLU_Sundials")
@@ -274,7 +324,7 @@ def parallel_download(urls, download_dir):
 
 # Get installation location
 parser = argparse.ArgumentParser(
-    description="Download, compile and install Sundials and SuiteSparse."
+    description="Download, compile and install SUNDIALS and SuiteSparse."
 )
 parser.add_argument(
     "--force",
@@ -296,10 +346,20 @@ def parallel_download(urls, download_dir):
     safe_remove_dir(os.path.join(download_dir, "build_sundials"))
     safe_remove_dir(os.path.join(download_dir, f"SuiteSparse-{SUITESPARSE_VERSION}"))
     safe_remove_dir(os.path.join(download_dir, f"sundials-{SUNDIALS_VERSION}"))
-    sundials_found, suitesparse_found = False, False
+    if platform.system() == "Darwin":
+        safe_remove_dir(os.path.join(install_dir, "lib", "libomp.dylib"))
+        safe_remove_dir(os.path.join(install_dir, "include", "omp.h"))
+        sundials_found, suitesparse_found, openmp_found = False, False, False
+    else:
+        sundials_found, suitesparse_found = False, False
 else:
     # Check whether the libraries are installed
-    sundials_found, suitesparse_found = check_libraries_installed(install_dir)
+    if platform.system() == "Darwin":
+        sundials_found, suitesparse_found = check_libraries_installed(install_dir)
+        openmp_found = check_openmp_installed_on_macos(install_dir)
+    else:  # Linux
+        sundials_found, suitesparse_found = check_libraries_installed(install_dir)
+
 
 if __name__ == "__main__":
     # Determine which libraries to download based on whether they were found
@@ -312,12 +372,22 @@ def parallel_download(urls, download_dir):
             ],
             download_dir,
         )
+
+        if platform.system() == "Darwin" and not openmp_found:
+            download_extract_library(OPENMP_URL, OPENMP_CHECKSUM, download_dir)
+            set_up_openmp(download_dir, install_dir)
+
         install_suitesparse(download_dir)
         install_sundials(download_dir, install_dir)
+
     else:
         if not sundials_found:
             # Only SUNDIALS is missing, download and install it
             parallel_download([(SUNDIALS_URL, SUNDIALS_CHECKSUM)], download_dir)
+            if platform.system() == "Darwin" and not openmp_found:
+                download_extract_library(OPENMP_URL, OPENMP_CHECKSUM, download_dir)
+                set_up_openmp(download_dir, install_dir)
+            # openmp needed for sundials on macOS
             install_sundials(download_dir, install_dir)
         if not suitesparse_found:
             # Only SuiteSparse is missing, download and install it

From b55169cb74cccd1ca52346466613d8e35137e30a Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 01:03:26 +0530
Subject: [PATCH 07/23] Remove unused compiler argument

---
 scripts/install_KLU_Sundials.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/install_KLU_Sundials.py b/scripts/install_KLU_Sundials.py
index 620ea54d1d..762596d6c7 100755
--- a/scripts/install_KLU_Sundials.py
+++ b/scripts/install_KLU_Sundials.py
@@ -116,7 +116,6 @@ def install_sundials(download_dir, install_dir):
 
         cmake_args += [
             "-DOpenMP_C_FLAGS=" + OpenMP_C_FLAGS,
-            "-DOpenMP_CXX_FLAGS=" + OpenMP_C_FLAGS,
             "-DOpenMP_C_LIB_NAMES=" + OpenMP_C_LIB_NAMES,
             "-DOpenMP_omp_LIBRARY=" + OpenMP_omp_LIBRARY,
         ]

From 6fb8ef02ef144d225bec2c177a2905f8fc912645 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 01:16:24 +0530
Subject: [PATCH 08/23] Fix rpath for libomp dylib at wheel repair

---
 .github/workflows/publish_pypi.yml |  8 ++++++--
 scripts/fix_libomp_rpath_macos.py  | 19 +++++++++++++++++++
 2 files changed, 25 insertions(+), 2 deletions(-)
 create mode 100644 scripts/fix_libomp_rpath_macos.py

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 740c0766dd..c9c404da1e 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -139,7 +139,9 @@ jobs:
         env:
           CIBW_BEFORE_BUILD_MACOS: >
             python -m pip install --upgrade cmake casadi setuptools wheel
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
+            python scripts/fix_macos_wheel.py
+            delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for ${{ matrix.os }}
@@ -173,7 +175,9 @@ jobs:
         run: python -m pipx run cibuildwheel --output-dir wheelhouse
         env:
           CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
-          CIBW_REPAIR_WHEEL_COMMAND: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
+            python scripts/fix_libomp_rpath_macos.py
+            delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64
diff --git a/scripts/fix_libomp_rpath_macos.py b/scripts/fix_libomp_rpath_macos.py
new file mode 100644
index 0000000000..6f92719645
--- /dev/null
+++ b/scripts/fix_libomp_rpath_macos.py
@@ -0,0 +1,19 @@
+# A helper script to fix the rpath of the OpenMP dynamic library. This
+# is to be used when building the wheels for PyBaMM on macOS (on both
+# amd64 and arm64 architectures).
+
+import os
+import subprocess
+
+homedir = os.path.expanduser("~")
+libomp_path = os.path.join(homedir, ".local/lib/libomp.dylib")
+
+subprocess.run(
+    [
+        "install_name_tool",
+        "-change",
+        "/usr/local/lib/libomp.dylib",
+        libomp_path,
+        libomp_path,
+    ]
+)

From 9185c355312d11ced582d6f9bd51308f74678d2d Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 01:18:21 +0530
Subject: [PATCH 09/23] Fix a failing link

---
 .lycheeignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.lycheeignore b/.lycheeignore
index 338303b4ba..1543b69f03 100644
--- a/.lycheeignore
+++ b/.lycheeignore
@@ -1,6 +1,7 @@
 # a list of links/files to be ignored by lychee link checker (see workflow file)
 https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v%7BSUITESPARSE_VERSION%7D.tar.gz
 https://github.com/LLNL/sundials/releases/download/v%7BSUNDIALS_VERSION%7D/sundials-%7BSUNDIALS_VERSION%7D.tar.gz
+https://mac.r-project.org/openmp/openmp-%7BOPENMP_VERSION%7D-darwin20-Release.tar.gz
 
 # Errors in docs/source/user_guide/getting_started.md
 file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/api_docs

From f907ca655cc4f7f03104c0926420f396dd773205 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 01:27:53 +0530
Subject: [PATCH 10/23] Revert "Fix rpath for libomp dylib at wheel repair"

This reverts commit 6fb8ef02ef144d225bec2c177a2905f8fc912645.
---
 .github/workflows/publish_pypi.yml |  8 ++------
 scripts/fix_libomp_rpath_macos.py  | 19 -------------------
 2 files changed, 2 insertions(+), 25 deletions(-)
 delete mode 100644 scripts/fix_libomp_rpath_macos.py

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index c9c404da1e..740c0766dd 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -139,9 +139,7 @@ jobs:
         env:
           CIBW_BEFORE_BUILD_MACOS: >
             python -m pip install --upgrade cmake casadi setuptools wheel
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
-            python scripts/fix_macos_wheel.py
-            delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for ${{ matrix.os }}
@@ -175,9 +173,7 @@ jobs:
         run: python -m pipx run cibuildwheel --output-dir wheelhouse
         env:
           CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
-            python scripts/fix_libomp_rpath_macos.py
-            delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_REPAIR_WHEEL_COMMAND: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64
diff --git a/scripts/fix_libomp_rpath_macos.py b/scripts/fix_libomp_rpath_macos.py
deleted file mode 100644
index 6f92719645..0000000000
--- a/scripts/fix_libomp_rpath_macos.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# A helper script to fix the rpath of the OpenMP dynamic library. This
-# is to be used when building the wheels for PyBaMM on macOS (on both
-# amd64 and arm64 architectures).
-
-import os
-import subprocess
-
-homedir = os.path.expanduser("~")
-libomp_path = os.path.join(homedir, ".local/lib/libomp.dylib")
-
-subprocess.run(
-    [
-        "install_name_tool",
-        "-change",
-        "/usr/local/lib/libomp.dylib",
-        libomp_path,
-        libomp_path,
-    ]
-)

From 77e33e2cdac4eb424f3c825153740551d86b46a1 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 01:55:26 +0530
Subject: [PATCH 11/23] Fix RPATHs for SuiteSparse and libomp

---
 scripts/install_KLU_Sundials.py | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/scripts/install_KLU_Sundials.py b/scripts/install_KLU_Sundials.py
index 762596d6c7..0bbdcc3ce6 100755
--- a/scripts/install_KLU_Sundials.py
+++ b/scripts/install_KLU_Sundials.py
@@ -68,11 +68,11 @@ def install_suitesparse(download_dir):
     env = os.environ.copy()
     for libdir in ["SuiteSparse_config", "AMD", "COLAMD", "BTF", "KLU"]:
         build_dir = os.path.join(suitesparse_src, libdir)
-        # We want to ensure that libsuitesparseconfig.dylib is not repeated in
-        # multiple paths at the time of wheel repair. Therefore, it should not be
-        # built with an RPATH since it is copied to the install prefix.
+        # Set an RPATH in order for libsuitesparseconfig.dylib to find libomp.dylib
         if libdir == "SuiteSparse_config":
-            env["CMAKE_OPTIONS"] = f"-DCMAKE_INSTALL_PREFIX={install_dir}"
+            env["CMAKE_OPTIONS"] = (
+                f"-DCMAKE_INSTALL_PREFIX={install_dir} -DCMAKE_INSTALL_RPATH={install_dir}/lib"
+            )
         else:
             # For AMD, COLAMD, BTF and KLU; do not set a BUILD RPATH but use an
             # INSTALL RPATH in order to ensure that the dynamic libraries are found
@@ -165,6 +165,17 @@ def set_up_openmp(download_dir, install_dir):
             os.path.join(install_dir, "include"),
         )
 
+    # fix rpath; for some reason the downloaded dylib has an absolute path
+    # to /usr/local/lib/, so use self-referential rpath
+    subprocess.check_call(
+        [
+            "install_name_tool",
+            "-id",
+            "@rpath/libomp.dylib",
+            f"{os.path.join(install_dir, 'lib', 'libomp.dylib')}",
+        ]
+    )
+
 
 def check_libraries_installed(install_dir):
     # Define the directories to check for SUNDIALS and SuiteSparse libraries

From 092af70895239015b740eabdde8eecca3ca6bd46 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 02:18:02 +0530
Subject: [PATCH 12/23] 11.1 for arm64 macOS and 11.0 for amd64 macOS

---
 scripts/install_KLU_Sundials.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/scripts/install_KLU_Sundials.py b/scripts/install_KLU_Sundials.py
index 0bbdcc3ce6..2b9d268bac 100755
--- a/scripts/install_KLU_Sundials.py
+++ b/scripts/install_KLU_Sundials.py
@@ -323,8 +323,12 @@ def parallel_download(urls, download_dir):
 # Build in parallel wherever possible
 os.environ["CMAKE_BUILD_PARALLEL_LEVEL"] = str(cpu_count())
 
-# Set macOS environment variables for compatibility
-os.environ["MACOSX_DEPLOYMENT_TARGET"] = "11.0"
+# Set macOS environment variables for compatibility. this is set to
+# 1. 11.1 for arm64 (libcasadi.dylib), and
+# 2. 11.0 for x86_64 (libomp.dylib)
+os.environ["MACOSX_DEPLOYMENT_TARGET"] = (
+    "11.1" if platform.machine == "arm64" else "11.0"
+)
 
 # Create download directory in PyBaMM dir
 pybamm_dir = os.path.split(os.path.abspath(os.path.dirname(__file__)))[0]

From b47c0343029e9e4894a495cf02003e002d8675c5 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 02:18:25 +0530
Subject: [PATCH 13/23] Set up Fortran compiler via GHA

---
 .github/workflows/publish_pypi.yml | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 740c0766dd..09eed0f0af 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -112,12 +112,15 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      # sometimes gfortran cannot be found, so reinstall gcc just to be sure
+      - uses: fortran-lang/setup-fortran@v1.6
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 13
+
       - name: Install SuiteSparse and SUNDIALS on macOS
         if: matrix.os == 'macos-12'
         run: |
-          brew install graphviz
-          brew reinstall gcc
           python -m pip install cmake wget
           python scripts/install_KLU_Sundials.py
 
@@ -137,6 +140,7 @@ jobs:
         if: matrix.os == 'macos-12'
         run: pipx run cibuildwheel --output-dir wheelhouse
         env:
+          MACOSX_DEPLOYMENT_TARGET: 11.1
           CIBW_BEFORE_BUILD_MACOS: >
             python -m pip install --upgrade cmake casadi setuptools wheel
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
@@ -162,10 +166,14 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
+      - uses: fortran-lang/setup-fortran@v1.6
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 13
+
       - name: Install SuiteSparse and SUNDIALS on macOS
         run: |
-          brew install graphviz
-          brew reinstall gcc
           python -m pip install cmake pipx
           python scripts/install_KLU_Sundials.py
 

From 4809a31b9f8cb5678541a19fad7277b3879f534d Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 02:25:22 +0530
Subject: [PATCH 14/23] Downgrade to gcc 12

---
 .github/workflows/publish_pypi.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 09eed0f0af..0bb2f38449 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -116,7 +116,7 @@ jobs:
         id: setup-fortran
         with:
           compiler: gcc
-          version: 13
+          version: 12
 
       - name: Install SuiteSparse and SUNDIALS on macOS
         if: matrix.os == 'macos-12'
@@ -170,7 +170,7 @@ jobs:
         id: setup-fortran
         with:
           compiler: gcc
-          version: 13
+          version: 12
 
       - name: Install SuiteSparse and SUNDIALS on macOS
         run: |
@@ -180,6 +180,7 @@ jobs:
       - name: Build wheels on macOS arm64
         run: python -m pipx run cibuildwheel --output-dir wheelhouse
         env:
+          MACOSX_DEPLOYMENT_TARGET: 11.1
           CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
           CIBW_REPAIR_WHEEL_COMMAND: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"

From b5d20cd9c8d4b6be06cd4a44ea0562a9406e7891 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 19:37:21 +0530
Subject: [PATCH 15/23] Try fix for macOS amd64 wheels first

---
 .github/workflows/publish_pypi.yml | 60 ++++++++++++++++++++++--------
 1 file changed, 45 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 0bb2f38449..60d6a0d6f5 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -112,18 +112,6 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      - uses: fortran-lang/setup-fortran@v1.6
-        id: setup-fortran
-        with:
-          compiler: gcc
-          version: 12
-
-      - name: Install SuiteSparse and SUNDIALS on macOS
-        if: matrix.os == 'macos-12'
-        run: |
-          python -m pip install cmake wget
-          python scripts/install_KLU_Sundials.py
-
       - name: Build wheels on Linux
         run: pipx run cibuildwheel --output-dir wheelhouse
         if: matrix.os == 'ubuntu-latest'
@@ -141,8 +129,50 @@ jobs:
         run: pipx run cibuildwheel --output-dir wheelhouse
         env:
           MACOSX_DEPLOYMENT_TARGET: 11.1
-          CIBW_BEFORE_BUILD_MACOS: >
-            python -m pip install --upgrade cmake casadi setuptools wheel
+          # Sourced from
+          # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
+          CIBW_BEFORE_ALL_MACOS: |
+            set -e -x
+
+            # download gfortran with proper macos minimum version (11.0)
+            curl -L https://github.com/isuruf/gcc/releases/download/gcc-11.3.0-2/gfortran-darwin-x86_64-native.tar.gz -o gfortran.tar.gz
+
+            GFORTRAN_SHA256=$(shasum --algorithm 256 gfortran.tar.gz)
+            KNOWN_SHA256="981367dd0ad4335613e91bbee453d60b6669f5d7e976d18c7bdb7f1966f26ae4  gfortran.tar.gz"
+            if [ "$GFORTRAN_SHA256" != "$KNOWN_SHA256" ]; then
+              echo "SHA256 mismatch for gfortran.tar.gz"
+              echo "expected: $KNOWN_SHA256"
+              echo "got: $GFORTRAN_SHA256"
+              exit 1
+            fi
+
+            mkdir -p gfortran_installed/
+            tar -xv -C gfortran_installed/ -f gfortran.tar.gz
+
+            export FC=$(pwd)/gfortran_installed/gfortran-darwin-x86_64-native/bin/gfortran
+            export PATH=$(pwd)/gfortran_installed/gfortran-darwin-x86_64-native/bin:$PATH
+
+            # link libgfortran.5.dylib, libgfortran.dylib, libquadmath.0.dylib, libquadmath.dylib, libgcc_s.1.dylib, libgcc_s.1.1.dylib
+            # and place them in $HOME/.local/lib, and then change rpath
+            # to $HOME/.local/lib
+
+            mkdir -p $HOME/.local/lib
+            lib_dir=$(pwd)/gfortran_installed/gfortran-darwin-x86_64-native/lib
+            for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.dylib libgcc_s.1.1.dylib; do
+              cp $lib_dir/$lib $HOME/.local/lib/
+              install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
+              # can be removed I think
+              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libgfortran.5.dylib
+              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libgfortran.dylib
+              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libquadmath.0.dylib
+              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libquadmath.dylib
+            done
+
+            export SDKROOT=${SDKROOT:-$(xcrun --show-sdk-path)}
+
+            python -m pip install cmake wget
+            python scripts/install_KLU_Sundials.py
+          CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade cmake casadi setuptools wheel delocate
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
@@ -182,7 +212,7 @@ jobs:
         env:
           MACOSX_DEPLOYMENT_TARGET: 11.1
           CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
-          CIBW_REPAIR_WHEEL_COMMAND: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64

From da25a4b5c3a0879dd20cfa92fd719947db9aeb54 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 20:43:15 +0530
Subject: [PATCH 16/23] Build on macos-13 image instead

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

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 60d6a0d6f5..a2902ba20c 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -99,7 +99,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-12]
+        os: [ubuntu-latest, macos-13]
     steps:
       - uses: actions/checkout@v4
         name: Check out PyBaMM repository
@@ -125,7 +125,7 @@ jobs:
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Build wheels on macOS amd64
-        if: matrix.os == 'macos-12'
+        if: matrix.os == 'macos-13'
         run: pipx run cibuildwheel --output-dir wheelhouse
         env:
           MACOSX_DEPLOYMENT_TARGET: 11.1

From 4bfe789b8c4781fdff221bc7087cf67fc5504f93 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 21:38:31 +0530
Subject: [PATCH 17/23] Debug further, try building against 11.0

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

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index a2902ba20c..d4c2dbfca9 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -128,7 +128,7 @@ jobs:
         if: matrix.os == 'macos-13'
         run: pipx run cibuildwheel --output-dir wheelhouse
         env:
-          MACOSX_DEPLOYMENT_TARGET: 11.1
+          MACOSX_DEPLOYMENT_TARGET: 11.0
           # Sourced from
           # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
           CIBW_BEFORE_ALL_MACOS: |

From 498151f1215308c13681bac3c7efa2719984e211 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 22:20:17 +0530
Subject: [PATCH 18/23] And now build for macOS arm64

---
 .github/workflows/publish_pypi.yml | 60 ++++++++++++++++++++++--------
 1 file changed, 45 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index d4c2dbfca9..794496684f 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -172,7 +172,7 @@ jobs:
 
             python -m pip install cmake wget
             python scripts/install_KLU_Sundials.py
-          CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade cmake casadi setuptools wheel delocate
+          CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade pip cmake casadi setuptools wheel delocate
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
@@ -196,22 +196,52 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      - uses: fortran-lang/setup-fortran@v1.6
-        id: setup-fortran
-        with:
-          compiler: gcc
-          version: 12
-
-      - name: Install SuiteSparse and SUNDIALS on macOS
-        run: |
-          python -m pip install cmake pipx
-          python scripts/install_KLU_Sundials.py
-
       - name: Build wheels on macOS arm64
-        run: python -m pipx run cibuildwheel --output-dir wheelhouse
+        run: |
+          python -m pip install cibuildwheel
+          python -m cibuildwheel --output-dir wheelhouse
         env:
-          MACOSX_DEPLOYMENT_TARGET: 11.1
-          CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
+          MACOSX_DEPLOYMENT_TARGET: 11.1  # CasADi requires macOS 11.1
+          # Sourced from
+          # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
+          CIBW_BEFORE_ALL_MACOS: |
+            set -e -x
+
+            # download gfortran with proper macos minimum version (11.0)
+            curl -L https://github.com/isuruf/gcc/releases/download/gcc-11.3.0-2/gfortran-darwin-arm64-native.tar.gz -o gfortran.tar.gz
+
+            GFORTRAN_SHA256=$(shasum --algorithm 256 gfortran.tar.gz)
+            KNOWN_SHA256="84364eee32ba843d883fb8124867e2bf61a0cd73b6416d9897ceff7b85a24604  gfortran.tar.gz"
+            if [ "$GFORTRAN_SHA256" != "$KNOWN_SHA256" ]; then
+              echo "SHA256 mismatch for gfortran.tar.gz"
+              echo "expected: $KNOWN_SHA256"
+              echo "got: $GFORTRAN_SHA256"
+              exit 1
+            fi
+
+            mkdir -p gfortran_installed/
+            tar -xv -C gfortran_installed/ -f gfortran.tar.gz
+
+            export FC=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/bin/gfortran
+            export PATH=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/bin:$PATH
+
+            # link libgfortran.5.dylib, libgfortran.dylib, libquadmath.0.dylib, libquadmath.dylib, libgcc_s.1.1.dylib
+            # and place them in $HOME/.local/lib, and then change rpath
+            # note: libgcc_s.1.dylib not present for arm64, skip for now
+            # to $HOME/.local/lib
+
+            mkdir -p $HOME/.local/lib
+            lib_dir=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/lib
+            for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.1.dylib; do
+              cp $lib_dir/$lib $HOME/.local/lib/
+              install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
+            done
+
+            export SDKROOT=${SDKROOT:-$(xcrun --show-sdk-path)}
+
+            python -m pip install cmake wget
+            python scripts/install_KLU_Sundials.py
+          CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade pip cmake casadi setuptools wheel delocate
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 

From 3c84d8dfff6d3664b1e118bc9635a603d5f7714f Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 22:29:32 +0530
Subject: [PATCH 19/23] Try building arm64 against 11.0

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

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 794496684f..e5d8a190c8 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -201,7 +201,7 @@ jobs:
           python -m pip install cibuildwheel
           python -m cibuildwheel --output-dir wheelhouse
         env:
-          MACOSX_DEPLOYMENT_TARGET: 11.1  # CasADi requires macOS 11.1
+          MACOSX_DEPLOYMENT_TARGET: 11.0
           # Sourced from
           # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
           CIBW_BEFORE_ALL_MACOS: |

From 3f822893223319ec0e162bb555014585ede2f223 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 23:20:01 +0530
Subject: [PATCH 20/23] Rename wheel from 11_1 to 11_0

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

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index e5d8a190c8..b41c190531 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -242,7 +242,10 @@ jobs:
             python -m pip install cmake wget
             python scripts/install_KLU_Sundials.py
           CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade pip cmake casadi setuptools wheel delocate
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          # Rename wheel for now: https://github.com/casadi/casadi/issues/3698
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
+            delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel} --require-target-macos-version 11.1
+            mv {dest_dir}/{wheel} | sed 's/macosx_11_1/macosx_11_0/' {dest_dir}/{wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64

From e0ad96ccd379cb7d1445d0a2516ed97913e1910e Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 23:49:54 +0530
Subject: [PATCH 21/23] Cleanup and fix up commands

---
 .github/workflows/publish_pypi.yml |  3 +--
 scripts/install_KLU_Sundials.py    | 13 +++----------
 2 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index b41c190531..e644e4d5be 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -242,10 +242,9 @@ jobs:
             python -m pip install cmake wget
             python scripts/install_KLU_Sundials.py
           CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade pip cmake casadi setuptools wheel delocate
-          # Rename wheel for now: https://github.com/casadi/casadi/issues/3698
+          # Use higher macOS target for now: https://github.com/casadi/casadi/issues/3698
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
             delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel} --require-target-macos-version 11.1
-            mv {dest_dir}/{wheel} | sed 's/macosx_11_1/macosx_11_0/' {dest_dir}/{wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64
diff --git a/scripts/install_KLU_Sundials.py b/scripts/install_KLU_Sundials.py
index 2b9d268bac..c0e046c48d 100755
--- a/scripts/install_KLU_Sundials.py
+++ b/scripts/install_KLU_Sundials.py
@@ -136,8 +136,8 @@ def install_sundials(download_dir, install_dir):
     subprocess.run(make_cmd, cwd=build_dir, check=True)
 
 
-# relevant for macOS only because recent Xcode Clang does not include OpenMP headers.
-# Other compilers (e.g. GCC) include OpenMP specification by default.
+# Relevant for macOS only because recent Xcode Clang versions do not include OpenMP headers.
+# Other compilers (e.g. GCC) include the OpenMP specification by default.
 def set_up_openmp(download_dir, install_dir):
     print("-" * 10, "Extracting OpenMP archive", "-" * 40)
 
@@ -323,13 +323,6 @@ def parallel_download(urls, download_dir):
 # Build in parallel wherever possible
 os.environ["CMAKE_BUILD_PARALLEL_LEVEL"] = str(cpu_count())
 
-# Set macOS environment variables for compatibility. this is set to
-# 1. 11.1 for arm64 (libcasadi.dylib), and
-# 2. 11.0 for x86_64 (libomp.dylib)
-os.environ["MACOSX_DEPLOYMENT_TARGET"] = (
-    "11.1" if platform.machine == "arm64" else "11.0"
-)
-
 # Create download directory in PyBaMM dir
 pybamm_dir = os.path.split(os.path.abspath(os.path.dirname(__file__)))[0]
 download_dir = os.path.join(pybamm_dir, "install_KLU_Sundials")
@@ -401,7 +394,7 @@ def parallel_download(urls, download_dir):
             if platform.system() == "Darwin" and not openmp_found:
                 download_extract_library(OPENMP_URL, OPENMP_CHECKSUM, download_dir)
                 set_up_openmp(download_dir, install_dir)
-            # openmp needed for sundials on macOS
+            # openmp needed for SUNDIALS on macOS
             install_sundials(download_dir, install_dir)
         if not suitesparse_found:
             # Only SuiteSparse is missing, download and install it

From 18dcbbd7455ab2c9308c075df7952979437461c4 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Thu, 16 May 2024 23:59:14 +0530
Subject: [PATCH 22/23] Rename wheel in dest dir instead

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

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index e644e4d5be..7411345081 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -245,6 +245,7 @@ jobs:
           # Use higher macOS target for now: https://github.com/casadi/casadi/issues/3698
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
             delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel} --require-target-macos-version 11.1
+            for file in {dest_dir}/*.whl; do mv "$file" "${file//macosx_11_1/macosx_11_0}"; done
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64

From 30a76b90c1b9ac91c32dec1eb7247356ed75e5f2 Mon Sep 17 00:00:00 2001
From: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Date: Fri, 17 May 2024 20:19:25 +0530
Subject: [PATCH 23/23] Cleanup plus references to SciPy license

---
 .github/workflows/publish_pypi.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 7411345081..01bf7ad95f 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -130,6 +130,7 @@ jobs:
         env:
           MACOSX_DEPLOYMENT_TARGET: 11.0
           # Sourced from
+          # License: BSD-3-Clause
           # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
           CIBW_BEFORE_ALL_MACOS: |
             set -e -x
@@ -161,11 +162,6 @@ jobs:
             for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.dylib libgcc_s.1.1.dylib; do
               cp $lib_dir/$lib $HOME/.local/lib/
               install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
-              # can be removed I think
-              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libgfortran.5.dylib
-              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libgfortran.dylib
-              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libquadmath.0.dylib
-              # install_name_tool -change $lib_dir/$lib $HOME/.local/lib/$lib $HOME/.local/lib/libquadmath.dylib
             done
 
             export SDKROOT=${SDKROOT:-$(xcrun --show-sdk-path)}
@@ -203,6 +199,7 @@ jobs:
         env:
           MACOSX_DEPLOYMENT_TARGET: 11.0
           # Sourced from
+          # License: BSD-3-Clause
           # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
           CIBW_BEFORE_ALL_MACOS: |
             set -e -x