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Migrate unit tests to GitHub #175

Merged
merged 66 commits into from
Oct 24, 2024
Merged

Migrate unit tests to GitHub #175

merged 66 commits into from
Oct 24, 2024

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WeinaJi
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@WeinaJi WeinaJi commented Jun 3, 2024 •
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Context

This PR migrates the unit test pipeline from GitLab to GitHub actions. Based on the existing simulation_test.yml, it adds the model building for neocortex and neocortex-mutiscale models, and launch the unit tests via pytest. For testing data, sub circuits of v5_sonata, v5_sonata + gap junctions, sscx-v7-plasticity are extracted by brainbuilder from the original circuits in gpfs and are stored locally.

Scope

  • Download neocortex mods from github repo
  • test-unit
  • test-integration
  • test-integration-e2e
  • test-scientific
  • test-scientific-ngv

Doc builds are tested on ReadTheDocs side for all PRs.

Testing

Currently the follow tests are skipped:

Review

  • PR description is complete
  • Coding style (imports, function length, New functions, classes or files) are good
  • Unit/Scientific test added
  • Updated Readme, in-code, developer documentation

@WeinaJi WeinaJi force-pushed the weji/actions_improve branch from dbf4d05 to 3136109 Compare June 3, 2024 13:16
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@WeinaJi WeinaJi force-pushed the weji/actions_improve branch from e9a45da to fc109a8 Compare June 3, 2024 13:38
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@WeinaJi WeinaJi force-pushed the weji/actions_improve branch from 0fb721f to 8650471 Compare September 10, 2024 13:17
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@WeinaJi WeinaJi changed the title download neocortex mods from github repo Migrate unit tests to GitHub Sep 11, 2024
matz-e
matz-e reviewed Sep 30, 2024
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Very impressive to get the whole testing done in 8 minutes!

I'm just wondering if we could factor the docs out into a separate workflow (in the future)

.github/workflows/simulation_test.yml Outdated Show resolved Hide resolved
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@jorblancoa jorblancoa force-pushed the weji/actions_improve branch from 50eff37 to 9998205 Compare October 2, 2024 14:41
@jorblancoa jorblancoa marked this pull request as ready for review October 2, 2024 14:41
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matz-e
matz-e previously approved these changes Oct 2, 2024
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Looks good!

tests/simulations/ngv/README.rst Outdated Show resolved Hide resolved
Weina Ji and others added 21 commits October 22, 2024 16:07
@jorblancoa
fix example run
d8d33a0
@jorblancoa
write PATH to GITHUB_ENV and remove repeated pkg install
9271b9f
@WeinaJi @jorblancoa
NEURODAMUS_NCX_V5=ON for neocortex model
b625911
@jorblancoa
Fix crash test
059a71a
@jorblancoa
Activate virtual env only once
2b7ab1d
@jorblancoa
fixup! Activate virtual env only once
d282bc8
@jorblancoa
Adapt crashmode test
2832c9c
@jorblancoa
Separate docs_build
e246172
@jorblancoa
fixup! Separate docs_build
135e231
@jorblancoa
fixup! Separate docs_build
e949655
@jorblancoa
Fix docs warning with latest sphinx
9d89fed
@jorblancoa
fixup! Fix docs warning with latest sphinx
195b10b
@jorblancoa
Fix an issue reading extra properties for cells where there is no syn…
1b6195c 
…apses.

Install latest libsonata branch
@jorblancoa
remove build docs workflow, enable PR builds on ReadTheDocs side
a85901d
@jorblancoa
don't copy circuit data iin test_cli_opts.py
c4c863e
@jorblancoa
Use tmp_path fixture instead of creating new tmp files
51c4f83
@jorblancoa
Add flake8 in github actions and fix issues
e0cbbee
@jorblancoa
Separate lint with flake8
6089882
@jorblancoa
Remove gitlab unit tests and tox
125ad95 
Enable memory load balancing test
@jorblancoa
Add stages that were defined in a template before
f04ddcf
@jorblancoa
Include common nse config
e0d8626
@jorblancoa jorblancoa force-pushed the weji/actions_improve branch from b4a2406 to e0d8626 Compare October 22, 2024 14:07
@jorblancoa
Adapt dry run test
6a048fc 
 - Reduce lower bound memory to 60.0
WeinaJi
WeinaJi commented Oct 23, 2024
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LGTM (but I can't approve it as the owner of the PR. )
@ferdonline ,can we merge this long PR ?

jorblancoa
jorblancoa previously approved these changes Oct 24, 2024
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@jorblancoa jorblancoa merged commit 629b989 into main Oct 24, 2024
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@jorblancoa jorblancoa deleted the weji/actions_improve branch October 24, 2024 15:21
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@matz-e matz-e matz-e left review comments

@jorblancoa jorblancoa jorblancoa approved these changes

@ferdonline ferdonline Awaiting requested review from ferdonline

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@WeinaJi @bbpbuildbot @ferdonline @matz-e @jorblancoa