Setting up various badges for the repository

.editorconfig

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+[*.sh]
+indent_style = space
+indent_size = 4
+space_redirects = true
+keep_padding = true
+never_split = true
+
+[unit/run_tests]
+indent_style = space
+indent_size = 4
+space_redirects = true
+keep_padding = true
+never_split = true

.github/linters/.clang-format

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+../../.clang-format

.github/linters/.markdown-lint.yml

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+../../.markdownlint.yml

.github/linters/.yaml-lint.yml

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+../../.yamllint.yml

.github/workflows/lint.yml

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+---
+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/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          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

.github/workflows/main.yml

@@ -1,30 +1,40 @@
+---
 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
       - 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}" \
+                          --build-arg coverage=true \
                           docker/platypus
+      - name: UploadCoverage
+        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
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.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:

.markdownlint.yml

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+---
+###########################
+###########################
+## 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

.pre-commit-config.yaml

@@ -1,11 +1,64 @@
+---
 repos:
-- 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/pre-commit/mirrors-clang-format
+    rev: v14.0.6
+    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:
+  #     - 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
+
+  # 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:
+    - 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