feat!: sharpen up type usage (#332)

close #285 * Clean up types and type annotations where possible. Not exhaustive -- there's some stuff that probably needs refactoring to make progress on -- but made some good progress, such that I think we can say the "types" issue is closed enough. * **maybe important**: by virtue of where json model dumps were happening, this introduced a small change to the order of the keys in some dicts that were getting sha512'd, which meant the ID changed during testing. I set JSON serialization to first sort keys in order so that this doesn't matter in the future, but this does entail a one-time change in digest ID. if that's bad, I can revert and try to figure out a workaround. * Also changed how stuff from GKS/VRS models are imported so that the code is a little more succinct. I think `models.Variation` style imports were a relic from a Python-JSONschema-objects custom and we don't need to do it anymore.
cancervariants · May 10, 2024 · 4855309 · 4855309
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diff --git a/.github/ISSUE_TEMPLATE/bug-report.yaml b/.github/ISSUE_TEMPLATE/bug-report.yaml
@@ -0,0 +1,85 @@
+name: Bug Report
+description: Report a bug.
+labels: ["bug"]
+body:
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: Provide a clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      description: Provide detailed steps to replicate the bug.
+      placeholder: |
+        1. In this environment...
+        2. With this config...
+        3. Run '...'
+        4. See error...
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Expected behavior
+      description: What did you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Current behavior
+      description: |
+        What actually happened?
+
+        Include full errors, stack traces, and/or relevant logs.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Possible reason(s)
+      description: Provide any insights into what might be causing the issue.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Suggested fix
+      description: Provide any suggestions on how to resolve the bug.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Branch, commit, and/or version
+      description: Provide the branch, commit, and/or version you're using.
+      placeholder: |
+        branch: issue-1
+        commit: abc123d
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots with descriptions to help explain your problem.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Environment details
+      description: Provide environment details (OS name and version, etc).
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional details
+      description: Provide any other additional details about the problem.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this fix."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: true
diff --git a/.github/ISSUE_TEMPLATE/feature-request.yaml b/.github/ISSUE_TEMPLATE/feature-request.yaml
@@ -0,0 +1,60 @@
+name: Feature Request
+description: Suggest an idea for this project.
+labels: ["enhancement"]
+body:
+  - type: textarea
+    attributes:
+      label: Feature description
+      description: Provide a clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Use case
+      description: |
+        Why do you need this feature? For example: "I'm always frustrated when..."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Proposed solution
+      description: Provide proposed solution.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Alternatives considered
+      description: Describe any alternative solutions you've considered.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Implementation details
+      description: Provide any technical details on how the feature might be implemented.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Potential Impact
+      description: |
+        Discuss any potential impacts of this feature on existing functionality or performance, if known.
+        Will this feature cause breaking changes?
+        What challenges might arise?
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Provide any other context or screenshots about the feature.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this feature."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: true
diff --git a/.github/workflows/branch_workflow_rules.yaml b/.github/workflows/branch_workflow_rules.yaml
@@ -0,0 +1,13 @@
+name: Branch workflow rules
+on:
+  pull_request:
+    types: [opened, reopened, edited]
+jobs:
+  check-branch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: check_branch_names
+        if: ${{ github.base_ref == 'main' && github.head_ref != 'staging' }}
+        run: |
+          echo "Head branch must be 'staging' when creating a PR where the base branch is 'main'"
+          exit 1
diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml
@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v3
 

diff --git a/.github/workflows/stale.yaml b/.github/workflows/stale.yaml
@@ -0,0 +1,24 @@
+name: "Make comments on stale issues and PRs"
+
+on:
+  schedule:
+    - cron: "30 13 * * *"
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v9
+        with:
+          remove-stale-when-updated: true
+
+          days-before-issue-stale: 45
+          stale-issue-label: stale
+          stale-issue-message: "This issue is stale because it has been open 45 days with no activity. Please make a comment for triaging or closing the issue."
+
+          days-before-pr-stale: 7
+          stale-pr-label: stale
+          stale-pr-message: "This PR is stale because it has been open 7 days with no activity. Please review this PR."
diff --git a/pyproject.toml b/pyproject.toml
@@ -15,13 +15,11 @@ 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 = ">=3.8"
+requires-python = ">=3.10"
 description = "A search interface for cancer variant interpretations assembled by aggregating and harmonizing across multiple cancer variant interpretation knowledgebases."
 license = {file = "LICENSE"}
 dependencies = [

diff --git a/src/metakb/cli.py b/src/metakb/cli.py
@@ -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
@@ -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: Optional[Path],
+    load_target_cdm: Path | None,
     load_latest_s3_cdms: bool,
     update_cached: bool,
 ) -> None:
@@ -228,7 +228,7 @@ def _load_normalizers_db() -> None:
 
 def _update_normalizer_db(
     name: str,
-    update_normalizer_db_fn: callable,
+    update_normalizer_db_fn: Callable[[str, bool, str, bool, bool, bool], None],
 ) -> None:
     """Update Normalizer DynamoDB database.
 
@@ -331,7 +331,7 @@ def _retrieve_s3_cdms() -> str:
         key=lambda f: f.key,
         reverse=True,
     )
-    newest_version: Optional[str] = None
+    newest_version: str | None = None
 
     for file in bucket:
         match = re.match(