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Remove fitness from spectrum #45

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Remove fitness from spectrum #45

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@mariacm12 mariacm12 commented Jun 17, 2025 •
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Description

Remove fitness from the codebase because it was too specific to the pipeline of ASAP Discovery. Removing fitness implies the removal of the FINT scoring mode in docking. Should solve #23

Todos

Notable points that this PR has either accomplished or will accomplish.

  • Remove dependencies
  • Remove fitness.py

Questions

  • Question 1 ..

Status

  • Ready to go

Developers certificate of origin

Castellanos Morales and others added 30 commits December 17, 2024 22:42
add rmsd-coloring
6506808
Fix chain visualization
9d54918
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
bb0c791 
for more information, see https://pre-commit.ci
Fix pre-commit-ci
327148d
Add the option to align struct directory and pdb file
218e340
Needed changes on seq_alignment
5ff8680
Implement fitness-alignment to align wrt fasta
2089987
Add more options to struct-alignment
2288c66
changes to fitness-alignment
4f850f8
Additions to align_seq_match
ca6553e
Merge branch 'main' of github.com:asapdiscovery/asapdiscovery into sp…
c549e26 
…ectrum-struct-changes
Fix merge conflicts
600e031
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
2dee96d 
for more information, see https://pre-commit.ci
precommit ci fixes
e6e328b
fix seq-align test
dcbaa12
struct-alignment tests
8bfe6bf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
f2719e2 
for more information, see https://pre-commit.ci
Add structure alignment tests
44c315a
Fix struct-alignment cfold test
08d0bd1
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
f01968d 
for more information, see https://pre-commit.ci
@hmacdope
Merge remote-tracking branch 'upstream/main' into spectrum-struct-cha…
dc0f3de 
…nges
@hmacdope
bump CI
983150c
@hmacdope
bump CI
f104935
Added a check for blast.csv file
b27e9b3
@ijpulidos
Bump CI
5e8902a
@mariacm12
Merge branch 'pydantic_2' into spectrum-struct-changes
7ce24c5
@ijpulidos
TODO to fix test here with "hidden" error
04900b8
@ijpulidos
Checking subprocess return code, print error
43fc57b
added mafft dependancy
5071f09
add mafft to ubuntu yaml
ad99f8d
@mariacm12 mariacm12 added this to the release 0.1 milestone Jun 17, 2025
@mariacm12 mariacm12 self-assigned this Jun 17, 2025
@mariacm12 mariacm12 changed the base branch from main to pydantic_2 June 17, 2025 21:13
@mariacm12 mariacm12 requested a review from ijpulidos June 17, 2025 22:02
@apayne97 apayne97 modified the milestones: release 0.1, release 0.2 Jun 24, 2025
@apayne97 apayne97 removed this from the release 0.8 milestone Aug 19, 2025
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@ijpulidos ijpulidos Awaiting requested review from ijpulidos

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@mariacm12 @apayne97 @hmacdope @ijpulidos