Initial Setup

.gitattributes

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+# Common settings that generally should always be used with your language specific settings
+
+# Auto detect text files and perform LF normalization
+# https://www.davidlaing.com/2012/09/19/customise-your-gitattributes-to-become-a-git-ninja/
+*          text=auto
+
+#
+# The above will handle all files NOT found below
+#
+
+# Documents
+*.bibtex   text diff=bibtex
+*.doc	        diff=astextplain
+*.DOC	        diff=astextplain
+*.docx          diff=astextplain
+*.DOCX          diff=astextplain
+*.dot           diff=astextplain
+*.DOT           diff=astextplain
+*.pdf           diff=astextplain
+*.PDF           diff=astextplain
+*.rtf           diff=astextplain
+*.RTF	        diff=astextplain
+*.md       text
+*.tex      text diff=tex
+*.adoc     text
+*.textile  text
+*.mustache text
+*.csv      text
+*.tab      text
+*.tsv      text
+*.txt      text
+*.sql      text
+
+# Graphics
+*.png      binary
+*.jpg      binary
+*.jpeg     binary
+*.gif      binary
+*.tif      binary
+*.tiff     binary
+*.ico      binary
+# SVG treated as an asset (binary) by default.
+*.svg      text
+# If you want to treat it as binary,
+# use the following line instead.
+# *.svg    binary
+*.eps      binary
+
+# Scripts
+*.bash     text eol=lf
+*.fish     text eol=lf
+*.sh       text eol=lf
+# These are explicitly windows files and should use crlf
+*.bat      text eol=crlf
+*.cmd      text eol=crlf
+*.ps1      text eol=crlf
+
+# Serialisation
+*.json     text
+*.toml     text
+*.xml      text
+*.yaml     text
+*.yml      text
+
+# Archives
+*.7z       binary
+*.gz       binary
+*.tar      binary
+*.tgz      binary
+*.zip      binary
+
+# Text files where line endings should be preserved
+*.patch    -text
+
+#
+# Exclude files from exporting
+#
+
+.gitattributes export-ignore
+.gitignore     export-ignore
+
+# Java sources
+*.java          text diff=java
+*.gradle        text diff=java
+*.gradle.kts    text diff=java
+
+# These files are text and should be normalized (Convert crlf => lf)
+*.css           text diff=css
+*.df            text
+*.htm           text diff=html
+*.html          text diff=html
+*.js            text
+*.jsp           text
+*.jspf          text
+*.jspx          text
+*.properties    text
+*.tld           text
+*.tag           text
+*.tagx          text
+*.xml           text
+
+# These generated analysis-results shouldn't be taken into account for language statistics
+analysis-results/** linguist-vendored
+
+# These files are binary and should be left untouched
+# (binary is a macro for -text -diff)
+*.class         binary
+*.dll           binary
+*.ear           binary
+*.jar           binary
+*.so            binary
+*.war           binary

.github/pull_request_template.md

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+### 🚀 Feature
+
+- 
+
+### ⚙️ Optimization
+
+- 
+
+### 🛠 Fix
+
+- 
+
+### 📖 Documentation
+
+- 

.github/workflows/analyze-code-graph.yml

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+name: Analyze Code Graph
+
+on:
+  workflow_call:
+    inputs:
+      analysis-name:
+        description: "The name of the project to analyze. E.g. MyProject-1.0.0"
+        required: true
+        type: string
+      artifacts-upload-name:
+        description: "The name of the artifacts uploaded with 'actions/upload-artifact' containing the content of the 'artifacts' directory for the analysis."
+        required: false
+        type: string
+        default: ''
+      sources-upload-name:
+        description: "The name of the sources uploaded with 'actions/upload-artifact' containing the content of the 'source' directory for the analysis."
+        required: false
+        type: string
+        default: ''
+      analysis-arguments:
+        description: "The arguments to pass to the analysis script (default='--profile Neo4jv5-low-memory')."
+        required: false
+        type: string
+        default: '--profile Neo4jv5-low-memory'
+      typescript-scan-heap-memory:
+        description: "The heap memory in MB to use for the TypeScript scan (default=4096)"
+        required: false
+        type: string
+        default: '4096'
+    outputs:
+      uploaded-analysis-results:
+        description: "The name of the artifact uploaded with 'actions/upload-artifact' containing the analysis results."
+        value: ${{ jobs.analyze-code-graph.outputs.uploaded-analysis-results-artifact-name }}
+
+jobs:
+  analyze-code-graph:
+    runs-on: ubuntu-latest
+    outputs:
+      uploaded-analysis-results-artifact-name: ${{ steps.set-analysis-results-artifact-name.outputs.uploaded-analysis-results-artifact-name }}
+    strategy:
+      matrix:
+        include:
+        - os: ubuntu-latest
+          java: 17
+          python: 3.11
+          miniforge: 24.9.0-0
+    steps:
+      - name: Assure that either artifacts-upload-name or sources-upload-name is set
+        if: inputs.artifacts-upload-name == '' && inputs.sources-upload-name == ''
+        run: echo "Please specify either the input parameter 'artifacts-upload-name' or 'sources-upload-name'."; exit 1
+      - name: Checkout code-graph-analysis-pipeline
+        uses: actions/checkout@v4
+        with:
+          repository: JohT/code-graph-analysis-pipeline
+          ref: 41f3e22b5bd65351474dd23effeee91fab849a12
+          path: code-graph-analysis-pipeline
+          persist-credentials: false
+
+      - name: (Java Setup) Java Development Kit (JDK) ${{ matrix.java }}
+        uses: actions/setup-java@v4
+        with:
+          distribution: "temurin"
+          java-version: ${{ matrix.java }}
+
+      # "Setup Python" can be skipped if jupyter notebook analysis-results aren't needed
+      - name: (Python Setup) Setup Cache for Conda package manager Miniforge
+        uses: actions/cache@v4
+        env:
+          # Increase this value to reset cache if etc/example-environment.yml has not changed
+          # Reference: https://github.com/conda-incubator/setup-miniconda#caching
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-environments-${{hashFiles('**/environment.yml', '.github/workflows/*.yml') }}
+
+      - name: (Python Setup) Use version ${{ matrix.python }} with Conda package manager Miniforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python }}
+          miniforge-version: ${{ matrix.miniforge }}
+          activate-environment: codegraph
+          environment-file: ./code-graph-analysis-pipeline/jupyter/environment.yml
+          auto-activate-base: false
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: (Python Setup) Conda environment info
+        shell: bash -el {0}
+        run: conda info
+
+      - name: (Code Analysis Setup) Add code-graph-analysis-pipeline temporarily to .gitignore
+        shell: bash
+        run: |
+          echo "" >> .gitignore
+          echo "# Code Graph Analysis Pipeline" >> .gitignore
+          echo "code-graph-analysis-pipeline/" >> .gitignore
+
+      - name: (Code Analysis Setup) Setup Cache Analysis Downloads
+        uses: actions/cache@v4
+        with:
+          path: ./code-graph-analysis-pipeline/temp/downloads
+          key:
+            ${{ runner.os }}-${{ hashFiles('**/*.sh') }}
+
+      - name: (Code Analysis Setup) Generate Neo4j Initial Password
+        id: generate-neo4j-initial-password
+        shell: bash
+        run: |
+          generated_password=$( LC_ALL=C tr -dc '[:graph:]' </dev/urandom | head -c 12; echo )
+          echo "::add-mask::$generated_password"
+          echo "neo4j-initial-password=$generated_password" >> "$GITHUB_OUTPUT"
+
+      - name: (Code Analysis Setup) Initialize Analysis
+        shell: bash
+        working-directory: code-graph-analysis-pipeline
+        env:
+          NEO4J_INITIAL_PASSWORD: ${{ steps.generate-neo4j-initial-password.outputs.neo4j-initial-password }}
+        run: ./init.sh ${{ inputs.analysis-name }}
+
+      - name: (Code Analysis Setup) Download sources for analysis
+        if: inputs.sources-upload-name != ''
+        uses: actions/download-artifact@v4
+        with:
+          name: ${{ inputs.sources-upload-name }}
+          path: code-graph-analysis-pipeline/temp/${{ inputs.analysis-name }}/source/${{ inputs.analysis-name }}
+
+      - name: (Code Analysis Setup) Download artifacts for analysis
+        if: inputs.artifacts-upload-name != ''
+        uses: actions/download-artifact@v4
+        with:
+          name: ${{ inputs.artifacts-upload-name }}
+          path: code-graph-analysis-pipeline/temp/${{ inputs.analysis-name }}/artifacts
+
+      - name: (Code Analysis) Analyze ${{ inputs.analysis-name }}
+        working-directory: code-graph-analysis-pipeline/temp/${{ inputs.analysis-name }}
+        # Shell type can be skipped if jupyter notebook analysis-results (and therefore conda) aren't needed
+        shell: bash -el {0}
+        env:
+          NEO4J_INITIAL_PASSWORD: ${{ steps.generate-neo4j-initial-password.outputs.neo4j-initial-password }}
+          ENABLE_JUPYTER_NOTEBOOK_PDF_GENERATION: "true"
+          IMPORT_GIT_LOG_DATA_IF_SOURCE_IS_PRESENT: "" # Options: "none", "aggregated", "full". default = "plugin" or ""
+        run: |
+          TYPESCRIPT_SCAN_HEAP_MEMORY=${{ inputs.typescript-scan-heap-memory }} ./../../scripts/analysis/analyze.sh ${{ inputs.analysis-arguments }}
+
+      - name: Assemble ENVIRONMENT_INFO
+        run: echo "ENVIRONMENT_INFO=-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}" >> $GITHUB_ENV
+
+      - name: Set artifact name for uploaded analysis results
+        id: set-analysis-results-artifact-name
+        run: echo "uploaded-analysis-results-artifact-name=code-analysis-results-java-${{ env.ENVIRONMENT_INFO }}" >> $GITHUB_OUTPUT
+
+      # Upload logs and unfinished analysis-results in case of an error for troubleshooting
+      - name: (Code Analysis Results) Archive failed run with logs and unfinished analysis-results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: java-code-analysis-logs-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+          path: |
+            ./code-graph-analysis-pipeline/temp/**/runtime/*
+            ./code-graph-analysis-pipeline/temp/**/reports/*
+          retention-days: 5
+
+      # Upload successful analysis-results in case they are needed for troubleshooting
+      - name: (Code Analysis Results) Archive successful analysis-results
+        if: success()
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ steps.set-analysis-results-artifact-name.outputs.uploaded-analysis-results-artifact-name }}
+          path: ./code-graph-analysis-pipeline/temp/**/reports/*
+          if-no-files-found: error
+          retention-days: 5
+
+    # Upload Database Export
+    # Only possible after an export with "./../../scripts/analysis/analyze.sh --report DatabaseCsvExport"
+    # Won't be done here because of performance and security concerns
+    #- name: Archive exported database
+    #  uses: actions/upload-artifact@v3
+    #  with:
+    #    name: typescript-code-analysis-database-export-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+    #    path: ./code-graph-analysis-pipeline/temp/**/import
+    #    if-no-files-found: error
+    #    retention-days: 5

.github/workflows/check-links-in-documentation.yml

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+name: Check links in documentation
+
+on:
+  pull_request:
+    branches:
+      - main
+    # Only watch root level Markdown documentation file changes
+    paths:
+      - 'README.md'
+      - '.github/workflows/check-links-in-documentation.yml' # also run when this file was changed
+  schedule:
+    - cron: "15 6 1 * *" # On the first day of each month at 6:15 o'clock
+
+jobs:
+  analysis-results:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout GIT Repository
+      uses: actions/checkout@v4
+
+    - name: Setup node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version-file: '.nvmrc'
+
+    - name: Skip on update of AxonFramework by bot (Renovate)
+      if: |
+        github.event_name == 'pull_request' && 
+        startsWith(github.event.pull_request.title, 'Update dependency AxonFramework') && 
+        github.event.pull_request.user.type == 'Bot'
+      run: |
+        echo "Skipping link check on AxonFramework updates since the updated links to the analysis-results will only be active " 
+        echo "skip_link_check=true" >> $GITHUB_ENV
+
+    - name: Check links in top level documentation Markdown files
+      if: ${{ ! env.skip_link_check}}
+      run: npx --yes [email protected] --verbose --alive=200,202,206 --retry README.md
+      # Temporarily, everything is done using command line options rather than with the config file, which doesn't seem to work.
+      # Maybe related to https://github.com/tcort/markdown-link-check/issues/379 ?

.github/workflows/check-renovate-config.yml

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+name: Check Renovate Configuration
+
+on:
+  pull_request:
+    branches:
+      - main
+    # Only watch root level Renovate configuration changes
+    paths:
+      - 'renovate.json*'
+
+jobs:
+  analysis-results:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout GIT Repository
+      uses: actions/checkout@v4
+
+    - name: Setup node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version-file: '.nvmrc'
+
+    - name: Run renovate-config-validator
+      run: npx --yes --package [email protected] -- renovate-config-validator