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Extension hangs at startup at "reactivating terminal message", spinner loops indefinitely #23963

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Extension hangs at startup at "reactivating terminal message", spinner loops indefinitely#23963
Assignees
DonJayamannekarthiknadiganthonykim1
Labels
*duplicateIssue identified as a duplicate of another issue(s)area-environmentsFeatures relating to handling interpreter environmentsbugIssue identified by VS Code Team member as probable bug
@corneliusroemer

Description

@corneliusroemer
corneliusroemer
opened on Aug 17, 2024

Type: Bug

Similar to issue #22512 (closed without resolution, hence can't comment there)

When starting vscode, Python extension never finishes loading, gets stuck at "Reactivating terminals".

I can't report issue due to that in the normal way.

Code 2024-08-17 19 15 28

Logs:

Python extension logs 
2024-08-17 19:03:46.464 [info] Experiment 'pythonaacf' is active
2024-08-17 19:03:46.464 [info] Experiment 'pythonCreateEnvOnPipInstall' is active
2024-08-17 19:03:46.464 [info] Experiment 'pythonRecommendTensorboardExt' is active
2024-08-17 19:03:46.464 [info] Experiment 'pythonTerminalEnvVarActivation' is active
2024-08-17 19:03:46.464 [info] Experiment 'pythonTestAdapter' is active
2024-08-17 19:03:46.464 [info] Native locator: Refresh started
2024-08-17 19:03:46.464 [info] Default formatter is set to ms-python.black-formatter for workspace /Users/corneliusromer/code/augur
2024-08-17 19:03:46.495 [info] > pyenv which python
2024-08-17 19:03:46.495 [info] cwd: .
2024-08-17 19:03:46.565 [warning] Unknown environment manager: Poetry
2024-08-17 19:03:46.804 [error] [
  'Failed to check whether to display prompt for conda inherit env setting, Class name = v, completed in 238ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:03:46.805 [error] [
  'getActivatedEnvironmentVariables, Class name = D, completed in 237ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Arg 2: undefined, Arg 3: undefined, Arg 4: "/bin/zsh"',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:03:46.805 [error] Failed to apply terminal env vars undefined [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:03:46.805 [error] Python Extension: interpreterManager.refresh [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:03:46.805 [error] [
  'Failed to intialize conda inherit env prompt, Class name = v, completed in 238ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:03:46.805 [error] [
  'Failed to activate a workspace, Class name = m, completed in 649ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Arg 2: {"started":1723914226015}, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:03:46.805 [error] Failure during activation. [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:03:46.805 [error] sendStartupTelemetry() failed. [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:03:46.863 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/bin/conda
2024-08-17 19:03:46.890 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/bioconda/bin/conda
2024-08-17 19:03:46.891 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/pango402/bin/conda
2024-08-17 19:03:46.895 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/mambabug/bin/conda
2024-08-17 19:03:46.895 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/pango3116/bin/conda
2024-08-17 19:03:46.896 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/mamba-dev/bin/conda
2024-08-17 19:03:46.897 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/smithy/bin/conda
2024-08-17 19:03:46.900 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/pangolin/bin/conda
2024-08-17 19:03:46.906 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/vcftools-build/bin/conda
2024-08-17 19:03:46.907 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/py11/bin/conda
2024-08-17 19:03:46.908 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/bioconda-utils/bin/conda
2024-08-17 19:03:46.908 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain-base/bin/conda
2024-08-17 19:03:46.908 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/py11-64/bin/conda
2024-08-17 19:03:46.909 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/snakemake-test/bin/conda
2024-08-17 19:03:46.909 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/general/bin/conda
2024-08-17 19:03:46.911 [info] Conda environment manager found at: /Users/corneliusromer/code/tsv-utils-feedstock/miniforge3/bin/conda
2024-08-17 19:03:46.911 [info] Conda environment manager found at: /Users/corneliusromer/code/conda-base/.dev-env/bin/conda
2024-08-17 19:03:46.911 [info] Conda environment manager found at: /Users/corneliusromer/Miniforge3/bin/conda
2024-08-17 19:03:46.911 [info] Conda environment manager found at: /Users/corneliusromer/miniforge3/bin/conda
2024-08-17 19:03:46.912 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/bin/conda
2024-08-17 19:03:46.913 [info] Native locator: Refresh finished in 859 ms
2024-08-17 19:03:53.643 [info] > /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/bin/conda info --json
2024-08-17 19:03:54.600 [info] > /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/bin/conda --version
2024-08-17 19:06:30.366 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:06:50.591 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:06:55.156 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:07:13.136 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:07:18.909 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:07:20.752 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:07:38.759 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:07:56.235 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:08:13.221 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/.vscode/settings.json
2024-08-17 19:08:38.590 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:08:40.623 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/augur/export_v2.py
2024-08-17 19:09:17.261 [info] Discover tests for workspace name: augur - uri: /Users/corneliusromer/code/augur/.vscode/settings.json
2024-08-17 19:09:27.421 [info] Experiment 'pythonaacf' is active
2024-08-17 19:09:27.422 [info] Experiment 'pythonCreateEnvOnPipInstall' is active
2024-08-17 19:09:27.422 [info] Experiment 'pythonRecommendTensorboardExt' is active
2024-08-17 19:09:27.422 [info] Experiment 'pythonTerminalEnvVarActivation' is active
2024-08-17 19:09:27.422 [info] Experiment 'pythonTestAdapter' is active
2024-08-17 19:09:27.422 [info] Native locator: Refresh started
2024-08-17 19:09:27.422 [info] Default formatter is set to charliermarsh.ruff for workspace /Users/corneliusromer/code/augur
2024-08-17 19:09:27.594 [info] > pyenv which python
2024-08-17 19:09:27.594 [info] cwd: .
2024-08-17 19:09:27.637 [warning] Unknown environment manager: Poetry
2024-08-17 19:09:27.686 [info] > conda info --json
2024-08-17 19:09:27.708 [error] Python Extension: interpreterManager.refresh [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:09:27.723 [error] [
  'Failed to check whether to display prompt for conda inherit env setting, Class name = v, completed in 0ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:09:27.723 [error] [
  'Failed to intialize conda inherit env prompt, Class name = v, completed in 1ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:09:27.723 [error] [
  'getActivatedEnvironmentVariables, Class name = D, completed in 1ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Arg 2: undefined, Arg 3: undefined, Arg 4: "/bin/zsh"',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:09:27.723 [error] Failed to apply terminal env vars undefined [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:09:27.723 [error] [
  'Failed to activate a workspace, Class name = m, completed in 317ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur/augur/export_v2.py>, Arg 2: {"started":1723914567219}, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:09:27.723 [error] Failure during activation. [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:09:27.723 [error] sendStartupTelemetry() failed. [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:09:27.745 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/bin/conda
2024-08-17 19:09:27.809 [info] Conda environment manager found at: /Users/corneliusromer/code/tsv-utils-feedstock/miniforge3/bin/conda
2024-08-17 19:09:27.831 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/py11-64/bin/conda
2024-08-17 19:09:27.871 [info] Conda environment manager found at: /Users/corneliusromer/code/conda-base/.dev-env/bin/conda
2024-08-17 19:09:27.897 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/snakemake-test/bin/conda
2024-08-17 19:09:28.680 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/bioconda-utils/bin/conda
2024-08-17 19:09:28.806 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/general/bin/conda
2024-08-17 19:09:28.832 [info] Conda environment manager found at: /Users/corneliusromer/Miniforge3/bin/conda
2024-08-17 19:09:28.885 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/pango3116/bin/conda
2024-08-17 19:09:28.908 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/mamba-dev/bin/conda
2024-08-17 19:09:28.921 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/bioconda/bin/conda
2024-08-17 19:09:28.934 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/vcftools-build/bin/conda
2024-08-17 19:09:28.987 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain-base/bin/conda
2024-08-17 19:09:29.001 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/pangolin/bin/conda
2024-08-17 19:09:29.079 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/py11/bin/conda
2024-08-17 19:09:29.091 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/mambabug/bin/conda
2024-08-17 19:09:29.103 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/smithy/bin/conda
2024-08-17 19:09:29.131 [info] Conda environment manager found at: /Users/corneliusromer/miniforge3/bin/conda
2024-08-17 19:09:29.145 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/pango402/bin/conda
2024-08-17 19:09:29.191 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/bin/conda
2024-08-17 19:09:29.261 [info] Native locator: Refresh finished in 2013 ms
2024-08-17 19:11:32.272 [info] Experiment 'pythonaacf' is active
2024-08-17 19:11:32.272 [info] Experiment 'pythonCreateEnvOnPipInstall' is active
2024-08-17 19:11:32.272 [info] Experiment 'pythonRecommendTensorboardExt' is active
2024-08-17 19:11:32.272 [info] Experiment 'pythonTerminalEnvVarActivation' is active
2024-08-17 19:11:32.272 [info] Experiment 'pythonTestAdapter' is active
2024-08-17 19:11:32.272 [info] Native locator: Refresh started
2024-08-17 19:11:32.272 [info] Default formatter is set to charliermarsh.ruff for workspace /Users/corneliusromer/code/augur
2024-08-17 19:11:32.272 [debug] Testing: Setting up watcher for /Users/corneliusromer/code/augur
2024-08-17 19:11:32.272 [debug] VS Code was not launched from the command line
2024-08-17 19:11:32.478 [debug] Dump environment variables {
    "BUN_INSTALL": "/Users/corneliusromer/.bun",
    "CLASSPATH": ".:/opt/homebrew/Cellar/antlr/4.13.1/antlr-4.13.1-complete.jar",
    "COLORTERM": "truecolor",
    "COMMAND_MODE": "unix2003",
    "CONDA_DEFAULT_ENV": "augur",
    "CONDA_EXE": "/opt/homebrew/Caskroom/miniforge/base/bin/conda",
    "CONDA_PREFIX": "/Users/corneliusromer/micromamba/envs/augur",
    "CONDA_PREFIX_1": "/Users/corneliusromer/micromamba/envs/augur",
    "CONDA_PYTHON_EXE": "/opt/homebrew/Caskroom/miniforge/base/bin/python",
    "CONDA_SHLVL": "1",
    "CR_PAT": "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",
    "EDITOR": "vim",
    "ELECTRON_NO_ATTACH_CONSOLE": "1",
    "GIT_SUBREPO_ROOT": "/Users/corneliusromer/code/git-subrepo",
    "GRADLE_HOME": "/Users/corneliusromer/.sdkman/candidates/gradle/current",
    "HISTSIZE": "1000000000",
    "HOME": "/Users/corneliusromer",
    "HOMEBREW_CELLAR": "/opt/homebrew/Cellar",
    "HOMEBREW_PREFIX": "/opt/homebrew",
    "HOMEBREW_REPOSITORY": "/opt/homebrew",
    "INFOPATH": "/opt/homebrew/share/info:",
    "JAVA_HOME": "/Users/corneliusromer/.sdkman/candidates/java/current",
    "LANG": "en_GB.UTF-8",
    "LESS": "-SNRi",
    "LOGNAME": "corneliusromer",
    "LaunchInstanceID": "7624F95A-998C-4E49-859F-5BCE8589A939",
    "MAMBA_EXE": "/opt/homebrew/bin/micromamba",
    "MAMBA_NO_BANNER": "1",
    "MAMBA_ROOT_PREFIX": "/Users/corneliusromer/micromamba",
    "MANPATH": "/Users/corneliusromer/.nvm/versions/node/v22.1.0/share/man:/Users/corneliusromer/code/git-subrepo/man::/opt/local/share/man::/Users/corneliusromer/.antidote/man",
    "MallocNanoZone": "0",
    "NVM_BIN": "/Users/corneliusromer/.nvm/versions/node/v22.1.0/bin",
    "NVM_CD_FLAGS": "-q",
    "NVM_DIR": "/Users/corneliusromer/.nvm",
    "NVM_INC": "/Users/corneliusromer/.nvm/versions/node/v22.1.0/include/node",
    "OLDPWD": "/Users/corneliusromer/code/nextclade_data_workflows/sars-cov-2",
    "ORIGINAL_XDG_CURRENT_DESKTOP": "undefined",
    "PWD": "/Users/corneliusromer/code/augur",
    "RBENV_SHELL": "zsh",
    "SAVEHIST": "1000000000",
    "SDKMAN_CANDIDATES_API": "https://api.sdkman.io/2",
    "SDKMAN_CANDIDATES_DIR": "/Users/corneliusromer/.sdkman/candidates",
    "SDKMAN_DIR": "/Users/corneliusromer/.sdkman",
    "SDKMAN_PLATFORM": "darwinarm64",
    "SECURITYSESSIONID": "186b2",
    "SHELL": "/bin/zsh",
    "SHLVL": "2",
    "SSH_AUTH_SOCK": "/private/tmp/com.apple.launchd.RZN3IZzVV6/Listeners",
    "STARSHIP_SESSION_KEY": "1180161525311162",
    "STARSHIP_SHELL": "zsh",
    "TERM": "xterm-256color",
    "TERM_PROGRAM": "Hyper",
    "TERM_PROGRAM_VERSION": "3.4.1",
    "TMPDIR": "/var/folders/qf/4kkcfypx0gbfb0t9336522_r0000gn/T/",
    "USER": "corneliusromer",
    "VSCODE_AMD_ENTRYPOINT": "vs/workbench/api/node/extensionHostProcess",
    "VSCODE_CLI": "1",
    "VSCODE_CODE_CACHE_PATH": "/Users/corneliusromer/Library/Application Support/Code/CachedData/fee1edb8d6d72a0ddff41e5f71a671c23ed924b9",
    "VSCODE_CRASH_REPORTER_PROCESS_TYPE": "extensionHost",
    "VSCODE_CWD": "/Users/corneliusromer/code/augur",
    "VSCODE_HANDLES_UNCAUGHT_ERRORS": "true",
    "VSCODE_IPC_HOOK": "/Users/corneliusromer/Library/Application Support/Code/1.92-main.sock",
    "VSCODE_NLS_CONFIG": "{\"userLocale\":\"en-gb\",\"osLocale\":\"en-gb\",\"resolvedLanguage\":\"en\",\"defaultMessagesFile\":\"/Applications/Visual Studio Code.app/Contents/Resources/app/out/nls.messages.json\",\"locale\":\"en\",\"availableLanguages\":{}}",
    "VSCODE_PID": "13538",
    "XML_CATALOG_FILES": "file:///Users/corneliusromer/micromamba/envs/augur/etc/xml/catalog file:///etc/xml/catalog",
    "XPC_FLAGS": "0x0",
    "XPC_SERVICE_NAME": "application.com.microsoft.VSCode.158551132.158551138.76FC77C5-40B3-4F26-8DC5-1766DB024D8A",
    "__CFBundleIdentifier": "com.microsoft.VSCode",
    "__CF_USER_TEXT_ENCODING": "0x1F5:0x0:0x2",
    "__CONDA_SHLVL_0_MAMBA_NO_BANNER": "1",
    "ELECTRON_RUN_AS_NODE": "1",
    "PATH": "/Users/corneliusromer/micromamba/envs/augur/bin:/Users/corneliusromer/.sdkman/candidates/java/current/bin:/Users/corneliusromer/.sdkman/candidates/gradle/current/bin:/opt/homebrew/opt/libpq/bin:/Users/corneliusromer/.bun/bin:/opt/homebrew/Caskroom/miniforge/base/condabin:/opt/homebrew/opt/gnu-sed/libexec/gnubin:/Users/corneliusromer/.rbenv/shims:/Users/corneliusromer/.nextstrain/cli-standalone:/opt/homebrew/opt/llvm/bin:/Users/corneliusromer/.nvm/versions/node/v22.1.0/bin:/Users/corneliusromer/code/git-subrepo/lib:/Users/corneliusromer/.cargo/bin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/Apple/usr/bin:/Library/TeX/texbin:/Applications/Wireshark.app/Contents/MacOS:/usr/local/share/dotnet:/Applications/quarto/bin:/Users/corneliusromer/.cargo/bin:/Users/corneliusromer/.local/bin:/Users/corneliusromer/.dotnet/tools:/opt/homebrew/opt/fzf/bin:/Users/corneliusromer/.local/bin:/Users/corneliusromer/code/bash_scripts:/Users/corneliusromer/micromamba/envs/bioconda-arm64/bin:/Users/corneliusromer/.pixi/bin:/Users/corneliusromer/go/bin"
}
2024-08-17 19:11:32.480 [info] > pyenv which python
2024-08-17 19:11:32.480 [info] cwd: .
2024-08-17 19:11:32.482 [debug] Extension ms-toolsai.jupyter accessed onDidChangeEnvironments with args: undefined
2024-08-17 19:11:32.482 [debug] Extension ms-toolsai.jupyter accessed getEnvironmentVariables with args: undefined
2024-08-17 19:11:32.482 [debug] Extension ms-toolsai.jupyter accessed onDidEnvironmentVariablesChange with args: undefined
2024-08-17 19:11:32.482 [debug] Extension ms-toolsai.jupyter accessed onDidEnvironmentVariablesChange with args: undefined
2024-08-17 19:11:32.482 [debug] Extension ms-toolsai.jupyter accessed onDidChangeEnvironments with args: undefined
2024-08-17 19:11:32.483 [debug] Extension ms-toolsai.jupyter accessed onDidChangeActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.483 [debug] Extension ms-toolsai.jupyter accessed onDidChangeEnvironments with args: undefined
2024-08-17 19:11:32.485 [warning] Unknown environment manager: Poetry
2024-08-17 19:11:32.487 [debug] [Error: Command failed: pyenv which python
/bin/sh: pyenv: command not found

	at genericNodeError (node:internal/errors:984:15)
	at wrappedFn (node:internal/errors:538:14)
	at ChildProcess.exithandler (node:child_process:423:12)
	at ChildProcess.emit (node:events:531:35)
	at maybeClose (node:internal/child_process:1105:16)
	at Socket.<anonymous> (node:internal/child_process:457:11)
	at Socket.emit (node:events:519:28)
	at Pipe.<anonymous> (node:net:338:12)] {
  code: 127,
  killed: false,
  signal: null,
  cmd: 'pyenv which python'
}
2024-08-17 19:11:32.509 [debug] Extension charliermarsh.ruff accessed onDidChangeActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.509 [debug] Extension charliermarsh.ruff accessed getActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.509 [debug] Extension ms-python.autopep8 accessed resolveEnvironment with args: {"id":"/Users/corneliusromer/micromamba/envs/augur/bin/python","path":"/Users/corneliusromer/micromamba/envs/augur/bin/python"}
2024-08-17 19:11:32.510 [debug] Extension charliermarsh.ruff accessed resolveEnvironment with args: {"id":"/Users/corneliusromer/micromamba/envs/augur/bin/python","path":"/Users/corneliusromer/micromamba/envs/augur/bin/python"}
2024-08-17 19:11:32.510 [debug] Extension ms-python.autopep8 accessed getActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.510 [debug] Extension ms-python.autopep8 accessed onDidChangeActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.513 [debug] Searching for conda.
2024-08-17 19:11:32.513 [debug] Probing conda binary: conda
2024-08-17 19:11:32.514 [info] > conda info --json
2024-08-17 19:11:32.522 [debug] Python API env change detected /usr/local/bin/python3 add
2024-08-17 19:11:32.526 [debug] Python API env change detected /Library/Developer/CommandLineTools/usr/bin/python3 add
2024-08-17 19:11:32.527 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/augur/bin/python add
2024-08-17 19:11:32.530 [error] [
  'Failed to check whether to display prompt for conda inherit env setting, Class name = v, completed in 21ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:11:32.530 [error] [
  'getActivatedEnvironmentVariables, Class name = D, completed in 22ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Arg 2: undefined, Arg 3: undefined, Arg 4: "/bin/zsh"',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:11:32.530 [error] Failed to apply terminal env vars undefined [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:11:32.530 [error] Python Extension: interpreterManager.refresh [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:11:32.530 [error] [
  'Failed to intialize conda inherit env prompt, Class name = v, completed in 23ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur>, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:11:32.530 [error] [
  'Failed to activate a workspace, Class name = m, completed in 274ms, has a falsy return value, Arg 1: <Uri:/Users/corneliusromer/code/augur/augur/export_v2.py>, Arg 2: {"started":1723914692041}, Return Value: undefined',
  [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
  	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
  	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
  	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
  	at process.processImmediate (node:internal/timers:478:21)] {
    code: -4,
    data: undefined
  }
]
2024-08-17 19:11:32.530 [error] Failure during activation. [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:11:32.530 [error] sendStartupTelemetry() failed. [s [Error]: Failed to resolve env "/Users/corneliusromer/micromamba/envs/augur"
	at ae (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1966664)
	at oe (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1964624)
	at Immediate.<anonymous> (/Users/corneliusromer/.vscode/extensions/ms-python.python-2024.13.2024081501-darwin-arm64/out/client/extension.js:2:1960918)
	at process.processImmediate (node:internal/timers:478:21)] {
  code: -4,
  data: undefined
}
2024-08-17 19:11:32.531 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/bioconda-arm64/bin/python add
2024-08-17 19:11:32.533 [debug] Python API env change detected /Users/corneliusromer/.virtualenvs/ena-read-docs/bin/python add
2024-08-17 19:11:32.536 [debug] Python API env change detected /Users/corneliusromer/.pixi/envs/python/bin/python add
2024-08-17 19:11:32.537 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/gofasta/python add
2024-08-17 19:11:32.540 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/iqtree/python add
2024-08-17 19:11:32.543 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/trimadap/python add
2024-08-17 19:11:32.545 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/auspice/python add
2024-08-17 19:11:32.547 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/tsv-utils-bioconda/python add
2024-08-17 19:11:32.555 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/nextclade/python add
2024-08-17 19:11:32.558 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/build-raxml/python add
2024-08-17 19:11:32.561 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/smdpcli/bin/python add
2024-08-17 19:11:32.563 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/augur/bin/python update
2024-08-17 19:11:32.576 [debug] Python API env change detected /Users/corneliusromer/code/ncov/.snakemake/conda/1eb5c34cec2847056d159ebb3ba309a0_/bin/python add
2024-08-17 19:11:32.584 [debug] Python API env change detected /opt/local/bin/python3.10 add
2024-08-17 19:11:32.587 [debug] Python API env change detected /Users/corneliusromer/.local/share/virtualenvs/ncov-ingest-PlHIQus7/bin/python add
2024-08-17 19:11:32.591 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/lapis-silo/bin/python add
2024-08-17 19:11:32.596 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/sreality/bin/python add
2024-08-17 19:11:32.604 [debug] Python API env change detected /Users/corneliusromer/Miniforge3/conda-bld/simplejson_1719492293018/_build_env/python add
2024-08-17 19:11:32.612 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/hyphy-x86/python add
2024-08-17 19:11:32.619 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/pango402/bin/conda
2024-08-17 19:11:32.624 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/pango402/bin/python add
2024-08-17 19:11:32.630 [debug] Python API env change detected /usr/bin/python3 add
2024-08-17 19:11:32.632 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_10/bin/python add
2024-08-17 19:11:32.635 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/zstdtest/python add
2024-08-17 19:11:32.641 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/bin/conda
2024-08-17 19:11:32.643 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/matchspec/python add
2024-08-17 19:11:32.646 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/testenv/python add
2024-08-17 19:11:32.649 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/iqtree-cmaple/python add
2024-08-17 19:11:32.652 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_17/bin/python add
2024-08-17 19:11:32.655 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/pl019/bin/python add
2024-08-17 19:11:32.658 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/bioconda-utils/bin/conda
2024-08-17 19:11:32.659 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/bioconda-utils/bin/python add
2024-08-17 19:11:32.662 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/iqtree-native/bin/python add
2024-08-17 19:11:32.666 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/auspice-dev/python add
2024-08-17 19:11:32.671 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/aliasor/bin/python add
2024-08-17 19:11:32.676 [debug] Python API env change detected /opt/local/bin/python3.11 add
2024-08-17 19:11:32.684 [debug] Extension charliermarsh.ruff accessed getActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.684 [debug] Extension ms-python.autopep8 accessed getActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.684 [debug] Extension ms-python.autopep8 accessed resolveEnvironment with args: {"id":"/Users/corneliusromer/micromamba/envs/augur/bin/python","path":"/Users/corneliusromer/micromamba/envs/augur/bin/python"}
2024-08-17 19:11:32.684 [debug] Extension charliermarsh.ruff accessed resolveEnvironment with args: "/Users/corneliusromer/micromamba/envs/augur/bin/python"
2024-08-17 19:11:32.684 [debug] Extension ms-python.autopep8 accessed getActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.684 [debug] Extension charliermarsh.ruff accessed resolveEnvironment with args: {"id":"/Users/corneliusromer/micromamba/envs/augur/bin/python","path":"/Users/corneliusromer/micromamba/envs/augur/bin/python"}
2024-08-17 19:11:32.684 [debug] Extension ms-python.autopep8 accessed resolveEnvironment with args: {"id":"/Users/corneliusromer/micromamba/envs/augur/bin/python","path":"/Users/corneliusromer/micromamba/envs/augur/bin/python"}
2024-08-17 19:11:32.691 [debug] Extension charliermarsh.ruff accessed getActiveEnvironmentPath with args: undefined
2024-08-17 19:11:32.691 [debug] Extension charliermarsh.ruff accessed resolveEnvironment with args: {"id":"/Users/corneliusromer/micromamba/envs/augur/bin/python","path":"/Users/corneliusromer/micromamba/envs/augur/bin/python"}
2024-08-17 19:11:32.692 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/bioconda-64/bin/python add
2024-08-17 19:11:32.701 [debug] Python API env change detected /usr/local/bin/python3.12 add
2024-08-17 19:11:32.706 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/grayskull/bin/python add
2024-08-17 19:11:32.712 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/managed-conda/bin/python add
2024-08-17 19:11:32.724 [info] Conda environment manager found at: /Users/corneliusromer/miniforge3/bin/conda
2024-08-17 19:11:32.726 [debug] Python API env change detected /Users/corneliusromer/miniforge3/bin/python add
2024-08-17 19:11:32.730 [debug] Python API env change detected /Users/corneliusromer/code/tsv-utils-feedstock/miniforge3/conda-bld/debug_1719963245734/_build_env/python add
2024-08-17 19:11:32.735 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/taxonium/bin/python add
2024-08-17 19:11:32.738 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/py36-64/bin/python add
2024-08-17 19:11:32.742 [info] Conda environment manager found at: /Users/corneliusromer/code/conda-base/.dev-env/bin/conda
2024-08-17 19:11:32.743 [debug] Python API env change detected /Users/corneliusromer/code/conda-base/.dev-env/bin/python add
2024-08-17 19:11:32.748 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/raxml/bin/python add
2024-08-17 19:11:32.753 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_18/bin/python add
2024-08-17 19:11:32.756 [info] Conda environment manager found at: /Users/corneliusromer/code/tsv-utils-feedstock/miniforge3/bin/conda
2024-08-17 19:11:32.757 [debug] Python API env change detected /Users/corneliusromer/code/tsv-utils-feedstock/miniforge3/bin/python add
2024-08-17 19:11:32.760 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/pyfastx/bin/python add
2024-08-17 19:11:32.765 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_16/bin/python add
2024-08-17 19:11:32.769 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/py38-test/bin/python add
2024-08-17 19:11:32.774 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/usher/python add
2024-08-17 19:11:32.784 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/cdk8s/bin/python add
2024-08-17 19:11:32.791 [info] Conda environment manager found at: /Users/corneliusromer/Miniforge3/bin/conda
2024-08-17 19:11:32.794 [debug] Python API env change detected /Users/corneliusromer/Miniforge3/bin/python add
2024-08-17 19:11:32.800 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/bioconda-arm/bin/python add
2024-08-17 19:11:32.806 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/general/bin/conda
2024-08-17 19:11:32.808 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/general/bin/python add
2024-08-17 19:11:32.813 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/augur-dev/bin/python add
2024-08-17 19:11:32.819 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/xopen-arm/bin/python add
2024-08-17 19:11:32.825 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/pangolinUsherSampled/bin/python add
2024-08-17 19:11:32.830 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/flu_frequencies/bin/python add
2024-08-17 19:11:32.836 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/pangolin/bin/conda
2024-08-17 19:11:32.838 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/pangolin/bin/python add
2024-08-17 19:11:32.846 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/khipu/bin/python add
2024-08-17 19:11:32.855 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/related-issues/bin/python add
2024-08-17 19:11:32.865 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/pathoplexus-nextclade/bin/python add
2024-08-17 19:11:32.871 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/test1/bin/python add
2024-08-17 19:11:32.880 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/opencv/bin/python add
2024-08-17 19:11:32.887 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/clangdev/python add
2024-08-17 19:11:32.892 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/py11/bin/conda
2024-08-17 19:11:32.894 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/py11/bin/python add
2024-08-17 19:11:32.900 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/sdow-backend/bin/python add
2024-08-17 19:11:32.908 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_16py11/bin/python add
2024-08-17 19:11:32.915 [debug] Python API env change detected /Users/corneliusromer/code/ncov/.snakemake/conda/07c1d165d433e95e46312a0a1caaede5_/bin/python add
2024-08-17 19:11:32.924 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/polars/bin/python add
2024-08-17 19:11:32.934 [debug] Python API env change detected /Users/corneliusromer/code/mamba/build/envs/test/bin/python add
2024-08-17 19:11:32.942 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/py11-64/bin/conda
2024-08-17 19:11:32.944 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/py11-64/bin/python add
2024-08-17 19:11:33.003 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/loculus-ena/bin/python add
2024-08-17 19:11:33.071 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/email-validator/python add
2024-08-17 19:11:33.130 [debug] Delay Trigger[Test Configuration Change]: triggered=1, called=1
2024-08-17 19:11:33.183 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/py39-test/bin/python add
2024-08-17 19:11:33.207 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/nbdevcf/bin/python add
2024-08-17 19:11:33.215 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/fh/bin/python add
2024-08-17 19:11:33.224 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/py12/bin/python add
2024-08-17 19:11:33.235 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/hyphy/bin/python add
2024-08-17 19:11:33.251 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/snakemake-dev/bin/python add
2024-08-17 19:11:33.274 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s7_3_2/bin/python add
2024-08-17 19:11:33.286 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/miniwdl/bin/python add
2024-08-17 19:11:33.294 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/loculus-ingest/bin/python add
2024-08-17 19:11:33.304 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_18py11/bin/python add
2024-08-17 19:11:33.314 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/default/bin/python add
2024-08-17 19:11:33.328 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/treetime/bin/python add
2024-08-17 19:11:33.338 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/lr_quant_benchmark/bin/python add
2024-08-17 19:11:33.347 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/obecni/bin/python add
2024-08-17 19:11:33.360 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/fhdev/bin/python add
2024-08-17 19:11:33.362 [debug] conda info --json: {
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    "/opt/homebrew/Caskroom/miniforge/base/envs/pyfastx",
    "/opt/homebrew/Caskroom/miniforge/base/envs/pypy",
    "/opt/homebrew/Caskroom/miniforge/base/envs/pypy-arm",
    "/opt/homebrew/Caskroom/miniforge/base/envs/pypy=7.3.11",
    "/opt/homebrew/Caskroom/miniforge/base/envs/r",
    "/opt/homebrew/Caskroom/miniforge/base/envs/snakefmt",
    "/opt/homebrew/Caskroom/miniforge/base/envs/snakemake",
    "/opt/homebrew/Caskroom/miniforge/base/envs/taxonium",
    "/opt/homebrew/Caskroom/miniforge/base/envs/testenv",
    "/opt/homebrew/Caskroom/miniforge/base/envs/treetime",
    "/opt/homebrew/Caskroom/miniforge/base/envs/treetime9",
    "/opt/homebrew/Caskroom/miniforge/base/envs/wf-artic"
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  "envs_dirs": [
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    "/Users/corneliusromer/.conda/envs"
  ],
  "netrc_file": null,
  "offline": false,
  "pkgs_dirs": [
    "/opt/homebrew/Caskroom/miniforge/base/pkgs",
    "/Users/corneliusromer/.conda/pkgs"
  ],
  "platform": "osx-arm64",
  "python_version": "3.11.9.final.0",
  "rc_path": "/Users/corneliusromer/.condarc",
  "requests_version": "2.32.3",
  "root_prefix": "/opt/homebrew/Caskroom/miniforge/base",
  "root_writable": true,
  "site_dirs": [],
  "solver": {
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    "user_agent": "solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.8"
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  "sys.executable": "/opt/homebrew/Caskroom/miniforge/base/bin/python",
  "sys.prefix": "/opt/homebrew/Caskroom/miniforge/base",
  "sys.version": "3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:34:54) [Clang 16.0.6 ]",
  "sys_rc_path": "/opt/homebrew/Caskroom/miniforge/base/.condarc",
  "user_agent": "conda/24.5.0 requests/2.32.3 CPython/3.11.9 Darwin/23.6.0 OSX/14.6.1 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.8",
  "user_rc_path": "/Users/corneliusromer/.condarc",
  "virtual_pkgs": [
    [
      "__archspec",
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    [
      "__conda",
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    [
      "__osx",
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    [
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}

2024-08-17 19:11:33.362 [debug] Found conda via filesystem probing: conda
2024-08-17 19:11:33.377 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/nextclade-sc2/bin/python add
2024-08-17 19:11:33.389 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/tsv-utils/python add
2024-08-17 19:11:33.402 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_1py11/bin/python add
2024-08-17 19:11:33.420 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_13py11/bin/python add
2024-08-17 19:11:33.432 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/pypy-arm/python add
2024-08-17 19:11:33.444 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/bioconda-test/python add
2024-08-17 19:11:33.458 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/augur-dev-arm/bin/python add
2024-08-17 19:11:33.470 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/mamba/python add
2024-08-17 19:11:33.482 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s8_10py11/bin/python add
2024-08-17 19:11:33.494 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/poseidon/python add
2024-08-17 19:11:33.503 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/loculus-submission/bin/python add
2024-08-17 19:11:33.513 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/otd/bin/python add
2024-08-17 19:11:33.526 [debug] Python API env change detected /Users/corneliusromer/code/tsv-utils-feedstock/miniforge3/conda-bld/debug_1719963245734/_h_env/python add
2024-08-17 19:11:33.536 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/loculus-nextclade/bin/python add
2024-08-17 19:11:33.561 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/flu_frequencies_test/bin/python add
2024-08-17 19:11:33.585 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/cmaple/python add
2024-08-17 19:11:33.593 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s7py11/bin/python add
2024-08-17 19:11:33.604 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/basetest/bin/python add
2024-08-17 19:11:33.614 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/biopython/bin/python add
2024-08-17 19:11:33.628 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/pypy-arm/python add
2024-08-17 19:11:33.638 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/osxtest/python add
2024-08-17 19:11:33.650 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/auspice/python add
2024-08-17 19:11:33.663 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/smithy/bin/conda
2024-08-17 19:11:33.666 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/smithy/bin/python add
2024-08-17 19:11:33.677 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/augur-dev/bin/python add
2024-08-17 19:11:33.687 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/snakemake-test/bin/conda
2024-08-17 19:11:33.690 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/snakemake-test/bin/python add
2024-08-17 19:11:33.702 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/snakemake/bin/python add
2024-08-17 19:11:33.713 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/wf-artic/python add
2024-08-17 19:11:33.725 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/snakemake/bin/python add
2024-08-17 19:11:33.736 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/mambabug/bin/conda
2024-08-17 19:11:33.742 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/mambabug/bin/python add
2024-08-17 19:11:33.752 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/nbdev/bin/python add
2024-08-17 19:11:33.763 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/snakefmt/bin/python add
2024-08-17 19:11:33.773 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/treetime9/bin/python add
2024-08-17 19:11:33.784 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/ldc/python add
2024-08-17 19:11:33.797 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/bioconda/bin/conda
2024-08-17 19:11:33.800 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/bioconda/bin/python add
2024-08-17 19:11:33.817 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/grayskullenv/bin/python add
2024-08-17 19:11:33.832 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/mamba-dev/bin/conda
2024-08-17 19:11:33.835 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/mamba-dev/bin/python add
2024-08-17 19:11:33.845 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/polars-book/bin/python add
2024-08-17 19:11:33.857 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/test/python add
2024-08-17 19:11:33.875 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/throwaway/python add
2024-08-17 19:11:33.888 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/matchspec/python add
2024-08-17 19:11:33.898 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain-base/bin/conda
2024-08-17 19:11:33.905 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain-base/bin/python add
2024-08-17 19:11:33.915 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/r/bin/python add
2024-08-17 19:11:33.927 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/xopen/bin/python add
2024-08-17 19:11:33.941 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/s7_32/bin/python add
2024-08-17 19:11:33.953 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain-reinstall/bin/python add
2024-08-17 19:11:33.968 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/mpox-nextclade/bin/python add
2024-08-17 19:11:33.980 [info] Conda environment manager found at: /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/bin/conda
2024-08-17 19:11:33.981 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/bin/python add
2024-08-17 19:11:33.999 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/conda-base/python add
2024-08-17 19:11:34.012 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/pypy/bin/python add
2024-08-17 19:11:34.022 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/nextstrain-base/bin/python add
2024-08-17 19:11:34.033 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/bin/python add
2024-08-17 19:11:34.043 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/treetime/bin/python add
2024-08-17 19:11:34.058 [debug] Python API env change detected /opt/homebrew/Caskroom/miniforge/base/envs/pypy=7.3.11/python add
2024-08-17 19:11:34.068 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/vcftools-build/bin/conda
2024-08-17 19:11:34.072 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/vcftools-build/bin/python add
2024-08-17 19:11:34.082 [info] Conda environment manager found at: /Users/corneliusromer/micromamba/envs/pango3116/bin/conda
2024-08-17 19:11:34.087 [debug] Python API env change detected /Users/corneliusromer/micromamba/envs/pango3116/bin/python add
2024-08-17 19:11:34.100 [debug] Python API env change detected /Library/Frameworks/Python.framework/Versions/3.12/bin/python3 add
2024-08-17 19:11:34.115 [debug] Python API env change detected /opt/homebrew/bin/python3.10 add
2024-08-17 19:11:34.127 [debug] Python API env change detected /opt/homebrew/bin/python3.11 add
2024-08-17 19:11:34.139 [debug] Python API env change detected /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12 add
2024-08-17 19:11:34.149 [debug] Python API env change detected /opt/homebrew/bin/python3 add
2024-08-17 19:11:34.150 [info] Native locator: Refresh finished in 2075 ms
2024-08-17 19:11:34.496 [debug] Delay Trigger[Test Configuration Change]: triggered=2, called=2
2024-08-17 19:11:35.478 [debug] Received shell integration sequence for zsh

Extension version: 2024.13.2024081501
VS Code version: Code 1.92.2 (Universal) (fee1edb8d6d72a0ddff41e5f71a671c23ed924b9, 2024-08-14T17:29:30.058Z)
OS version: Darwin arm64 23.6.0
Modes:

System Info
Item Value
CPUs Apple M1 Pro (10 x 2400)
GPU Status 2d_canvas: enabled
canvas_oop_rasterization: enabled_on
direct_rendering_display_compositor: disabled_off_ok
gpu_compositing: enabled
multiple_raster_threads: enabled_on
opengl: enabled_on
rasterization: enabled
raw_draw: disabled_off_ok
skia_graphite: disabled_off
video_decode: enabled
video_encode: enabled
webgl: enabled
webgl2: enabled
webgpu: enabled
webnn: disabled_off
Load (avg) 5, 4, 4
Memory (System) 32.00GB (0.08GB free)
Process Argv . --crash-reporter-id a2d96ad4-dac0-4355-b505-a26375c755d4
Screen Reader no
VM 0%
A/B Experiments 
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pythoncenvpt:31062603
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impr_priority:31102340
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pythonrstrctxt:31112756
flighttreat:31119336
wkspc-onlycs-t:31111718
nativeloc1:31118318
wkspc-ranged-t:31118572

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*duplicateIssue identified as a duplicate of another issue(s)area-environmentsFeatures relating to handling interpreter environmentsbugIssue identified by VS Code Team member as probable bug

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