bugfix agent vqueue & refactor tools/deps

[kpango]

Signed-off-by: kpango kpango@vdaas.org

Description:

1. bugfix agent vqueue cache deletion logic
2. small changes to make command
   • fix sysctl params before k3d deployment (workaround for new linux kernel)
   • remove traefik from k3d deployment and add contour for IngressControler
   • use contour operator for kind deployment instead of raw contour deploy
   • patch metrics server to insecure for dev environment deploy k3d and kind works with it
   • change default e2e target to lb gateway from meta gateway
   • change default charts's dev.yaml deployment configuration's dimension to 784 (suitable for fashion-mnist dataset)
3. refactor small things

Related Issue:

How Has This Been Tested?:

Environment:

• Go Version: 1.16.4
• Docker Version: 19.03.8
• Kubernetes Version: 1.18.2
• NGT Version: 1.12.3

Types of changes:

• Bug fix [type/bug]
• New feature [type/feature]
• Add tests [type/test]
• Security related changes [type/security]
• Add documents [type/documentation]
• Refactoring [type/refactoring]
• Update dependencies [type/dependency]
• Update benchmarks and performances [type/bench]
• Update CI [type/ci]

Changes to Core Features:

• Have you added an explanation of what your changes do and why you'd like us to include them?
• Have you written new tests for your core changes, as applicable?
• Have you successfully ran tests with your changes locally?

Checklist:

• I have read the CONTRIBUTING document.
• I have checked open Pull Requests for the similar feature or fixes?
• I have added tests and benchmarks to cover my changes.
• I have ensured all new and existing tests passed.
• I have commented my code, particularly in hard-to-understand areas
• I have updated the documentation accordingly.

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[github-actions]

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File is not gofumpt-ed (gofumpt)

[codecov]

Codecov Report

Merging #1250 (4248bfe) into master (4b9130d) will increase coverage by 0.51%.
The diff coverage is 25.00%.

@@            Coverage Diff             @@
##           master    #1250      +/-   ##
==========================================
+ Coverage   17.54%   18.05%   +0.51%     
==========================================
  Files         498      501       +3     
  Lines       30845    31198     +353     
==========================================
+ Hits         5411     5633     +222     
- Misses      25155    25266     +111     
- Partials      279      299      +20     

Impacted Files	Coverage Δ
pkg/agent/core/ngt/handler/grpc/handler.go	0.00% <0.00%> (ø)
pkg/agent/core/ngt/service/ngt.go	0.00% <0.00%> (ø)
pkg/agent/core/ngt/service/vqueue/queue.go	0.00% <0.00%> (ø)
internal/safety/safety.go	95.65% <100.00%> (ø)
internal/db/storage/blob/s3/reader/reader.go	63.73% <0.00%> (-30.77%)	⬇️
internal/errgroup/group.go	92.42% <0.00%> (-1.52%)	⬇️
internal/worker/worker.go	83.33% <0.00%> (ø)
internal/net/option.go	89.65% <0.00%> (ø)
internal/net/net.go	49.18% <0.00%> (ø)
internal/net/dialer.go	79.42% <0.00%> (ø)

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[hlts2]

Thank you.
LGTM

[kevindiu]

LGTM

[kevindiu]

should we update patch version due to the fix?

[kpango]

I think so I'll check other PR that we can include next release.