From 9586d63efabc09c61245c554dac5bbd66d420fe1 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 4 Jun 2024 11:52:16 +0100
Subject: [PATCH 01/26] Trying to add code coverage reporting to CI

---
 .github/workflows/main.yml |  4 ++++
 docker/platypus/Dockerfile |  7 +++++--
 upload-coverage.sh         | 11 +++++++++++
 3 files changed, 20 insertions(+), 2 deletions(-)
 create mode 100644 upload-coverage.sh

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2792d3b3..07a29e32 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -28,3 +28,7 @@ jobs:
                           --build-arg build_git_sha=${PRCOMMITSHA:-$GITHUB_SHA} \
                           --build-arg build_git_repo=${PRREPOSITORY:-$GITHUB_REPOSITORY} \
                           docker/platypus
+      - name: UploadCoverage
+        run: |
+          ci_env=`bsah <(curl -s https://codecov.io/env)`
+          docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash opt/platypus/upload-coverage.sh
diff --git a/docker/platypus/Dockerfile b/docker/platypus/Dockerfile
index 86ebd142..327c7455 100644
--- a/docker/platypus/Dockerfile
+++ b/docker/platypus/Dockerfile
@@ -12,6 +12,9 @@ ARG build_git_repo=aurora-multiphysics/platypus
 # By default we install everything under /opt
 ARG WORKDIR=opt
 
+# By default, build without code coverage flags
+ARG coverage=false
+
 # Get Platypus with Hephaestus
 RUN cd /$WORKDIR && \
     git clone https://github.com/$build_git_repo && \
@@ -32,8 +35,8 @@ RUN cd /$WORKDIR/platypus/contrib/hephaestus/build && \
 
 # Build Platypus
 RUN cd /$WORKDIR/platypus && \
-    make -j$compile_cores
+    make -j$compile_cores coverage=$coverage
 
 # Test Platypus
 RUN cd /$WORKDIR/platypus && \
-    make test
+    make test linkcoverage=$coverage
diff --git a/upload-coverage.sh b/upload-coverage.sh
new file mode 100644
index 00000000..3cee8b60
--- /dev/null
+++ b/upload-coverage.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
+curl -Os https://cli.codecov.io/latest/linux/codecov
+curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM
+curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM.sig
+gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM
+
+shasum -a 256 -c codecov.SHA256SUM
+sudo chmod +x codecov
+./codecov --verbose upload-process --fail-on-error

From f4c9da6c2cbd79ae910462dd70869194bbe9ef19 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 4 Jun 2024 13:22:20 +0100
Subject: [PATCH 02/26] Fixed typo in CI

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

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 07a29e32..0aaa5fbc 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -30,5 +30,5 @@ jobs:
                           docker/platypus
       - name: UploadCoverage
         run: |
-          ci_env=`bsah <(curl -s https://codecov.io/env)`
+          ci_env=`bash <(curl -s https://codecov.io/env)`
           docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash opt/platypus/upload-coverage.sh

From 3c12cef26862c9d79f09965a3a2e202932e3b5e8 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 4 Jun 2024 13:52:59 +0100
Subject: [PATCH 03/26] Fix coverage upload script

---
 upload-coverage.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/upload-coverage.sh b/upload-coverage.sh
index 3cee8b60..ffbc082e 100644
--- a/upload-coverage.sh
+++ b/upload-coverage.sh
@@ -7,5 +7,6 @@ curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM.sig
 gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM
 
 shasum -a 256 -c codecov.SHA256SUM
-sudo chmod +x codecov
+chmod +x codecov
+
 ./codecov --verbose upload-process --fail-on-error

From bd1a37274094c7163001ef8c452a556b39c21673 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 4 Jun 2024 14:35:46 +0100
Subject: [PATCH 04/26] Trying to fix coverage upload

---
 upload-coverage.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/upload-coverage.sh b/upload-coverage.sh
index ffbc082e..6e4b09b8 100644
--- a/upload-coverage.sh
+++ b/upload-coverage.sh
@@ -9,4 +9,5 @@ gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM
 shasum -a 256 -c codecov.SHA256SUM
 chmod +x codecov
 
-./codecov --verbose upload-process --fail-on-error
+cd /opt/platypus
+./codecov --verbose

From ecda8723c556155c073edb3520327d861c244085 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 4 Jun 2024 14:55:30 +0100
Subject: [PATCH 05/26] More attempts at fixing

---
 upload-coverage.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/upload-coverage.sh b/upload-coverage.sh
index 6e4b09b8..23e4b2ce 100644
--- a/upload-coverage.sh
+++ b/upload-coverage.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+cd /opt/platypus
+
 curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
 curl -Os https://cli.codecov.io/latest/linux/codecov
 curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM
@@ -9,5 +11,4 @@ gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM
 shasum -a 256 -c codecov.SHA256SUM
 chmod +x codecov
 
-cd /opt/platypus
 ./codecov --verbose

From 317946dbc4fd2a0529706fe18b4b41621726169f Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 4 Jun 2024 15:25:32 +0100
Subject: [PATCH 06/26] Trying to use old approach to upload codecov

---
 upload-coverage.sh | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/upload-coverage.sh b/upload-coverage.sh
index 23e4b2ce..664c8915 100644
--- a/upload-coverage.sh
+++ b/upload-coverage.sh
@@ -2,13 +2,4 @@
 
 cd /opt/platypus
 
-curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
-curl -Os https://cli.codecov.io/latest/linux/codecov
-curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM
-curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM.sig
-gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM
-
-shasum -a 256 -c codecov.SHA256SUM
-chmod +x codecov
-
-./codecov --verbose
+bash <(curl -s https://codecov.io/bash)

From 513af5d697b51287c29b7b26d2921c85f5b66aa3 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Wed, 5 Jun 2024 16:03:28 +0100
Subject: [PATCH 07/26] Added support for clang-format linting

---
 .github/workflows/lint.yml                    | 36 +++++++++++++++++++
 include/base/PlatypusApp.h                    |  1 -
 include/problem/MFEMProblem.h                 | 11 +++---
 .../ElementVectorL2Difference.C               |  6 ++--
 4 files changed, 47 insertions(+), 7 deletions(-)
 create mode 100644 .github/workflows/lint.yml

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 00000000..65ed6650
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,36 @@
+name: Lint
+
+on:
+  push:
+    branches:
+       - main
+  pull_request:
+    branches:
+       - main
+
+permissions: { }
+
+jobs:
+  build:
+    name: Lint
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: read
+      # To report GitHub Actions status checks
+      statuses: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          # super-linter needs the full git history to get the
+          # list of files that changed across commits
+          fetch-depth: 0
+
+      - name: Super-linter
+        uses: super-linter/super-linter/slim@v6.6.0
+        env:
+          # To report GitHub Actions status checks
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/include/base/PlatypusApp.h b/include/base/PlatypusApp.h
index 15b1e2e4..bfa1962b 100644
--- a/include/base/PlatypusApp.h
+++ b/include/base/PlatypusApp.h
@@ -14,4 +14,3 @@ class PlatypusApp : public MooseApp
   static void registerAll(Factory & f, ActionFactory & af, Syntax & s);
   static void associateSyntax(Syntax & syntax, ActionFactory & action_factory);
 };
-
diff --git a/include/problem/MFEMProblem.h b/include/problem/MFEMProblem.h
index dee49f69..1be63adc 100644
--- a/include/problem/MFEMProblem.h
+++ b/include/problem/MFEMProblem.h
@@ -147,7 +147,8 @@ class MFEMProblem : public ExternalProblem
   void setMOOSEElementalVarData(MooseVariableFieldBase & moose_variable);
 
   /**
-   * Template method for adding kernels. We can only add kernels using equation system problem builders.
+   * Template method for adding kernels. We can only add kernels using equation system problem
+   * builders.
    */
   template <class T>
   void addKernel(std::string var_name, std::shared_ptr<hephaestus::Kernel<T>> kernel)
@@ -156,13 +157,15 @@ class MFEMProblem : public ExternalProblem
 
     EquationSystemProblemBuilderInterface * eqn_system_problem_builder{nullptr};
 
-    if ((eqn_system_problem_builder = dynamic_cast<EquationSystemProblemBuilderInterface *>(mfem_problem_builder.get())))
+    if ((eqn_system_problem_builder =
+             dynamic_cast<EquationSystemProblemBuilderInterface *>(mfem_problem_builder.get())))
     {
       eqn_system_problem_builder->AddKernel(std::move(var_name), std::move(kernel));
     }
-    else 
+    else
     {
-      mooseError("Cannot add kernel with name '" + var_name + "' because there is no equation system.");
+      mooseError("Cannot add kernel with name '" + var_name +
+                 "' because there is no equation system.");
     }
   }
 
diff --git a/src/postprocessors/ElementVectorL2Difference.C b/src/postprocessors/ElementVectorL2Difference.C
index a2b70acb..7a47903f 100644
--- a/src/postprocessors/ElementVectorL2Difference.C
+++ b/src/postprocessors/ElementVectorL2Difference.C
@@ -47,13 +47,15 @@ ElementVectorL2Difference::computeQpIntegral()
   return difference_vector.norm_sq(); // dot product of difference vector.
 }
 
-void ElementVectorL2Difference::checkVectorVariables() const
+void
+ElementVectorL2Difference::checkVectorVariables() const
 {
   auto & coupled_vector_variables = getCoupledVectorMooseVars();
 
   if (coupled_vector_variables.size() != 2)
   {
-    mooseError("There are ", coupled_vector_variables.size(), " coupled vector variables. Expected 2.");
+    mooseError(
+        "There are ", coupled_vector_variables.size(), " coupled vector variables. Expected 2.");
   }
 
   auto first = coupled_vector_variables[0];

From f6e0bb45c191b46a818213f3eab1566aaf6dc6e8 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Wed, 5 Jun 2024 16:03:43 +0100
Subject: [PATCH 08/26] Another attempt to upload coverage data

---
 upload-coverage.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/upload-coverage.sh b/upload-coverage.sh
index 664c8915..fbff8588 100644
--- a/upload-coverage.sh
+++ b/upload-coverage.sh
@@ -2,4 +2,9 @@
 
 cd /opt/platypus
 
+for filename in `find src -name "*.C"`; 
+do 
+  gcov -n -o . $filename > /dev/null; 
+done
+
 bash <(curl -s https://codecov.io/bash)

From 0f1a51bdb1e17d6039f9eb095d47b6225b61205d Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Wed, 5 Jun 2024 16:03:58 +0100
Subject: [PATCH 09/26] Add a couple initial badges to the README

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 76ce82bc..ea27f3e1 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,9 @@
 Platypus
 =====
 
+![build](https://github.com/aurora-multiphysics/platypus/actions/workflows/main.yml/badge.svg?branch=main)
+[![GitHub License](https://img.shields.io/github/license/aurora-multiphysics/platypus)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html)
+
 Platypus is a MOOSE-based application created to enable custom MOOSE problems to be set up and solved using the [MFEM](https://github.com/mfem/mfem) finite element library as an alternative backend to libMesh. It is based off of the MOOSE electromagnetics app [Apollo](https://github.com/aurora-multiphysics/apollo) that uses MFEM for solving electromagnetics problems in a variety of formulations.
 
 Platypus is under active development and is being updated frequently.

From afd9035e067e7fc7c8b90f99900e18c5691b88ab Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 16:27:15 +0100
Subject: [PATCH 10/26] Applied shellcheck linting

---
 .gitlab-ci.yml                          | 140 ------------------------
 scripts/build-platypus-csd3-cclake.sh   |  72 ++++++------
 scripts/build-platypus-csd3-sapphire.sh |  88 +++++++--------
 scripts/install-format-hook.sh          |   4 +-
 scripts/upload-coverage.sh              |  10 ++
 upload-coverage.sh                      |  10 --
 6 files changed, 92 insertions(+), 232 deletions(-)
 delete mode 100644 .gitlab-ci.yml
 mode change 100644 => 100755 scripts/build-platypus-csd3-cclake.sh
 mode change 100644 => 100755 scripts/build-platypus-csd3-sapphire.sh
 create mode 100755 scripts/upload-coverage.sh
 delete mode 100644 upload-coverage.sh

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
deleted file mode 100644
index 333b21d8..00000000
--- a/.gitlab-ci.yml
+++ /dev/null
@@ -1,140 +0,0 @@
-image: ubuntu:latest
-
-variables:
-  GIT_SUBMODULE_STRATEGY: recursive
-
-stages:
-  - build
-  - test
-  - quality
-  - security
-  - deploy
-
-# Build the software, along with all tests
-build:
-  stage: build
-  script:
-    - mkdir build
-    - cd build
-    - cmake ..
-    - make -j
-    - cd ..
-  artifacts:
-    paths:
-    - build/
-    - bin/
-    - lib/
-    expire_in: 1 day
-
-# Run tests
-
-.template: &coverage_template
-  stage: test
-  before_script:
-    - apt install gcovr
-    - cd build
-    - cmake .. -DBUILD_TYPE=TEST
-    - make -j
-#   after_script:
-#     - make gcovr
-  coverage: '/^lines: (\d+.\d+)%/'
-
-
-unit_tests:
-  <<: *coverage_template
-  script:
-    - ../bin/unit_tests
-    - make gcovr
-    - mv gcovr unit_test_coverage
-  artifacts:
-    paths:
-    - build/unit_test_coverage
-    expire_in: 1 week
-
-integration_tests:
-  <<: *coverage_template
-  script:
-    - ../bin/integration_tests
-    - make gcovr
-    - mv gcovr integration_test_coverage
-  artifacts:
-    paths:
-    - build/integration_test_coverage
-    expire_in: 1 week
-
-regression_tests:
-  <<: *coverage_template
-  script:
-    - ../bin/regression_tests
-    - make gcovr
-    - mv gcovr regression_test_coverage
-  artifacts:
-    paths:
-    - build/regression_test_coverage
-    expire_in: 1 week
-
-format_tests:
-  stage: test
-  script:
-    - find ./{test,src}/ -iname *.h -o -iname *.cpp -o -iname *.hpp | xargs clang-format-8 -style=file | clang-format-diff-8 > out.txt
-    - if [[ -s out.txt ]]; then false; fi
-  allow_failure: true
-
-# Code quality
-cyclomatic_complexity:
-  stage: quality
-  script:
-    - python /home/lizard/lizard.py --CCN=15 --length=100 --arguments=10 src
-
-static_analysis:
-  stage: quality
-  script:
-    - script -c "cppcheck src --enable=all" cppcheck.out
-  artifacts:
-    paths:
-    - cppcheck.out
-    expire_in: 1 week
-
-similarity:
-  stage: quality
-  script:
-    - script -c "sim_c++ -aRn src/*" similarity.out
-  artifacts:
-    paths:
-    - similarity.out
-    expire_in: 1 week
-
-
-flaws:
-  stage: security
-  script:
-    - script -c "flawfinder src" flawfinder.out
-  artifacts:
-    paths:
-    - flawfinder.out
-    expire_in: 1 week
-
-pages:
-  stage: deploy
-  script:
-    # assuming build folder in the build stage is kept
-    - mkdir builddoc && cd builddoc
-    - cmake ..
-    - make doc
-    # doxygen output folder name is controlled in defined Doxygen.in
-    # gitlab pages request document must put into `public` folder of the repo directory
-    - mv public/html ../public
-    - cd ..
-    - mv build/unit_test_coverage public/unit_coverage
-    - mv build/integration_test_coverage public/integration_coverage
-    - mv build/regression_test_coverage public/regression_coverage
-  dependencies:
-    - unit_tests
-    - integration_tests
-    - regression_tests
-  only:
-    - master
-  artifacts:
-    paths:
-    - public
-  allow_failure: true # TODO change to false
diff --git a/scripts/build-platypus-csd3-cclake.sh b/scripts/build-platypus-csd3-cclake.sh
old mode 100644
new mode 100755
index 8dd20206..e372fe5f
--- a/scripts/build-platypus-csd3-cclake.sh
+++ b/scripts/build-platypus-csd3-cclake.sh
@@ -1,8 +1,8 @@
 #!/bin/bash
 #set -ue
 
-export STACK_SRC=`mktemp -d /tmp/moose_stack_src.XXXXXX`
-export WORKDIR=`pwd`
+export STACK_SRC=$(mktemp -d /tmp/moose_stack_src.XXXXXX)
+export WORKDIR=$(pwd)
 export compile_cores=32
 export OMPI_MCA_mca_base_component_show_load_errors=0
 
@@ -14,18 +14,18 @@ function load_modules() {
 }
 
 function build_petsc() {
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     curl -LJO https://github.com/xiaoyeli/superlu_dist/archive/refs/tags/v8.1.0.tar.gz
     if [ -d "$WORKDIR/petsc" ] ; then
        return
     fi
     mkdir petsc
-    cd petsc
+    cd petsc || exit 1
     curl -L -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.19.3.tar.gz
     tar -xf petsc-3.19.3.tar.gz -C .
-    cd petsc-3.19.3
+    cd petsc-3.19.3 || exit 1
     ./configure \
-	--prefix=$WORKDIR/petsc \
+	--prefix="$WORKDIR"/petsc \
         CXXOPTFLAGS='-O3 -march=cascadelake -funroll-loops' COPTFLAGS='-O3 -march=cascadelake -funroll-loops' FOPTFLAGS='-O3 -march=cascadelake' \
 	--with-debugging=0 \
 	--with-ssl=0 \
@@ -40,16 +40,16 @@ function build_petsc() {
     --download-metis=1 \
     --download-ptscotch=1 \
     --download-parmetis=1 \
-    --download-superlu_dist=$WORKDIR/superlu_dist-8.1.0.tar.gz \
+    --download-superlu_dist="$WORKDIR"/superlu_dist-8.1.0.tar.gz \
     --download-scalapack=1 \
     --download-mumps=1 \
     --download-slepc=1 \
     --with-64-bit-indices=1 \
     --with-mpi-dir=/usr/local/Cluster-Apps/openmpi/gcc/9.3/4.0.4 \
-    PETSC_DIR=`pwd` PETSC_ARCH=arch-linux-c-opt
+    PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
     make
-    make PETSC_DIR=$WORKDIR/petsc/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install
-    make PETSC_DIR=$WORKDIR/petsc PETSC_ARCH="" check
+    make PETSC_DIR="$WORKDIR"/petsc/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install
+    make PETSC_DIR="$WORKDIR"/petsc PETSC_ARCH="" check
     cd ..
     cd ..
     export PETSC_DIR=$WORKDIR/petsc
@@ -57,16 +57,16 @@ function build_petsc() {
 
 function build_moose() {
     export MOOSE_JOBS=32
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     if [ -d "$WORKDIR/moose" ] ; then
        return
     fi
 #    _build_mpich33
     load_modules
     #build_vtk_git
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     git clone https://github.com/idaholab/moose
-    cd moose
+    cd moose || exit 1
     git checkout master
     if [ ! -f "$WORKDIR/petsc/lib/libpetsc.so" ] ; then
       echo "PETSc Install Unsuccessful"
@@ -82,20 +82,20 @@ function build_moose() {
     export FC=mpif90
     if [ -d "$WORKDIR/vtk" ] ; then
       echo "building libmesh with VTK"
-      METHODS='opt' ./scripts/update_and_rebuild_libmesh.sh --with-mpi --with-cxx-std=2017 --with-vtk-include=$WORKDIR/vtk/include/vtk-9.1 --with-vtk-lib=$WORKDIR/vtk/lib64
+      METHODS='opt' ./scripts/update_and_rebuild_libmesh.sh --with-mpi --with-cxx-std=2017 --with-vtk-include="$WORKDIR"/vtk/include/vtk-9.1 --with-vtk-lib="$WORKDIR"/vtk/lib64
     else
       echo "Building libmesh withOUT VTK"
       METHODS='opt' ./scripts/update_and_rebuild_libmesh.sh --with-mpi
     fi
     ./configure --with-derivative-size=200 --with-ad-indexing-type=global
     METHODS='opt' ./scripts/update_and_rebuild_wasp.sh
-    cd framework
+    cd framework || exit 1
     METHOD=opt make -j32
     cd ..
-    cd modules
+    cd modules || exit 1
     METHOD=opt make -j32
     cd ..
-    cd test
+    cd test || exit 1
     METHOD=opt make -j32
     ./run_tests -j32
     cd ..
@@ -103,16 +103,16 @@ function build_moose() {
 }
 
 function build_mfem() {
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     if [ -d "$WORKDIR/mfem" ] ; then
        return
     fi
     git clone https://github.com/Heinrich-BR/mfem.git
-    cd mfem 
+    cd mfem || exit 1
     git checkout SubmeshBoundary
-    sed -i "s|list|# list|g" $WORKDIR/mfem/config/cmake/modules/FindNetCDF.cmake
+    sed -i "s|list|# list|g" "$WORKDIR"/mfem/config/cmake/modules/FindNetCDF.cmake
     mkdir build
-    cd build
+    cd build || exit 1
     echo "Building MFEM"
     cmake .. \
         -DCMAKE_BUILD_TYPE=Release \
@@ -120,41 +120,41 @@ function build_mfem() {
         -DMFEM_SHARED=YES \
         -DMFEM_USE_OPENMP=YES \
         -DMFEM_THREAD_SAFE=NO \
-        -DHYPRE_DIR=/$WORKDIR/petsc/ \
-        -DBLAS_LIBRARIES=/$WORKDIR/petsc/lib/libfblas.a \
-        -DLAPACK_LIBRARIES=/$WORKDIR/petsc/lib/libflapack.a \
+        -DHYPRE_DIR=/"$WORKDIR"/petsc/ \
+        -DBLAS_LIBRARIES=/"$WORKDIR"/petsc/lib/libfblas.a \
+        -DLAPACK_LIBRARIES=/"$WORKDIR"/petsc/lib/libflapack.a \
         -DMFEM_USE_MPI=YES \
         -DMFEM_USE_METIS_5=YES \
-        -DMETIS_DIR=/$WORKDIR/petsc/ \
-        -DParMETIS_DIR=/$WORKDIR/petsc/ \
+        -DMETIS_DIR=/"$WORKDIR"/petsc/ \
+        -DParMETIS_DIR=/"$WORKDIR"/petsc/ \
         -DMFEM_USE_SUPERLU=YES \
-        -DSuperLUDist_DIR=/$WORKDIR/petsc/ \
+        -DSuperLUDist_DIR=/"$WORKDIR"/petsc/ \
         -DMFEM_USE_NETCDF=YES \
-        -DNETCDF_LIBRARIES=$WORKDIR/moose/libmesh/installed/lib/libnetcdf.so \
-        -DNETCDF_INCLUDE_DIRS=$WORKDIR/moose/libmesh/contrib/netcdf/netcdf-c-4.6.2/include \
+        -DNETCDF_LIBRARIES="$WORKDIR"/moose/libmesh/installed/lib/libnetcdf.so \
+        -DNETCDF_INCLUDE_DIRS="$WORKDIR"/moose/libmesh/contrib/netcdf/netcdf-c-4.6.2/include \
         -DHDF5_DIR=/usr/local/Cluster-Apps/hdf5/openmpi/gcc/9.3/1.12.0 \
         -DCMAKE_POLICY_DEFAULT_CMP0057=NEW
     make -j"$compile_cores"
-    cd miniapps/common
+    cd miniapps/common || exit 1
     make -j"$compile_cores"
 }
 
 function build_platypus() {
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     if [ -d "$WORKDIR/platypus" ] ; then
        return
     fi
 
     git clone https://github.com/aurora-multiphysics/platypus.git
-    cd platypus
+    cd platypus || exit 1
     git checkout master
     git submodule update --init --recursive
-    cd contrib/hephaestus/
+    cd contrib/hephaestus/ || exit 1
     mkdir build
-    cd build
-    cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DMFEM_DIR=/$WORKDIR/mfem/build -DMFEM_COMMON_INCLUDES=/$WORKDIR/mfem/miniapps/common  ..
+    cd build || exit 1
+    cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DMFEM_DIR=/"$WORKDIR"/mfem/build -DMFEM_COMMON_INCLUDES=/"$WORKDIR"/mfem/miniapps/common  ..
     make -j1
-    cd /$WORKDIR/platypus
+    cd /"$WORKDIR"/platypus || exit 1
     make -j"$compile_cores"
 }
 
diff --git a/scripts/build-platypus-csd3-sapphire.sh b/scripts/build-platypus-csd3-sapphire.sh
old mode 100644
new mode 100755
index c3d14427..2c8a2b53
--- a/scripts/build-platypus-csd3-sapphire.sh
+++ b/scripts/build-platypus-csd3-sapphire.sh
@@ -25,12 +25,12 @@ function load_modules() {
     module load python/3.8
     module load ninja
 
-    export STACK_SRC=`mktemp -d /tmp/moose_stack_src.XXXXXX`
-    export WORKDIR=`pwd`
+    export STACK_SRC=$(mktemp -d /tmp/moose_stack_src.XXXXXX)
+    export WORKDIR=$(pwd)
     export compile_cores=8
     export OMPI_MCA_mca_base_component_show_load_errors=0
 
-    USER=`whoami`
+    USER=$(whoami)
     BUILD_DIR_NAME=${WORKDIR}
 
     ROOT_PATH=/home/${USER}/rds/rds-ukaea-ap001/${USER}
@@ -52,7 +52,7 @@ function load_modules() {
 
     export PATH=${BUILD_PATH}:${PATH}
 
-    cd ${WORKDIR}
+    cd "${WORKDIR}" || exit 1
 
     #Need to set some compiler flags via config file"
     echo "-std=c++17" >> icpx.cfg
@@ -72,7 +72,7 @@ function load_modules() {
 }
 
 function _build_hdf5() {
-    cd ${WORKDIR}
+    cd "${WORKDIR}" || exit 1
     mkdir -p ${HDF5_DIR_NAME} || { echo "Failed to create ${HDF5_DIR_NAME}" ; exit 1 ; }
 
     HDF5_MAJ_VER=1.10
@@ -84,9 +84,9 @@ function _build_hdf5() {
         || { echo "Failed to download hdf5" ; exit 1 ; }
     tar -xf hdf5-${HDF5_VER}.tar.gz
 
-    cd hdf5-${HDF5_VER}
+    cd hdf5-${HDF5_VER} || exit 1
     make clean
-    ./configure --prefix=${HDF5_INSTALL_PATH} --enable-cxx --enable-fortran --enable-build-mode=production
+    ./configure --prefix="${HDF5_INSTALL_PATH}" --enable-cxx --enable-fortran --enable-build-mode=production
     make install -j ${compile_cores}
     if [ $? -eq 2 ]; then
         echo "HDF5 Build failed"
@@ -96,7 +96,7 @@ function _build_hdf5() {
 }
 
 function _build_petsc() {
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     # echo "Downloading SuperLU_dist"
     # curl -kLJO https://github.com/xiaoyeli/superlu_dist/archive/refs/tags/v8.1.0.tar.gz
     # curl -kLJO https://github.com/xiaoyeli/superlu_dist/archive/refs/tags/v8.1.0.tar.gz
@@ -104,23 +104,23 @@ function _build_petsc() {
     #    return
     # fi
     mkdir -p petsc
-    cd petsc
+    cd petsc || exit 1
     curl -kL -O http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.19.3.tar.gz
     tar -xf petsc-3.19.3.tar.gz -C .
-    cd petsc-3.19.3
+    cd petsc-3.19.3 || exit 1
     ./configure \
     --with-cc=$CC --with-cxx=$CXX --with-fc=$FC -CXXPP=cpp \
-		       --prefix=${WORKDIR}/${PETSC_DIR_NAME} \
+		       --prefix="${WORKDIR}"/${PETSC_DIR_NAME} \
 		       --download-hypre=1 \
 		       --with-shared-libraries \
 		       --with-debugging=no \
-		       --with-hdf5-dir=${WORKDIR}/${HDF5_DIR_NAME} \
-		       --with-blaslapack-dir=${MKLROOT} \
+		       --with-hdf5-dir="${WORKDIR}"/${HDF5_DIR_NAME} \
+		       --with-blaslapack-dir="${MKLROOT}" \
 		       --download-metis=1 \
 		       --download-parmetis=1 \
 		       --download-ptscotch=1 \
 		       --download-mumps=1 \
-		       --download-superlu_dist=${WORKDIR}/superlu_dist-8.1.0.tar.gz \
+		       --download-superlu_dist="${WORKDIR}"/superlu_dist-8.1.0.tar.gz \
 		       --download-scalapack=1 \
 		       --download-slepc=1 \
 		       --with-mpi=1 \
@@ -128,13 +128,13 @@ function _build_petsc() {
 		       --with-fortran-bindings=0 \
 		       --with-sowing=0 \
 		       --with-64-bit-indices \
-		       --with-make-np=${SLURM_NTASKS} \
+		       --with-make-np="${SLURM_NTASKS}" \
 		       COPTFLAGS='-O3 -fno-slp-vectorize' \
 		       CXXOPTFLAGS='-O3 -fno-slp-vectorize' \
                FOPTFLAGS='-O3 -fno-slp-vectorize' \
-	           PETSC_DIR=`pwd` PETSC_ARCH=arch-linux-c-opt
+	           PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
     make
-    make PETSC_DIR=${WORKDIR}/${PETSC_DIR_NAME}/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install \
+    make PETSC_DIR="${WORKDIR}"/${PETSC_DIR_NAME}/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install \
 	|| { echo "Failed to build petsc" ; exit 1 ; }
     cd ..
     cd ..
@@ -143,13 +143,13 @@ function _build_petsc() {
 
 function build_moose() {
     export MOOSE_JOBS=32
-    cd $WORKDIR 
+    cd "$WORKDIR" || exit 1
     # if [ -d "$WORKDIR/moose" ] ; then
     #    return
     # fi
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     git clone https://github.com/idaholab/moose
-    cd moose
+    cd moose || exit 1
     git checkout ${MOOSE_COMMIT} || { echo "Checkout failed" ; exit 1 ; }
     if [ ! -f "$WORKDIR/petsc/lib/libpetsc.so" ] ; then
       echo "PETSc Install Unsuccessful"
@@ -198,13 +198,13 @@ function build_moose() {
   
     ./configure --with-derivative-size=200 --with-ad-indexing-type=global
     METHODS='opt' ./scripts/update_and_rebuild_wasp.sh
-    cd framework
+    cd framework || exit 1
     METHOD=opt make -j"$compile_cores"
     cd ..
-    cd modules
+    cd modules || exit 1
     METHOD=opt make -j"$compile_cores"
     cd ..
-    cd test
+    cd test || exit 1
     METHOD=opt make -j"$compile_cores"
     ./run_tests -j"$compile_cores"
     cd ..
@@ -212,69 +212,69 @@ function build_moose() {
 }
 
 function build_gslib() {
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     if [ -d "$WORKDIR/gslb" ] ; then
        return
     fi
     git clone https://github.com/Nek5000/gslib.git
-    cd gslib
+    cd gslib || exit 1
     make CFLAGS='-O2 -fPIC'
 }
 
 function build_mfem() {
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     # if [ -d "$WORKDIR/mfem" ] ; then
     #    return
     # fi
     git clone https://github.com/Heinrich-BR/mfem.git
-    cd mfem
+    cd mfem || exit 1
     git checkout SubmeshBoundary
-    sed -i "s|list|# list|g" $WORKDIR/mfem/config/cmake/modules/FindNetCDF.cmake
+    sed -i "s|list|# list|g" "$WORKDIR"/mfem/config/cmake/modules/FindNetCDF.cmake
     mkdir build
-    cd build
+    cd build || exit 1
     echo "Building MFEM"
     cmake .. \
         -DCMAKE_BUILD_TYPE=Release \
 	    -DCMAKE_POSITION_INDEPENDENT_CODE=YES \
 	    -DMFEM_USE_OPENMP=NO \
 	    -DMFEM_THREAD_SAFE=NO \
-        -DHYPRE_DIR=/$WORKDIR/petsc/ \
+        -DHYPRE_DIR=/"$WORKDIR"/petsc/ \
         -DMFEM_USE_LAPACK=YES \
         -DMFEM_USE_MPI=YES \
         -DMFEM_USE_METIS_5=YES \
-        -DMETIS_DIR=/$WORKDIR/petsc/ \
-        -DParMETIS_DIR=/$WORKDIR/petsc/ \
+        -DMETIS_DIR=/"$WORKDIR"/petsc/ \
+        -DParMETIS_DIR=/"$WORKDIR"/petsc/ \
         -DMFEM_USE_SUPERLU=YES \
-        -DSuperLUDist_DIR=/$WORKDIR/petsc/ \
+        -DSuperLUDist_DIR=/"$WORKDIR"/petsc/ \
         -DSuperLUDist_VERSION_OK=YES \
         -DMFEM_USE_NETCDF=YES \
-        -DNETCDF_LIBRARIES=$WORKDIR/moose/libmesh/installed/lib/libnetcdf.so \
-        -DNETCDF_INCLUDE_DIRS=$WORKDIR/moose/libmesh/contrib/netcdf/netcdf-c-4.6.2/include \
-        -DHDF5_DIR=/$WORKDIR/${HDF5_DIR_NAME}/ \
+        -DNETCDF_LIBRARIES="$WORKDIR"/moose/libmesh/installed/lib/libnetcdf.so \
+        -DNETCDF_INCLUDE_DIRS="$WORKDIR"/moose/libmesh/contrib/netcdf/netcdf-c-4.6.2/include \
+        -DHDF5_DIR=/"$WORKDIR"/${HDF5_DIR_NAME}/ \
         -DMFEM_USE_GSLIB=YES \
-      	-DGSLIB_DIR=/$WORKDIR/gslib/build
+        -DGSLIB_DIR=/"$WORKDIR"/gslib/build
     make -j"$compile_cores"
-    cd miniapps/common
+    cd miniapps/common || exit 1
     make -j"$compile_cores"
 }
 
 function build_platypus() {
-    cd $WORKDIR
+    cd "$WORKDIR" || exit 1
     # if [ -d "$WORKDIR/platypus" ] ; then
     #    return
     # fi
 
     git clone https://github.com/aurora-multiphysics/platypus.git
-    cd platypus
+    cd platypus || exit 1
     git checkout ${PLATYPUS_COMMIT}
     git submodule update --init --recursive
-    cd contrib/hephaestus/
+    cd contrib/hephaestus/ || exit 1
     # git checkout master
     mkdir build
-    cd build
-    cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DMFEM_DIR=/$WORKDIR/mfem/build ..
+    cd build || exit 1
+    cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DMFEM_DIR=/"$WORKDIR"/mfem/build ..
     ninja
-    cd /$WORKDIR/platypus
+    cd /"$WORKDIR"/platypus || exit 1
     make -j"$compile_cores"
 }
 
diff --git a/scripts/install-format-hook.sh b/scripts/install-format-hook.sh
index 44a2037a..004318a2 100755
--- a/scripts/install-format-hook.sh
+++ b/scripts/install-format-hook.sh
@@ -20,7 +20,7 @@ else
     echo "$patch"
     exit 1
 fi
-' > $hookfile
+' > "$hookfile"
 
-chmod a+x $hookfile
+chmod a+x "$hookfile"
 
diff --git a/scripts/upload-coverage.sh b/scripts/upload-coverage.sh
new file mode 100755
index 00000000..7157dc51
--- /dev/null
+++ b/scripts/upload-coverage.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+cd /opt/platypus || exit 1
+
+for filename in $(find build -name "*.C"); 
+do 
+  gcov -n -o . "$filename" > /dev/null; 
+done
+
+bash <(curl -s https://codecov.io/bash)
diff --git a/upload-coverage.sh b/upload-coverage.sh
deleted file mode 100644
index fbff8588..00000000
--- a/upload-coverage.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-cd /opt/platypus
-
-for filename in `find src -name "*.C"`; 
-do 
-  gcov -n -o . $filename > /dev/null; 
-done
-
-bash <(curl -s https://codecov.io/bash)

From 8df4908aa35d0cb26866d24aac238a7f0caaf5cc Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 16:27:46 +0100
Subject: [PATCH 11/26] Adjusted path to coverage upload script

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

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0aaa5fbc..9fe98b45 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -31,4 +31,4 @@ jobs:
       - name: UploadCoverage
         run: |
           ci_env=`bash <(curl -s https://codecov.io/env)`
-          docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash opt/platypus/upload-coverage.sh
+          docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash opt/platypus/scripts/upload-coverage.sh

From 86f54051ce1b32d35c5914af1e0b6b96f607e64a Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 17:50:23 +0100
Subject: [PATCH 12/26] Configured linters and tried to correct issues with
 them

---
 .github/linters/.clang-format      |  1 +
 .github/linters/.markdown-lint.yml | 35 ++++++++++++++++++++++++++++++
 .github/linters/.yaml-lint.yml     | 11 ++++++++++
 .github/workflows/lint.yml         | 12 ++++++++++
 .github/workflows/main.yml         | 12 +++++-----
 .pre-commit-config.yaml            |  3 ++-
 doc/config.yml                     |  1 +
 docker/platypus-deps/Dockerfile    | 18 +++++++--------
 docker/platypus/Dockerfile         | 20 ++++++++---------
 platypus.yaml                      |  7 +++---
 10 files changed, 92 insertions(+), 28 deletions(-)
 create mode 120000 .github/linters/.clang-format
 create mode 100644 .github/linters/.markdown-lint.yml
 create mode 100644 .github/linters/.yaml-lint.yml

diff --git a/.github/linters/.clang-format b/.github/linters/.clang-format
new file mode 120000
index 00000000..2d112372
--- /dev/null
+++ b/.github/linters/.clang-format
@@ -0,0 +1 @@
+../../.clang-format
\ No newline at end of file
diff --git a/.github/linters/.markdown-lint.yml b/.github/linters/.markdown-lint.yml
new file mode 100644
index 00000000..a694d1b7
--- /dev/null
+++ b/.github/linters/.markdown-lint.yml
@@ -0,0 +1,35 @@
+---
+###########################
+###########################
+## Markdown Linter rules ##
+###########################
+###########################
+
+# Linter rules doc:
+# - https://github.com/DavidAnson/markdownlint
+#
+# Note:
+# To comment out a single error:
+#   <!-- markdownlint-disable -->
+#   any violations you want
+#   <!-- markdownlint-restore -->
+#
+
+###############
+# Rules by id #
+###############
+MD004: false                  # Unordered list style
+MD007:
+  indent: 2                   # Unordered list indentation
+MD013:
+  line_length: 100            # Line length 80 is far too short
+MD026:
+  punctuation: ".,;:!。，；:"  # List of not allowed
+MD029: false                  # Ordered list item prefix
+MD033: false                  # Allow inline HTML
+MD041: false                  # Allow MOOSE configuration data before first heading
+
+#################
+# Rules by tags #
+#################
+blank_lines: false  # Error on blank lines
diff --git a/.github/linters/.yaml-lint.yml b/.github/linters/.yaml-lint.yml
new file mode 100644
index 00000000..b0bc8c54
--- /dev/null
+++ b/.github/linters/.yaml-lint.yml
@@ -0,0 +1,11 @@
+extends: default
+
+ignore:
+  - syntax.yaml
+
+line-length:
+    level: warning
+    max: 100
+    allow-non-breakable-words: true
+    allow-non-breakable-inline-mappings: true
+ 
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 65ed6650..14a25bd2 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -1,3 +1,4 @@
+---
 name: Lint
 
 on:
@@ -31,6 +32,17 @@ jobs:
 
       - name: Super-linter
         uses: super-linter/super-linter/slim@v6.6.0
+        with:
+          VALIDATE_ANSIBLE: false
+          VALIDATE_CHECKOV: false
+          VALIDATE_CPP: false
+          VALIDATE_JSCPD: false
+          VALIDATE_PYTHON_BLACK: false
+          VALIDATE_PYTHON_FLAKE8: false
+          VALIDATE_PYTHON_ISORT: false
+          VALIDATE_PYTHON_MYPY: false
+          VALIDATE_PYTHON_PYLINT: false
+          VALIDATE_PYTHON_RUFF: false
         env:
           # To report GitHub Actions status checks
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9fe98b45..3eb03a4e 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,3 +1,4 @@
+---
 name: BuildTest
 on:
   push:
@@ -17,18 +18,19 @@ jobs:
     steps:
       # First check out the repository to get the docker file
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       # Print the context for this GitHub workflow
       - name: PrintGithubContext
-        run: echo ${PRCOMMITSHA:-$GITHUB_SHA} ${PRREPOSITORY:-$GITHUB_REPOSITORY}
+        run: echo "${PRCOMMITSHA:-$GITHUB_SHA}" "${PRREPOSITORY:-$GITHUB_REPOSITORY}"
       # Now build in a container with all deps
       - name: DockerBuildTest
         run: |
              docker build -t ci-platypus-ubuntu \
-                          --build-arg build_git_sha=${PRCOMMITSHA:-$GITHUB_SHA} \
-                          --build-arg build_git_repo=${PRREPOSITORY:-$GITHUB_REPOSITORY} \
+                          --build-arg build_git_sha="${PRCOMMITSHA:-$GITHUB_SHA}" \
+                          --build-arg build_git_repo="${PRREPOSITORY:-$GITHUB_REPOSITORY}" \
                           docker/platypus
       - name: UploadCoverage
         run: |
-          ci_env=`bash <(curl -s https://codecov.io/env)`
+          ci_env=$(bash <(curl -s https://codecov.io/env))
+          # shellcheck disable=SC2086
           docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash opt/platypus/scripts/upload-coverage.sh
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b8aee6cb..60809f66 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,3 +1,4 @@
+---
 repos:
 - repo: https://github.com/pre-commit/mirrors-clang-format
   rev: v14.0.6
@@ -8,4 +9,4 @@ repos:
   rev: v1.3.5
   hooks:
   - id: clang-tidy
-    args: [-p=./build, -config-file=./.clang-tidy, --warnings-as-errors=*, -extra-arg=-std=c++17, -extra-arg=-stdlib=libstdc++]
\ No newline at end of file
+    args: [-p=./build, -config-file=./.clang-tidy, --warnings-as-errors=*, -extra-arg=-std=c++17, -extra-arg=-stdlib=libstdc++]
diff --git a/doc/config.yml b/doc/config.yml
index 0cfa7005..95128cfc 100644
--- a/doc/config.yml
+++ b/doc/config.yml
@@ -1,3 +1,4 @@
+---
 Content:
     Platypus:
         root_dir: ${ROOT_DIR}/doc/content
diff --git a/docker/platypus-deps/Dockerfile b/docker/platypus-deps/Dockerfile
index 2b2bf6a3..d6b90fcf 100644
--- a/docker/platypus-deps/Dockerfile
+++ b/docker/platypus-deps/Dockerfile
@@ -9,8 +9,8 @@ ARG compile_cores=4
 ARG WORKDIR=opt
 
 # Configure MOOSE
+WORKDIR /$WORKDIR
 RUN export MOOSE_JOBS=$compile_cores && \
-    cd /$WORKDIR && \
     git clone https://github.com/idaholab/moose && \
     cd moose && \
     git checkout master && \
@@ -25,23 +25,23 @@ RUN export MOOSE_JOBS=$compile_cores && \
     ./configure --with-derivative-size=200
 
 # Build WASP
-RUN cd /$WORKDIR/moose/scripts && \
-    METHODS=opt ./update_and_rebuild_wasp.sh
+WORKDIR /$WORKDIR/moose/scripts
+RUN METHODS=opt ./update_and_rebuild_wasp.sh
 
 # Build MOOSE
-RUN cd /$WORKDIR/moose/framework && \
-    METHOD=opt make -j$compile_cores
+WORKDIR /$WORKDIR/moose/framework
+RUN METHOD=opt make -j$compile_cores
 
-RUN cd /$WORKDIR/moose/test && \
-    METHOD=opt make -j$compile_cores
+WORKDIR /$WORKDIR/moose/test
+RUN METHOD=opt make -j$compile_cores
 
 # This is needed or it mpiexec complains because docker runs as root
 # Discussion on this issue https://github.com/open-mpi/ompi/issues/4451
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
-# RUN cd /$WORKDIR/moose/test && \
-#     ./run_tests -j"$compile_cores" --re='(?!initial_condition.newton_with_exact_initialization)'
+# WORKDIR /$WORKDIR/moose/test
+# RUN ./run_tests -j"$compile_cores" --re='(?!initial_condition.newton_with_exact_initialization)'
 
 # ENV OMPI_ALLOW_RUN_AS_ROOT=
 # ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=
diff --git a/docker/platypus/Dockerfile b/docker/platypus/Dockerfile
index 327c7455..cedb9970 100644
--- a/docker/platypus/Dockerfile
+++ b/docker/platypus/Dockerfile
@@ -16,27 +16,27 @@ ARG WORKDIR=opt
 ARG coverage=false
 
 # Get Platypus with Hephaestus
-RUN cd /$WORKDIR && \
-    git clone https://github.com/$build_git_repo && \
+WORKDIR /$WORKDIR 
+RUN git clone https://github.com/$build_git_repo && \
     cd platypus && \
     git checkout $build_git_sha && \
     git submodule update --init --recursive
 
 # Build Hephaestus
-RUN cd /$WORKDIR/platypus/contrib/hephaestus/ && \
-    mkdir build && \
+WORKDIR /$WORKDIR/platypus/contrib/hephaestus/
+RUN mkdir build && \
     cd build && \
     cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DMFEM_DIR=/$WORKDIR/mfem/build .. && \
     ninja
 
 # Test Hephaestus
-RUN cd /$WORKDIR/platypus/contrib/hephaestus/build && \
-    ninja test
+WORKDIR /$WORKDIR/platypus/contrib/hephaestus/build
+RUN ninja test
 
 # Build Platypus
-RUN cd /$WORKDIR/platypus && \
-    make -j$compile_cores coverage=$coverage
+WORKDIR /$WORKDIR/platypus
+RUN make -j$compile_cores coverage=$coverage
 
 # Test Platypus
-RUN cd /$WORKDIR/platypus && \
-    make test linkcoverage=$coverage
+WORKDIR /$WORKDIR/platypus
+RUN make test linkcoverage=$coverage
diff --git a/platypus.yaml b/platypus.yaml
index ff87e7db..99471ace 100644
--- a/platypus.yaml
+++ b/platypus.yaml
@@ -1,9 +1,10 @@
+---
 DMETHOD: opt
 Werror: reorder
 compiler_type: gcc
 documentation: true
 installation_type: in_tree
 registered_apps:
-- WASPAPP
-- PLATYPUSAPP
-- PLATYPUSTESTAPP
+  - WASPAPP
+  - PLATYPUSAPP
+  - PLATYPUSTESTAPP

From 5cddb1a50ff5bedcaad62f2ffd70239f04d7781f Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 18:12:50 +0100
Subject: [PATCH 13/26] Fixed path to upload script

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

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3eb03a4e..577d6be6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -33,4 +33,4 @@ jobs:
         run: |
           ci_env=$(bash <(curl -s https://codecov.io/env))
           # shellcheck disable=SC2086
-          docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash opt/platypus/scripts/upload-coverage.sh
+          docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash /opt/platypus/scripts/upload-coverage.sh

From a465503d1a0b1fb85eb13fafbf05ced6e4a53e9c Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 19:00:51 +0100
Subject: [PATCH 14/26] Applied shfmt

---
 .editorconfig                           |  6 ++
 scripts/build-platypus-csd3-cclake.sh   | 78 ++++++++++----------
 scripts/build-platypus-csd3-sapphire.sh | 96 ++++++++++++++-----------
 scripts/install-format-hook.sh          |  3 +-
 scripts/upload-coverage.sh              |  5 +-
 unit/run_tests                          | 16 ++---
 6 files changed, 109 insertions(+), 95 deletions(-)
 create mode 100644 .editorconfig

diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 00000000..cae7cdab
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,6 @@
+[{*.sh,run_tests}]
+indent_style = space
+indent_size = 4
+space_redirects = true
+keep_padding = true
+never_split = true
\ No newline at end of file
diff --git a/scripts/build-platypus-csd3-cclake.sh b/scripts/build-platypus-csd3-cclake.sh
index e372fe5f..9b51d8ef 100755
--- a/scripts/build-platypus-csd3-cclake.sh
+++ b/scripts/build-platypus-csd3-cclake.sh
@@ -16,8 +16,8 @@ function load_modules() {
 function build_petsc() {
     cd "$WORKDIR" || exit 1
     curl -LJO https://github.com/xiaoyeli/superlu_dist/archive/refs/tags/v8.1.0.tar.gz
-    if [ -d "$WORKDIR/petsc" ] ; then
-       return
+    if [ -d "$WORKDIR/petsc" ]; then
+        return
     fi
     mkdir petsc
     cd petsc || exit 1
@@ -25,28 +25,28 @@ function build_petsc() {
     tar -xf petsc-3.19.3.tar.gz -C .
     cd petsc-3.19.3 || exit 1
     ./configure \
-	--prefix="$WORKDIR"/petsc \
+        --prefix="$WORKDIR"/petsc \
         CXXOPTFLAGS='-O3 -march=cascadelake -funroll-loops' COPTFLAGS='-O3 -march=cascadelake -funroll-loops' FOPTFLAGS='-O3 -march=cascadelake' \
-	--with-debugging=0 \
-	--with-ssl=0 \
-	--with-pic=1 \
-	--with-openmp=1 \
-	--with-mpi=1 \
-	--with-shared-libraries=1 \
-    --with-fortran-bindings=0 \
-    --with-sowing=0 \
-    --download-hypre=1 \
-    --download-fblaslapack=1 \
-    --download-metis=1 \
-    --download-ptscotch=1 \
-    --download-parmetis=1 \
-    --download-superlu_dist="$WORKDIR"/superlu_dist-8.1.0.tar.gz \
-    --download-scalapack=1 \
-    --download-mumps=1 \
-    --download-slepc=1 \
-    --with-64-bit-indices=1 \
-    --with-mpi-dir=/usr/local/Cluster-Apps/openmpi/gcc/9.3/4.0.4 \
-    PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
+        --with-debugging=0 \
+        --with-ssl=0 \
+        --with-pic=1 \
+        --with-openmp=1 \
+        --with-mpi=1 \
+        --with-shared-libraries=1 \
+        --with-fortran-bindings=0 \
+        --with-sowing=0 \
+        --download-hypre=1 \
+        --download-fblaslapack=1 \
+        --download-metis=1 \
+        --download-ptscotch=1 \
+        --download-parmetis=1 \
+        --download-superlu_dist="$WORKDIR"/superlu_dist-8.1.0.tar.gz \
+        --download-scalapack=1 \
+        --download-mumps=1 \
+        --download-slepc=1 \
+        --with-64-bit-indices=1 \
+        --with-mpi-dir=/usr/local/Cluster-Apps/openmpi/gcc/9.3/4.0.4 \
+        PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
     make
     make PETSC_DIR="$WORKDIR"/petsc/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install
     make PETSC_DIR="$WORKDIR"/petsc PETSC_ARCH="" check
@@ -58,19 +58,19 @@ function build_petsc() {
 function build_moose() {
     export MOOSE_JOBS=32
     cd "$WORKDIR" || exit 1
-    if [ -d "$WORKDIR/moose" ] ; then
-       return
+    if [ -d "$WORKDIR/moose" ]; then
+        return
     fi
-#    _build_mpich33
+    # _build_mpich33
     load_modules
-    #build_vtk_git
+    # build_vtk_git
     cd "$WORKDIR" || exit 1
     git clone https://github.com/idaholab/moose
     cd moose || exit 1
     git checkout master
-    if [ ! -f "$WORKDIR/petsc/lib/libpetsc.so" ] ; then
-      echo "PETSc Install Unsuccessful"
-      return
+    if [ ! -f "$WORKDIR/petsc/lib/libpetsc.so" ]; then
+        echo "PETSc Install Unsuccessful"
+        return
     fi
 
     export PETSC_DIR=$WORKDIR/petsc
@@ -80,12 +80,12 @@ function build_moose() {
     export F90=mpif90
     export F77=mpif77
     export FC=mpif90
-    if [ -d "$WORKDIR/vtk" ] ; then
-      echo "building libmesh with VTK"
-      METHODS='opt' ./scripts/update_and_rebuild_libmesh.sh --with-mpi --with-cxx-std=2017 --with-vtk-include="$WORKDIR"/vtk/include/vtk-9.1 --with-vtk-lib="$WORKDIR"/vtk/lib64
+    if [ -d "$WORKDIR/vtk" ]; then
+        echo "building libmesh with VTK"
+        METHODS='opt' ./scripts/update_and_rebuild_libmesh.sh --with-mpi --with-cxx-std=2017 --with-vtk-include="$WORKDIR"/vtk/include/vtk-9.1 --with-vtk-lib="$WORKDIR"/vtk/lib64
     else
-      echo "Building libmesh withOUT VTK"
-      METHODS='opt' ./scripts/update_and_rebuild_libmesh.sh --with-mpi
+        echo "Building libmesh withOUT VTK"
+        METHODS='opt' ./scripts/update_and_rebuild_libmesh.sh --with-mpi
     fi
     ./configure --with-derivative-size=200 --with-ad-indexing-type=global
     METHODS='opt' ./scripts/update_and_rebuild_wasp.sh
@@ -104,8 +104,8 @@ function build_moose() {
 
 function build_mfem() {
     cd "$WORKDIR" || exit 1
-    if [ -d "$WORKDIR/mfem" ] ; then
-       return
+    if [ -d "$WORKDIR/mfem" ]; then
+        return
     fi
     git clone https://github.com/Heinrich-BR/mfem.git
     cd mfem || exit 1
@@ -141,8 +141,8 @@ function build_mfem() {
 
 function build_platypus() {
     cd "$WORKDIR" || exit 1
-    if [ -d "$WORKDIR/platypus" ] ; then
-       return
+    if [ -d "$WORKDIR/platypus" ]; then
+        return
     fi
 
     git clone https://github.com/aurora-multiphysics/platypus.git
diff --git a/scripts/build-platypus-csd3-sapphire.sh b/scripts/build-platypus-csd3-sapphire.sh
index 2c8a2b53..e4f5819c 100755
--- a/scripts/build-platypus-csd3-sapphire.sh
+++ b/scripts/build-platypus-csd3-sapphire.sh
@@ -8,7 +8,7 @@
 #SBATCH --cpus-per-task=1
 #SBATCH -o out_%j_%A_%a
 #SBATCH --exclusive
-. /etc/profile.d/modules.sh  
+. /etc/profile.d/modules.sh
 
 #TODO:
 # - Remove xdr requirement from moose/scripts/configure_libmesh
@@ -59,7 +59,7 @@ function load_modules() {
     echo "-Wno-tautological-constant-compare" >> icpx.cfg
     export ICPXCFG=${WORKDIR}/icpx.cfg
 
-    export CC=mpiicc 
+    export CC=mpiicc
     export CXX=mpiicpc
     export FC=mpiifort
     export F77=mpiifort
@@ -68,20 +68,26 @@ function load_modules() {
     export I_MPI_CXX=icpx
     export I_MPI_F90=ifx
     export I_MPI_FC=ifx
-    export I_MPI_F77=ifx  
+    export I_MPI_F77=ifx
 }
 
 function _build_hdf5() {
     cd "${WORKDIR}" || exit 1
-    mkdir -p ${HDF5_DIR_NAME} || { echo "Failed to create ${HDF5_DIR_NAME}" ; exit 1 ; }
+    mkdir -p ${HDF5_DIR_NAME} || {
+        echo "Failed to create ${HDF5_DIR_NAME}"
+        exit 1
+    }
 
     HDF5_MAJ_VER=1.10
     HDF5_MIN_VER=10
     HDF5_VER=${HDF5_MAJ_VER}.${HDF5_MIN_VER}
     echo "Downloading HDF5"
     curl -kLJO \
-        https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_MAJ_VER}/hdf5-${HDF5_VER}/src/hdf5-${HDF5_VER}.tar.gz \
-        || { echo "Failed to download hdf5" ; exit 1 ; }
+        https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_MAJ_VER}/hdf5-${HDF5_VER}/src/hdf5-${HDF5_VER}.tar.gz ||
+        {
+            echo "Failed to download hdf5"
+            exit 1
+        }
     tar -xf hdf5-${HDF5_VER}.tar.gz
 
     cd hdf5-${HDF5_VER} || exit 1
@@ -92,7 +98,7 @@ function _build_hdf5() {
         echo "HDF5 Build failed"
         exit 1
     fi
-    echo "HDF5 built" 
+    echo "HDF5 built"
 }
 
 function _build_petsc() {
@@ -109,33 +115,36 @@ function _build_petsc() {
     tar -xf petsc-3.19.3.tar.gz -C .
     cd petsc-3.19.3 || exit 1
     ./configure \
-    --with-cc=$CC --with-cxx=$CXX --with-fc=$FC -CXXPP=cpp \
-		       --prefix="${WORKDIR}"/${PETSC_DIR_NAME} \
-		       --download-hypre=1 \
-		       --with-shared-libraries \
-		       --with-debugging=no \
-		       --with-hdf5-dir="${WORKDIR}"/${HDF5_DIR_NAME} \
-		       --with-blaslapack-dir="${MKLROOT}" \
-		       --download-metis=1 \
-		       --download-parmetis=1 \
-		       --download-ptscotch=1 \
-		       --download-mumps=1 \
-		       --download-superlu_dist="${WORKDIR}"/superlu_dist-8.1.0.tar.gz \
-		       --download-scalapack=1 \
-		       --download-slepc=1 \
-		       --with-mpi=1 \
-		       --with-cxx-dialect=C++17 \
-		       --with-fortran-bindings=0 \
-		       --with-sowing=0 \
-		       --with-64-bit-indices \
-		       --with-make-np="${SLURM_NTASKS}" \
-		       COPTFLAGS='-O3 -fno-slp-vectorize' \
-		       CXXOPTFLAGS='-O3 -fno-slp-vectorize' \
+        --with-cc=$CC --with-cxx=$CXX --with-fc=$FC -CXXPP=cpp \
+         --prefix="${WORKDIR}"/${PETSC_DIR_NAME} \
+         --download-hypre=1 \
+         --with-shared-libraries \
+         --with-debugging=no \
+         --with-hdf5-dir="${WORKDIR}"/${HDF5_DIR_NAME} \
+         --with-blaslapack-dir="${MKLROOT}" \
+         --download-metis=1 \
+         --download-parmetis=1 \
+         --download-ptscotch=1 \
+         --download-mumps=1 \
+         --download-superlu_dist="${WORKDIR}"/superlu_dist-8.1.0.tar.gz \
+         --download-scalapack=1 \
+         --download-slepc=1 \
+         --with-mpi=1 \
+         --with-cxx-dialect=C++17 \
+         --with-fortran-bindings=0 \
+         --with-sowing=0 \
+         --with-64-bit-indices \
+         --with-make-np="${SLURM_NTASKS}" \
+         COPTFLAGS='-O3 -fno-slp-vectorize' \
+         CXXOPTFLAGS='-O3 -fno-slp-vectorize' \
                FOPTFLAGS='-O3 -fno-slp-vectorize' \
-	           PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
+            PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
     make
-    make PETSC_DIR="${WORKDIR}"/${PETSC_DIR_NAME}/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install \
-	|| { echo "Failed to build petsc" ; exit 1 ; }
+    make PETSC_DIR="${WORKDIR}"/${PETSC_DIR_NAME}/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install ||
+        {
+            echo "Failed to build petsc"
+            exit 1
+        }
     cd ..
     cd ..
     export PETSC_DIR=$WORKDIR/petsc
@@ -150,10 +159,13 @@ function build_moose() {
     cd "$WORKDIR" || exit 1
     git clone https://github.com/idaholab/moose
     cd moose || exit 1
-    git checkout ${MOOSE_COMMIT} || { echo "Checkout failed" ; exit 1 ; }
-    if [ ! -f "$WORKDIR/petsc/lib/libpetsc.so" ] ; then
-      echo "PETSc Install Unsuccessful"
-      return
+    git checkout ${MOOSE_COMMIT} || {
+        echo "Checkout failed"
+        exit 1
+    }
+    if [ ! -f "$WORKDIR/petsc/lib/libpetsc.so" ]; then
+        echo "PETSc Install Unsuccessful"
+        return
     fi
     export PETSC_DIR=$WORKDIR/petsc
     export PETSC_ARCH=arch-linux-c-opt
@@ -195,7 +207,7 @@ function build_moose() {
     export I_MPI_F90=ifx
     export I_MPI_F77=ifx
     export I_MPI_C=icx
-  
+
     ./configure --with-derivative-size=200 --with-ad-indexing-type=global
     METHODS='opt' ./scripts/update_and_rebuild_wasp.sh
     cd framework || exit 1
@@ -213,8 +225,8 @@ function build_moose() {
 
 function build_gslib() {
     cd "$WORKDIR" || exit 1
-    if [ -d "$WORKDIR/gslb" ] ; then
-       return
+    if [ -d "$WORKDIR/gslb" ]; then
+        return
     fi
     git clone https://github.com/Nek5000/gslib.git
     cd gslib || exit 1
@@ -235,9 +247,9 @@ function build_mfem() {
     echo "Building MFEM"
     cmake .. \
         -DCMAKE_BUILD_TYPE=Release \
-	    -DCMAKE_POSITION_INDEPENDENT_CODE=YES \
-	    -DMFEM_USE_OPENMP=NO \
-	    -DMFEM_THREAD_SAFE=NO \
+        -DCMAKE_POSITION_INDEPENDENT_CODE=YES \
+        -DMFEM_USE_OPENMP=NO \
+        -DMFEM_THREAD_SAFE=NO \
         -DHYPRE_DIR=/"$WORKDIR"/petsc/ \
         -DMFEM_USE_LAPACK=YES \
         -DMFEM_USE_MPI=YES \
diff --git a/scripts/install-format-hook.sh b/scripts/install-format-hook.sh
index 004318a2..27f45815 100755
--- a/scripts/install-format-hook.sh
+++ b/scripts/install-format-hook.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-REPO_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/../"
+REPO_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}")"  && pwd)/../"
 hookfile="$REPO_DIR/.git/hooks/pre-commit"
 
 if [[ -f $hookfile ]]; then
@@ -23,4 +23,3 @@ fi
 ' > "$hookfile"
 
 chmod a+x "$hookfile"
-
diff --git a/scripts/upload-coverage.sh b/scripts/upload-coverage.sh
index 7157dc51..8fbbabde 100755
--- a/scripts/upload-coverage.sh
+++ b/scripts/upload-coverage.sh
@@ -2,9 +2,8 @@
 
 cd /opt/platypus || exit 1
 
-for filename in $(find build -name "*.C"); 
-do 
-  gcov -n -o . "$filename" > /dev/null; 
+for filename in $(find build -name "*.C"); do
+    gcov -n -o . "$filename" > /dev/null
 done
 
 bash <(curl -s https://codecov.io/bash)
diff --git a/unit/run_tests b/unit/run_tests
index f79debb7..8c95970b 100755
--- a/unit/run_tests
+++ b/unit/run_tests
@@ -3,16 +3,14 @@
 APPLICATION_NAME=platypus
 # If $METHOD is not set, use opt
 if [ -z $METHOD ]; then
-  export METHOD=opt
+    export METHOD=opt
 fi
 
-if [ -e ./unit/$APPLICATION_NAME-unit-$METHOD ]
-then
-  ./unit/$APPLICATION_NAME-unit-$METHOD
-elif [ -e ./$APPLICATION_NAME-unit-$METHOD ]
-then
-  ./$APPLICATION_NAME-unit-$METHOD
+if [ -e ./unit/$APPLICATION_NAME-unit-$METHOD ]; then
+    ./unit/$APPLICATION_NAME-unit-$METHOD
+elif [ -e ./$APPLICATION_NAME-unit-$METHOD ]; then
+    ./$APPLICATION_NAME-unit-$METHOD
 else
-  echo "Executable missing!"
-  exit 1
+    echo "Executable missing!"
+    exit 1
 fi

From 6b66e2bfe659b222b240ffc85e3e5922acd34775 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 19:03:03 +0100
Subject: [PATCH 15/26] Applied clang-format

---
 test/include/base/PlatypusTestApp.h | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/include/base/PlatypusTestApp.h b/test/include/base/PlatypusTestApp.h
index ff8133e2..82119365 100644
--- a/test/include/base/PlatypusTestApp.h
+++ b/test/include/base/PlatypusTestApp.h
@@ -13,4 +13,3 @@ class PlatypusTestApp : public MooseApp
   static void registerApps();
   static void registerAll(Factory & f, ActionFactory & af, Syntax & s, bool use_test_objs = false);
 };
-

From dc2c3af8871dc274b6bccbd3bd6666c75721f4a0 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 19:03:50 +0100
Subject: [PATCH 16/26] Ignore some unavoidable hadolint errors

---
 docker/platypus-deps/Dockerfile | 1 +
 docker/platypus/Dockerfile      | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/docker/platypus-deps/Dockerfile b/docker/platypus-deps/Dockerfile
index d6b90fcf..7188db5c 100644
--- a/docker/platypus-deps/Dockerfile
+++ b/docker/platypus-deps/Dockerfile
@@ -10,6 +10,7 @@ ARG WORKDIR=opt
 
 # Configure MOOSE
 WORKDIR /$WORKDIR
+# hadolint ignore=DL3003
 RUN export MOOSE_JOBS=$compile_cores && \
     git clone https://github.com/idaholab/moose && \
     cd moose && \
diff --git a/docker/platypus/Dockerfile b/docker/platypus/Dockerfile
index cedb9970..5e0832cd 100644
--- a/docker/platypus/Dockerfile
+++ b/docker/platypus/Dockerfile
@@ -17,6 +17,7 @@ ARG coverage=false
 
 # Get Platypus with Hephaestus
 WORKDIR /$WORKDIR 
+# hadolint ignore=DL3003
 RUN git clone https://github.com/$build_git_repo && \
     cd platypus && \
     git checkout $build_git_sha && \
@@ -24,6 +25,7 @@ RUN git clone https://github.com/$build_git_repo && \
 
 # Build Hephaestus
 WORKDIR /$WORKDIR/platypus/contrib/hephaestus/
+# hadolint ignore=DL3003
 RUN mkdir build && \
     cd build && \
     cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DMFEM_DIR=/$WORKDIR/mfem/build .. && \

From b3b7b0ccdc25e70f3ec251828ca6643543d327a3 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 19:04:34 +0100
Subject: [PATCH 17/26] Fix YAML formatting

---
 .github/linters/.yaml-lint.yml     | 67 ++++++++++++++++++++++++++----
 .github/workflows/lint.yml         | 13 +++---
 .github/workflows/main.yml         |  6 +--
 .github/workflows/weekly_build.yml |  3 +-
 .pre-commit-config.yaml            | 18 ++++----
 5 files changed, 79 insertions(+), 28 deletions(-)

diff --git a/.github/linters/.yaml-lint.yml b/.github/linters/.yaml-lint.yml
index b0bc8c54..c8bf34bd 100644
--- a/.github/linters/.yaml-lint.yml
+++ b/.github/linters/.yaml-lint.yml
@@ -1,11 +1,62 @@
-extends: default
-
-ignore:
-  - syntax.yaml
-
-line-length:
+---
+###########################################
+# These are the rules used for            #
+# linting all the yaml files in the stack #
+# NOTE:                                   #
+# You can disable line with:              #
+# # yamllint disable-line                 #
+###########################################
+rules:
+  braces:
+    level: warning
+    min-spaces-inside: 0
+    max-spaces-inside: 0
+    min-spaces-inside-empty: 1
+    max-spaces-inside-empty: 5
+  brackets:
+    level: warning
+    min-spaces-inside: 0
+    max-spaces-inside: 0
+    min-spaces-inside-empty: 1
+    max-spaces-inside-empty: 5
+  colons:
+    level: warning
+    max-spaces-before: 0
+    max-spaces-after: 1
+  commas:
+    level: warning
+    max-spaces-before: 0
+    min-spaces-after: 1
+    max-spaces-after: 1
+  comments: disable
+  comments-indentation: disable
+  document-end: disable
+  document-start:
     level: warning
-    max: 100
+    present: true
+  empty-lines:
+    level: warning
+    max: 2
+    max-start: 0
+    max-end: 0
+  hyphens:
+    level: warning
+    max-spaces-after: 1
+  indentation:
+    level: warning
+    spaces: consistent
+    indent-sequences: true
+    check-multi-line-strings: false
+  key-duplicates: enable
+  line-length:
+    level: warning
+    max: 80
     allow-non-breakable-words: true
     allow-non-breakable-inline-mappings: true
- 
+  new-line-at-end-of-file: disable
+  new-lines:
+    type: unix
+  trailing-spaces: disable
+
+ignore:
+  - syntax.yaml
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 14a25bd2..b64233a8 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -4,12 +4,12 @@ name: Lint
 on:
   push:
     branches:
-       - main
+      - main
   pull_request:
     branches:
-       - main
+      - main
 
-permissions: { }
+permissions: {}
 
 jobs:
   build:
@@ -32,7 +32,9 @@ jobs:
 
       - name: Super-linter
         uses: super-linter/super-linter/slim@v6.6.0
-        with:
+        env:
+          # To report GitHub Actions status checks
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           VALIDATE_ANSIBLE: false
           VALIDATE_CHECKOV: false
           VALIDATE_CPP: false
@@ -43,6 +45,3 @@ jobs:
           VALIDATE_PYTHON_MYPY: false
           VALIDATE_PYTHON_PYLINT: false
           VALIDATE_PYTHON_RUFF: false
-        env:
-          # To report GitHub Actions status checks
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 577d6be6..58586fbc 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,17 +3,17 @@ name: BuildTest
 on:
   push:
     branches:
-       - main
+      - main
   pull_request:
     branches:
-       - main
+      - main
 
 jobs:
   docker-build-test-ubuntu:
     runs-on: ubuntu-latest
     name: BuildTestUbuntu
     env:
-      PRCOMMITSHA : ${{ github.event.pull_request.head.sha }}
+      PRCOMMITSHA: ${{ github.event.pull_request.head.sha }}
       PRREPOSITORY: ${{ github.event.pull_request.head.repo.full_name }}
     steps:
       # First check out the repository to get the docker file
diff --git a/.github/workflows/weekly_build.yml b/.github/workflows/weekly_build.yml
index cf78d9f7..1c8dbc98 100644
--- a/.github/workflows/weekly_build.yml
+++ b/.github/workflows/weekly_build.yml
@@ -1,9 +1,10 @@
+---
 name: Publish Docker Images
 on:
   workflow_dispatch:
   schedule:
     # Schedule to update image every Monday morning at 04:00.
-    - cron:  '00 4 * * 1'
+    - cron: '00 4 * * 1'
 
 jobs:
   push-platypus-deps-image-to-docker-hub:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 60809f66..db7a527b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,12 +1,12 @@
 ---
 repos:
-- repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v14.0.6
-  hooks:
-  - id: clang-format
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v14.0.6
+    hooks:
+      - id: clang-format
 
-- repo: https://github.com/pocc/pre-commit-hooks
-  rev: v1.3.5
-  hooks:
-  - id: clang-tidy
-    args: [-p=./build, -config-file=./.clang-tidy, --warnings-as-errors=*, -extra-arg=-std=c++17, -extra-arg=-stdlib=libstdc++]
+  - repo: https://github.com/pocc/pre-commit-hooks
+    rev: v1.3.5
+    hooks:
+      - id: clang-tidy
+        args: [-p=./build, -config-file=./.clang-tidy, --warnings-as-errors=*, -extra-arg=-std=c++17, -extra-arg=-stdlib=libstdc++]

From 40e5b30937dbda59d73a95ad629f1d2fce910a6d Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 19:05:23 +0100
Subject: [PATCH 18/26] Fixed very long line

---
 README.md | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ea27f3e1..faf018b8 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,12 @@ Platypus
 ![build](https://github.com/aurora-multiphysics/platypus/actions/workflows/main.yml/badge.svg?branch=main)
 [![GitHub License](https://img.shields.io/github/license/aurora-multiphysics/platypus)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html)
 
-Platypus is a MOOSE-based application created to enable custom MOOSE problems to be set up and solved using the [MFEM](https://github.com/mfem/mfem) finite element library as an alternative backend to libMesh. It is based off of the MOOSE electromagnetics app [Apollo](https://github.com/aurora-multiphysics/apollo) that uses MFEM for solving electromagnetics problems in a variety of formulations.
+Platypus is a MOOSE-based application created to enable custom MOOSE
+problems to be set up and solved using the
+[MFEM](https://github.com/mfem/mfem) finite element library as an
+alternative backend to libMesh. It is based off of the MOOSE
+electromagnetics app
+[Apollo](https://github.com/aurora-multiphysics/apollo) that uses MFEM
+for solving electromagnetics problems in a variety of formulations.
 
 Platypus is under active development and is being updated frequently.

From a3d9408b40fb6b68be91c5e4890b041b38e6930a Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 19:18:05 +0100
Subject: [PATCH 19/26] Fixed a few more YAML formatting errors

---
 .github/linters/.yaml-lint.yml | 2 +-
 .github/workflows/lint.yml     | 2 +-
 .github/workflows/main.yml     | 3 ++-
 .pre-commit-config.yaml        | 7 ++++++-
 4 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/.github/linters/.yaml-lint.yml b/.github/linters/.yaml-lint.yml
index c8bf34bd..4c44381e 100644
--- a/.github/linters/.yaml-lint.yml
+++ b/.github/linters/.yaml-lint.yml
@@ -50,7 +50,7 @@ rules:
   key-duplicates: enable
   line-length:
     level: warning
-    max: 80
+    max: 100
     allow-non-breakable-words: true
     allow-non-breakable-inline-mappings: true
   new-line-at-end-of-file: disable
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index b64233a8..c1356c40 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -9,7 +9,7 @@ on:
     branches:
       - main
 
-permissions: {}
+permissions: { }
 
 jobs:
   build:
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 58586fbc..48311070 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -33,4 +33,5 @@ jobs:
         run: |
           ci_env=$(bash <(curl -s https://codecov.io/env))
           # shellcheck disable=SC2086
-          docker run $ci_env -e CI=true ci-platypus-ubuntu:latest bash /opt/platypus/scripts/upload-coverage.sh
+          docker run $ci_env -e CI=true ci-platypus-ubuntu:latest \
+                 bash /opt/platypus/scripts/upload-coverage.sh
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index db7a527b..4cd0ef39 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,4 +9,9 @@ repos:
     rev: v1.3.5
     hooks:
       - id: clang-tidy
-        args: [-p=./build, -config-file=./.clang-tidy, --warnings-as-errors=*, -extra-arg=-std=c++17, -extra-arg=-stdlib=libstdc++]
+        args:
+          - "-p=./build"
+          - "-config-file=./.clang-tidy"
+          - "--warnings-as-errors=*"
+          - "-extra-arg=-std=c++17"
+          - "-extra-arg=-stdlib=libstdc++"

From b2fe79c9e354e36bb912efd84e86b0b3c788f686 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 19:43:16 +0100
Subject: [PATCH 20/26] Fixed remaining shellcheck errors

---
 .github/workflows/lint.yml              |  1 -
 scripts/build-platypus-csd3-cclake.sh   |  8 +++++---
 scripts/build-platypus-csd3-sapphire.sh | 14 +++++++-------
 scripts/upload-coverage.sh              |  3 ++-
 unit/run_tests                          |  8 ++++----
 5 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index c1356c40..ce30aa9f 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -33,7 +33,6 @@ jobs:
       - name: Super-linter
         uses: super-linter/super-linter/slim@v6.6.0
         env:
-          # To report GitHub Actions status checks
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           VALIDATE_ANSIBLE: false
           VALIDATE_CHECKOV: false
diff --git a/scripts/build-platypus-csd3-cclake.sh b/scripts/build-platypus-csd3-cclake.sh
index 9b51d8ef..226bfeba 100755
--- a/scripts/build-platypus-csd3-cclake.sh
+++ b/scripts/build-platypus-csd3-cclake.sh
@@ -1,8 +1,10 @@
 #!/bin/bash
 #set -ue
 
-export STACK_SRC=$(mktemp -d /tmp/moose_stack_src.XXXXXX)
-export WORKDIR=$(pwd)
+STACK_SRC=$(mktemp -d /tmp/moose_stack_src.XXXXXX)
+export STACK_SRC
+WORKDIR=$(pwd)
+export WORKDIR
 export compile_cores=32
 export OMPI_MCA_mca_base_component_show_load_errors=0
 
@@ -46,7 +48,7 @@ function build_petsc() {
         --download-slepc=1 \
         --with-64-bit-indices=1 \
         --with-mpi-dir=/usr/local/Cluster-Apps/openmpi/gcc/9.3/4.0.4 \
-        PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
+        PETSC_DIR="$(pwd)" PETSC_ARCH=arch-linux-c-opt
     make
     make PETSC_DIR="$WORKDIR"/petsc/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install
     make PETSC_DIR="$WORKDIR"/petsc PETSC_ARCH="" check
diff --git a/scripts/build-platypus-csd3-sapphire.sh b/scripts/build-platypus-csd3-sapphire.sh
index e4f5819c..d4644414 100755
--- a/scripts/build-platypus-csd3-sapphire.sh
+++ b/scripts/build-platypus-csd3-sapphire.sh
@@ -8,6 +8,7 @@
 #SBATCH --cpus-per-task=1
 #SBATCH -o out_%j_%A_%a
 #SBATCH --exclusive
+# shellcheck source=/dev/null
 . /etc/profile.d/modules.sh
 
 #TODO:
@@ -25,8 +26,10 @@ function load_modules() {
     module load python/3.8
     module load ninja
 
-    export STACK_SRC=$(mktemp -d /tmp/moose_stack_src.XXXXXX)
-    export WORKDIR=$(pwd)
+    STACK_SRC=$(mktemp -d /tmp/moose_stack_src.XXXXXX)
+    export STACK_SRC
+    WORKDIR=$(pwd)
+    export WORKDIR
     export compile_cores=8
     export OMPI_MCA_mca_base_component_show_load_errors=0
 
@@ -35,16 +38,13 @@ function load_modules() {
 
     ROOT_PATH=/home/${USER}/rds/rds-ukaea-ap001/${USER}
     BUILD_PATH=${ROOT_PATH}/${BUILD_DIR_NAME}
-    USR_PATH=${BUILD_PATH}/usr
 
     HDF5_MAJ_VER=1.10
     HDF5_MIN_VER=10
     HDF5_DIR_NAME=hdf5
     HDF5_INSTALL_PATH=${WORKDIR}/${HDF5_DIR_NAME}
 
-    PETSC_COMMIT=38aca504f6ea08cc814f159b2c9bcf837a5876f3
     PETSC_DIR_NAME=petsc
-    PETSC_INSTALL_DIR=${BUILD_PATH}/petsc
 
     MOOSE_COMMIT=4e99faf9804480e7be302895ff9b8ded5b9944ea
 
@@ -116,7 +116,7 @@ function _build_petsc() {
     cd petsc-3.19.3 || exit 1
     ./configure \
         --with-cc=$CC --with-cxx=$CXX --with-fc=$FC -CXXPP=cpp \
-         --prefix="${WORKDIR}"/${PETSC_DIR_NAME} \
+         --prefix="${WORKDIR}/${PETSC_DIR_NAME}" \
          --download-hypre=1 \
          --with-shared-libraries \
          --with-debugging=no \
@@ -138,7 +138,7 @@ function _build_petsc() {
          COPTFLAGS='-O3 -fno-slp-vectorize' \
          CXXOPTFLAGS='-O3 -fno-slp-vectorize' \
                FOPTFLAGS='-O3 -fno-slp-vectorize' \
-            PETSC_DIR=$(pwd) PETSC_ARCH=arch-linux-c-opt
+            PETSC_DIR="$(pwd)" PETSC_ARCH=arch-linux-c-opt
     make
     make PETSC_DIR="${WORKDIR}"/${PETSC_DIR_NAME}/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install ||
         {
diff --git a/scripts/upload-coverage.sh b/scripts/upload-coverage.sh
index 8fbbabde..a3a33d23 100755
--- a/scripts/upload-coverage.sh
+++ b/scripts/upload-coverage.sh
@@ -2,7 +2,8 @@
 
 cd /opt/platypus || exit 1
 
-for filename in $(find build -name "*.C"); do
+for filename in build/**/*.C
+do
     gcov -n -o . "$filename" > /dev/null
 done
 
diff --git a/unit/run_tests b/unit/run_tests
index 8c95970b..e0132af4 100755
--- a/unit/run_tests
+++ b/unit/run_tests
@@ -2,14 +2,14 @@
 
 APPLICATION_NAME=platypus
 # If $METHOD is not set, use opt
-if [ -z $METHOD ]; then
+if [ -z "$METHOD" ]; then
     export METHOD=opt
 fi
 
-if [ -e ./unit/$APPLICATION_NAME-unit-$METHOD ]; then
+if [ -e ./unit/"$APPLICATION_NAME"-unit-"$METHOD" ]; then
     ./unit/$APPLICATION_NAME-unit-$METHOD
-elif [ -e ./$APPLICATION_NAME-unit-$METHOD ]; then
-    ./$APPLICATION_NAME-unit-$METHOD
+elif [ -e ./"$APPLICATION_NAME"-unit-"$METHOD" ]; then
+    ./"$APPLICATION_NAME"-unit-"$METHOD"
 else
     echo "Executable missing!"
     exit 1

From 629534660f009ec0335cca0d81a8aa32394c0d98 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 20:06:46 +0100
Subject: [PATCH 21/26] Fixed a few more formatting errors in bash script

---
 scripts/build-platypus-csd3-sapphire.sh | 46 ++++++++++++-------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/scripts/build-platypus-csd3-sapphire.sh b/scripts/build-platypus-csd3-sapphire.sh
index d4644414..6873ebb2 100755
--- a/scripts/build-platypus-csd3-sapphire.sh
+++ b/scripts/build-platypus-csd3-sapphire.sh
@@ -116,29 +116,29 @@ function _build_petsc() {
     cd petsc-3.19.3 || exit 1
     ./configure \
         --with-cc=$CC --with-cxx=$CXX --with-fc=$FC -CXXPP=cpp \
-         --prefix="${WORKDIR}/${PETSC_DIR_NAME}" \
-         --download-hypre=1 \
-         --with-shared-libraries \
-         --with-debugging=no \
-         --with-hdf5-dir="${WORKDIR}"/${HDF5_DIR_NAME} \
-         --with-blaslapack-dir="${MKLROOT}" \
-         --download-metis=1 \
-         --download-parmetis=1 \
-         --download-ptscotch=1 \
-         --download-mumps=1 \
-         --download-superlu_dist="${WORKDIR}"/superlu_dist-8.1.0.tar.gz \
-         --download-scalapack=1 \
-         --download-slepc=1 \
-         --with-mpi=1 \
-         --with-cxx-dialect=C++17 \
-         --with-fortran-bindings=0 \
-         --with-sowing=0 \
-         --with-64-bit-indices \
-         --with-make-np="${SLURM_NTASKS}" \
-         COPTFLAGS='-O3 -fno-slp-vectorize' \
-         CXXOPTFLAGS='-O3 -fno-slp-vectorize' \
-               FOPTFLAGS='-O3 -fno-slp-vectorize' \
-            PETSC_DIR="$(pwd)" PETSC_ARCH=arch-linux-c-opt
+        --prefix="${WORKDIR}/${PETSC_DIR_NAME}" \
+        --download-hypre=1 \
+        --with-shared-libraries \
+        --with-debugging=no \
+        --with-hdf5-dir="${WORKDIR}"/${HDF5_DIR_NAME} \
+        --with-blaslapack-dir="${MKLROOT}" \
+        --download-metis=1 \
+        --download-parmetis=1 \
+        --download-ptscotch=1 \
+        --download-mumps=1 \
+        --download-superlu_dist="${WORKDIR}"/superlu_dist-8.1.0.tar.gz \
+        --download-scalapack=1 \
+        --download-slepc=1 \
+        --with-mpi=1 \
+        --with-cxx-dialect=C++17 \
+        --with-fortran-bindings=0 \
+        --with-sowing=0 \
+        --with-64-bit-indices \
+        --with-make-np="${SLURM_NTASKS}" \
+        COPTFLAGS='-O3 -fno-slp-vectorize' \
+        CXXOPTFLAGS='-O3 -fno-slp-vectorize' \
+        FOPTFLAGS='-O3 -fno-slp-vectorize' \
+        PETSC_DIR="$(pwd)" PETSC_ARCH=arch-linux-c-opt
     make
     make PETSC_DIR="${WORKDIR}"/${PETSC_DIR_NAME}/petsc-3.19.3 PETSC_ARCH=arch-linux-c-opt install ||
         {

From f4f1027aa1a6f1d30be5cc66a24c5f7839d336c6 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 20:07:01 +0100
Subject: [PATCH 22/26] Build with coverage flags

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

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 48311070..3dcf8ea2 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -28,6 +28,7 @@ jobs:
              docker build -t ci-platypus-ubuntu \
                           --build-arg build_git_sha="${PRCOMMITSHA:-$GITHUB_SHA}" \
                           --build-arg build_git_repo="${PRREPOSITORY:-$GITHUB_REPOSITORY}" \
+                          --build-arg coverage=true \
                           docker/platypus
       - name: UploadCoverage
         run: |

From 662d4edba7bd30f1014d65570fa32b8e2516f5ce Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 7 Jun 2024 20:43:59 +0100
Subject: [PATCH 23/26] Added pre-commit hooks for same linters as used in CI

---
 .github/linters/.markdown-lint.yml | 36 +----------------
 .github/linters/.yaml-lint.yml     | 63 +-----------------------------
 .markdownlint.yml                  | 35 +++++++++++++++++
 .pre-commit-config.yaml            | 61 ++++++++++++++++++++++++-----
 .yamllint.yml                      | 62 +++++++++++++++++++++++++++++
 5 files changed, 150 insertions(+), 107 deletions(-)
 mode change 100644 => 120000 .github/linters/.markdown-lint.yml
 mode change 100644 => 120000 .github/linters/.yaml-lint.yml
 create mode 100644 .markdownlint.yml
 create mode 100644 .yamllint.yml

diff --git a/.github/linters/.markdown-lint.yml b/.github/linters/.markdown-lint.yml
deleted file mode 100644
index a694d1b7..00000000
--- a/.github/linters/.markdown-lint.yml
+++ /dev/null
@@ -1,35 +0,0 @@
----
-###########################
-###########################
-## Markdown Linter rules ##
-###########################
-###########################
-
-# Linter rules doc:
-# - https://github.com/DavidAnson/markdownlint
-#
-# Note:
-# To comment out a single error:
-#   <!-- markdownlint-disable -->
-#   any violations you want
-#   <!-- markdownlint-restore -->
-#
-
-###############
-# Rules by id #
-###############
-MD004: false                  # Unordered list style
-MD007:
-  indent: 2                   # Unordered list indentation
-MD013:
-  line_length: 100            # Line length 80 is far too short
-MD026:
-  punctuation: ".,;:!。，；:"  # List of not allowed
-MD029: false                  # Ordered list item prefix
-MD033: false                  # Allow inline HTML
-MD041: false                  # Allow MOOSE configuration data before first heading
-
-#################
-# Rules by tags #
-#################
-blank_lines: false  # Error on blank lines
diff --git a/.github/linters/.markdown-lint.yml b/.github/linters/.markdown-lint.yml
new file mode 120000
index 00000000..7e62b3d9
--- /dev/null
+++ b/.github/linters/.markdown-lint.yml
@@ -0,0 +1 @@
+../../.markdownlint.yml
\ No newline at end of file
diff --git a/.github/linters/.yaml-lint.yml b/.github/linters/.yaml-lint.yml
deleted file mode 100644
index 4c44381e..00000000
--- a/.github/linters/.yaml-lint.yml
+++ /dev/null
@@ -1,62 +0,0 @@
----
-###########################################
-# These are the rules used for            #
-# linting all the yaml files in the stack #
-# NOTE:                                   #
-# You can disable line with:              #
-# # yamllint disable-line                 #
-###########################################
-rules:
-  braces:
-    level: warning
-    min-spaces-inside: 0
-    max-spaces-inside: 0
-    min-spaces-inside-empty: 1
-    max-spaces-inside-empty: 5
-  brackets:
-    level: warning
-    min-spaces-inside: 0
-    max-spaces-inside: 0
-    min-spaces-inside-empty: 1
-    max-spaces-inside-empty: 5
-  colons:
-    level: warning
-    max-spaces-before: 0
-    max-spaces-after: 1
-  commas:
-    level: warning
-    max-spaces-before: 0
-    min-spaces-after: 1
-    max-spaces-after: 1
-  comments: disable
-  comments-indentation: disable
-  document-end: disable
-  document-start:
-    level: warning
-    present: true
-  empty-lines:
-    level: warning
-    max: 2
-    max-start: 0
-    max-end: 0
-  hyphens:
-    level: warning
-    max-spaces-after: 1
-  indentation:
-    level: warning
-    spaces: consistent
-    indent-sequences: true
-    check-multi-line-strings: false
-  key-duplicates: enable
-  line-length:
-    level: warning
-    max: 100
-    allow-non-breakable-words: true
-    allow-non-breakable-inline-mappings: true
-  new-line-at-end-of-file: disable
-  new-lines:
-    type: unix
-  trailing-spaces: disable
-
-ignore:
-  - syntax.yaml
diff --git a/.github/linters/.yaml-lint.yml b/.github/linters/.yaml-lint.yml
new file mode 120000
index 00000000..54a3654b
--- /dev/null
+++ b/.github/linters/.yaml-lint.yml
@@ -0,0 +1 @@
+../../.yamllint.yml
\ No newline at end of file
diff --git a/.markdownlint.yml b/.markdownlint.yml
new file mode 100644
index 00000000..a694d1b7
--- /dev/null
+++ b/.markdownlint.yml
@@ -0,0 +1,35 @@
+---
+###########################
+###########################
+## Markdown Linter rules ##
+###########################
+###########################
+
+# Linter rules doc:
+# - https://github.com/DavidAnson/markdownlint
+#
+# Note:
+# To comment out a single error:
+#   <!-- markdownlint-disable -->
+#   any violations you want
+#   <!-- markdownlint-restore -->
+#
+
+###############
+# Rules by id #
+###############
+MD004: false                  # Unordered list style
+MD007:
+  indent: 2                   # Unordered list indentation
+MD013:
+  line_length: 100            # Line length 80 is far too short
+MD026:
+  punctuation: ".,;:!。，；:"  # List of not allowed
+MD029: false                  # Ordered list item prefix
+MD033: false                  # Allow inline HTML
+MD041: false                  # Allow MOOSE configuration data before first heading
+
+#################
+# Rules by tags #
+#################
+blank_lines: false  # Error on blank lines
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4cd0ef39..2e66799f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,13 +5,54 @@ repos:
     hooks:
       - id: clang-format
 
-  - repo: https://github.com/pocc/pre-commit-hooks
-    rev: v1.3.5
-    hooks:
-      - id: clang-tidy
-        args:
-          - "-p=./build"
-          - "-config-file=./.clang-tidy"
-          - "--warnings-as-errors=*"
-          - "-extra-arg=-std=c++17"
-          - "-extra-arg=-stdlib=libstdc++"
+  # - repo: https://github.com/pocc/pre-commit-hooks
+  #   rev: v1.3.5
+  #   hooks:
+  #     - id: clang-tidy
+  #       args:
+  #         - "-p=./build"
+  #         - "-config-file=./.clang-tidy"
+  #         - "--warnings-as-errors=*"
+  #         - "-extra-arg=-std=c++17"
+  #         - "-extra-arg=-stdlib=libstdc++"
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: 2.7.3
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
+
+  - repo: https://github.com/scop/pre-commit-shfmt
+    rev: v3.8.0-1
+    hooks:
+      - id: shfmt
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+
+  - repo: https://github.com/hadolint/hadolint
+    rev: v2.12.0
+    hooks:
+      - id: hadolint
+
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.41.0
+    hooks:
+    - id: markdownlint-fix
+
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.1
+    hooks:
+      - id: actionlint
+
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.16.1
+    hooks:
+      - id: gitleaks
diff --git a/.yamllint.yml b/.yamllint.yml
new file mode 100644
index 00000000..4c44381e
--- /dev/null
+++ b/.yamllint.yml
@@ -0,0 +1,62 @@
+---
+###########################################
+# These are the rules used for            #
+# linting all the yaml files in the stack #
+# NOTE:                                   #
+# You can disable line with:              #
+# # yamllint disable-line                 #
+###########################################
+rules:
+  braces:
+    level: warning
+    min-spaces-inside: 0
+    max-spaces-inside: 0
+    min-spaces-inside-empty: 1
+    max-spaces-inside-empty: 5
+  brackets:
+    level: warning
+    min-spaces-inside: 0
+    max-spaces-inside: 0
+    min-spaces-inside-empty: 1
+    max-spaces-inside-empty: 5
+  colons:
+    level: warning
+    max-spaces-before: 0
+    max-spaces-after: 1
+  commas:
+    level: warning
+    max-spaces-before: 0
+    min-spaces-after: 1
+    max-spaces-after: 1
+  comments: disable
+  comments-indentation: disable
+  document-end: disable
+  document-start:
+    level: warning
+    present: true
+  empty-lines:
+    level: warning
+    max: 2
+    max-start: 0
+    max-end: 0
+  hyphens:
+    level: warning
+    max-spaces-after: 1
+  indentation:
+    level: warning
+    spaces: consistent
+    indent-sequences: true
+    check-multi-line-strings: false
+  key-duplicates: enable
+  line-length:
+    level: warning
+    max: 100
+    allow-non-breakable-words: true
+    allow-non-breakable-inline-mappings: true
+  new-line-at-end-of-file: disable
+  new-lines:
+    type: unix
+  trailing-spaces: disable
+
+ignore:
+  - syntax.yaml

From 4249c1248b42a608870df0e7025015cbe85e98d2 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Mon, 10 Jun 2024 13:26:10 +0100
Subject: [PATCH 24/26] Fixed remaining issues with pre-commit hooks/linting

---
 .editorconfig                  | 11 +++++++++--
 .pre-commit-config.yaml        | 14 ++++++++++----
 scripts/install-format-hook.sh |  7 ++++---
 scripts/upload-coverage.sh     |  3 +--
 unit/run_tests                 |  2 +-
 5 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index cae7cdab..4c9b9224 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -1,6 +1,13 @@
-[{*.sh,run_tests}]
+[*.sh]
 indent_style = space
 indent_size = 4
 space_redirects = true
 keep_padding = true
-never_split = true
\ No newline at end of file
+never_split = true
+
+[unit/run_tests]
+indent_style = space
+indent_size = 4
+space_redirects = true
+keep_padding = true
+never_split = true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2e66799f..e0d6aa26 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,6 +5,7 @@ repos:
     hooks:
       - id: clang-format
 
+  # Not yet figured out how to configure this properly
   # - repo: https://github.com/pocc/pre-commit-hooks
   #   rev: v1.3.5
   #   hooks:
@@ -32,11 +33,16 @@ repos:
     hooks:
       - id: shellcheck
 
-  - repo: https://github.com/hadolint/hadolint
-    rev: v2.12.0
-    hooks:
-      - id: hadolint
+  # Hadolint isn't trivial to install
+  # - repo: https://github.com/hadolint/hadolint
+  #   rev: v2.12.0
+  #   hooks:
+  #     - id: hadolint
 
+  # Note: needs node.js >= 18, which is more recent than version
+  # distributed with Ubuntu 22.4. The latest versions of node.js can
+  # be installed using the instructions at
+  # https://github.com/nodesource/distributions?tab=readme-ov-file#debian-and-ubuntu-based-distributions
   - repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.41.0
     hooks:
diff --git a/scripts/install-format-hook.sh b/scripts/install-format-hook.sh
index 27f45815..86e1958a 100755
--- a/scripts/install-format-hook.sh
+++ b/scripts/install-format-hook.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-REPO_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}")"  && pwd)/../"
+REPO_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/../"
 hookfile="$REPO_DIR/.git/hooks/pre-commit"
 
 if [[ -f $hookfile ]]; then
@@ -8,7 +8,8 @@ if [[ -f $hookfile ]]; then
     exit 1
 fi
 
-echo '#!/bin/bash
+cat << 'EOF' > "$hookfile"
+#!/bin/bash
 patch=$(git clang-format --diff -- $(git diff --staged --name-only -- src include tests unit))
 if [[ "$patch" =~ "no modified files to format" || "$patch" =~ "clang-format did not modify any files" ]]; then
     echo "" > /dev/null
@@ -20,6 +21,6 @@ else
     echo "$patch"
     exit 1
 fi
-' > "$hookfile"
+EOF
 
 chmod a+x "$hookfile"
diff --git a/scripts/upload-coverage.sh b/scripts/upload-coverage.sh
index a3a33d23..99843299 100755
--- a/scripts/upload-coverage.sh
+++ b/scripts/upload-coverage.sh
@@ -2,8 +2,7 @@
 
 cd /opt/platypus || exit 1
 
-for filename in build/**/*.C
-do
+for filename in build/**/*.C; do
     gcov -n -o . "$filename" > /dev/null
 done
 
diff --git a/unit/run_tests b/unit/run_tests
index e0132af4..2fef62c7 100755
--- a/unit/run_tests
+++ b/unit/run_tests
@@ -7,7 +7,7 @@ if [ -z "$METHOD" ]; then
 fi
 
 if [ -e ./unit/"$APPLICATION_NAME"-unit-"$METHOD" ]; then
-    ./unit/$APPLICATION_NAME-unit-$METHOD
+    ./unit/"$APPLICATION_NAME"-unit-"$METHOD"
 elif [ -e ./"$APPLICATION_NAME"-unit-"$METHOD" ]; then
     ./"$APPLICATION_NAME"-unit-"$METHOD"
 else

From 74127010ada110e653592ecfda12beee0dff1479 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 11 Jun 2024 15:55:06 +0100
Subject: [PATCH 25/26] Trying (yet again) to upload to codecov

---
 .github/workflows/main.yml | 2 ++
 scripts/upload-coverage.sh | 5 -----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3dcf8ea2..65fa04a1 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,3 +36,5 @@ jobs:
           # shellcheck disable=SC2086
           docker run $ci_env -e CI=true ci-platypus-ubuntu:latest \
                  bash /opt/platypus/scripts/upload-coverage.sh
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/scripts/upload-coverage.sh b/scripts/upload-coverage.sh
index 99843299..980963ef 100755
--- a/scripts/upload-coverage.sh
+++ b/scripts/upload-coverage.sh
@@ -1,9 +1,4 @@
 #!/bin/bash
 
 cd /opt/platypus || exit 1
-
-for filename in build/**/*.C; do
-    gcov -n -o . "$filename" > /dev/null
-done
-
 bash <(curl -s https://codecov.io/bash)

From 915351c66669518dfc8cbb3aa944eeca534d1a54 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Wed, 12 Jun 2024 11:25:56 +0100
Subject: [PATCH 26/26] Added two more badges

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index faf018b8..d2f13404 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,9 @@
 Platypus
 =====
 
+![lint](https://github.com/aurora-multiphysics/platypus/actions/workflows/lint.yml/badge.svg?branch=main)
 ![build](https://github.com/aurora-multiphysics/platypus/actions/workflows/main.yml/badge.svg?branch=main)
+[![codecov](https://codecov.io/gh/aurora-multiphysics/platypus/graph/badge.svg?token=WV2DE9DT53)](https://codecov.io/gh/aurora-multiphysics/platypus)
 [![GitHub License](https://img.shields.io/github/license/aurora-multiphysics/platypus)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html)
 
 Platypus is a MOOSE-based application created to enable custom MOOSE