Linter

.github/pull_request_template.md

@@ -1,7 +1,7 @@
-# Pull request description:
+# Pull request description
 
 
-## Changes or fixes:
+## Changes or fixes
 
 
-## Examples:
+## Examples

.github/workflows/CDImage.yml

@@ -39,12 +39,17 @@ jobs:
     - name: Log in to GitHub Container Registry
       run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
 
+    - name: Set MACH3_VERSION
+      run: echo "MACH3_VERSION=${{ github.head_ref }}" >> "$GITHUB_ENV"
+      env:
+        GITHUB_HEAD_REF: ${{ github.head_ref }}
+
     - name: Build Docker image
       run: |
         if [ "${{ github.ref_type }}" == 'tag' ]; then
-          docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}${{ github.ref_name }} --build-arg MACH3_VERSION=${{ github.ref_name }}
+          docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}${{ github.ref_name }} --build-arg MACH3_VERSION="${MACH3_VERSION}"
         else
-          docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }} --build-arg MACH3_VERSION=develop
+          docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }} --build-arg MACH3_VERSION="develop"
         fi
 
     - name: Push Docker image

.github/workflows/CIBuild.yml

@@ -43,5 +43,8 @@ jobs:
     - name: Log in to GitHub Container Registry
       run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
 
+    - name: Set environment variable for MACH3_VERSION
+      run: echo "MACH3_VERSION=${{ github.head_ref }}" >> "$GITHUB_ENV"
+
     - name: Build the Docker image
-      run: docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag }} --build-arg MACH3_VERSION=${{ github.head_ref }} --build-arg CMAKE_OPTIONS="${{ matrix.cmakeoptions }}"
+      run: docker build . --file ${{ matrix.file }} --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag }} --build-arg MACH3_VERSION=${{ env.MACH3_VERSION }} --build-arg CMAKE_OPTIONS="${{ matrix.cmakeoptions }}"

.github/workflows/CIValidations.yml

@@ -63,15 +63,16 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-
     - name: Get MaCh3 Validations
       run: |
         cd /opt/
         git clone https://github.com/mach3-software/MaCh3Tutorial.git MaCh3Validations
         cd MaCh3Validations
         mkdir build
         cd build
-        cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
+        cmake ../ -DMaCh3_Branch="${{ env.GITHUB_HEAD_REF }}"
+      env:
+        GITHUB_HEAD_REF: ${{ github.head_ref }}
 
     - name: Build MaCh3 Validations
       run: |

.github/workflows/Linter.yml

@@ -0,0 +1,29 @@
+---
+# Lint our code and throw error if something is looking fishy in the changes
+name: Super Linter
+
+on:
+  pull_request:
+    branches: [develop]
+
+jobs:
+  super-linter:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Run Super Linter
+        uses: github/super-linter@v7
+        env:
+          VALIDATE_MARKDOWN: true  # Enable Markdown linting
+          VALIDATE_DOCKERFILE: true  # Enable Dockerfile linting
+          VALIDATE_YAML: true  # Enable YAML linting
+          VALIDATE_GITHUB_ACTIONS: true  # Enable GitHub Actions workflow linting
+          VALIDATE_PYTHON: true  # Enable Python linting
+          VALIDATE_ALL_CODEBASE: false  # Lint the entire codebase
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # GitHub token for permissions
+          DISABLE_LINTERS: "CPP"  # Disable linting for other languages

.github/workflows/Meme.yml

@@ -0,0 +1,16 @@
+# Add random meme whenever PR is opened
+name: "Random Meme"
+
+on:
+  pull_request:
+    types: [opened, reopened]
+
+jobs:
+  test:
+    name: setup environment
+    runs-on: ubuntu-latest
+    steps:
+      - name: Memes
+        uses: deep5050/memes-on-issues-action@main
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/Newsletter.yml

@@ -16,21 +16,21 @@ jobs:
 
       - name: Count the total number of commits in MaCh3
         run: |
-          echo "commit_count=$(git rev-list --count HEAD)" >> $GITHUB_ENV
+          echo "commit_count=$(git rev-list --count HEAD)" >> "$GITHUB_ENV"
 
       - name: Count commits in the last week for MaCh3
         run: |
-          echo "commits_last_week=$(git rev-list --count --since='1 week ago' HEAD)" >> $GITHUB_ENV
+          echo "commits_last_week=$(git rev-list --count --since='1 week ago' HEAD)" >> "$GITHUB_ENV"
 
       - name: Get the most recent tag for MaCh3
         run: |
           latest_tag=$(git describe --tags --abbrev=0)
-          echo "latest_tag=${latest_tag}" >> $GITHUB_ENV
+          echo "latest_tag=${latest_tag}" >> "$GITHUB_ENV"
 
       - name: Get the current date
         run: |
           current_date=$(date +"%d/%m/%Y")
-          echo "current_date=${current_date}" >> $GITHUB_ENV
+          echo "current_date=${current_date}" >> "$GITHUB_ENV"
 
       - name: Checkout the MaCh3Tutorial repository
         uses: actions/checkout@v4
@@ -41,16 +41,16 @@ jobs:
 
       - name: Count the total number of commits in MaCh3Tutorial
         run: |
-          echo "tutorial_commit_count=$(git -C MaCh3Tutorial rev-list --count HEAD)" >> $GITHUB_ENV
+          echo "tutorial_commit_count=$(git -C MaCh3Tutorial rev-list --count HEAD)" >> "$GITHUB_ENV"
 
       - name: Count commits in the last week for MaCh3Tutorial
         run: |
-          echo "tutorial_commits_last_week=$(git -C MaCh3Tutorial rev-list --count --since='1 week ago' HEAD)" >> $GITHUB_ENV
+          echo "tutorial_commits_last_week=$(git -C MaCh3Tutorial rev-list --count --since='1 week ago' HEAD)" >> "$GITHUB_ENV"
 
       - name: Get the most recent tag for MaCh3Tutorial
         run: |
           tutorial_latest_tag=$(git -C MaCh3Tutorial describe --tags --abbrev=0)
-          echo "tutorial_latest_tag=${tutorial_latest_tag}" >> $GITHUB_ENV
+          echo "tutorial_latest_tag=${tutorial_latest_tag}" >> "$GITHUB_ENV"
 
       - name: Checkout the MaCh3-PythonUtils repository
         uses: actions/checkout@v4
@@ -61,16 +61,16 @@ jobs:
 
       - name: Count the total number of commits in MaCh3-PythonUtils
         run: |
-          echo "python_utils_commit_count=$(git -C MaCh3-PythonUtils rev-list --count HEAD)" >> $GITHUB_ENV
+          echo "python_utils_commit_count=$(git -C MaCh3-PythonUtils rev-list --count HEAD)" >> "$GITHUB_ENV"
 
       - name: Count commits in the last week for MaCh3-PythonUtils
         run: |
-          echo "python_utils_commits_last_week=$(git -C MaCh3-PythonUtils rev-list --count --since='1 week ago' HEAD)" >> $GITHUB_ENV
+          echo "python_utils_commits_last_week=$(git -C MaCh3-PythonUtils rev-list --count --since='1 week ago' HEAD)" >> "$GITHUB_ENV"
 
       - name: Get the most recent tag for MaCh3-PythonUtils
         run: |
           python_utils_latest_tag=$(git -C MaCh3-PythonUtils describe --tags --abbrev=0)
-          echo "python_utils_latest_tag=${python_utils_latest_tag}" >> $GITHUB_ENV
+          echo "python_utils_latest_tag=${python_utils_latest_tag}" >> "$GITHUB_ENV"
 
       - name: Create a new GitHub Discussion
         uses: abirismyname/[email protected]

.github/workflows/TagTutorial.yml

@@ -25,10 +25,10 @@ jobs:
           cd MaCh3Tutorial/
 
           # Extract the tag name from GITHUB_REF
-          TAG_NAME=$(echo "${GITHUB_REF#refs/tags/}")
+          TAG_NAME="${GITHUB_REF#refs/tags/}"
 
           # Create the new tag
-          git tag $TAG_NAME
+          git tag "$TAG_NAME"
 
           # Push the tag to the MaCh3Tutorial repository
-          git push https://${{ secrets.MACH3_VALIDATIONS_PAT }}@github.com/mach3-software/MaCh3Tutorial.git $TAG_NAME
+          git push https://${{ secrets.MACH3_VALIDATIONS_PAT }}@github.com/mach3-software/MaCh3Tutorial.git "$TAG_NAME"

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-## How to Contribute Code to MaCh3
+# How to Contribute Code to MaCh3
 The gitflow development policy should be followed, with the master and develop branches only being committed to via pull request.
 
 New features should be developed on branches in this repository with the branch naming: `feature_FEATURENAME`
@@ -8,59 +8,58 @@ Please see [here](https://www.atlassian.com/git/tutorials/comparing-workflows/gi
 ## Doxygen
 When making comments try following Doxygen type of comments
 
-```
+```cpp
 // I like comments
 void Foo(){}
 ```
 try
-```
+```cpp
 /// @brief I like comments
 void Foo(){}
 ```
 After making release or tag please
-```
+```bash
 cd Doc
 doxygen Doxyfile
 ```
 to produce both html and latex file. To produce book like pdf file:
-```
+```bash
 cd latex
 pdflatex refman.tex
 ```
 
 ## Logger
 MaCh3 is using spdlog logger see [here](https://github.com/gabime/spdlog/tree/master). And wraps it around MaCh3 names [here](https://github.com/mach3-software/MaCh3/blob/develop/manager/MaCh3Logger.h)
 It is advised to use it. For example rather than
-```
+```cpp
 std::cout<< " Error: Something is wrong" <<std::endl;
 ```
 it is advised to used logger
-```
+```cpp
 MACH3LOG_ERROR("Something is wrong");
 ```
 To pass argument to logger use following syntax:
-```
+```cpp
 MACH3LOG_INFO("I like {}, do you like {}", FirsString, SecondString);
 ```
 Logger by default will print whole float. Normally to show only several significant figures you would use `std::precision(2)`. To obtain same thing with logger please use `{:.2f}` like this:
-```
+```cpp
 MACH3LOG_INFO("Here is full LLH but I only show 2 significant figures {:.2f}", LLH);
 ```
 
 ## Config Syntax
 MaCh3 currently uses yaml as config handler. To help unify syntax over the code there are several YamlHelper function available [here](https://github.com/mach3-software/MaCh3/blob/develop/manager/YamlHelper.h). Most important is `GetFromManager`. For code below which checks if config entry exist and if doesn't set some default value
 
-```
+```cpp
 bool AsimovFit = false;
 
 if(config[AsimovFit])
 {
   AsimovFit = config[AsimovFit].as<bool>;
 }
-
 ```
 This can be replaced with:
-```
+```cpp
 bool AsimovFit = GetFromManager<bool>(config[AsimovFit], false);
 ```
 
@@ -70,23 +69,23 @@ Some fits require lot's of RAM. Easiest and fastest solution to reduce RAM is us
 ## Error handling
 MaCh3 uses custom error handling implemented [here](https://github.com/mach3-software/MaCh3/blob/develop/manager/MaCh3Exception.h)
 Instead of throw
-```
+```cpp
 throw;
 ```
 it is advised to use:
 
-```
+```cpp
 throw MaCh3Exception(__FILE__ , __LINE__ , "Some message");
 ```
 or
-```
+```cpp
 throw MaCh3Exception(__FILE__ , __LINE__ );
 ```
 This way we can ensure error messages are unified and user always get hints where in the code problem occurred. If current MaCh3Exception is not sufficient consider implementing new or expanding current exceptions in MaCh3Exception.h.
 
 ## Formatting
 To ensure a unified style in MaCh3 software you can use a clang-format file which has instructions about formatting code.
-```
+```bash
 clang-format --assume-filename=/path/to/your/.clang-format=${MaCh3_ROOT}/../.clang-format blarb.cpp
 ```
 Please see [here](https://clang.llvm.org/docs/ClangFormat.html) and [here](https://root.cern/contribute/coding_conventions/) for more details.

Diagnostics/README.md

@@ -1,4 +1,4 @@
-### Diagnostic
+# Diagnostic
 **ProcessMCMC** - The main app you want to use for analysing the ND280 chain. It prints posterior distribution after burn-in the cut. Moreover, you can compare two/three different chains. There are a few options you can modify easily inside the app like selection, burn-in cut, and whether to plot xse+flux or only flux. Other functionality
 <ol>
 <li> Produce a covariance matrix with multithreading (which requires lots of RAM due to caching) </li>
@@ -14,12 +14,12 @@
 **DiagMCMC** - Perform MCMC diagnostic like autocorrelation or trace plots.
 
 **RHat** - Performs RHat diagnostic to study if all used chains converged to the same stationary distribution.
-```
+```bash
 ./RHat Ntoys MCMCchain_1.root MCMCchain_2.root MCMCchain_3.root ... [how many you like]
 ```
 
 **CombineMaCh3Chains** - will combine chains files produced by **MCMC**, enforcing the condition that all the files to combine were made using the exact same software versions and config files
-```
+```bash
 CombineMaCh3Chains [-h] [-c [0-9]] [-f] [-o <output file>] file1.root [file2.root, file3.root ...]
 ```
 *fileX.root* are the individual spline files to combine, can specify any number, need at least one