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add gru-npu consent group #645

Merged
merged 3 commits into from
Feb 23, 2022
Merged

add gru-npu consent group #645

merged 3 commits into from
Feb 23, 2022

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chris-s-friedman
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🚨 remove whitespace at end of comments
@chris-s-friedman
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looks like CI checks failing on a pip install issue

ERROR: Cannot install -r dev-requirements.txt (line 7) and click==7.1.2 because these package versions have conflicting dependencies.

The conflict is caused by:
    The user requested click==7.1.2
    black 22.1.0 depends on click>=8.0.0

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
WARNING: You are using pip version 21.2.4; however, version 22.0.3 is available.
You should consider upgrading via the '/usr/local/bin/python -m pip install --upgrade pip' command.

Exited with code exit status 1

CircleCI received exit code 1

@fiendish
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fiendish commented Feb 23, 2022

So either update click or pin a lower version of black :)

most recent version of black requires click >= 8
@chris-s-friedman
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chris-s-friedman commented Feb 23, 2022

any ideas on why test_invalid_ingest_subset_stages would start failing now? the most recent PRs haven't changed the tests and i wouldn't expect this pr to change anything related to this test...

unless the new version of click breaks things....

@fiendish
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The new click version changed some output strings.

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2022-02-23T20:05:18.1257895Z E assert 'invalid choice' in "Usage: test [OPTIONS] INGEST_PACKAGE_PATH\nTry 'test --help' for help.\n\nError: Invalid value for '--stages': 'foo' is not one of 'e', 'et', 'etl', 't', 'tl', 'l'.\n"

2022-02-23T20:05:18.1269037Z E assert 'invalid choice' in "Usage: test [OPTIONS] INGEST_PACKAGE_PATH\nTry 'test --help' for help.\n\nError: Invalid value for '--stages': 'el' is not one of 'e', 'et', 'etl', 't', 'tl', 'l'.\n"

2022-02-23T20:05:18.1280658Z E assert 'invalid choice' in "Usage: test [OPTIONS] INGEST_PACKAGE_PATH\nTry 'test --help' for help.\n\nError: Invalid value for '--stages': 'te' is not one of 'e', 'et', 'etl', 't', 'tl', 'l'.\n"

2022-02-23T20:05:18.1292195Z E assert 'invalid choice' in "Usage: test [OPTIONS] INGEST_PACKAGE_PATH\nTry 'test --help' for help.\n\nError: Invalid value for '--stages': 'lte' is not one of 'e', 'et', 'etl', 't', 'tl', 'l'.\n"

2022-02-23T20:05:18.1302738Z E assert 'invalid choice' in "Usage: test [OPTIONS] INGEST_PACKAGE_PATH\nTry 'test --help' for help.\n\nError: Invalid value for '--stages': 'lt' is not one of 'e', 'et', 'etl', 't', 'tl', 'l'.\n"

@fiendish
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fiendish commented Feb 23, 2022

Output comparison tests are always fragile. Adjust the tests to look for "Invalid value" instead of "invalid choice".

@chris-s-friedman
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Updated with 0786441 . looks like this is the only thing that looked for invalid choice.

click v8 now ouputs invalid value instead of invalid choice

:pencil2: Invalid not invalid

:rotating_light: format on save shouldn't have reshaped this
@chris-s-friedman chris-s-friedman merged commit 1da6dd7 into master Feb 23, 2022
@chris-s-friedman chris-s-friedman deleted the add-gru_npu branch February 23, 2022 20:49
chris-s-friedman added a commit that referenced this pull request Feb 23, 2022
## Release 1.11.0

### Summary

- Emojis: ? x3, ✨ x3
- Categories: Additions x3, Other Changes x3

### New features and changes

- [#645](#645) -  add gru-npu consent group - [1da6dd7](1da6dd7) by [chris-s-friedman](https://github.com/chris-s-friedman)
- [#644](#644) -  ✨ specify external IDs for clinical markers - [c1f6c1c](c1f6c1c) by [chris-s-friedman](https://github.com/chris-s-friedman)
- [#643](#643) - ✨ Add new sequencing center Tempus - [87f5cdf](87f5cdf) by [youngnm](https://github.com/youngnm)
- [#642](#642) -  Sql query tutorial - [92889ef](92889ef) by [chris-s-friedman](https://github.com/chris-s-friedman)
- [#641](#641) - ✨ Add NIH and Methylation constants - [6a1e70b](6a1e70b) by [youngnm](https://github.com/youngnm)
- [#639](#639) - ✨ add CSIR sequencing Center - [81e5752](81e5752) by [chris-s-friedman](https://github.com/chris-s-friedman)
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3 participants