fix: handle cases where gene_context is not found

.github/workflows/checks.yml

@@ -25,8 +25,13 @@ jobs:
  steps:
  - uses: actions/checkout@v3
 
- - name: black
- uses: psf/black@stable
+ - name: Setup Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: 3.11
+
+ - name: Install dependencies
+ run: python3 -m pip install ".[dev]"
 
- - name: ruff
- uses: chartboost/ruff-action@v1
+ - name: Check style
+ run: python3 -m ruff check . && ruff format --check .

.gitignore

@@ -16,10 +16,7 @@ dist/
 
 .mypy_cache/
 
-variation/data/seqrepo/
-variation/data/uta_20180821
-variation/data/notebooks
-variation/data/*.txt
+src/variation/data
 
 Pipfile.lock
 

.pre-commit-config.yaml

@@ -2,20 +2,15 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v1.4.0
+ rev: v4.5.0
  hooks:
  - id: check-added-large-files
  - id: detect-private-key
  - id: trailing-whitespace
  - id: end-of-file-fixer
-- repo: https://github.com/psf/black
- rev: 23.7.0
- hooks:
- - id: black
- language_version: python3.11
 - repo: https://github.com/astral-sh/ruff-pre-commit
- # Ruff version.
- rev: v0.0.280
+ rev: v0.2.0
  hooks:
+ - id: ruff-format
  - id: ruff
  args: [ --fix, --exit-non-zero-on-fix ]

Pipfile

@@ -12,8 +12,7 @@ variation-normalizer = {editable = true, path = "."}
 jupyter = "*"
 ipykernel = "*"
 psycopg2-binary = "*"
-ruff = "*"
-black = "*"
+ruff = "==0.2.0"
 
 [packages]
 "biocommons.seqrepo" = "*"

README.md

@@ -156,20 +156,26 @@ Next, view the OpenAPI docs on your local machine:
 
 ### Init coding style tests
 
-Code style is managed by [Ruff](https://github.com/astral-sh/ruff) and checked prior to commit.
+Code style is managed by [Ruff](https://docs.astral.sh/ruff/) and checked prior to commit.
+
+Check style with `ruff`:
+
+```shell
+python3 -m ruff format . && python3 -m ruff check --fix .
+```
 
 We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.
 
 This ensures:
 
-* Check code style
-* Check for added large files
-* Detect AWS Credentials
-* Detect Private Key
+* Style correctness
+* No large files
+* AWS credentials are present
+* Private key is present
 
-Before first commit run:
+Pre-commit *must* be installed before your first commit. Use the following command:
 
-```shell
+```commandline
 pre-commit install
 ```
 

codebuild/deploy_eb_env_dev.py

@@ -43,6 +43,6 @@
  "Status"
  ]
  print(eb_provisioned_product_status)
-except Exception as e: # noqa: E722
+except Exception as e:
  print(e)
  print("The EB environment is already running....")

pyproject.toml

@@ -1,41 +1,159 @@
+[project]
+name = "variation-normalizer"
+authors = [
+ {name = "Alex Wagner"},
+ {name = "Kori Kuzma"},
+ {name = "James Stevenson"}
+]
+readme = "README.md"
+classifiers = [
+ "Development Status :: 3 - Alpha",
+ "Framework :: FastAPI",
+ "Framework :: Pydantic",
+ "Framework :: Pydantic :: 2",
+ "Intended Audience :: Science/Research",
+ "Intended Audience :: Developers",
+ "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",
+]
+requires-python = ">=3.8"
+description = "VICC normalization routine for variations"
+license = {file = "LICENSE"}
+dependencies = [
+ "biocommons.seqrepo",
+ "fastapi",
+ "uvicorn",
+ "pydantic ==2.*",
+ "ga4gh.vrs[extras] ~= 2.0.0a2",
+ "gene-normalizer ~=0.3.0.dev1",
+ "boto3",
+ "cool-seq-tool ~=0.4.0.dev1",
+ "bioutils"
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = ["pytest>=6.0", "pytest-cov", "pytest-asyncio"]
+dev = ["pre-commit", "ruff==0.2.0", "psycopg2-binary", "jupyter", "ipykernel"]
+
+[project.urls]
+Homepage = "https://github.com/cancervariants/variation-normalization"
+Documentation = "https://github.com/cancervariants/variation-normalization"
+Changelog = "https://github.com/cancervariants/variation-normalization/releases"
+Source = "https://github.com/cancervariants/variation-normalization"
+"Bug Tracker" = "https://github.com/cancervariants/variation-normalization/issues"
+
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta:__legacy__"
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "variation.version.__version__"}
+
+# Scanning for namespace packages in the ``src`` directory is true by
+# default in pyproject.toml, so you do NOT need to include the
+# `tool.setuptools.packages.find` if it looks like the following:
+# [tool.setuptools.packages.find]
+# namespaces = true
+# where = ["src"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=src --cov-report term-missing"
+testpaths = ["tests"]
 
-[tool.black]
-line-length = 88
+[tool.coverage.run]
+branch = true
 
 [tool.ruff]
-# pycodestyle (E, W)
-# Pyflakes (F)
-# flake8-annotations (ANN)
-# flake8-quotes (Q)
-# pydocstyle (D)
-# pep8-naming (N)
-# isort (I)
-select = ["E", "W", "F", "ANN", "Q", "D", "N", "I"]
+src = ["src"]
 
-fixable = ["I", "F401"]
+lint.select = [
+ "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
+ "E", "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+ "I", # https://docs.astral.sh/ruff/rules/#isort-i
+ "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+ "D", # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+ "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+ "ANN", # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+ "ASYNC", # https://docs.astral.sh/ruff/rules/#flake8-async-async
+ "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+ "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+ "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+ "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+ "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
+ "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+ "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
+ "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+ "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+ "PGH", # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+ "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+]
 
+lint.fixable = [
+ "I",
+ "F401",
+ "D",
+ "UP",
+ "ANN",
+ "B",
+ "C4",
+ "G",
+ "PIE",
+ "PT",
+ "RSE",
+ "SIM",
+ "RUF"
+]
+# ANN101 - missing-type-self
+# ANN003 - missing-type-kwargs
+# D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
+# D206 - indent-with-spaces*
+# D213 - multi-line-summary-second-line
+# D300 - triple-single-quotes*
 # D400 - ends-in-period
 # D415 - ends-in-punctuation
-# ANN101 - missing-type-self
-# ANN003 - missing-type-kwargs
-# E501 - line-too-long
-ignore = ["D205", "D400", "D415", "ANN101", "ANN003", "E501"]
-
-[tool.ruff.flake8-quotes]
-docstring-quotes = "double"
+# E111 - indentation-with-invalid-multiple*
+# E114 - indentation-with-invalid-multiple-comment*
+# E117 - over-indented*
+# E501 - line-too-long*
+# W191 - tab-indentation*
+# PGH003 - blanket-type-ignore
+# *ignored for compatibility with formatter
+lint.ignore = [
+ "ANN101", "ANN003",
+ "D203", "D205", "D206", "D213", "D300", "D400", "D415",
+ "E111", "E114", "E117", "E501",
+ "W191",
+ "PGH003",
+ "S321",
+]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
+# ANN201 - Missing type annotation
 # ANN102 - missing-type-cls
 # N805 - invalid-first-argument-name-for-method
-# F821 - undefined-name
-# F401 - unused-import
-"tests/*" = ["ANN001", "ANN2", "ANN102"]
-"setup.py" = ["F821"]
-"*__init__.py" = ["F401"]
-"variation/schemas/*" = ["ANN201", "N805", "ANN001"]
+# S101 - assert
+# B011 - assert-false
+# RUF001 - ambiguous-unicode-character-string
+"tests/*" = ["ANN001", "ANN102", "ANN2", "S101", "B011"]
+"src/variation/schemas/*" = ["ANN001", "ANN201", "N805", "S101"]
+"codebuild/*" = ["T201"]
+
+[tool.ruff.lint.flake8-bugbear]
+# Allow default arguments like, e.g., `data: List[str] = fastapi.Query(None)`.
+extend-immutable-calls = ["fastapi.Query"]

variation/__init__.py → src/variation/__init__.py

@@ -3,7 +3,7 @@
 from os import environ
 
 if "VARIATION_NORM_EB_PROD" in environ:
- LOG_FN = "/tmp/variation.log"
+ LOG_FN = "/var/variation.log"
 else:
  LOG_FN = "variation.log"