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Merge pull request #349 from JohT/feature/improve-documentation
Improve Documentation
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‎.github/workflows/internal-check-links-in-documentation.yml

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- 'COMMANDS.md'
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- 'GETTING_STARTED.md'
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- 'INTEGRATION.md'
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- 'CHANGELOG.md'
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- '.github/workflows/internal-check-links-in-documentation.yml' # also run when this file was changed
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schedule:
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- cron: "15 6 1 * *" # On the first day of each month at 6:15 o'clock
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- name: Check links in top level documentation Markdown files
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if: ${{ ! env.skip_link_check}}
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run: npx --yes [email protected] --verbose --alive=200,202,206 --retry README.md COMMANDS.md GETTING_STARTED.md INTEGRATION.md
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run: npx --yes [email protected] --verbose --alive=200,202,206 --retry README.md COMMANDS.md GETTING_STARTED.md INTEGRATION.md CHANGELOG.md
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# Temporarily, everything is done using command line options rather than with the config file, which doesn't seem to work.
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# Maybe related to https://github.com/tcort/markdown-link-check/issues/379 ?

‎CHANGELOG.md

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# Code Graph Analysis Pipeline - Changelog
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This document describes the changes to the Code Graph Analysis Pipeline. The changes are grouped by version and date. The latest version is at the top.
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## v2.0.0 (2024-12-15) TypeScript Source Code Analysis
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For all details see: https://github.com/JohT/code-graph-analysis-pipeline/releases/tag/v2.0.0
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### 🌟 Highlights 🌟
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* ✨[TypeScript](https://github.com/jqassistant-plugin/jqassistant-typescript-plugin) ✨ Source Code Analysis (experimental)
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* [Git](https://github.com/kontext-e/jqassistant-git-plugin) data included
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* [Npm package.json](https://github.com/jqassistant-plugin/jqassistant-npm-plugin) data included
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* Multiple source folders
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* Symbolic links
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* Incoming and Outgoing dependencies considering Java subpackages
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* [Path finding algorithms](https://neo4j.com/docs/graph-data-science/current/algorithms/pathfinding) reports
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* [Bridges](https://neo4j.com/docs/graph-data-science/current/algorithms/bridges) centrality algorithm report
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* JavaEE and Spring REST endpoint reports
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### 🚀 Features
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* Skip analysis for empty projections by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/114
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* Small Improvements by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/117
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* Incoming and outgoing package dependencies with sub packages by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/124
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* Introduce Typescript Analysis by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/112
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* Separate report reference documentation generation by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/143
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* Add optional data validation before Jupyter notebook execution. by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/144
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* Assure that t-SNE perplexity parameter is lower than the sample size for small graphs by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/147
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* Use pnpm as package manager for react-router by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/148
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* Migrate from sklearn.manifold TSNE to openTSNE for visualizing node embeddings by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/155
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* Provide script to import git log as csv by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/157
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* Add parent git commit nodes and connect them by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/159
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* Use latest stable open graph-data-science version 2.6.7 by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/161
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* Use latest stable open-graph-data-science version 2.6.8 by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/162
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* Ignore duplicate Typescript analysis json files scan by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/173
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* Fix missing declarationCount property on DEPENDS_ON relationships by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/183
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* Add file distance to DEPENDS_ON relationships by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/184
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* Support npm package.json files by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/185
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* Add script to sort out external Java jar libraries. by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/186
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* Support multiple source directories by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/178
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* Support Typescript scan for existing sources without clone by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/191
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* Refine nodes and relationships for multi typescript project graphs by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/194
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* Support scanning files outside "artifacts" and switch to plugin for git data by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/195
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* Use Renovate to update jQAssistant plugins by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/198
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* Fix error when tsconfig has file as reference path. by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/200
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* Improve useability by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/203
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* Auto detect latest git tag if no version is specified by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/208
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* Detect, mark and filter test related modules in Typescript analysis by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/209
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* Improve file and npm relationships for Typescript projects by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/210
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* Add statistics about resolved external Typescript modules by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/215
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* Scan every Typescript source directory separately. by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/224
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* Support scanning large code bases by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/229
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* Improvements for Typescript by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/231
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* Support Typescript version numbers by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/223
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* Scan each contained Typescript package when the scan of the whole source repository failed by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/244
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* Fix missing support for dashes in profile names. by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/245
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* Improve RESOLVES_TO relationships between external and internal Typescript modules by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/248
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* Improve internal dependencies reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/255
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* Fix minor Typescript issues by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/259
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* Improve naming of external Typescript nodes by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/260
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* Improve Typescript scanning and git import by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/265
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* Improvements for large scala Typescript analysis by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/268
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* Fix missing IS_IMPLEMENTED_IN relationship for Typescript declarations by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/277
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* Fix broken link check using workaround by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/279
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* Install Typescript project dependencies explicitly by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/280
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* Update jQAssistant TypeScript Plugin to v1.3.2 by @renovate in https://github.com/JohT/code-graph-analysis-pipeline/pull/282
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* Add details to algorithm result code unit names by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/285
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### 📈 Reports
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* Add reports containing JavaEE and Spring REST resources by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/102
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* Add Graph visualizations for Typescript Modules by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/142
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* Add graph data science algorithms for Typescript by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/137
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* Add external dependencies reports for Typescript by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/154
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* Add internal dependencies reports for Typescript by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/167
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* Add Overview reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/174
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* Add visibility reports for Typescript by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/175
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* Introduce path finding algorithm reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/216
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* Add Bridges centrality algorithm report by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/283
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## v1.0.1 (2023-12-16) Fix Graph Visualization
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For all details see: https://github.com/JohT/code-graph-analysis-pipeline/releases/tag/v1.0.1
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### ⚙️ Optimization
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* Update and add old results by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/91
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* Improve visualization error handling by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/89
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### 🛠 Fixes
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* Fix JavaScript Graph Visualization by running it after all CSV reports that write data into the Graph by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/89
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### 📦 Dependency Updates
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* Update dependency AxonFramework/AxonFramework to v4.9.1 by @renovate in https://github.com/JohT/code-graph-analysis-pipeline/pull/90
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## v1.0.0 (2023-12-09) First major version release
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### 🚀 Features
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* Update to Neo4j v5 and jQAssistant CLI 2.0 by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/6
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* Introduce explore mode to start a manual analysis by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/13/commits/53d60458589d5bfae07958fad57f0533f9eb9cb1
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* Support for open packaged graph-data-science plugin by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/15
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* Support query parameters by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/42
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### 📈 Reports
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* Graph Visualization by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/24
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* Render visualization as png using puppeteer by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/26
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* Add artifact reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/31
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* Add node embeddings reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/47
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* Add reports with metrics about detected communities by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/73
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* Add java specific queries and reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/83
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### 📖 Documentation
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* Auto-generate reference documentation by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/22
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* Bring documentation up-to-date by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/74
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### ⚙️ Optimization
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* Rename "package dependencies" to "internal dependencies" by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/12
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* Separate artifacts and their download from the analysis by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/13
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* Performance Tuning by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/19
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* Update old analysis reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/23
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* Parametrize Topological Sort by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/51
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* Refine Community Detection by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/52
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* Fail-fast approach for error handling by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/54
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* Optimize centrality reports using in-memory mutate by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/55
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* Optimize Similarity using in-memory mutation by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/60
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* Minor improvements and refinements by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/88
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### 🛠 Fixes
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* Fix missing Jupyter reports by @JohT in https://github.com/JohT/code-graph-analysis-pipeline/pull/72
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## v0.9.0 (2023-06-26) Initial Release Version
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For all details see: https://github.com/JohT/code-graph-analysis-pipeline/releases/tag/v0.9.0
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### 🚀 Features
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* Analyze static code structure, dependencies, metrics, ...
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* Fully automated [pipeline](./.github/workflows/code-reports.yml) from tool installation and artifact download to report generation
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* Runtime and library independent automation using [shell scripts](./scripts/SCRIPTS.md)
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* Comprehensive list of [Cypher queries](./cypher/CYPHER.md)
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* Example Analysis for [AxonFramework](https://github.com/AxonFramework/AxonFramework)
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### 📖 Jupyter Notebook Reports
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* [External Dependencies](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/external-dependencies-java/ExternalDependenciesJava.md) contains detailed information about external library usage ([Notebook](./jupyter/ExternalDependenciesJava.ipynb)).
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* [Object Oriented Design Quality Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-java/ObjectOrientedDesignMetricsJava.md) is based on [OO Design Quality Metrics by Robert Martin](https://api.semanticscholar.org/CorpusID:18246616) ([Notebook](./jupyter/ObjectOrientedDesignMetricsJava.ipynb)).
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* [Overview](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/overview-java/OverviewJava.md) contains overall statistics and details about methods and their complexity. ([Notebook](./jupyter/OverviewJava.ipynb)).
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* [Internal Dependencies](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/internal-dependencies-java/InternalDependenciesJava.md) is based on [Analyze java package metrics in a graph database](https://joht.github.io/johtizen/data/2023/04/21/java-package-metrics-analysis.html) and also includes cyclic dependencies ([Notebook](./jupyter/InternalDependenciesJava.ipynb)).
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* [Visibility Metrics](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-java/VisibilityMetricsJava.md) ([Notebook](./jupyter/VisibilityMetricsJava.ipynb)).
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* [Wordcloud](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/wordcloud/Wordcloud.md) contains a visual representation of package and class names ([Notebook](./jupyter/Wordcloud.ipynb)).
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### 📖 Graph Data Science Reports
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Here are some reports that utilize Neo4j's [Graph Data Science Library](https://neo4j.com/product/graph-data-science):
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* [Centrality](./scripts/reports/CentralityCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/centrality-csv/Package_Centrality_Page_Rank.csv))
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* [Community Detection](./scripts/reports/CommunityCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/community-csv/Package_communityLeidenId_Community__Metrics.csv))
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* [Similarity](./scripts/reports/SimilarityCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/similarity-csv/Package_Similarity.csv))
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### 📖 Other Reports
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* [External Dependencies (CSV)](./scripts/reports/ExternalDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/external-dependencies-csv/External_package_usage_overall.csv))
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* [Object Oriented Design Metrics (CSV)](./scripts/reports/ObjectOrientedDesignMetricsCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/object-oriented-design-metrics-csv/MainSequenceAbstractnessInstabilityDistanceJava.csv))
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* [Overview (CSV)](./scripts/reports/OverviewCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/overview-csv/Cyclomatic_Method_Complexity.csv))
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* [Internal Dependencies - Cyclic (CSV)](./scripts/reports/PackageDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/internal-dependencies-csv/Cyclic_Dependencies_Breakdown_Backward_Only.csv))
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* [Internal Dependencies - Interface Segregation (CSV)](./scripts/reports/PackageDependenciesCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/internal-dependencies-csv/InterfaceSegregationCandidates.csv))
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* [Visibility Metrics (CSV)](./scripts/reports/VisibilityMetricsCsv.sh) ([Example](https://github.com/JohT/code-graph-analysis-examples/blob/main/analysis-results/AxonFramework/latest/visibility-metrics-csv/RelativeVisibilityPerArtifact.csv))

‎COMMANDS.md

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The following command shows how to use [markdown-link-check](https://github.com/tcort/markdown-link-check) to for example check the links in the [README.md](./README.md) file:
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```script
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npx --yes markdown-link-check --quiet --progress --config=markdown-lint-check-config.json README.md COMMANDS.md GETTING_STARTED.md INTEGRATION.md
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npx --yes markdown-link-check --quiet --progress --config=markdown-lint-check-config.json README.md COMMANDS.md GETTING_STARTED.md INTEGRATION.md CHANGELOG.md
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```
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## Manual Setup

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