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Virtual site class #876

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Virtual site class #876

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PR Summary:

PR Checklist

  • Includes appropriate unit test(s)
  • Appropriate docstring(s) are added/updated
  • Code is (approximately) PEP8 compliant
  • Issue(s) raised/addressed?

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codecov bot commented Mar 6, 2025 •
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Codecov Report

Attention: Patch coverage is 64.82759% with 51 lines in your changes missing coverage. Please review.

Project coverage is 93.57%. Comparing base (4b1c0ad) to head (8b7ac3d).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
gmso/core/virtual_type.py 62.50% 33 Missing ⚠️
gmso/formats/mol2.py 19.04% 17 Missing ⚠️
gmso/core/forcefield.py 91.66% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #876      +/-   ##
==========================================
- Coverage   94.15%   93.57%   -0.59%     
==========================================
  Files          65       67       +2     
  Lines        6979     7124     +145     
==========================================
+ Hits         6571     6666      +95     
- Misses        408      458      +50

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github-advanced-security[bot]
github-advanced-security bot found potential problems Mar 11, 2025
View reviewed changes
@Zeerakkhan47
Update virtual_site.py
e89d635 
deleted duplicate class VirtualSite(site)
github-advanced-security[bot]
github-advanced-security bot found potential problems Mar 11, 2025
View reviewed changes
pre-commit-ci bot and others added 13 commits March 11, 2025 19:38
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
5af7e4d 
for more information, see https://pre-commit.ci
@Zeerakkhan47
added xsd info for virtual site type
22f3c8c
@Zeerakkhan47
edited tip4p_2005xml by adding VirtualSiteTypes
bd40072
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
618da83 
for more information, see https://pre-commit.ci
@Zeerakkhan47
Added tests for reading example xml with virtual sites
2558cfc
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
25a9de0 
for more information, see https://pre-commit.ci
@chrisjonesBSU @Zeerakkhan47
update docker file
6dcb58d
@pre-commit-ci @Zeerakkhan47
[pre-commit.ci] pre-commit autoupdate
2c71327 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.4 → v0.9.6](astral-sh/ruff-pre-commit@v0.9.4...v0.9.6)
@CalCraven @Zeerakkhan47
Fix handling for 3-site settles by passing a tag to write_top gromacs…
9d4415a 
… function
@pre-commit-ci @Zeerakkhan47
[pre-commit.ci] pre-commit autoupdate
f3e4e7f 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.9.7](astral-sh/ruff-pre-commit@v0.9.6...v0.9.7)
@pre-commit-ci @Zeerakkhan47
[pre-commit.ci] pre-commit autoupdate
ae0acf9 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.7 → v0.9.9](astral-sh/ruff-pre-commit@v0.9.7...v0.9.9)
- [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1)
@pre-commit-ci @Zeerakkhan47
[pre-commit.ci] pre-commit autoupdate
3ac80fc 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.9 → v0.9.10](astral-sh/ruff-pre-commit@v0.9.9...v0.9.10)
@pre-commit-ci @Zeerakkhan47
[pre-commit.ci] pre-commit autoupdate
8bef127 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.10 → v0.11.0](astral-sh/ruff-pre-commit@v0.9.10...v0.11.0)
@chrisjonesBSU chrisjonesBSU linked an issue Mar 20, 2025 that may be closed by this pull request
General virtual site data structure in GMSO #874
Open
@chrisjonesBSU chrisjonesBSU mentioned this pull request Mar 25, 2025
Closed
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Successfully merging this pull request may close these issues.

General virtual site data structure in GMSO
3 participants
@Zeerakkhan47 @chrisjonesBSU @CalCraven