docs

docs/Makefile

@@ -6,7 +6,7 @@
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = source
-BUILDDIR      = build
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/source/conf.py

@@ -22,7 +22,7 @@
 author = "LinkML Authors"
 
 
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 
 # -- General configuration ---------------------------------------------------
 
@@ -65,8 +65,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-# html_theme = 'alabaster'
-html_theme = "sphinx_rtd_theme"
+html_theme = "alabaster"
+# html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

src/semdsl/__init__.py

@@ -1,13 +1,7 @@
 """semdsl package."""
-import importlib_metadata
+__version__ = "0.0.0"
 
-try:
-    __version__ = importlib_metadata.version(__name__)
-except importlib_metadata.PackageNotFoundError:
-    # package is not installed
-    __version__ = "0.0.0"  # pragma: no cover
-
-from semdsl.datamodel.semdsl_model import *
+from semdsl.datamodel.semdsl_model import SchemaGrammar
 from semdsl.dsl_engine import DSLEngine
 
 __all__ = [

src/semdsl/dsl_engine.py

@@ -2,7 +2,7 @@
 from dataclasses import dataclass
 from pathlib import Path
 from types import ModuleType
-from typing import Any, Optional, TextIO, Type, Union
+from typing import Optional, TextIO, Type, Union
 
 import yaml
 from lark import Tree

src/semdsl/importers/importer.py

@@ -1,11 +1,6 @@
-import sys
 from abc import abstractmethod
-from dataclasses import dataclass, field
-from io import StringIO
-from types import ModuleType
-from typing import Any, TextIO
-
-from linkml_runtime.utils.compile_python import compile_python
+from dataclasses import dataclass
+from typing import Any
 
 from semdsl.datamodel.semdsl_model import SchemaGrammar
 

src/semdsl/importers/schema_importer.py

@@ -1,4 +1,3 @@
-from copy import copy
 from dataclasses import dataclass
 from io import StringIO
 from typing import List, Optional, TextIO, Union
@@ -188,7 +187,7 @@ def _add_enum(self, sg: SchemaGrammar, enum: EnumDefinition):
         sym = self._enum_symbol(enum.name)
         rule = ProductionRule(is_terminal=True, lhs_symbol=sym)
         disj = Disjunction(operands=[])
-        for text, pv in enum.permissible_values.items():
+        for text in enum.permissible_values.keys():
             seq = AtomicSequence(elements=[])
             self._add_terminal(seq, text)
             disj.operands.append(seq)

src/semdsl/mapper/mapper.py

@@ -8,7 +8,7 @@
 from linkml_runtime.linkml_model import SlotDefinition
 
 from semdsl.datamodel.semdsl_model import AtomicSequence, Disjunction, SchemaGrammar
-from semdsl.view.view import rule_by_non_terminal, rule_lhs_symbol
+from semdsl.view.view import rule_lhs_symbol
 
 logger = logging.getLogger(__name__)
 
@@ -54,7 +54,6 @@ def transform(
                 if tgt_class not in sv.all_classes():
                     raise ValueError(f"Unknown class {tgt_class}")
                 target = tgt_class
-            rule = rule_by_non_terminal(self.schemagrammar, token.value)
             is_object = (
                 tgt_class and not class_defs[tgt_class].abstract and not class_defs[tgt_class].mixin
             )

src/semdsl/view/view.py

@@ -27,15 +27,15 @@ def rule_lhs_symbol(rule: ProductionRule) -> Optional[str]:
 def _sequence_lhs_symbol(sequence: Sequence) -> Optional[str]:
     if isinstance(sequence, Disjunction):
         if len(sequence.operands) != 1:
-            raise ValueError(f"Disjunction {sequence} must have exactly one operand; in {rule}")
+            raise ValueError(f"Disjunction {sequence} must have exactly one operand")
         return lhs_symbol(sequence.operands[0])
     if isinstance(sequence, AtomicSequence):
         if len(sequence.elements) != 1:
-            raise ValueError(f"AtomicSequence {sequence} must have exactly one element; in {rule}")
+            raise ValueError(f"AtomicSequence {sequence} must have exactly one element")
         el = sequence.elements[0]
         if not isinstance(el, NonTerminal):
             raise ValueError(
-                f"AtomicSequence {sequence} must have exactly one NonTerminal element; in {rule}"
+                f"AtomicSequence {sequence} must have exactly one NonTerminal element"
             )
         return el.name
     raise AssertionError(f"Unexpected sequence type {type(sequence)}")

src/semdsl/writers/lark_writer.py

@@ -1,8 +1,6 @@
 from dataclasses import dataclass
 from typing import Union
 
-from linkml_runtime.utils.compile_python import compile_python
-
 from semdsl.datamodel.semdsl_model import (
     AtomicSequence,
     Disjunction,

tests/test_cli.py

@@ -7,7 +7,7 @@
 from linkml_runtime import SCHEMA_DIRECTORY, SchemaView
 
 from semdsl.cli import main
-from tests import EXAMPLE_CLUE_DIR, EXAMPLE_DIR, OUTPUT_DIR
+from tests import OUTPUT_DIR
 from tests.input.examples.arithmetic import ARITHMETIC_DSL, ARITHMETIC_EXAMPLE, ARITHMETIC_MODEL
 from tests.input.examples.clue import CLUE_MODEL
 from tests.input.examples.linkml_lite import LINKML_DSL, LINKML_EXAMPLE

tests/test_engine.py

@@ -6,7 +6,7 @@
 from lark import Token
 from linkml_runtime import SchemaView
 
-from semdsl.datamodel.semdsl_model import AtomicSequence, ProductionRule, SchemaGrammar
+from semdsl.datamodel.semdsl_model import SchemaGrammar
 from semdsl.dsl_engine import DSLEngine
 from semdsl.mapper.mapper import Mapper
 from semdsl.writers.lark_writer import LarkWriter

tests/test_importers/test_schema_importer.py

@@ -2,8 +2,9 @@
 
 import unittest
 
+from lark import UnexpectedCharacters, UnexpectedToken
+
 from semdsl import DSLEngine
-from tests import EXAMPLE_DIR
 from tests.input.examples.arithmetic import ARITHMETIC_MODEL
 
 CLUE_SCHEMA = """
@@ -85,7 +86,7 @@ def test_schema_guided(self):
         for case in cases:
             passes, ser, target_class, expected = case
             if not passes:
-                with self.assertRaises(Exception):
+                with self.assertRaises((UnexpectedCharacters, UnexpectedToken)) :
                     obj = engine.parse_as_object(ser, target_class=target_class)
                 continue
             obj = engine.parse_as_object(ser, target_class=target_class)

tests/test_importers/test_schema_importer_metamodel.py

@@ -27,6 +27,6 @@ def test_model(self):
         mod = writer.compile(sg)
         print(f"Compiled to {mod}")
         mapper = Mapper(schemaview=self.schemaview, schemagrammar=sg)
-        print("Parsing: SchemaDefinition(id=x name=y)")
+        print(mapper)
         tree = mod.grammar.parse("SchemaDefinition(id=x name=y)")
-        # print(tree.pretty())
+        print(tree.pretty())

tox.ini

@@ -4,64 +4,41 @@
 # and then run "tox" from this directory.
 
 [tox]
-# To use a PEP 517 build-backend you are required to configure tox to use an isolated_build:
-# https://tox.readthedocs.io/en/latest/example/package.html
-isolated_build = True
-skipsdist = True
-
+isolated_build = true
 envlist =
-    # always keep coverage-clean first
-    coverage-clean
     lint
     flake8
-    mypy
-    docstr-coverage
     py
 
 [testenv]
-whitelist_externals =
-    poetry
 commands =
-    poetry run pytest
-description = Run unit tests with pytest. This is a special environment that does not get a name, and
-              can be referenced with "py".
-
-[testenv:coverage-clean]
-deps = coverage
-skip_install = true
-commands = coverage erase
+    coverage run -p -m pytest --durations=20 {posargs:tests}
+    coverage combine
+    coverage xml
+deps =
+    pytest
+    coverage
 
 [testenv:lint]
 deps =
     black
     isort
 skip_install = true
 commands =
-    black src/ tests/
-    isort src/ tests/
+    black .
+    isort .
 description = Run linters.
 
-[testenv:doclint]
-deps =
-    rstfmt
-skip_install = true
-commands =
-    rstfmt docs/source/
-description = Run documentation linters.
-
 [testenv:flake8]
 skip_install = true
 deps =
-    darglint
     flake8<5.0.0
-    flake8-black
     flake8-bandit
+    flake8-black
     flake8-bugbear
     flake8-colors
-    flake8-docstrings
     flake8-isort
-    flake8-print
-    pydocstyle
+    pep8-naming
 commands =
     flake8 src/ tests/
 description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming).
@@ -72,22 +49,34 @@ description = Run the flake8 tool with several plugins (bandit, docstrings, impo
 #########################
 [flake8]
 ignore =
-    DAR101 # Missing parameter(s) in Docstring: - with_git_hash
-    DAR201 # Missing "Returns" in Docstring: - return
-    DAR301 # Missing "Yields" in Docstring: - yield
-    E111 # indentation is not a multiple of 4
-    T201 # print found.
-
-[testenv:mypy]
-deps = mypy
-skip_install = true
-commands = mypy --install-types --non-interactive --ignore-missing-imports src/
-description = Run the mypy tool to check static typing on the project.
-
-[testenv:docstr-coverage]
-skip_install = true
-deps =
-    docstr-coverage
-commands =
-    docstr-coverage src/ tests/ --skip-private --skip-magic
-description = Run the docstr-coverage tool to check documentation coverage
+    E203
+    W503
+    C901 # needs code change so ignoring for now.
+    E731 # needs code change so ignoring for now.
+    S101 # asserts are fine
+    S106 # flags false positives with test_table_filler
+    N801 # mixed case is bad but there's a lot of auto-generated code
+    N815 # same ^
+    S404 # Consider possible security implications associated with the subprocess module.
+    S108 # Probable insecure usage of temp file/directory.
+    S307 # Use of possibly insecure function - consider using safer ast.literal_eval.
+    S603 # subprocess call - check for execution of untrusted input.
+    S607 # Starting a process with a partial executable path ["open" in both cases]
+    S608 # Possible SQL injection vector through string-based query construction.
+    B024 # StreamingWriter is an abstract base class, but it has no abstract methods. 
+         # Remember to use @abstractmethod, @abstractclassmethod and/or @abstractproperty decorators.
+    B027 # empty method in an abstract base class, but has no abstract decorator. Consider adding @abstractmethod
+    N803 # math-oriented classes can ignore this (e.g. hypergeometric.py)
+    N806 # math-oriented classes can ignore this (e.g. hypergeometric.py)
+    B019
+    S113 # new check - deal with this later
+
+max-line-length = 120
+max-complexity = 13
+import-order-style = pycharm
+application-import-names =
+    semdsl
+    tests
+exclude =
+    datamodel   ## datamodels are auto-generated
+    tests/input/examples