[ENH, VIZ] updating draw() for using a graph layout that allows us to fix node positions

[siebert-julien]

Fixes #24

Changes proposed in this pull request:

• adding a pos argument to the draw function
• adding an example for drawing graphs with fixed layout
• adding a test for draw

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[adam2392]

Some minor edits. Great work and thanks for also writing up an example!

I pushed a commit to main to fix a CI issue. You probably will see some issues with formatting, which you can fix locally. You can check:

poetry run poe apply_format
poetry run poe lint
poetry run poe type_check
poetry run poe build_docs

For more information, see https://github.com/py-why/pywhy-graphs/blob/main/CONTRIBUTING.md

[siebert-julien]

Hi @adam2392 I accepted the minor changes you requested.

I also run the formatting checks.

I had no problem with poetry run poe apply_format and poetry run poe type_check.

Unfortunately poetry run poe lint was taking ages, I had to kill it.

I hope everything is fine now.

[adam2392]

Unfortunately poetry run poe lint was taking ages, I had to kill it.

This could be because not all the dev dependencies were installed (e.g. flake8, etc.). Can you try running:

poetry install --only style? I should add a check whether or not the libs are even installed. I think flake8 times out for some reason if you don't have it installed rather than raising an error... not sure why. Here is the output I get when running locally.

(pywhy-graphs) adam2392@Adams-MacBook-Pro pywhy-graphs % poetry run poe lint
Poe => flake8
./tests/test_draw.py:1:1: F401 'pywhy_graphs' imported but unused
./tests/test_draw.py:5:1: F401 'pywhy_graphs.CPDAG' imported but unused
./tests/test_draw.py:5:1: F401 'pywhy_graphs.PAG' imported but unused
./tests/test_draw.py:11:101: E501 line too long (111 > 100 characters)
./tests/test_draw.py:29:101: E501 line too long (131 > 100 characters)
./tests/test_draw.py:47:101: E501 line too long (105 > 100 characters)
./tests/test_draw.py:61:101: E501 line too long (131 > 100 characters)
./examples/draw_and_compare_graphs_with_same_layout.py:8:101: E501 line too long (114 > 100 characters)
./examples/draw_and_compare_graphs_with_same_layout.py:15:101: E501 line too long (106 > 100 characters)
./examples/draw_and_compare_graphs_with_same_layout.py:17:101: E501 line too long (119 > 100 characters)
./examples/draw_and_compare_graphs_with_same_layout.py:42:101: E501 line too long (102 > 100 characters)
./pywhy_graphs/viz/draw.py:16:101: E501 line too long (111 > 100 characters)
Poe => bandit -r pywhy_graphs -c pyproject.toml
[main]  INFO    profile include tests: None
[main]  INFO    profile exclude tests: None
[main]  INFO    cli include tests: None
[main]  INFO    cli exclude tests: None
[main]  INFO    using config: pyproject.toml
[main]  INFO    running on Python 3.9.13
Run started:2022-12-21 00:29:26.630414

Test results:
        No issues identified.

Code scanned:
        Total lines of code: 1785
        Total lines skipped (#nosec): 0

Run metrics:
        Total issues (by severity):
                Undefined: 0
                Low: 0
                Medium: 0
                High: 0
        Total issues (by confidence):
                Undefined: 0
                Low: 0
                Medium: 0
                High: 0
Files skipped (0):
Poe => codespell pywhy_graphs/ doc/ examples/ --ignore-words=.codespellignore --skip **/_build/*
examples/draw_and_compare_graphs_with_same_layout.py:42: softwares ==> software
Poe => pydocstyle .
Error: Subtasks _flake8, _codespell returned non-zero exit status 

[adam2392]

Almost there!

• Can you add a changelog entry in docs/whats_new/v0.1.rst?
• The CIs should work now and will show you the issues w/ the code formatting. Lmk if the poetry install of the Dev dependencies do not work well.

[codecov-commenter]

Codecov Report

Merging #26 (cb89339) into main (8c2ff2e) will increase coverage by 0.71%.
The diff coverage is 17.24%.

@@            Coverage Diff             @@
##             main      #26      +/-   ##
==========================================
+ Coverage   68.27%   68.99%   +0.71%     
==========================================
  Files          14       14              
  Lines         788      803      +15     
  Branches      208      213       +5     
==========================================
+ Hits          538      554      +16     
+ Misses        204      197       -7     
- Partials       46       52       +6     

Impacted Files	Coverage Δ
pywhy_graphs/viz/draw.py	36.36% <17.24%> (+36.36%)	⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[adam2392]

The CircleCI error: /home/circleci/project/docs/whats_new/v0.1.rst:34: WARNING: py:func reference target not found: pywhy_graphs.viz.draw can be fixed by adding draw function to the api.rst file.

There I would create another section for "Visualization of causal graphs" and you can follow the pattern shown for other functions to add draw somewhere there.

[siebert-julien]

@adam2392 The CI fails on building the doc. I am out of idea why this is the case (at first I thought the URL syntax was the root cause, but I think I fixed that). Any idea?

Concerning the style dependencies, they were all installed properly. The problem seems to come from flake8 that does not respond for some reasons (I haven't investigated that).

[adam2392]

@adam2392 The CI fails on building the doc. I am out of idea why this is the case (at first I thought the URL syntax was the root cause, but I think I fixed that). Any idea?

Concerning the style dependencies, they were all installed properly. The problem seems to come from flake8 that does not respond for some reasons (I haven't investigated that).

No worries. I fixed it. See #26 (comment).

[adam2392]

Thanks @siebert-julien for the code contribution! Will merge once CI gives the green light.