Bug in CPDAG drawing

[aryan26roy]

Checklist

• I have verified that the issue exists against the main branch.
• I have read the relevant section in the contribution guide on reporting bugs.
• I have checked the issues list for similar or identical bug reports.
• I have checked the pull requests list for existing proposed fixes.
• I have checked the CHANGELOG and the commit log to find out if the bug was already fixed in the main branch.
• I have included in the "Description" section below a traceback from any exceptions related to this bug.
• I have included in the "Related issues or possible duplicates" section beloew all related issues and possible duplicate issues (If there are none, check this box anyway).
• I have included in the "Environment" section below the name of the operating system and Python version that I was using when I discovered this bug.
• I have included in the "Environment" section below the output of pip freeze.
• I have included in the "Steps to reproduce" section below a minimally reproducible example.

Description

When drawing a CPDAG with 4 nodes (even 3 nodes) the drawing shows more edges than the edge list displays.

{'directed': OutEdgeView([('xy', 'x'), ('x', 'z')]), 'undirected': EdgeView([])}

{'directed': OutEdgeView([('xy', 'x'), ('x', 'z'), ('z', 'w')]), 'undirected': EdgeView([])}

Python traceback:

Related issues or possible duplicates

• None

Environment

OS: Ubuntu 22.10

Python version: 3.10.7

Output of pip freeze:

accessible-pygments==0.0.4
alabaster==0.7.13
ananke==0.1
attrs==22.2.0
Babel==2.12.1
backcall==0.2.0
bandit==1.7.4
beautifulsoup4==4.12.0
black==22.12.0
CacheControl==0.12.11
causal-learn==0.1.3.3
certifi==2022.12.7
cffi==1.15.1
charset-normalizer==3.1.0
cleo==2.0.1
click==8.1.3
cloudpickle==2.2.1
codespell==2.2.4
contourpy==1.0.7
crashtest==0.4.1
cryptography==40.0.1
cycler==0.11.0
Cython==0.29.33
decorator==5.1.1
distlib==0.3.6
docutils==0.19
dowhy==0.9.1
dulwich==0.20.50
dunamai==1.16.0
econml==0.14.0
exceptiongroup==1.1.1
filelock==3.10.7
flake8==5.0.4
fonttools==4.39.3
-e git+ssh://[email protected]/scikit-hep/formulate.git@1658ad732fb441c11ce8fac08e3a4eda0d43d44f#egg=formulate
gitdb==4.0.10
GitPython==3.1.31
graphviz==0.20.1
html5lib==1.1
idna==3.4
imagesize==1.4.1
importlib-metadata==6.1.0
iniconfig==2.0.0
ipython==7.34.0
isort==5.12.0
jaraco.classes==3.2.3
jedi==0.18.2
jeepney==0.8.0
Jinja2==3.1.2
joblib==1.2.0
jsonschema==4.17.3
keyring==23.13.1
kiwisolver==1.4.4
lark==1.1.5
latexcodec==2.0.1
lightgbm==3.3.5
llvmlite==0.39.1
lockfile==0.12.2
MarkupSafe==2.1.2
matplotlib==3.7.1
matplotlib-inline==0.1.6
mccabe==0.7.0
more-itertools==9.1.0
mpmath==1.3.0
msgpack==1.0.5
mypy==0.971
mypy-extensions==1.0.0
networkx==2.8.8
numba==0.56.4
numpy==1.23.5
numpydoc==1.5.0
packaging==23.0
paho-mqtt==1.6.1
pandas==1.5.3
parso==0.8.3
pastel==0.2.1
pathspec==0.11.0
patsy==0.5.3
pbr==5.11.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==9.4.0
pkginfo==1.9.6
platformdirs==3.1.0
pluggy==1.0.0
poethepoet==0.16.5
poetry==1.3.0
poetry-core==1.4.0
poetry-dynamic-versioning==0.21.4
poetry-plugin-export==1.3.0
pre-commit-hooks @ file:///home/aryan/.cache/pre-commit/repolkdstyo6
prompt-toolkit==3.0.38
ptyprocess==0.7.0
pybtex==0.24.0
pybtex-docutils==1.0.2
pycodestyle==2.9.1
pycparser==2.21
pydata-sphinx-theme==0.13.3
pydocstyle==6.3.0
pydot==1.4.2
pyflakes==2.5.0
Pygments==2.14.0
pyparsing==3.0.9
pyrsistent==0.19.3
pytest==7.3.0
python-dateutil==2.8.2
pytz==2023.3
-e git+ssh://[email protected]/aryan26roy/pywhy-graphs.git@c13d202c7af244ff94a1c8d29d7740e62a3e7c93#egg=pywhy_graphs
PyYAML==6.0
rapidfuzz==2.13.7
requests==2.28.2
requests-toolbelt==0.10.1
ruamel.yaml==0.17.21
ruamel.yaml.clib==0.2.7
ruff==0.0.263
scikit-learn==1.1.3
scipy==1.10.1
SecretStorage==3.3.3
shap==0.40.0
shellingham==1.5.0.post1
six==1.16.0
slicer==0.0.7
smmap==5.0.0
snowballstemmer==2.2.0
soupsieve==2.4
sparse==0.14.0
Sphinx==5.3.0
sphinx-copybutton==0.5.1
sphinx-gallery==0.12.2
sphinx-issues==3.0.1
sphinx_design==0.3.0
sphinxcontrib-applehelp==1.0.4
sphinxcontrib-bibtex==2.5.0
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.1
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
statsmodels==0.13.5
stevedore==5.0.0
sympy==1.11.1
sync-with-poetry @ file:///home/aryan/.cache/pre-commit/repoat95e_7n
threadpoolctl==3.1.0
tokenize-rt==5.0.0
toml==0.10.2
tomli==2.0.1
tomlkit==0.7.2
tqdm==4.65.0
traitlets==5.9.0
trove-classifiers==2023.3.9
typing_extensions==4.5.0
urllib3==1.26.15
virtualenv==20.21.0
wcwidth==0.2.6
webencodings==0.5.1
zipp==3.15.0

Steps to reproduce

Example source:

import pywhy_graphs
from pywhy_graphs import CPDAG
from pywhy_graphs.viz import draw



cpdag = CPDAG()

cpdag.add_edge("xy", "x", cpdag.directed_edge_name)
cpdag.add_edge("x", "z", cpdag.directed_edge_name)
cpdag.add_edge("z", "w", cpdag.directed_edge_name) # comment out the edges to see it reproduced with less number of edges.

print(cpdag.edges())

dot_graph = draw(cpdag, name="bug")
dot_graph.render(outfile="cpdag.png", view=True)

[aryan26roy]

@adam2392 I hope the MVP is good.

[adam2392]

Thanks!