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Refactor tests#27

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sfmig merged 55 commits intomainbrainglobe/brainglobe-workflows:mainfrom smg/tests-refactorbrainglobe/brainglobe-workflows:smg/tests-refactorCopy head branch name to clipboardDec 16, 2023

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Commits

Commits on Dec 1, 2023

• proto benchmarking smoke test (WIP)

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• added git URL to monkeypatched asv but not fully working yet (WIP)

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• rename workflows directory

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• rename and reorganise default configs and cellfinder main workflow script

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• update benchmarks to new locations of modules

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• update modules locations in tests

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Commits on Dec 4, 2023

• replace argparse by typer

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• add test for setup logger

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• pass logger by name

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• unit tests for setup steps (WIP)

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Commits on Dec 6, 2023

• rename path variable in config. add unit tests for setup steps.

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• replace message by message pattern for regex

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• fix to retrieve custom logger

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• remove notes about logger issue

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• small edits to comments

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• make two modules for unit tests (workflows and benchmarks)

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• renaming modules and add test for setup_workflow

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• remove old workflow tests and conftest

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• take logger name from module

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• add integration tests and conftest for fixtures shared between unit and integration

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• change logger name source in logger test

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• rename tests for benchmarks

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• add entrypoint and preliminary tests (WIP)

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• remove benchmarks results

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• fix CLI test

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Commits on Dec 7, 2023

• remove condition for logger one handler only

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• add docstrings and typing

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• remove conftest and move some integration tests to unit

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• recover conftest for shared fixtures

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• parametrise integration tests

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• move shared fixtures from unit to conftest.py

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• change argument for CLI via main using typer

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• move custom logger fixture to conftest under unit tests

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• fix for brainglobe workflows benchmark test

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• mark benchmark tests as skip for now

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• replace typer by argparse (WIP)

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• add test for config parser

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• argparse fix but not the best

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• change parser and test to always receive a list

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• add default to main and move parser out of main

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Commits on Dec 8, 2023

• fix typing of List

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• add init file for benchmarks

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• reorganise fixtures in conftest

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• add wrapper fn for entrypoint

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Commits on Dec 11, 2023

• edit asv to fetch repo from this branch (for benchmarks PR)

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• edit paths to asv config (for benchmarks PR)

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• small edits from PR review comments

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• Apply suggestions from code review

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• add teardown comment to benchmark test (currently skipped)

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• remove dvcs from monkeypatched asv config in benchmark test (currently skipped)

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• fill in docstring for benchmark test (currently skipped)

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• mypy fix

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• fix linting

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• logger_name in lowercase

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Commits on Dec 14, 2023

• Merge branch 'main' into smg/tests-refactor

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