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Input restrictions for EFGF lifted and some general refactoring and fixing #20

Merged
merged 27 commits into from
Feb 2, 2024
Merged

Input restrictions for EFGF lifted and some general refactoring and fixing #20

merged 27 commits into from
Feb 2, 2024

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JonasSchaub
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@JonasSchaub
Commented-out input restrictions;
b2f66c1
@JonasSchaub
Moved test classes into the same folder as the tested classes; moved …
b9c3dab 
…test resources into the respective package structure; added tests to EFGFTest for cases that formerly represented illegal inputs;
@JonasSchaub
Updated copyright year
82d8d0d
@JonasSchaub
Started refactoring code according to internal conventions;
565e448
@JonasSchaub
Continued refactoring;
436b40a
@JonasSchaub
Refactoring of markAtoms method
b165266
@JonasSchaub
Overhaul of extractGroups
6b222c5
@JonasSchaub
Overhaul of expandGeneralizedEnvironments, WIP
9699ef1
@JonasSchaub
Continued refactoring
d6f9004
@JonasSchaub
Overhaul of more methods, WIP
9d8edf6
@JonasSchaub
Overhaul of partitionIntoGroups()
b13a14c
@JonasSchaub
Finished refactoring of EFGF for now;
a241b13
@JonasSchaub
Added new environment mode to only extract marked atoms; added factor…
2531267 
…y methods; added convenience method for accessing valid atomic numbers
@JonasSchaub
Transferred some utility methods for input testing and preprocessing …
c755e3f 
…from utility class to EFGF;
@JonasSchaub
Additional documentation;
8b36bc1
@JonasSchaub
Overhaul of EFGFTest;
8682e11
@JonasSchaub
Fixed failing javadoc build
53704f8
@JonasSchaub
Pseudo atoms are not identified as hetero atoms anymore;
ab4d3c4
@JonasSchaub
Moved ChEBI analysis to evaluation test;
5aa839a
@JonasSchaub
Added molecule from test find 1 to test for extracting only marked at…
a9b58d5 
…oms;
@JonasSchaub
Test for charge neutralization;
82531db
@JonasSchaub
Started cleaning up tests;
77c822e
@JonasSchaub
Started looking at evaluation test;
f97e24a
@JonasSchaub
Finished cleaning up the evaluation test; some more refactoring and d…
6214bac 
…ocumentation;
@JonasSchaub
Fixed hydrogen bug and disabled evaluation test;
9f4f57c
@JonasSchaub JonasSchaub self-assigned this Feb 1, 2024
@sonarcloud SonarCloud
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sonarcloud bot commented Feb 2, 2024

Quality Gate Failed Quality Gate failed

Failed conditions

67.0% Coverage on New Code (required ≥ 80%)

See analysis details on SonarCloud

@JonasSchaub JonasSchaub merged commit 3ef7f6d into production Feb 2, 2024
4 of 5 checks passed
@JonasSchaub JonasSchaub deleted the input_restrictions branch February 2, 2024 09:22
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