fix polygons at gdstk level before shapely meshing preprocessing

[simbilod]

@HelgeGehring

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.25%.

Quality metrics	Before	After	Change
Complexity	9.67 🙂	9.61 🙂	-0.06 👍
Method Length	97.40 🙂	98.92 🙂	1.52 👎
Working memory	12.47 😞	12.88 😞	0.41 👎
Quality	54.74% 🙂	54.49% 🙂	-0.25% 👎

Other metrics	Before	After	Change
Lines	1296	1317	21

Changed files	Quality Before	Quality After	Quality Change
gdsfactory/simulation/gmsh/mesh.py	70.54% 🙂	69.32% 🙂	-1.22% 👎
gdsfactory/simulation/gmsh/meshtracker.py	73.08% 🙂	73.08% 🙂	0.00%
gdsfactory/simulation/gmsh/parse_gds.py	73.07% 🙂	71.43% 🙂	-1.64% 👎
gdsfactory/simulation/gmsh/uz_xsection_mesh.py	48.01% 😞	47.83% 😞	-0.18% 👎
gdsfactory/simulation/gmsh/xy_xsection_mesh.py	44.43% 😞	43.63% 😞	-0.80% 👎
gdsfactory/simulation/gmsh/xyz_mesh.py	37.46% 😞	37.46% 😞	0.00%

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
gdsfactory/simulation/gmsh/xyz_mesh.py	xyz_mesh	30 😞	669 ⛔	18 ⛔	15.09% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
gdsfactory/simulation/gmsh/uz_xsection_mesh.py	uz_xsection_mesh	14 🙂	362 ⛔	32 ⛔	22.66% ⛔	Try splitting into smaller methods. Extract out complex expressions
gdsfactory/simulation/gmsh/xy_xsection_mesh.py	xy_xsection_mesh	9 🙂	249 ⛔	28 ⛔	31.34% 😞	Try splitting into smaller methods. Extract out complex expressions
gdsfactory/simulation/gmsh/xyz_mesh.py	add_volume	10 🙂	325 ⛔	15 😞	34.89% 😞	Try splitting into smaller methods. Extract out complex expressions
gdsfactory/simulation/gmsh/mesh.py	mesh_from_polygons	4 ⭐	143 😞	18 ⛔	48.84% 😞	Try splitting into smaller methods. Extract out complex expressions

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[codecov]

Codecov Report

Merging #1396 (189b838) into main (594121f) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #1396   +/-   ##
=======================================
  Coverage   69.50%   69.50%           
=======================================
  Files         366      366           
  Lines       22002    22002           
  Branches     3156     3156           
=======================================
  Hits        15292    15292           
  Misses       5806     5806           
  Partials      904      904           

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[HelgeGehring]

Amazing! I'm just wondering, do you think growing and shrinking it by np.finfo(float).eps would be sufficient? With shapely that was once exactly what was needed 🤔

[tvt173]

Amazing! I'm just wondering, do you think growing and shrinking it by np.finfo(float).eps would be sufficient? With shapely that was once exactly what was needed 🤔

you should be able to even grow/shrink by the grid size, since anything smaller than that is physically irrelevant. that would be a good default for atol also... i.e. default=None, and if None, use active_pdk.grid_size

[simbilod]

Implemented, thank you for the suggestion @tvt173 @HelgeGehring

[joamatab]

Thank you Simon!