From 3e30553fad3bbc637acc9f58ef3dc5889dbdfc68 Mon Sep 17 00:00:00 2001
From: Tony Craig <apcraig@users.noreply.github.com>
Date: Wed, 1 May 2024 12:56:21 -0700
Subject: [PATCH] Fix Github Actions for macos system update (#948)

Github Actions broke again after default macos system update.

Clang was not picking up the C system files. Had to change the implementation and add -isysroot to the CFLAGS option. At the same time, removed prior implementation where the system files were linked into /usr/local/include, this was no longer working.
---
 .github/workflows/test-cice.yml                   | 3 +--
 configuration/scripts/machines/Macros.conda_macos | 3 ++-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-cice.yml b/.github/workflows/test-cice.yml
index e7e41de11..20d944d88 100644
--- a/.github/workflows/test-cice.yml
+++ b/.github/workflows/test-cice.yml
@@ -46,7 +46,6 @@ jobs:
         run: |
           sudo xcode-select -r
           sudo xcode-select -s /Library/Developer/CommandLineTools
-          sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/
           echo "xcrun --show-sdk-path: $(xcrun --show-sdk-path)"
           echo "xcode-select -p: $(xcode-select -p)"
       - name: system info
@@ -55,7 +54,7 @@ jobs:
           type wget
           type curl
           type csh
-          echo "readlink \$(which csh): $(python -c 'import os, sys; print os.path.realpath(sys.argv[1])' $(which csh))"
+          echo "readlink \$(which csh): $(python -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' $(which csh))"
           echo "csh --version: $(csh --version)"
           echo "uname -a: $(uname -a)"
           echo "sw_vers: $(sw_vers)"
diff --git a/configuration/scripts/machines/Macros.conda_macos b/configuration/scripts/machines/Macros.conda_macos
index 6f26da0fc..f8b95aa76 100644
--- a/configuration/scripts/machines/Macros.conda_macos
+++ b/configuration/scripts/machines/Macros.conda_macos
@@ -47,7 +47,8 @@ SDKPATH = $(shell xcrun --show-sdk-path)
 ifeq ($(strip $(SDKPATH)),)
   CFLAGS_HOST := 
 else
-  CFLAGS_HOST = -isysroot $(SDKPATH)
+  CFLAGS_HOST := -isysroot $(SDKPATH)
+  CFLAGS += -isysroot $(SDKPATH)
   LD += -L$(SDKPATH)/usr/lib
 endif