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refactor: Remove plugins #1245

Merged
merged 228 commits into from
Sep 13, 2023
Merged

refactor: Remove plugins #1245

merged 228 commits into from
Sep 13, 2023

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ivadym
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@ivadym ivadym commented Sep 8, 2023

This PR:

Remove unused plugin CLI module.

Removed:

  • Plugin CLI

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

mathiasbio added 30 commits June 9, 2023 16:39
@mathiasbio
Nothing to see here.
760e666
@mathiasbio
comment out cadd for testing
3c62c64
@mathiasbio
correcting bug
c97cae2
@mathiasbio
add missing function import
b36419f
@mathiasbio
fix pytest ini
f712f13
@mathiasbio
fixing qc workflow
a14d0f9
@mathiasbio
removing duplicate fixtures after merge
13677bc
@mathiasbio
correcting qc workflow to work with WGS cases too
a327a76
@mathiasbio
add test for qc wgs workflow
f7327ee
@mathiasbio
add vcfdir to qc workflow
ce9325c
@mathiasbio
fixing qc for wgs
55d1630
@mathiasbio
removed concatenation rule
55b0780
@mathiasbio
fixing pytest
f1df90f
@mathiasbio
removing duplicate and deprecated test functions
9db7778
@mathiasbio
black reformat
933301a
@mathiasbio
fixing bug in PON workflow
6a4cc41
@mathiasbio
changing PON to use default sentieon alignment workflow, up to dedup
eb549f3
@mathiasbio
adding sentieon env variables
edda0c3
@mathiasbio
remove deprecated function
a52f564
@mathiasbio
remove deprecated variables
136286f
@mathiasbio
fixing bug
ae2a089
@mathiasbio
fixing bug
d22ba0e
@mathiasbio
removing tmp from input umi
ba0cf0e
@mathiasbio
refactor and fix qcworkflow bug
5e7269b
@mathiasbio
fix bug
99b2409
@mathiasbio
add new fixtures for new tests
90dc14d
@mathiasbio
refactor code
3e44042
@mathiasbio
refactor and cleanup
63360b6
@mathiasbio
add new tests
79ae219
@mathiasbio
black
fd7d5f8
@ivadym ivadym requested a review from a team as a code owner September 8, 2023 15:21
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codecov bot commented Sep 8, 2023 •
edited
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Codecov Report

Patch coverage is 100.00% of modified lines.

Files Changed Coverage
BALSAMIC/constants/metrics.py ø
BALSAMIC/utils/scheduler.py ø
BALSAMIC/commands/base.py 100.00%
BALSAMIC/commands/config/base.py 100.00%
BALSAMIC/commands/config/case.py 100.00%
BALSAMIC/commands/config/pon.py 100.00%
BALSAMIC/commands/init/base.py 100.00%
BALSAMIC/commands/options.py 100.00%
BALSAMIC/commands/report/base.py 100.00%
BALSAMIC/commands/report/deliver.py 100.00%
... and 14 more

📢 Thoughts on this report? Let us know!.

mathiasbio
mathiasbio approved these changes Sep 12, 2023
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Nice! I took an extra look in the code and we're not using these plugins anywhere. So sadly, poor plugins, your time has come... 🥲 💀
🔥 🔥 🔥 🔥 🔥 🔥 🔥 🔥 🔥 🔥 🔥 🔥 🔥

Base automatically changed from run-cache-version to develop September 13, 2023 07:02
@sonarqubecloud
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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 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@ivadym ivadym merged commit 20a8b21 into develop Sep 13, 2023
@ivadym ivadym deleted the remove-plugins branch September 13, 2023 07:16
@ivadym ivadym self-assigned this Sep 22, 2023
@ivadym ivadym mentioned this pull request Nov 6, 2023
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@mathiasbio mathiasbio mathiasbio approved these changes

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