fix: correct dependencies and env management #315
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....uh, no idea what is going on with the CI checks |
korikuzma
requested changes
Dec 9, 2022
| @@ -13,7 +13,7 @@ boto3 = "*" | |||
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| [dev-packages] | |||
| thera-py = {editable = true, path = "."} | |||
| disease-normalizer = "==0.2.15" | |||
| disease-normalizer = "~=0.2.16" | |||
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Should also do the same for ga4gh.vrsatile.pydantic!
| @@ -30,7 +30,7 @@ test = | |||
| pytest-cov | |||
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| dev = | |||
| disease-normalizer == 0.2.15 | |||
| disease-normalizer ~=0.2.16 | |||
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Same comment as above, do the same for ga4gh.vrsatile.pydantic
| @@ -79,6 +79,8 @@ def update_normalizer_db(normalizer: str, aws_instance: str, db_url: str, | |||
| environ[AWS_ENV_VAR_NAME] = aws_env_name | |||
| confirm_aws_db_use(aws_env_name.upper()) | |||
| environ[SKIP_AWS_DB_ENV_NAME] = "true" # this is already checked above | |||
| endpoint_url = "" | |||
| db = Database() | |||
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You could either delete this + move line 91 outside the else condition or you can change line 83 to db = Database(db_url=endpoint_url)
jsstevenson
changed the title
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close #311. Also handle some other dependency compatibility issues and the main errors in #314 (but leaving that issue open to add documentation/maybe tweak CLI options). Also add the GtoP data extraction update that was merged to the dev branch earlier.