bring everything up to date and improve class and function description

.github/workflows/test_package.yml

@@ -22,10 +22,14 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: '4.3.2'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install -r requirements_dev.txt
     - name: Test with pytest
       run: |
-        python -m pytest
+        python -m pytest --cov=causalAssembly tests/

.lintr

@@ -0,0 +1,5 @@
+linters: linters_with_defaults(
+    line_length_linter = line_length_linter(120L),
+    object_name_linter = NULL,
+    indentation_linter = NULL
+    )

Makefile

@@ -1,28 +1,50 @@
 #Makefile for causalAssembly
 
+
 MAKEFILE_PATH := $(abspath $(lastword $(MAKEFILE_LIST)))
 CURRENT_DIR := $(notdir $(patsubst %/,%,$(dir $(MAKEFILE_PATH))))
 
 VENV_NAME := venv_${CURRENT_DIR}
 PYTHON=${VENV_NAME}/bin/python
 
+ALLOWED_LICENSES := "$(shell tr -s '\n' ';' < allowed_licenses.txt)"
+ALLOWED_PACKAGES := $(shell tr -s '\n' ' ' < allowed_packages.txt)
+
 sync-venv:
 	: # Create or update default virtual environment to latest pinned
 	: # dependencies
 	test -d $(VENV_NAME) || \
 		python3.10 -m virtualenv $(VENV_NAME); \
-		${PYTHON} -m pip install -U pip; \
-		${PYTHON} -m pip install pip-tools
-	. $(VENV_NAME)/bin/activate && pip-sync requirements_dev.txt
-	#. $(VENV_NAME)/bin/activate && pip install --no-deps -e .
+		${PYTHON} -m pip install -U uv; \
+	. $(VENV_NAME)/bin/activate && uv pip sync requirements_dev.txt
+	. $(VENV_NAME)/bin/activate && uv pip install --no-deps -e .
 
 requirements:
 	: # Update requirements_dev.txt if only new library is added
 	: # Assumes virtual environment with pip-tools installed is activated
-	pip-compile --extra dev -o requirements_dev.txt pyproject.toml --annotation-style line --no-emit-index-url --no-emit-trusted-host --allow-unsafe --resolver=backtracking
+	uv pip compile pyproject.toml --output-file=requirements.txt  --annotation-style=line
+	uv pip compile pyproject.toml --extra=dev --output-file=requirements_dev.txt  --annotation-style=line
 
 
 update-requirements:
 	: # Update requirements_dev.txt if dependencies should be updated
 	: # Assumes virtual environment with pip-tools installed is activated
-	pip-compile --extra dev -o requirements_dev.txt pyproject.toml --annotation-style line --no-emit-index-url --no-emit-trusted-host --allow-unsafe --resolver=backtracking --upgrade
+	uv pip compile pyproject.toml --output-file=requirements.txt  --annotation-style=line --upgrade
+	uv pip compile pyproject.toml --extra=dev --output-file=requirements_dev.txt  --annotation-style=line --upgrade
+
+
+precommit:
+	: # Run precommit on all files locally (this runs only the pre-commit and not the pre-push hooks)
+	pre-commit install
+	pre-commit run --all-files
+
+test:
+	: # Run pytest
+	python -m pytest
+
+licenses:
+	: # Create file with used licenses and check if these are permissive
+	pip-licenses --order=license --ignore-packages ${ALLOWED_PACKAGES} --allow-only=${ALLOWED_LICENSES} > licenses.txt
+
+clean-branches:
+	git branch --merged | grep  -v '\\*\\|main\\|develop' | xargs -n 1 -r git branch -d

README.md

@@ -6,7 +6,7 @@
 This repo provides details regarding $\texttt{causalAssembly}$, a causal discovery benchmark data tool based on complex production data.
 Theoretical details and information regarding construction are presented in the [paper](https://arxiv.org/abs/2306.10816):
 
-    Göbler, K., Windisch, T., Pychynski, T., Sonntag, S., Roth, M., & Drton, M. causalAssembly: Generating Realistic Production Data for Benchmarking Causal Discovery, to appear in Proceedings of the 3rd Conference on Causal Learning and Reasoning (CLeaR), 2024, 
+    Göbler, K., Windisch, T., Pychynski, T., Sonntag, S., Roth, M., & Drton, M. causalAssembly: Generating Realistic Production Data for Benchmarking Causal Discovery, to appear in Proceedings of the 3rd Conference on Causal Learning and Reasoning (CLeaR), 2024,
 ## Authors
 * [Konstantin Goebler](mailto:[email protected])
 * [Steffen Sonntag](mailto:[email protected])

VERSION

@@ -1 +1 @@
-1.1.3
+1.2.0

allowed_licenses.txt

@@ -0,0 +1,24 @@
+Apache-2.0
+Apache 2.0
+Apache License 2.0
+APACHE SOFTWARE LICENSE
+BOSCH-INTERNAL
+BSD 3-Clause
+BSD License
+BSD
+3-Clause BSD License
+BSD (3-Clause)
+ISC
+ISC License (ISCL)
+Other/Proprietary License
+MIT
+MIT License
+CMU License (MIT-CMU)
+GPL-2.0-or-later
+GNU General Public License v2 or later (GPLv2+)
+Python Software Foundation License
+The Unlicense (Unlicense)
+Historical Permission Notice and Disclaimer (HPND)
+MPL-2.0
+NVIDIA Proprietary Software
+UNKNOWN

allowed_packages.txt

@@ -0,0 +1,8 @@
+causalAssembly
+rpy2
+chardet
+certifi
+dbx
+mdpcommonlib
+pathspec
+text-unidecode

benchmarks/run.py

@@ -1,4 +1,5 @@
-""" Utility classes and functions related to causalAssembly.
+"""Utility classes and functions related to causalAssembly.
+
 Copyright (c) 2023 Robert Bosch GmbH
 
 This program is free software: you can redistribute it and/or modify