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WIP-refactoring nesting #57

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wants to merge 23 commits into from
Closed

WIP-refactoring nesting #57

wants to merge 23 commits into from

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AlexPatrie
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In an effort to lower the generalized "cognitive complexity" score assessed by SonarCloud, this pr and branch serves as an effort to lower all cognitive complexity-assessments-points > 1 to be <= 0. Please refer to Issue "Lowering Cognitive complexity as per SonarCloud" for more information.

@AlexPatrie
Added explicit typing to biosimulators_copasi.core
03bab4a
@AlexPatrie
More explicit typing particularly in tuples specifying the type and i…
bbc5885 
…ndex position
@AlexPatrie
Minor tweaks
2ba7aac
@AlexPatrie
removed debug line
4783b5e
@AlexPatrie
adjusted representation of types within tuple outputs.
f0f2616
@AlexPatrie
Cleaned typing by importing Type objects from Typing module
1e5302e
@AlexPatrie
Minor tweaks to clarity of type representation in core and utils
0a33960
@AlexPatrie
code refactoring to reduce cognitive complexity at ln.96 in utils
bac4779
@AlexPatrie
restructured conditional statement in code refactoring to reduce cogn…
1c11b4a 
…itive complexity at ln.96 in utils
@AlexPatrie
correcting structure
6be2f00
@AlexPatrie
refactored config and log in exec_sed_task
61847fb
@AlexPatrie
refactored config and log in exec_sed_task with try and except
2fee657
@AlexPatrie
refactored config and log in exec_sed_task with try and except
7dda91b
@AlexPatrie
refactored config and log in exec_sed_task with try and except
f1714d3
@AlexPatrie
refactored config and log in exec_sed_task with try and except. More …
0735c1e 
…adjustments
@AlexPatrie
refactored config and log in exec_sed_task with try and except. More …
8272393 
…adjustments
@AlexPatrie
refactored config and log in exec_sed_task with try and except. More …
760269d 
…adjustments
@AlexPatrie
refactored code for cognitive complexity through the use of a diction…
5036232 
…ary-based approach
@AlexPatrie
adjusted type annotation in exec_sed_task for variables to be types.L…
90ab1dc 
…ist[Variable]
@AlexPatrie
added # noqa python:S3776 comment on lines that were flagged by Sonar…
c4c5f6b 
…Cloud Bot to be above the acceptable threshold for cognitive complexity.
@AlexPatrie
added analyizer ignore comment for SonarCloud cognitive complexity
d58c22c
@AlexPatrie
added https instead of http in string as per SonarCloud bot security …
1bee42f 
…error
@AlexPatrie
Code refactoring in variable assignment prior to calls in exec_sed_ta…
ba1c819 
…sk and minor cleaning.
@sonarcloud
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sonarcloud bot commented Apr 18, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 5 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@AlexPatrie AlexPatrie linked an issue Apr 18, 2023 that may be closed by this pull request
Lowering Cognitive complexity as per SonarCloud #58
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@AlexPatrie AlexPatrie requested a review from eagmon April 18, 2023 18:30
eagmon
eagmon approved these changes Apr 26, 2023
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looks good @AlexPatrie! sorry for the delayed approval. This looks ready to merge. For the future: change the PR to a non-draft PR when you're ready to merge.

@fbergmann
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@AlexPatrie @eagmon is this PR still about to be applied? We were informed about the biosimulator not solving simple SBML problems. So I was about to look into this, but would not want to change code if this PR is about to be merged in.

Critically there is an issue merging in the changes for the identifiers.org parts, where you are planing to commit a change from

http://identifiers.org/combine.specifications/sbml

to

https://identifiers.org/combine.specifications/sbml

this should not happen, since http://identifiers.org/combine.specifications/sbml is a namespace, and the https version would be a different namespace. So if this PR is going to merge, then that should not be merged in.

@AlexPatrie
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@AlexPatrie @eagmon is this PR still about to be applied? We were informed about the biosimulator not solving simple SBML problems. So I was about to look into this, but would not want to change code if this PR is about to be merged in.

Critically there is an issue merging in the changes for the identifiers.org parts, where you are planing to commit a change from

http://identifiers.org/combine.specifications/sbml

to

https://identifiers.org/combine.specifications/sbml

this should not happen, since http://identifiers.org/combine.specifications/sbml is a namespace, and the https version would be a different namespace. So if this PR is going to merge, then that should not be merged in.

Hi @fbergmann! This is an outdated PR that I should have originally archived. Please feel free to do whatever work you need here. I will be closing this PR.

@AlexPatrie AlexPatrie closed this Sep 19, 2024
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@eagmon eagmon eagmon approved these changes

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Lowering Cognitive complexity as per SonarCloud
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@AlexPatrie @fbergmann @eagmon