From 9bc600afbe3752d0e13120a2b4044b35d7ab5cf8 Mon Sep 17 00:00:00 2001
From: Ben Lawrence <ben.lawrence@nanoporetech.com>
Date: Wed, 23 Oct 2024 10:31:04 +0100
Subject: [PATCH] Check that subprocesses don't error out

This should make the cause of some CI failures easier to spot since
they'll fail early rather than halfway through the build.
---
 cmake/DoradoVersion.cmake     | 13 +++++++++++--
 cmake/HDF5.cmake              | 21 +++++++++++++--------
 cmake/Htslib.cmake            |  7 +++++--
 cmake/InstallRedistLibs.cmake | 12 ++++++++++--
 cmake/Koi.cmake               | 22 ++++++++++++++++++----
 cmake/Torch.cmake             |  7 ++++++-
 cmake/UpdateSubmodules.cmake  | 12 ++++++------
 cmake/VbzPlugin.cmake         | 12 ++++++++++--
 8 files changed, 79 insertions(+), 27 deletions(-)

diff --git a/cmake/DoradoVersion.cmake b/cmake/DoradoVersion.cmake
index b185318d9..c105c8de2 100644
--- a/cmake/DoradoVersion.cmake
+++ b/cmake/DoradoVersion.cmake
@@ -4,8 +4,17 @@ set(DORADO_VERSION_REV 0)
 
 find_package(Git QUIET)
 if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
-  execute_process(COMMAND ${GIT_EXECUTABLE} log -1 --pretty=format:%h OUTPUT_VARIABLE DORADO_SHORT_HASH WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
-  execute_process(COMMAND ${GIT_EXECUTABLE} diff --quiet RESULT_VARIABLE IS_DIRTY WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+  execute_process(
+    COMMAND ${GIT_EXECUTABLE} log -1 --pretty=format:%h
+    OUTPUT_VARIABLE DORADO_SHORT_HASH
+    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+    COMMAND_ERROR_IS_FATAL ANY
+  )
+  execute_process(
+    COMMAND ${GIT_EXECUTABLE} diff --quiet
+    RESULT_VARIABLE IS_DIRTY
+    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+  )
   if(IS_DIRTY)
     string(APPEND DORADO_SHORT_HASH "+dirty")
   endif()
diff --git a/cmake/HDF5.cmake b/cmake/HDF5.cmake
index 142ca2eb4..2571d44ba 100644
--- a/cmake/HDF5.cmake
+++ b/cmake/HDF5.cmake
@@ -19,15 +19,20 @@ elseif(WIN32)
         # Need a zlib build for HDF to use
         download_and_extract(https://github.com/madler/zlib/archive/refs/tags/v${ZLIB_VER}.tar.gz zlib-${ZLIB_VER})
         set(HDF5_ZLIB_BUILD_DIR ${CMAKE_BINARY_DIR}/zlib-${ZLIB_VER}/build)
-        execute_process(COMMAND
-            cmake
-                -S ${DORADO_3RD_PARTY_DOWNLOAD}/zlib-${ZLIB_VER}/zlib-${ZLIB_VER}
-                -B ${HDF5_ZLIB_BUILD_DIR}
-                -A x64
-                -D CMAKE_INSTALL_PREFIX=${HDF5_ZLIB_INSTALL_DIR}
-                -D CMAKE_CONFIGURATION_TYPES=Release
+        execute_process(
+            COMMAND
+                cmake
+                    -S ${DORADO_3RD_PARTY_DOWNLOAD}/zlib-${ZLIB_VER}/zlib-${ZLIB_VER}
+                    -B ${HDF5_ZLIB_BUILD_DIR}
+                    -A x64
+                    -D CMAKE_INSTALL_PREFIX=${HDF5_ZLIB_INSTALL_DIR}
+                    -D CMAKE_CONFIGURATION_TYPES=Release
+            COMMAND_ERROR_IS_FATAL ANY
+        )
+        execute_process(
+            COMMAND cmake --build ${HDF5_ZLIB_BUILD_DIR} --config Release --target install
+            COMMAND_ERROR_IS_FATAL ANY
         )
-        execute_process(COMMAND cmake --build ${HDF5_ZLIB_BUILD_DIR} --config Release --target install)
 
         # HDF5 itself
         download_and_extract(https://cdn.oxfordnanoportal.com/software/analysis/${HDF_VER}-win.zip ${HDF_VER})
diff --git a/cmake/Htslib.cmake b/cmake/Htslib.cmake
index caabc1a39..86dff1f8e 100644
--- a/cmake/Htslib.cmake
+++ b/cmake/Htslib.cmake
@@ -18,8 +18,11 @@ if(NOT TARGET htslib) # lazy include guard
         find_program(MAKE_COMMAND make REQUIRED)
         find_program(AUTOCONF_COMMAND autoconf REQUIRED)
         find_program(AUTOHEADER_COMMAND autoheader REQUIRED)
-        execute_process(COMMAND bash -c "${AUTOCONF_COMMAND} -V | sed 's/.* //; q'"
-            OUTPUT_VARIABLE AUTOCONF_VERS)
+        execute_process(
+            COMMAND bash -c "${AUTOCONF_COMMAND} -V | sed 's/.* //; q'"
+            OUTPUT_VARIABLE AUTOCONF_VERS
+            COMMAND_ERROR_IS_FATAL ANY
+        )
         if (AUTOCONF_VERS VERSION_GREATER_EQUAL 2.70 AND NOT CMAKE_GENERATOR STREQUAL "Xcode")
             set(AUTOCONF_COMMAND autoreconf --install)
         endif()
diff --git a/cmake/InstallRedistLibs.cmake b/cmake/InstallRedistLibs.cmake
index 1984c0770..a3eb479c3 100644
--- a/cmake/InstallRedistLibs.cmake
+++ b/cmake/InstallRedistLibs.cmake
@@ -31,14 +31,22 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
                 get_filename_component(target_name ${target} NAME)
                 get_filename_component(link_name ${link} NAME)
                 if (NOT target_name STREQUAL link_name)
-                    execute_process(COMMAND ln -rfs ${target_name} ${link_name} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+                    execute_process(
+                        COMMAND ln -rfs ${target_name} ${link_name}
+                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                        COMMAND_ERROR_IS_FATAL ANY
+                    )
                     install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${link_name} DESTINATION lib COMPONENT redist_libs)
 
                     # create links to the versioned links above
                     # e.g. libcublas.so => libcublas.so.11
                     string(REGEX REPLACE "[.]so[.0-9]*$" ".so" base_link ${link_name})
                     if (NOT base_link STREQUAL link_name)
-                        execute_process(COMMAND ln -rfs ${link_name} ${base_link} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+                        execute_process(
+                            COMMAND ln -rfs ${link_name} ${base_link}
+                            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                            COMMAND_ERROR_IS_FATAL ANY
+                        )
                         install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${base_link} DESTINATION lib COMPONENT redist_libs)
                     endif()
                 endif()
diff --git a/cmake/Koi.cmake b/cmake/Koi.cmake
index a58f5faae..54403e452 100644
--- a/cmake/Koi.cmake
+++ b/cmake/Koi.cmake
@@ -31,13 +31,27 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux" OR WIN32)
         if(NOT EXISTS ${KOI_DIR})
             if(DEFINED GITLAB_CI_TOKEN)
                 message("Cloning Koi using CI token")
-                execute_process(COMMAND git clone https://gitlab-ci-token:${GITLAB_CI_TOKEN}@git.oxfordnanolabs.local/machine-learning/koi.git ${KOI_DIR})
+                execute_process(
+                    COMMAND git clone https://gitlab-ci-token:${GITLAB_CI_TOKEN}@git.oxfordnanolabs.local/machine-learning/koi.git ${KOI_DIR}
+                    COMMAND_ERROR_IS_FATAL ANY
+                )
             else()
                 message("Cloning Koi using ssh")
-                execute_process(COMMAND git clone git@git.oxfordnanolabs.local:machine-learning/koi.git ${KOI_DIR})
+                execute_process(
+                    COMMAND git clone git@git.oxfordnanolabs.local:machine-learning/koi.git ${KOI_DIR}
+                    COMMAND_ERROR_IS_FATAL ANY
+                )
             endif()
-            execute_process(COMMAND git checkout v${KOI_VERSION} WORKING_DIRECTORY ${KOI_DIR})
-            execute_process(COMMAND git submodule update --init --checkout WORKING_DIRECTORY ${KOI_DIR})
+            execute_process(
+                COMMAND git checkout v${KOI_VERSION}
+                WORKING_DIRECTORY ${KOI_DIR}
+                COMMAND_ERROR_IS_FATAL ANY
+            )
+            execute_process(
+                COMMAND git submodule update --init --checkout
+                WORKING_DIRECTORY ${KOI_DIR}
+                COMMAND_ERROR_IS_FATAL ANY
+            )
         endif()
         add_subdirectory(${KOI_DIR}/koi/lib)
 
diff --git a/cmake/Torch.cmake b/cmake/Torch.cmake
index 3999adc5d..469def886 100644
--- a/cmake/Torch.cmake
+++ b/cmake/Torch.cmake
@@ -214,7 +214,12 @@ else()
         file(STRINGS "${TORCH_LIB}/build-version" TORCH_BUILD_VERSION)
     else()
         set(PYTORCH_BUILD_VERSION "import torch; print('%s+cu%s' % (torch.__version__, torch.version.cuda.replace('.', '')), end='')")
-        execute_process(COMMAND python3 -c "${PYTORCH_BUILD_VERSION}" OUTPUT_VARIABLE TORCH_BUILD_VERSION WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+        execute_process(
+            COMMAND python3 -c "${PYTORCH_BUILD_VERSION}"
+            OUTPUT_VARIABLE TORCH_BUILD_VERSION
+            WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+            COMMAND_ERROR_IS_FATAL ANY
+        )
     endif()
     message(STATUS "TORCH_BUILD_VERSION: ${TORCH_BUILD_VERSION}")
 endif()
diff --git a/cmake/UpdateSubmodules.cmake b/cmake/UpdateSubmodules.cmake
index 1ae5b59ea..a1e7de202 100644
--- a/cmake/UpdateSubmodules.cmake
+++ b/cmake/UpdateSubmodules.cmake
@@ -3,17 +3,17 @@ option(GIT_SUBMODULE "Check submodules during build" ON)
 function(git_submodule_update)
     find_package(Git QUIET)
     if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
-        
+
         if(GIT_SUBMODULE)
             message(STATUS "Submodule update")
-            
+
             file(LOCK ${CMAKE_SOURCE_DIR} DIRECTORY)
             execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
-              WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-              RESULT_VARIABLE GIT_SUBMOD_RESULT
-	    )
+                WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+                RESULT_VARIABLE GIT_SUBMOD_RESULT
+            )
             file(LOCK ${CMAKE_SOURCE_DIR} DIRECTORY RELEASE)
-                
+
             if(NOT GIT_SUBMOD_RESULT EQUAL "0")
                 message(FATAL_ERROR "git submodule update --init --recursive failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
             endif()
diff --git a/cmake/VbzPlugin.cmake b/cmake/VbzPlugin.cmake
index eb41df61f..82b3495d8 100644
--- a/cmake/VbzPlugin.cmake
+++ b/cmake/VbzPlugin.cmake
@@ -15,8 +15,12 @@ function(add_hdf_vbz_plugin)
                 -B ${ZSTD_BUILD_DIR}
                 -A x64
                 -D CMAKE_CONFIGURATION_TYPES=Release
+            COMMAND_ERROR_IS_FATAL ANY
+        )
+        execute_process(
+            COMMAND cmake --build ${ZSTD_BUILD_DIR} --config Release
+            COMMAND_ERROR_IS_FATAL ANY
         )
-        execute_process(COMMAND cmake --build ${ZSTD_BUILD_DIR} --config Release)
 
         # On windows we need to tell hdf_plugins where we put the built zstd lib
         set(CONAN_INCLUDE_DIRS_RELEASE ${DORADO_3RD_PARTY_SOURCE}/zstd/lib)
@@ -35,8 +39,12 @@ function(add_hdf_vbz_plugin)
                 -S ${DORADO_3RD_PARTY_SOURCE}/zstd/build/cmake
                 -B ${ZSTD_BUILD_DIR}
                 -D CMAKE_INSTALL_PREFIX=${ZSTD_INSTALL_DIR}
+            COMMAND_ERROR_IS_FATAL ANY
+        )
+        execute_process(
+            COMMAND cmake --build ${ZSTD_BUILD_DIR} --target install
+            COMMAND_ERROR_IS_FATAL ANY
         )
-        execute_process(COMMAND cmake --build ${ZSTD_BUILD_DIR} --target install)
 
         list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/dorado/3rdparty/hdf_plugins/cmake")
         # Findzstd.cmake uses conan variables to determine where things are.