From da97bf3f67e27c3513b66646393418a3774a11ba Mon Sep 17 00:00:00 2001
From: Menno Fraters <menno.fraters@tutanota.com>
Date: Sun, 13 Oct 2024 23:46:38 +0200
Subject: [PATCH 1/5] fix pip enviroment.

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8266ae763..4e7439904 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -286,7 +286,7 @@ jobs:
         run: echo $PATH && export PATH=$PATH:/home/runner/.local/bin && echo $PATH && export PYTHONPATH=$PYTHONPATH:/home/runner/.local/bin
       
       - name: Install coveralls
-        run: pip install --user cpp-coveralls 
+        run: pipx install cpp-coveralls 
         shell: bash
          
       - name: Create Build Environment

From eda972b131e2a0e1a45ffa6c24a852297ec56954 Mon Sep 17 00:00:00 2001
From: Menno Fraters <menno.fraters@tutanota.com>
Date: Mon, 14 Oct 2024 00:00:51 +0200
Subject: [PATCH 2/5] add -fprofile-update=atomic flag to coverage.

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 25a57c1a4..f5152d838 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -351,8 +351,8 @@ SET(FORCE_COLORED_OUTPUT ON CACHE BOOL "Forces colored output when compiling wit
 
 IF ( CMAKE_BUILD_TYPE STREQUAL Coverage )
   SET(CMAKE_VERBOSE_MAKEFILE on )
-  SET(WB_COMPILER_OPTIONS_PRIVATE_COVERAGE_NEW --coverage -fprofile-arcs -ftest-coverage -g)
-  SET(WB_COMPILER_OPTIONS_PRIVATE_COVERAGE_OLD "--coverage -fprofile-arcs -ftest-coverage -g")
+  SET(WB_COMPILER_OPTIONS_PRIVATE_COVERAGE_NEW --coverage -fprofile-arcs -ftest-coverage -g -fprofile-update=atomic)
+  SET(WB_COMPILER_OPTIONS_PRIVATE_COVERAGE_OLD "--coverage -fprofile-arcs -ftest-coverage -g -fprofile-update=atomic")
 
   ## for old versions of cmake
   SET(WB_FORTRAN_COMPILER_FLAGS_COVERAGE "--coverage")

From 2527ce2a37fecf5b60b4aeaaabc5ce1e2e0769ca Mon Sep 17 00:00:00 2001
From: Menno Fraters <menno.fraters@tutanota.com>
Date: Mon, 14 Oct 2024 00:01:24 +0200
Subject: [PATCH 3/5] fix benchmarks

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

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 058d5fe48..81d2d0bcc 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -181,7 +181,7 @@ jobs:
             cat ${{github.workspace}}/result_${{matrix.benchmark_number}}.csv | cargo run --release analyze --disable-dynamic-printing > ${{github.workspace}}/benchmark_${{matrix.benchmark_number}}_results/analyze_${{matrix.benchmark_number}}.log ||:;
             cat ${{github.workspace}}/benchmark_${{matrix.benchmark_number}}_results/analyze_${{matrix.benchmark_number}}.log
     
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: benchmark_${{matrix.benchmark_number}}_results
         path: benchmark_${{matrix.benchmark_number}}_results/

From 76aba9d7bc5fc0a5cf2d4c91d63776fa6931088c Mon Sep 17 00:00:00 2001
From: Menno Fraters <menno.fraters@tutanota.com>
Date: Mon, 14 Oct 2024 00:03:10 +0200
Subject: [PATCH 4/5] fix draft paper test

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

diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
index 8271cf3da..4f9477693 100644
--- a/.github/workflows/draft-pdf.yml
+++ b/.github/workflows/draft-pdf.yml
@@ -14,7 +14,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: doc/JOSS/1.0/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

From dd3b08a49d2942b8bab8a5c69c1fd39c9d54dda0 Mon Sep 17 00:00:00 2001
From: Menno Fraters <menno.fraters@tutanota.com>
Date: Mon, 14 Oct 2024 00:04:43 +0200
Subject: [PATCH 5/5] fix spelling of truncation.

---
 tests/unit_tests/unit_test_world_builder.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/unit_tests/unit_test_world_builder.cc b/tests/unit_tests/unit_test_world_builder.cc
index a8d7aa44f..2ed45045a 100644
--- a/tests/unit_tests/unit_test_world_builder.cc
+++ b/tests/unit_tests/unit_test_world_builder.cc
@@ -3473,10 +3473,10 @@ TEST_CASE("WorldBuilder Types: Segment Object")
 {
 #define TYPE Segment
   const WorldBuilder::Point<2> thickness(1,2,invalid);
-  const WorldBuilder::Point<2> top_trucation(3,4,invalid);
+  const WorldBuilder::Point<2> top_truncation(3,4,invalid);
   const WorldBuilder::Point<2> angle(5,6,invalid);
   Objects::TYPE<Features::FaultModels::Temperature::Interface, Features::FaultModels::Composition::Interface, Features::FaultModels::Grains::Interface>
-  type (1.0, thickness, top_trucation, angle,
+  type (1.0, thickness, top_truncation, angle,
         std::vector<std::shared_ptr<Features::FaultModels::Temperature::Interface> >(),
         std::vector<std::shared_ptr<Features::FaultModels::Composition::Interface> >(),
         std::vector<std::shared_ptr<Features::FaultModels::Grains::Interface> >());