Update and reduction

populationgenomics · Jun 3, 2024 · f8b2a04 · f8b2a04
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diff --git a/.markdownlint.json b/.markdownlint.json
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,49 +5,38 @@ repos:
     rev: v4.5.0
     hooks:
       - id: check-yaml
-        exclude: '\.*conda/.*'
       - id: end-of-file-fixer
       - id: trailing-whitespace
-        exclude: '\.txt$|\.tsv$'
+        exclude: '\.txt|\.tsv$'
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: detect-private-key
       - id: debug-statements
       - id: check-added-large-files
+        exclude: '\.*.interval_list'
 
-  - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.38.0
+  # this home-brewed tool checks for any instances of CPG[number]+ in code or documentation
+  # and blocks addition of those files/prompts for the IDs to be removed
+  # it may not be useful in all instances (e.g. for private repos containing IDs)
+  - repo: https://github.com/populationgenomics/pre-commits
+    rev: "v0.1.3"
     hooks:
-      - id: markdownlint
-
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-        name: isort (python)
+      - id: cpg-id-checker
 
   - repo: https://github.com/ambv/black
-    rev: 23.12.1
+    rev: 24.3.0
     hooks:
       - id: black
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.11
+    rev: v0.4.7
     hooks:
       - id: ruff
 
+  # Static type analysis (as much as it's possible in python using type hints)
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: "v1.10.0"
     hooks:
       - id: mypy
-        args:
-          [
-            --pretty,
-            --show-error-codes,
-            --no-strict-optional,
-            --ignore-missing-imports,
-            --install-types,
-            --non-interactive,
-          ]
-        additional_dependencies: [types-PyYAML==6.0.4, types-toml]
+        args: [--pretty, --show-error-codes, --install-types, --non-interactive]
diff --git a/README.md b/README.md
@@ -4,3 +4,7 @@ Template repository based on the [CPG team-docs](https://github.com/populationge
 
 This contains python and markdown linting configuration, and a github linting action.
 Before making a new repository based on this template, it may be worth auditing the versions of linting tools and GitHub Actions listed in _.pre-commit-config.yaml_ and _.github/workflows_.
+
+As of `03-06-2024` this repository has been reduced to using Ruff and MyPy
+- Ruff implements linting, import sorting, formatting (since 0.1.2 Ruff has implemented Black-style formatting)
+- MyPy implements static type checking based on type hints and syntax
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,41 +1,42 @@
 [tool.black]
-line-length = 88
+line-length = 120
 skip-string-normalization = true
+exclude = '''
+/(
+  seqr-loading-pipelines
+  | gnomad_methods
+  | venv
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
+'''
 
-[tool.isort]
-py_version = 311
-profile = "black"
-line_length = 88
-sections = ["FUTURE", "STDLIB", "THIRDPARTY", "HAIL", "CPG", "FIRSTPARTY", "LOCALFOLDER"]
-known_hail = [
-    "hail",
-    "hailtop",
-]
-# Adjust these for each repository, e.g., removing those that should be
-# local rather than CPG. Also fill in extend_skip below if there are any
-# subdirectories that should be ignored.
-known_cpg = [
-    "analysis_runner",
-    "cpg_infra",
-    "cpg_utils",
-    "cpg_workflows",
-    "gnomad",
-    "hail_scripts",
-    "metamist",
-]
-# extend_skip = ["list", "submodules", "etc", here"]
+[tool.mypy]
+ignore_missing_imports = true
 
 [tool.ruff]
-line-length = 88
+line-length = 120
+extend-exclude = ["venv", ".mypy_cache", ".tox", ".venv", "build", "dist"]
 
-# ignore pydocstyle, flake8-boolean-trap (FBT)
-select = ["A", "B", "C",  "E", "F", "G", "I", "N", "Q", "S", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
+[tool.ruff.format]
+indent-style = 'space'
+quote-style = "single"
+skip-magic-trailing-comma = true
 
-fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "FBT", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
+[tool.ruff.lint]
+# ignore pydocstyle, flake8-boolean-trap (FBT)
+select = ["A", "B", "C",  "E", "F", "G", "I", "N", "Q", "S", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
+fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "FBT", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]
 
 ignore = [
     "ANN101",  # Missing type annotation for self in method
+    "ANN102",  # Missing type annotation for `cls` in classmethod
     "ANN201",  # Missing return type annotation for public function
+    "ANN204",  # Missing type annotation for special method `__init__`
+    "ANN401",  # Dynamically typed expressions (typing.Any) are disallowed in `**kwargs`
     "E501",    # Line length too long
     "E731",    # Do not assign a lambda expression, use a def
     "E741",    # Ambiguous variable name
@@ -48,5 +49,145 @@ ignore = [
     "PT018",   # Assertion should be broken down into multiple parts
     "Q000",    # Single quotes found but double quotes preferred
     "S101",    # Use of assert detected
-    "I001", # Import block is un-sorted (we use isort directly as ruff sort isn't fully supported)
+    "SLF001",  # Private member accessed: `_preemptible`
+
+    "ARG001",  # Unused function argument
+    "ARG002",  # Unused method argument
+
+    "PLR2004", # Magic value used
+
+    "ANN001",
+    "ANN202",
+    "C408",
+    "TID252",
+    "RET504",
+    "ERA001",
+    "UP032",
+    "RUF100",
+    "ISC001",
+    "PIE804",
+    "F401",
+    "C901",
+    "W605",
+    "RET505",
+    "ANN003",
+    "RUF013",
+    "UP031",
+    "RUF010",
+    "B006",
+    "ANN002",
+    "B023",
+    "EXE001",
+    "G001",
+    "SIM108",
+    "RUF005",
+    "G002",
+    "PD901",
+    "N999",
+    "SIM118",
+    "SIM102",
+    "PLW2901",
+    "S603",
+    "ARG005",
+    "PGH003",
+    "B904",
+    "N802",
+    "ISC003",
+    "ANN205",
+    "S607",
+    "RUF015",
+    "E701",
+    "N818",
+    "PIE790",
+    "N803",
+    "A002",
+    "RUF012",
+    "W291",
+    "S113",
+    "S311",
+    "N806",
+    "PLR5501",
+    "F403",
+    "SIM115",
+    "B007",
+    "F841",
+    "C405",
+    "C419",
+    "SIM300",
+    "PD011",
+    "UP015",
+    "S602",
+    "Q002",
+    "ISC002",
+    "COM819",
+    "C416",
+    "DTZ005",
+    "G003",
+    "S608",
+    "PIE808",
+    "B008",
+    "S108",
+    "E402",
+    "S605",
+    "F821",
+    "RET507",
+    "RET503",
+    "UP030",
+    "UP026",
+    "PLR1714",
+    "C403",
+    "PLR1711",
+    "PIE810",
+    "DTZ011",
+    "S105",
+    "BLE001",
+    "C401",
+    "C400",
+    "PLR0402",
+    "SIM201",
+    "RET506",
+    "C417",
+    "PD010",
+    "PLW1510",
+    "A001",
+    "W292",
+    "PYI024",
+    "Q003",
+    "S301",
+    "RET501",
+    "PD003",
+    "SIM117",
+    "RUF002",
+    "UP027",
+    "SIM105",
+    "E713",
+    "S324",
+    "S310",
+    "Q001",
+    "UP020",
+    "S506",
+    "N805",
+    "E712",
+    "E401",
+    "SIM212",
+    "DTZ002",
+    "COM812",  # missing-trailing-comma "The following rules may cause conflicts when used with the formatter"
+]
+
+# we use the ruff implementation of isort, instead of using both separately
+[tool.ruff.lint.isort]
+section-order = ["future", "standard-library", "third-party", "hail", "cpg", "first-party", "local-folder"]
+split-on-trailing-comma = false
+
+[tool.ruff.lint.isort.sections]
+hail = ["hail", "hailtop"]
+
+cpg = [
+    "analysis_runner",
+    "cpg_infra",
+    "cpg_utils",
+    "cpg_workflows",
+    "gnomad",
+    "hail_scripts",
+    "metamist",
 ]
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,4 +1,2 @@
 bump2version
-black
 pre-commit
-pylint