Upgrade Python 3.11 #396
Upgrade Python 3.11 #396
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With Tibanna, you need to change the lambda declaration as well ie: https://github.com/4dn-dcic/tibanna/blob/master/tibanna/lambdas/check_task_awsem.py#L10
Will approve once done
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@willronchetti, there's no testing in GA for this? Does foursight pick up the slack?
My other comments are not blocking.
.github/workflows/main-publish.yml
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| # This workflow contains a single job called "build" | ||
| build: | ||
| # The type of runner that the job will run on | ||
| runs-on: ubuntu-20.04 |
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can this work with 22.04?
| @@ -5,6 +5,9 @@ clean: | |||
| lint: | |||
| flake8 tibanna | |||
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| build: | |||
| poetry install | |||
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I'd add make configure here. You'll need to make a target.
And install looks redundant with build. Rather than eliminate it, to stay compatible, I suggest it should identify itself a synonym and then be implemented by make build.
pyproject.toml
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| python-lambda-4dn = "0.12.3" | ||
| boto3 = "^1.9.0" | ||
| botocore = "^1.12.1" | ||
| boto3 = "^1.28.51" |
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Maybe add boto3-stubs and botocore-stubs in dev-dependencies.
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There are unit tests on GA for this, yes |
Ah, I see. @dmichaels-harvard it looks like main.yml workflow got overlooked, unless it's too expensive to run more than one (@willronchetti?) |
| @@ -22,6 +22,7 @@ Version updates | |||
| **Sep 15, 2023** The latest version is now 4.0.0_. | |||
| - Support for Python 3.7 has been dropped | |||
| - Added support for Python 3.9 and 3.10 | |||
| - Added support for Python 3.11 | |||
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Sep 21, 2023 The latest version is now 5.0.0_.
- Added support for Python 3.11
| @@ -43,7 +43,7 @@ API().run_workflow(input_json='myrun.json') | |||
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| Note: Starting `0.8.2`, Tibanna supports local CWL/WDL files as well as shell commands and Snakemake workflows. | |||
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| Note 2: As of Tibanna version `2.0.0`, Python 3.6 is no longer supported. Please switch to Python 3.8! Python 3.7 is also supported as a fallback, but please prefer 3.8 if you can. | |||
| Note 2: As of Tibanna version `2.0.0`, Python 3.7 (and lower) is no longer supported. Please switch to Python 3.11! Python 3.8 is also supported as a fallback, but please prefer 3.11 if you can. | |||
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Tibanna 3 supports Python 3.7. Better include a new block:
Note 3: As of Tibanna version 5.0.0, Python 3.7 (and lower) is no longer supported. Please switch to Python 3.11!
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Looks good. I deployed this version to cgap-wolf and ran a test workflow successfully.
- Do the local tests run successfully with Python 3.11? You need 4DN account credentials sourced to run these. I would have run that myself, but somehow I am having trouble to set up a 3.11 environment.
- I left some minor comments above
- Build error must be fixed
- Needs version bump
- Let me know when you release the Pypi package. I need to build and upload the corresponding Docker image at the same time.
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