Ruff format and lint

.github/workflows/codespell.yml

@@ -6,7 +6,11 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
+    types:
+    - opened
+    - reopened
+    - synchronize
+    - ready_for_review
 
 permissions:
   contents: read
@@ -18,6 +22,6 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/deploy_documentation.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Set up Python3
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.12
         cache: 'poetry'
 
     - name: Install dependencies

.github/workflows/main.yaml

@@ -7,8 +7,13 @@ name: Build and test
 on:
   push:
     branches: [ main ]
+
   pull_request:
-    branches: [ main ]
+      types:
+          - opened
+          - reopened
+          - synchronize
+          - ready_for_review
 
 jobs:
   lint:
@@ -25,14 +30,14 @@ jobs:
         run: |
           pip install tox
 
-      - name: Check code quality with flake8
-        run: tox -e flake8
+      - name: Check code quality with ruff
+        run: tox -e lint_stats
 
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+        python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13' ]
 
     steps:
       - uses: actions/checkout@v4

pyproject.toml

@@ -1,50 +1,65 @@
-[tool.poetry]
+[project]
 name = "linkml-map"
 version = "0.0.0"
 description = "a framework for specifying and executing mappings between data models"
-authors = ["cmungall <cjm@berkeleybop.org>"]
 readme = "README.md"
+authors = [
+    {name = "cmungall", email = "cjm@berkeleybop.org"},
+]
+requires-python = "<=3.13,>=3.9"
+dynamic = [ "version" ]
+
+dependencies = [
+    "asteval<1,>=0",
+    "click<9,>=8",
+    "curies",
+    "jinja2<4,>=3",
+    "linkml-runtime>=1.7.2",
+    "pydantic>=2.0.0",
+    "pyyaml",
+]
+
+[project.optional-dependencies]
+duckdb = [
+    "duckdb<1,>=0",
+]
+graphviz = [
+    "graphviz<1.0.0,>=0.20.1",
+]
+units = [
+    "lark<2,>=1",
+    "pint<1,>=0",
+    "ucumvert<1,>=0",
+]
+dev = [
+    "deepdiff<7.0.0,>=6.7.1",
+    "deptry<1.0.0,>=0.21.1",
+    "jupyter<2.0.0,>=1.0.0",
+    "linkml>=1.7.0",
+    "mkdocs-mermaid2-plugin<1.0.0,>=0.6.0",
+    "mkdocs-windmill",
+    "mkdocstrings[crystal,python]",
+    "mknotebooks<1.0.0,>=0.8.0",
+    "pytest>=7.3.1",
+    "ruff>=0.11.2",
+    "tox>=4.24.2",
+]
+
+[project.scripts]
+linkml-map = "linkml_map.cli.cli:main"
 
-[tool.poetry.dependencies]
-python = "^3.9"
-asteval = "^0"
-click = "^8"
-curies = "*"
-duckdb = { version = "^0", optional = true }
-graphviz = { version = "^0.20.1", optional = true }
-jinja2 = "^3"
-lark = { version = "^1", optional = true }
-linkml-runtime = ">=1.7.2"
-pint = { version = "^0", optional = true }
-pydantic = ">=2.0.0"
-pyyaml = "*"
-ucumvert = { version = "^0", optional = true }
-
-[tool.poetry.extras]
-duckdb = ["duckdb"]
-graphviz = ["graphviz"]
-units = ["lark", "pint", "ucumvert"]
-
-[tool.poetry.group.dev.dependencies]
-deepdiff = "^6.7.1"
-deptry = "^0.21.1"
-jupyter = "^1.0.0"
-linkml = ">=1.7.0"
-mkdocs-mermaid2-plugin = "^0.6.0"
-mkdocs-windmill = "*"
-mkdocstrings = {extras = ["crystal", "python"], version = "*"}
-mknotebooks = "^0.8.0"
-pytest = "^7.3.1"
-tox = "*"
+[tool.poetry]
+requires-poetry = ">=2.0"
+version = "0.0.0"
+
+[tool.poetry.requires-plugins]
+poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = ["plugin"] }
 
 [tool.poetry-dynamic-versioning]
 enable = true
 vcs = "git"
 style = "pep440"
 
-[tool.poetry.scripts]
-linkml-map = "linkml_map.cli.cli:main"
-
 [tool.deptry]
 known_first_party = ["linkml_map"]
 extend_exclude = ["docs"]
@@ -53,19 +68,123 @@ extend_exclude = ["docs"]
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
 build-backend = "poetry_dynamic_versioning.backend"
 
-[tool.black]
-line-length = 100
-target-version = ["py39", "py310", "py311"]
-
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-include_trailing_comma = true
-reverse_relative = true
 
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
 [tool.codespell]
 skip = '.git,*.pdf,*.svg,go.sum,*.lock'
 check-hidden = true
 ignore-regex = '(^\s*"image/\S+": ".*|\b(KEGG.BRITE|mor.nlm.nih.gov)\b)'
 ignore-words-list = 'infarction,amination,assertIn,brite,ehr,mor,brite,nin,mirgate'
+
+[tool.ruff]
+line-length = 100
+target-version = "py312"
+
+[tool.ruff.format]
+exclude = [
+  "docs/",
+  "src/linkml_map/datamodel",
+  "tests/input"
+]
+
+[tool.ruff.lint]
+exclude = [
+  "docs/",
+  "src/linkml_map/datamodel",
+  "tests/input"
+]
+
+select = [
+    # core
+    "F", # Pyflakes
+    "E", # pycodestyle errors
+    "W", # pycodestyle warnings
+    "C90", # mccabe +
+    "I", # isort
+    "N", # pep8-naming
+    "D", # pydocstyle
+    "UP", # pyupgrade
+    # extensions
+    "YTT", # flake8-2020
+    "ANN", # flake8-annotations
+    "ASYNC", # flake8-async
+    "S", # flake8-bandit
+    "BLE", # flake8-blind-except
+    "FBT", # flake8-boolean-trap
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    # "COM", # flake8-commas
+    # "CPY", # flake8-copyright
+    "C4", # flake8-comprehensions
+    "DTZ", # flake8-datetimez
+    "T10", # flake8-debugger
+    # "DJ", # flake8-django
+    "EM", # flake8-errmsg
+    "EXE", # flake8-executable
+    "FA", # flake8-future-annotations
+    "ISC", # flake8-implicit-str-concat
+    "ICN", # flake8-import-conventions
+    "G", # flake8-logging-format
+    "INP", # flake8-no-pep420
+    "PIE", # flake8-pie
+    "T20", # flake8-print
+    "PYI", # flake8-pyi
+    "PT", # flake8-pytest-style
+    "Q", # flake8-quotes
+    "RSE", # flake8-raise
+    "RET", # flake8-return
+    "SLF", # flake8-self
+    "SLOT", # flake8-slots
+    "SIM", # flake8-simplify
+    "TID", # flake8-tidy-imports
+    "TCH", # flake8-type-checking
+    "INT", # flake8-gettext
+    "ARG", # flake8-unused-arguments
+    # "PTH", # flake8-use-pathlib
+    # "TD", # flake8-todos
+    # "FIX", # flake8-fixme
+    "ERA", # eradicate
+    "PD", # pandas-vet
+    "PGH", # pygrep-hooks
+    "PL", # Pylint
+    "TRY", # tryceratops
+    "FLY", # flynt
+    "NPY", # NumPy-specific rules
+    "AIR", # Airflow
+    "PERF", # Perflint
+    "FURB", # refurb
+    "LOG", # flake8-logging
+    "RUF", # Ruff-specific rules
+]
+
+ignore = [
+    # UP007: non-pep604-annotation-union - fix when 3.9 is dropped
+    "UP007",
+    # D200: unnecessary-multiline-docstring
+    "D200",
+    # D203: one-blank-line-before-class (conflicts with D211)
+    "D203",
+    # D212: multi-line-summary-first-line (conflicts with D213)
+    "D212",
+    # E203: whitespace before ',', ';', or ':'
+    "E203",
+    # E501: line length (specified elsewhere)
+    "E501",
+    # ISC001: conflicts with Ruff's formatter
+    "ISC001",
+    # C901: complex-structure - needs code change
+    "C901",
+    # E731: lambda-assignment - needs code change
+    "E731",
+    # B024: abstract-base-class-without-abstract-method
+    "B024",
+    # T201: print
+    "T201"
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**/*.py" = ["S101"] # use of assert
+
+[tool.ruff.lint.mccabe]
+# Flag errors (`C901`) whenever the complexity level exceeds 15.
+max-complexity = 15

src/linkml_map/compiler/graphviz_compiler.py

@@ -45,8 +45,7 @@ class GraphvizObject(CompiledSpecification):
     digraph: Digraph = None
 
     def render(self, file_path: str, format="png", view=False) -> None:
-        """
-        Renders a graphviz graph to a file.
+        """Render a graphviz graph to a file.
         :param file_path:
         :return:
         """
@@ -55,7 +54,7 @@ def render(self, file_path: str, format="png", view=False) -> None:
 
 class GraphvizCompiler(Compiler):
     """
-    Compiles a Transformation Specification to GraphViz.
+    Compile a Transformation Specification to GraphViz.
     """
 
     def compile(

src/linkml_map/transformer/object_transformer.py

@@ -21,7 +21,7 @@
 from linkml_map.utils.dynamic_object import DynObj, dynamic_object
 from linkml_map.utils.eval_utils import eval_expr, eval_expr_with_mapping
 
-DICT_OBJ = Dict[str, Any]
+DICT_OBJ = dict[str, Any]
 
 
 logger = logging.getLogger(__name__)
@@ -297,7 +297,11 @@ def map_object(
         return tgt_attrs
 
     def _perform_unit_conversion(
-        self, slot_derivation: SlotDerivation, source_obj: Any, sv: SchemaView, source_type: str
+        self,
+        slot_derivation: SlotDerivation,
+        source_obj: Any,
+        sv: SchemaView,
+        source_type: str,
     ) -> Union[float, Dict]:
         uc = slot_derivation.unit_conversion
         curr_v = source_obj.get(slot_derivation.populated_from, None)
@@ -309,13 +313,12 @@ def _perform_unit_conversion(
                 from_unit = curr_v.get(uc.source_unit_slot, None)
                 if from_unit is None:
                     raise ValueError(
-                        f"Could not determine unit from {curr_v}" f" using {uc.source_unit_slot}"
+                        f"Could not determine unit from {curr_v} using {uc.source_unit_slot}"
                     )
                 magnitude = curr_v.get(uc.source_magnitude_slot, None)
                 if magnitude is None:
                     raise ValueError(
-                        f"Could not determine magnitude from {curr_v}"
-                        f" using {uc.source_magnitude_slot}"
+                        f"Could not determine magnitude from {curr_v} using {uc.source_magnitude_slot}"
                     )
             else:
                 if slot.unit.ucum_code:
@@ -358,21 +361,18 @@ def _multivalued_to_singlevalued(self, vs: List[Any], slot_derivation: SlotDeriv
             delimiter = stringification.delimiter
             if delimiter:
                 return delimiter.join(vs)
-            elif stringification.syntax:
+            if stringification.syntax:
                 if stringification.syntax == SerializationSyntaxType.JSON:
                     return json.dumps(vs)
-                elif stringification.syntax == SerializationSyntaxType.YAML:
+                if stringification.syntax == SerializationSyntaxType.YAML:
                     return yaml.dump(vs, default_flow_style=True).strip()
-                else:
-                    raise ValueError(f"Unknown syntax: {stringification.syntax}")
-            else:
-                raise ValueError(f"Cannot convert multivalued to single valued: {vs}; no delimiter")
+                raise ValueError(f"Unknown syntax: {stringification.syntax}")
+            raise ValueError(f"Cannot convert multivalued to single valued: {vs}; no delimiter")
         if len(vs) > 1:
             raise ValueError(f"Cannot coerce multiple values {vs}")
         if len(vs) == 0:
             return None
-        else:
-            return vs[0]
+        return vs[0]
 
     def _singlevalued_to_multivalued(self, v: Any, slot_derivation: SlotDerivation) -> List[Any]:
         stringification = slot_derivation.stringification
@@ -443,5 +443,4 @@ def transform_enum(self, source_value: str, enum_name: str, source_obj: Any) ->
                 return pv_deriv.name
         if enum_deriv.mirror_source:
             return str(source_value)
-        else:
-            return None
+        return None