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structure generation overhaul #296

Merged
merged 20 commits into from
Nov 21, 2024
Merged

structure generation overhaul #296

merged 20 commits into from
Nov 21, 2024

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rolan701
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rolan701 and others added 20 commits November 14, 2024 19:02
hope this isn't awful
added move_point compatibility
no_tabs brought back
fixed trailing whitespace
needed for my structgen changes
added import copy
made dist a float
caveats for more unforseen instances of core3D building
fixed writemol2
smart generation default change and addition to mcomplex
changed writemol2 to hopefully pass test
no_tabs fix 1
no_tabs fix 2
obConversion.SetOutFormat("xyz")
obConversion.WriteFile(OBMol,fname+'BABEL.xyz')

# check if overextended H:

Check warning

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'dist' is unnecessary as it is
redefined
before this value is used.
This assignment to 'dist' is unnecessary as it is
redefined
before this value is used.
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codecov bot commented Nov 21, 2024

Codecov Report

Attention: Patch coverage is 33.33333% with 124 lines in your changes missing coverage. Please review.

Project coverage is 37.29%. Comparing base (7765d71) to head (7a86b90).
Report is 21 commits behind head on main.

Files with missing lines Patch % Lines
molSimplify/Scripts/structgen.py 16.53% 106 Missing ⚠️
molSimplify/Classes/mol3D.py 69.64% 17 Missing ⚠️
molSimplify/Scripts/inparse.py 66.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #296      +/-   ##
==========================================
+ Coverage   37.23%   37.29%   +0.05%     
==========================================
  Files          90       90              
  Lines       30025    30210     +185     
==========================================
+ Hits        11179    11266      +87     
- Misses      18846    18944      +98     
Flag Coverage Δ
unittests 37.29% <33.33%> (+0.05%) ⬆️

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@rolan701
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Big change merge, work with overwrite and smart_generation

@rolan701 rolan701 merged commit 1c8fb7e into hjkgrp:main Nov 21, 2024
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