Merge branch 'staging' into update-deps

cancervariants · Jul 15, 2024 · f3ee80f · f3ee80f
2 parents d612810 + a659989
commit f3ee80f
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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: false
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: false
diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml
@@ -9,10 +9,10 @@ jobs:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -23,10 +23,10 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install pypa/build
@@ -25,7 +25,7 @@ jobs:
       - name: Build a binary wheel and a source tarball
         run: python3 -m build
       - name: Store the distribution packages
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
@@ -42,7 +42,7 @@ jobs:
       id-token: write # IMPORTANT: mandatory for trusted publishing
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: python-package-distributions
           path: dist/

diff --git a/.github/workflows/stale.yaml b/.github/workflows/stale.yaml
@@ -0,0 +1,27 @@
+name: "Stalebot for issues and PRs"
+
+on:
+  schedule:
+    - cron: "30 13 * * 1-5"
+
+jobs:
+  stale-high-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml
+    with:
+      days-before-issue-stale: 90
+      days-before-pr-stale: 1
+      labels: priority:high
+
+  stale-medium-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml
+    with:
+      days-before-issue-stale: 135
+      days-before-pr-stale: 3
+      labels: priority:medium
+
+  stale-low-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml
+    with:
+      days-before-issue-stale: 180
+      days-before-pr-stale: 7
+      labels: priority:low
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,15 +2,18 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0  # pre-commit-hooks version
   hooks:
   - id: check-added-large-files
   - id: detect-private-key
   - id: trailing-whitespace
   - id: end-of-file-fixer
+  - id: check-merge-conflict
+  - id: detect-aws-credentials
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.2.0
+  rev: v0.5.0  # ruff version
   hooks:
     - id: ruff-format
     - id: ruff
       args: [ --fix, --exit-non-zero-on-fix ]
+minimum_pre_commit_version: 3.7.1
diff --git a/Pipfile b/Pipfile
@@ -7,12 +7,12 @@ verify_ssl = true
 pytest = "*"
 pytest-asyncio = "*"
 pytest-cov = "*"
-pre-commit = "*"
+pre-commit = ">=3.7.1"
 variation-normalizer = {editable = true, path = "."}
 jupyter = "*"
 ipykernel = "*"
 psycopg2-binary = "*"
-ruff = "==0.2.0"
+ruff = "==0.5.0"
 
 [packages]
 "biocommons.seqrepo" = "*"

diff --git a/pyproject.toml b/pyproject.toml
@@ -40,7 +40,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 test = ["pytest>=6.0", "pytest-cov", "pytest-asyncio"]
-dev = ["pre-commit", "ruff==0.2.0", "psycopg2-binary", "jupyter", "ipykernel"]
+dev = ["pre-commit>=3.7.1", "ruff==0.5.0", "psycopg2-binary", "jupyter", "ipykernel"]
 
 [project.urls]
 Homepage = "https://github.com/cancervariants/variation-normalization"
@@ -72,6 +72,9 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
+extend-exclude = [
+    "codebuild/*"
+]
 
 [tool.ruff.lint]
 select = [
@@ -90,16 +93,22 @@ select = [
   "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
   "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
   "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
   "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+  "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
   "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
   "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
   "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
   "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
   "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
   "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+  "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
   "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+  "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
   "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
   "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+  "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
+  "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
   "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
 fixable = [
@@ -110,15 +119,19 @@ fixable = [
   "ANN",
   "B",
   "C4",
+  "LOG",
   "G",
   "PIE",
   "PT",
   "RSE",
   "SIM",
+  "PERF",
+  "FURB",
   "RUF"
 ]
-# ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
+# ANN101 - missing-type-self
+# ANN102 - missing-type-cls
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
 # D206 - indent-with-spaces*
@@ -134,7 +147,7 @@ fixable = [
 # PGH003 - blanket-type-ignore
 # *ignored for compatibility with formatter
 ignore = [
-  "ANN101", "ANN003",
+  "ANN003", "ANN101", "ANN102",
   "D203", "D205", "D206", "D213", "D300", "D400", "D415",
   "E111", "E114", "E117", "E501",
   "W191",
@@ -146,15 +159,22 @@ ignore = [
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
 # ANN201 - Missing type annotation
-# ANN102 - missing-type-cls
 # N805 - invalid-first-argument-name-for-method
 # S101 - assert
 # B011 - assert-false
+# SLF001 - private-member-access
+# INP001 - implicit-namespace-package
 # RUF001 - ambiguous-unicode-character-string
-"tests/*" = ["ANN001", "ANN102", "ANN2", "S101", "B011"]
+# ARG002 - unused-method-argument
+"tests/*" = ["ANN001", "ANN2", "S101", "B011", "SLF001", "INP001"]
 "src/variation/schemas/*" = ["ANN001", "ANN201", "N805", "S101"]
-"codebuild/*" = ["T201"]
+"codebuild/*" = ["T201", "INP001"]
+"src/variation/validators/*" = ["ARG002"]
+"src/variation/translators/*" = ["ARG002"]
 
 [tool.ruff.lint.flake8-bugbear]
 # Allow default arguments like, e.g., `data: List[str] = fastapi.Query(None)`.
 extend-immutable-calls = ["fastapi.Query"]
+
+[tool.ruff.format]
+docstring-code-format = true
diff --git a/src/variation/__init__.py b/src/variation/__init__.py
@@ -1,30 +1 @@
 """The Variation Normalization package."""
-import logging
-from os import environ
-
-if "VARIATION_NORM_EB_PROD" in environ:
-    LOG_FN = "/tmp/variation.log"  # noqa: S108
-else:
-    LOG_FN = "variation.log"
-
-logging.basicConfig(
-    filename=LOG_FN, format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s"
-)
-logger = logging.getLogger("variation")
-logger.setLevel(logging.DEBUG)
-logger.handlers = []
-
-logging.getLogger("cool_seq_tool").setLevel(logging.INFO)
-logging.getLogger("boto3").setLevel(logging.INFO)
-logging.getLogger("botocore").setLevel(logging.INFO)
-logging.getLogger("urllib3").setLevel(logging.INFO)
-logging.getLogger("python_jsonschema_objects").setLevel(logging.INFO)
-logging.getLogger("hgvs.parser").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.seqaliasdb.seqaliasdb").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO)
-logging.getLogger("asyncio").setLevel(logging.INFO)
-
-if "VARIATION_NORM_EB_PROD" in environ:
-    ch = logging.StreamHandler()
-    ch.setLevel(logging.INFO)
-    logger.addHandler(ch)
diff --git a/src/variation/classifiers/__init__.py b/src/variation/classifiers/__init__.py
@@ -1,4 +1,5 @@
 """Classifier package level import."""
+
 from .amplification_classifier import AmplificationClassifier
 from .cdna_deletion_classifier import CdnaDeletionClassifier
 from .cdna_delins_classifier import CdnaDelInsClassifier