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Revert "feat!: sharpen up type usage (#332)" (#340)
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This reverts commit 4855309.
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jsstevenson authored May 13, 2024
1 parent 4855309 commit 9c35be7
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Showing 29 changed files with 423 additions and 585 deletions.
85 changes: 0 additions & 85 deletions .github/ISSUE_TEMPLATE/bug-report.yaml

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60 changes: 0 additions & 60 deletions .github/ISSUE_TEMPLATE/feature-request.yaml

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13 changes: 0 additions & 13 deletions .github/workflows/branch_workflow_rules.yaml

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2 changes: 1 addition & 1 deletion .github/workflows/checks.yaml
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Expand Up @@ -5,7 +5,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.10", "3.11", "3.12"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
steps:
- uses: actions/checkout@v3

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24 changes: 0 additions & 24 deletions .github/workflows/stale.yaml

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4 changes: 3 additions & 1 deletion pyproject.toml
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Expand Up @@ -15,11 +15,13 @@ classifiers = [
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
requires-python = ">=3.10"
requires-python = ">=3.8"
description = "A search interface for cancer variant interpretations assembled by aggregating and harmonizing across multiple cancer variant interpretation knowledgebases."
license = {file = "LICENSE"}
dependencies = [
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8 changes: 4 additions & 4 deletions src/metakb/cli.py
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Expand Up @@ -4,10 +4,10 @@
import logging
import re
import tempfile
from collections.abc import Callable
from os import environ
from pathlib import Path
from timeit import default_timer as timer
from typing import Optional
from zipfile import ZipFile

import asyncclick as click
Expand Down Expand Up @@ -117,7 +117,7 @@ async def update_metakb_db(
force_load_normalizers_db: bool,
normalizers_db_url: str,
load_latest_cdms: bool,
load_target_cdm: Path | None,
load_target_cdm: Optional[Path],
load_latest_s3_cdms: bool,
update_cached: bool,
) -> None:
Expand Down Expand Up @@ -228,7 +228,7 @@ def _load_normalizers_db() -> None:

def _update_normalizer_db(
name: str,
update_normalizer_db_fn: Callable[[str, bool, str, bool, bool, bool], None],
update_normalizer_db_fn: callable,
) -> None:
"""Update Normalizer DynamoDB database.
Expand Down Expand Up @@ -331,7 +331,7 @@ def _retrieve_s3_cdms() -> str:
key=lambda f: f.key,
reverse=True,
)
newest_version: str | None = None
newest_version: Optional[str] = None

for file in bucket:
match = re.match(
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