Update documentation

Author: JohT

COMMANDS.md

@@ -8,6 +8,7 @@
     - [Examples](#examples)
         - [Start an analysis with CSV reports only](#start-an-analysis-with-csv-reports-only)
         - [Start an analysis with Jupyter reports only](#start-an-analysis-with-jupyter-reports-only)
+        - [Start an analysis with Python reports only](#start-an-analysis-with-python-reports-only)
         - [Start an analysis with PDF generation](#start-an-analysis-with-pdf-generation)
         - [Start an analysis without importing git log data](#start-an-analysis-without-importing-git-log-data)
         - [Only run setup and explore the Graph manually](#only-run-setup-and-explore-the-graph-manually)
@@ -102,6 +103,14 @@ If only the Jupyter reports are needed e.g. when the CSV reports had already bee
 ./../../scripts/analysis/analyze.sh --report Jupyter
 ```
 
+#### Start an analysis with Python reports only
+
+If you only need Python reports, e.g. to skip Chromium Browser dependency, the this can be done with:
+
+```shell
+./../../scripts/analysis/analyze.sh --report Python
+```
+
 #### Start an analysis with PDF generation
 
 Note: Generating a PDF from a Jupyter notebook using [nbconvert](https://nbconvert.readthedocs.io) takes some time and might even fail due to a timeout error.

GETTING_STARTED.md

@@ -84,16 +84,22 @@ Use these optional command line options as needed:
   ./../../scripts/analysis/analyze.sh --report Csv
   ```
 
-- Jupyter notebook reports when Python and Conda are installed:
+- Jupyter notebook reports when Python and Conda are installed (and Chromium Browser for PDF generation):
 
   ```shell
   ./../../scripts/analysis/analyze.sh --report Jupyter
   ```
 
+- Python reports when Python and Conda are installed (without Chromium Browser for PDF generation):
+
+  ```shell
+  ./../../scripts/analysis/analyze.sh --report Python
+  ```
+
 - Graph visualizations when Node.js and npm are installed:
 
   ```shell
-  ./../../scripts/analysis/analyze.sh --report Jupyter
+  ./../../scripts/analysis/analyze.sh --report Visualization
   ```
 
 - All reports with Python, Conda, Node.js and npm installed:

README.md

@@ -148,6 +148,9 @@ The [Code Structure Analysis Pipeline](./.github/workflows/internal-java-code-an
   - [Neo4j Python Driver](https://neo4j.com/docs/api/python-driver)
   - [openTSNE](https://github.com/pavlin-policar/openTSNE)
   - [wordcloud](https://github.com/amueller/word_cloud)
+  - [umap](https://umap-learn.readthedocs.io)
+  - [scikit-learn](https://scikit-learn.org)
+  - [optuna](https://optuna.org)
 - [Graph Visualization](./graph-visualization/README.md) uses [node.js](https://nodejs.org/de) and the dependencies listed in [package.json](./graph-visualization/package.json).
 - [HPCC-Systems (High Performance Computing Cluster) Web-Assembly (JavaScript)](https://github.com/hpcc-systems/hpcc-js-wasm) containing a wrapper for GraphViz to visualize graph structures.
 - [GraphViz](https://gitlab.com/graphviz/graphviz) for CLI Graph Visualization