linkml 1.8.1__py3-none-any.whl → 1.8.2__py3-none-any.whl

linkml/utils/logictools.py

@@ -1,7 +1,7 @@
 import operator
 from copy import deepcopy
 from itertools import product
-from typing import Any, Collection, List, Optional, Tuple
+from typing import Any, Collection, List, Optional, Tuple, Type
 
 
 def member_of(item: Any, collection: Collection[Any]) -> bool:
@@ -25,6 +25,8 @@ OPS = {
 
 
 class Expression:
+    """Base class for logic expressions"""
+
     def __eq__(self, other: "Expression"):
         if isinstance(other, Expression):
             return self._ordered_str() == other._ordered_str()
@@ -60,6 +62,7 @@ class Expression:
 
     def __contains__(self, other: Any):
         return Term("contains", self, other)
+        return Term("contains", self, other)
 
     def _ordered_str(self, **kwargs):
         return str(self)
@@ -69,6 +72,8 @@ class Expression:
 
 
 class Variable(Expression):
+    """A variable in a logic expression"""
+
     def __init__(self, name: str):
         self.name = name
 
@@ -80,6 +85,8 @@ class Variable(Expression):
 
 
 class Top(Expression):
+    """True expression"""
+
     def __str__(self):
         return "T"
 
@@ -88,6 +95,8 @@ class Top(Expression):
 
 
 class Bottom(Expression):
+    """False expression"""
+
     def __str__(self):
         return "F"
 
@@ -96,6 +105,8 @@ class Bottom(Expression):
 
 
 class Not(Expression):
+    """Negation of an expression"""
+
     def __init__(self, operand: Expression):
         self.operand = operand
 
@@ -107,6 +118,8 @@ class Not(Expression):
 
 
 class And(Expression):
+    """Conjunction of expressions"""
+
     def __init__(self, *operands: Expression):
         self.operands: List[Expression] = list(operands)
 
@@ -306,6 +319,45 @@ def distribute_and_over_or(expr: Expression) -> Expression:
 
 
 def is_contradiction(expr: Expression, apply_dnf=False) -> Optional[bool]:
+    """
+    Check if the given expression is a contradiction.
+
+    >>> a = Variable("a")
+    >>> b = Variable("b")
+    >>> c = Variable("c")
+    >>> d = Variable("d")
+    >>> F = Bottom()
+    >>> T = Top()
+    >>> is_contradiction(T)
+    False
+    >>> is_contradiction(F)
+    True
+    >>> is_contradiction(~T)
+    True
+    >>> is_contradiction(~F)
+    False
+    >>> is_contradiction(~~T)
+    False
+    >>> is_contradiction(~~F)
+    True
+    >>> is_contradiction(F & F)
+    True
+    >>> is_contradiction(F & T)
+    True
+    >>> is_contradiction(F | T)
+    False
+    >>> is_contradiction(a & F )
+    True
+    >>> is_contradiction(a & ~a)
+    True
+    >>> assert is_contradiction(a & T) is None
+    >>> assert is_contradiction(a) is None
+    >>> assert is_contradiction(And(a)) is None
+
+    :param expr:
+    :param apply_dnf:
+    :return:
+    """
     if apply_dnf:
         expr = to_dnf(expr)
         expr = simplify(expr)
@@ -354,6 +406,32 @@ def evals_to_true(expr: Expression, apply_dnf=False) -> Optional[bool]:
     """
     Two-valued logic
 
+    >>> a = Variable("a")
+    >>> b = Variable("b")
+    >>> c = Variable("c")
+    >>> d = Variable("d")
+    >>> F = Bottom()
+    >>> T = Top()
+    >>> evals_to_true(T)
+    True
+    >>> evals_to_true(F)
+    False
+    >>> evals_to_true(~T)
+    False
+    >>> evals_to_true(~F)
+    True
+    >>> evals_to_true(a & b)
+    False
+    >>> evals_to_true(a | b)
+    False
+    >>> evals_to_true(a & a)
+    False
+
+    Note that this does not perform unification, so the following does not evaluate to True
+
+    >>> evals_to_true(a & ~a)
+    False
+
     :param expr:
     :param apply_dnf:
     :return:
@@ -363,7 +441,7 @@ def evals_to_true(expr: Expression, apply_dnf=False) -> Optional[bool]:
     if isinstance(expr, And):
         return all([evals_to_true(operand) for operand in expr.operands])
     elif isinstance(expr, Not):
-        if is_contradiction(expr.operand) is False:
+        if is_contradiction(expr.operand) is True:
             return True
         else:
             return False
@@ -378,32 +456,6 @@ def evals_to_true(expr: Expression, apply_dnf=False) -> Optional[bool]:
         return False
 
 
-def is_tautology(expr):
-    """
-    Checks if the given propositional logic formula is a tautology.
-
-    A formula is a tautology if it is true under every possible valuation of its variables.
-
-    Args:
-        expr (Expression): The input formula which is an instance of Expression or its subclasses.
-
-    Returns:
-        bool: True if the formula is a tautology, False otherwise.
-    """
-    if isinstance(expr, Or):
-        for i in range(len(expr.operands)):
-            for j in range(i + 1, len(expr.operands)):
-                if isinstance(expr.operands[i], Not) and expr.operands[i].operand == expr.operands[j]:
-                    return True
-                elif isinstance(expr.operands[j], Not) and expr.operands[j].operand == expr.operands[i]:
-                    return True
-    elif isinstance(expr, And):
-        for operand in expr.operands:
-            if is_tautology(operand):
-                return True
-    return False
-
-
 def eliminate_redundant(expr: Expression) -> Expression:
     if isinstance(expr, And):
         visited = set()
@@ -444,6 +496,23 @@ def simplify(expr: Expression) -> Expression:
     """
     Simplifies the given propositional logic formula.
 
+    >>> a = Variable("a")
+    >>> b = Variable("b")
+    >>> c = Variable("c")
+    >>> d = Variable("d")
+    >>> simplify(a & b)
+    (a & b)
+    >>> simplify(a | b)
+    (a | b)
+    >>> simplify(a & a)
+    a
+    >>> simplify(a | a)
+    a
+    >>> simplify(a & ~a)
+    F
+    >>> simplify(a | ~a)
+    T
+
     :param expr:
     :return:
     """
@@ -521,6 +590,30 @@ COMPOSITIONS = {
 
 
 def _unsat(x: Expression, y: Expression) -> bool:
+    """
+    Check if two terms are unsatisfiable when combined.
+
+    >>> a = Variable("a")
+    >>> b = Variable("b")
+    >>> _unsat( a < b, a > b)
+    True
+    >>> _unsat( a < b, a < b)
+    False
+    >>> _unsat( a <= b, b >= a)
+    False
+    >>> _unsat( a < b, a <= b)
+    False
+    >>> _unsat( a < b, b <= a)
+    False
+    >>> _unsat( IsIn(a, [1, 2]), IsIn(a, [2, 3]))
+    False
+    >>> _unsat( IsIn(a, [1, 2]), IsIn(a, [3, 4]))
+    True
+
+    :param x:
+    :param y:
+    :return:
+    """
     if isinstance(x, Term) and isinstance(y, Term):
         if x.operands[0] == y.operands[0]:
             xp = x.predicate
@@ -547,7 +640,27 @@ def _unsat(x: Expression, y: Expression) -> bool:
     return False
 
 
-def compose_operators(boolean_op, op1, v1, op2, v2) -> Optional[Tuple]:
+def compose_operators(boolean_op: Type[Expression], op1: str, v1: Any, op2: str, v2: Any) -> Optional[Tuple]:
+    """
+    Compose two expressions.
+
+    >>> assert compose_operators(And, '<', 1, '<', 2) == (operator.__lt__, 1)
+    >>> assert compose_operators(Or, '<', 1, '<', 2) == (operator.__lt__, 2)
+    >>> assert compose_operators(Or, '=', 1, '=', 2) is None
+    >>> assert compose_operators(And, '=', 1, '=', 2) is None
+    >>> assert compose_operators(And, "in", [1, 2], "in", [2, 3]) == (member_of, [2])
+    >>> assert compose_operators(Or, "in", [1, 2], "in", [2, 3]) == (member_of, [1, 2, 3])
+    >>> assert compose_operators(And, "in", [1], "in", [3]) == (member_of, [])
+    >>> assert compose_operators(And, "in", [1], "in", UniversalSet()) == (member_of, [1])
+    >>> assert compose_operators(Or, "in", [1], "in", UniversalSet()) == (member_of, UniversalSet())
+
+    :param boolean_op:
+    :param op1:
+    :param v1:
+    :param op2:
+    :param v2:
+    :return: New expression OR None if the expressions cannot be reduced
+    """
     rev_op_map = {v: k for k, v in OPS.items()}
     if not (op1 in rev_op_map and op2 in rev_op_map):
         return None

linkml/utils/schema_builder.py

@@ -101,12 +101,13 @@ class SchemaBuilder:
                     for k, v in slots.items():
                         cls.slots.append(k)
                         self.add_slot(SlotDefinition(k, **v), replace_if_present=replace_if_present)
-                for s in slots:
-                    cls.slots.append(s.name if isinstance(s, SlotDefinition) else s)
-                    if isinstance(s, str) and s in self.schema.slots:
-                        # top-level slot already exists
-                        continue
-                    self.add_slot(s, replace_if_present=replace_if_present)
+                else:
+                    for s in slots:
+                        cls.slots.append(s.name if isinstance(s, SlotDefinition) else s)
+                        if isinstance(s, str) and s in self.schema.slots:
+                            # top-level slot already exists
+                            continue
+                        self.add_slot(s, replace_if_present=replace_if_present)
             if slot_usage:
                 if isinstance(slot_usage, dict):
                     for k, v in slot_usage.items():

linkml/utils/schema_fixer.py

@@ -382,7 +382,7 @@ class SchemaFixer:
         return schema
 
 
-@click.group()
+@click.group(name="fix")
 @click.option("-v", "--verbose", count=True)
 @click.option("-q", "--quiet")
 def main(verbose: int, quiet: bool):

linkml/utils/sqlutils.py

@@ -270,7 +270,7 @@ class SQLStore:
             return obj
 
 
-@click.group()
+@click.group(name="sqldb")
 @click.option("-v", "--verbose", count=True)
 @click.option("-q", "--quiet")
 @click.option(

linkml/validator/cli.py

@@ -64,7 +64,7 @@ def _resolve_loaders(loader_config: Iterable[Union[str, Dict[str, Dict[str, str]
 DEPRECATED = "[DEPRECATED: only used in legacy mode]"
 
 
-@click.command()
+@click.command(name="validate")
 @click.option(
     "-s",
     "--schema",
@@ -132,6 +132,9 @@ def cli(
     include_range_class_descendants: bool,
     include_context: bool,
 ):
+    """
+    Validate data according to a LinkML Schema
+    """
     if legacy_mode:
         from linkml.validators import jsonschemavalidator
 

linkml/validators/jsonschemavalidator.py

@@ -114,7 +114,7 @@ class JsonSchemaDataValidator(DataValidator):
             yield f"{best_error.message} in {best_error.json_path}"
 
 
-@click.command()
+@click.command(name="jsonschema")
 @click.option("--module", "-m", help="Path to python datamodel module")
 @click.option(
     "--input-format",

linkml/validators/sparqlvalidator.py

@@ -85,7 +85,7 @@ class SparqlDataValidator(DataValidator):
         return self.schema
 
 
-@click.command()
+@click.command(name="sparql")
 @click.option("--named-graph", "-G", multiple=True, help="Constrain query to a named graph")
 @click.option("--input", "-i", help="Input file to validate")
 @click.option("--endpoint-url", "-U", help="URL of sparql endpoint")

linkml/workspaces/example_runner.py

@@ -255,7 +255,7 @@ class ExampleRunner:
             return dict_obj
 
 
-@click.command()
+@click.command(name="examples")
 @click.option("--schema", "-s", required=True, help="Path to linkml schema yaml file")
 @click.option("--prefixes", "-P", help="Path to prefixes")
 @click.option("--input-directory", "-e", help="folder containing positive examples that MUST pass validation")

{linkml-1.8.1.dist-info → linkml-1.8.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.8.1
+Version: 1.8.2
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -36,7 +36,7 @@ Requires-Dist: jinja2 (>=3.1.0)
 Requires-Dist: jsonasobj2 (>=1.0.3,<2.0.0)
 Requires-Dist: jsonschema[format] (>=4.0.0)
 Requires-Dist: linkml-dataops
-Requires-Dist: linkml-runtime (==1.8.0)
+Requires-Dist: linkml-runtime (>=1.8.1,<2.0.0)
 Requires-Dist: openpyxl
 Requires-Dist: parse
 Requires-Dist: prefixcommons (>=0.1.7)

{linkml-1.8.1.dist-info → linkml-1.8.2.dist-info}/RECORD

@@ -1,11 +1,17 @@
 linkml/__init__.py,sha256=0REu65rXiOk3F1CYLzq60HiSZ2DfFySfGS6QFljZ01s,3663
 linkml/_version.py,sha256=udxv6OEqcE89DTVMYPtetXYg8IA8Sgc6yW26-6f8C3M,310
+linkml/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml/cli/__main__.py,sha256=oPa7Fl2DQP40UivpIWNRr1CgwT2SQM0rhE478155zBY,80
+linkml/cli/main.py,sha256=-VaV8Z6rhadMOIHS9kdeV30NdXsE6jG3kVpvGbkF2wY,5184
 linkml/generators/PythonGenNotes.md,sha256=wb9BPLLhF6378OKLbwSBAwmniLpwrcT5_bbfCHfLme8,51006
 linkml/generators/README.md,sha256=RMzT8EblC_GEdPy5WyfXHDBXlFI6k6mz3Cx2sdpcyWI,4438
 linkml/generators/__init__.py,sha256=dQ2EUKy_MctEVEzbC3XzEJL5YmYwjYfsa44mG2zKn7g,1517
 linkml/generators/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml/generators/common/build.py,sha256=hXf2gf1ox2hiR-D6N-qXt5w5QkISLlo1A-_GurY3yHo,2897
+linkml/generators/common/lifecycle.py,sha256=UOJXlIyWQkvsn0Dao9_ZDzlamJtiINyVJQ6SRj66L9s,4910
+linkml/generators/common/template.py,sha256=bjcSNiC85MYl9oGhk0ZpqwZpRxxy_NqxG8XBV-TXXDY,3338
 linkml/generators/common/type_designators.py,sha256=lgVcIRJJ-yCvVGeP9U_gQZpm77UmJBQo9Bh3lGJITno,1956
-linkml/generators/csvgen.py,sha256=R8VQdWXj43LNf5isJElo3MStsiNBSSF4ywIRS1c3_v0,3243
+linkml/generators/csvgen.py,sha256=O20K3IuDxomGJAyNFJmm1_HbPyl6xUK0l-aKY0A3KcM,3253
 linkml/generators/docgen/class.md.jinja2,sha256=-JmjYHgYOaaBYd5r-Tr5dkk0CLM_lX0kHdocPQtRsjU,3504
 linkml/generators/docgen/class_diagram.md.jinja2,sha256=gzskx4hOpU_s6BqOXdYZ9DwKxuClnsEgDzPurm30PeY,3469
 linkml/generators/docgen/common_metadata.md.jinja2,sha256=gy9J8rghBfKDKimwtHj_XuHY4PJRRYHLXVlBHqWrUzU,1604
@@ -13,70 +19,70 @@ linkml/generators/docgen/enum.md.jinja2,sha256=mXnUrRkleY2bOTEyAZ5c4pcUnqhs6BNa8
 linkml/generators/docgen/index.md.jinja2,sha256=wXUYTmayPLFltC0vbGE_Mf6m3GkkWav7FOEjCvEpHp4,1466
 linkml/generators/docgen/index.tex.jinja2,sha256=Go_EA-_N4JUpbOYbk3OY11mz5yV70VF2l2sMtgIPWw4,501
 linkml/generators/docgen/schema.md.jinja2,sha256=xlENfnzNRYgPT_0tdqNFxgklVM4Qf5BuzhFVvSMDuxs,70
-linkml/generators/docgen/slot.md.jinja2,sha256=ZGa-kaNvi5LknvFRIjKQyRpSynr1SlkLrpEmWDNPwDA,3226
+linkml/generators/docgen/slot.md.jinja2,sha256=dJHugIv9OPTi3FIn8Iez7CzjQizdXrcn0hcmCmXSgV4,3339
 linkml/generators/docgen/subset.md.jinja2,sha256=EPln_fjlhlkmwEGEp2iPX-9Xm2vVodPZLlRBlYCB_sA,2705
 linkml/generators/docgen/type.md.jinja2,sha256=QmCMJZrFwP33eHkggBVtypbyrxTb-XZn9vHOYojVaYk,635
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-linkml/generators/graphqlgen.py,sha256=ClJdD6fVjBI8rsIJ3DIuwdQScAJG0gYYKwS8SrFqVZk,2149
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+linkml/generators/excelgen.py,sha256=MQRRm1wDbg7auUQH9tGb5aRyrp-e4gjXsY10aoLb9LI,7708
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 linkml/generators/javagen/example_template.java.jinja2,sha256=ec4CVTv_0zS7V5Y-1E6H4lRraya10gfX7BEMBlu38X4,444
 linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMltvrYyVeut7l2Q-tzK7AOiVmWs,1729
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-linkml/generators/jsonschemagen.py,sha256=sQXlaT_UOiJfbRoxH-hFY4nM0ELdjRlCFnS8HqVzqb8,28263
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 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/generators/linkmlgen.py,sha256=1_Kt_7rD42WvCTjq0yaq1Of7jEDZR_uusyzAT-qWMHk,3471
-linkml/generators/markdowngen.py,sha256=mwydWkrF-WzsTiKwJqqe9NUya5VaTj7ywKqodP85A44,34449
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-linkml/generators/pydanticgen/__init__.py,sha256=-972x-uV0atgveW_n5qvG1WelKANvsk9ZseZOIH_tNI,663
-linkml/generators/pydanticgen/array.py,sha256=EYqAkT2_wE82kZ-niUWAC5U3V8EvjjyfSH7tz5GYKWo,19461
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+linkml/generators/protogen.py,sha256=a4KUyKj525tuE2YenEJQ_IkbNKnnhVH_N-qTEmMBVY4,2524
+linkml/generators/pydanticgen/__init__.py,sha256=5SUFNcrh-6MLfMqptR6wPsR2v1Gyrl3wii-yu6kdnQM,700
+linkml/generators/pydanticgen/array.py,sha256=mF_vhmlPfd9yVlVyANvT9GgLP6iQLSheqaowT5Jp6Jo,16120
 linkml/generators/pydanticgen/black.py,sha256=BaJ7b-kMUbIN_cKRT3yCaMEbFwxzj1_U7w4fKQnkL44,723
-linkml/generators/pydanticgen/build.py,sha256=Ia8qy4C16b-KqO_fw4tGQW_Eo4grCVyX7RsuJ3uRTtk,2681
-linkml/generators/pydanticgen/includes.py,sha256=0CZi8vs6Z2eVvMOWhbTphCYoI3X8E9-8LgSaCBeiuCY,1174
-linkml/generators/pydanticgen/pydanticgen.py,sha256=kaUBENnVEGpFs3gGK8kQbR2ZoZ1eg9Jiz0yNtXajbEw,34900
-linkml/generators/pydanticgen/template.py,sha256=gffWyzJNmjw2Kf1UszRp97qGrnkAGd4UnLimU2nEsEA,21154
-linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=S_T-M7n_eeM3LW5gQUuTPH1-Oc1CEtL7Bve7qAFouYQ,688
-linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=48y64MnC9rjNSV-nKLMeDuHN4gm15UsInhnKxh65zoM,834
-linkml/generators/pydanticgen/templates/class.py.jinja,sha256=V_lyvFcZ9QhlKZi2bL5iff8RjHir2SQTTypOzQMOfmk,744
+linkml/generators/pydanticgen/build.py,sha256=_NQzXK_wWJ-EAHBi1nqZCEWSTYy7KWkc5w-mRsEXycI,3936
+linkml/generators/pydanticgen/includes.py,sha256=kDAwonKbhTFzrFa2TrmTYuOSHXuzDy5WHgBaI5nVY6c,504
+linkml/generators/pydanticgen/pydanticgen.py,sha256=TCQG5O0GFT1GDsrMby79jDujWFJ3D_pXW8sUB3vw3L0,49059
+linkml/generators/pydanticgen/template.py,sha256=alt5yXyf2zdh93rLhyuIu9Ctb9C3O1oM62Upr4JH6Cw,21000
+linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=uMyVKpO5uQkAFlIvIBwA6FFZl_BSIotfwCorrSwMA3Q,873
+linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=6KRQ1ZVHh1uwZnYL3qxBnyit8_DNE7D-4l2-1wsRsG0,406
+linkml/generators/pydanticgen/templates/class.py.jinja,sha256=GqR2t5y0vLmvUpT2vyP5VX42PO9AkAnGE-U2RZPa9AI,690
 linkml/generators/pydanticgen/templates/conditional_import.py.jinja,sha256=YheknDrxvepiJUzeItSL5aSbAkCdR1k0a6m6aTA4qNM,240
 linkml/generators/pydanticgen/templates/enum.py.jinja,sha256=572XFQyEMZfL-G_Cj68T-NI_mUnDoFOAVJOGIKu2Hb8,338
-linkml/generators/pydanticgen/templates/footer.py.jinja,sha256=WuWGJjkWDQcEPL2bGk5fdGuhO0gQRUJzpo4CQHHxQNQ,385
+linkml/generators/pydanticgen/templates/footer.py.jinja,sha256=t_24p1xmqdbfxGqz_XCXSTvkkWt26_2w_RcQjGIAWlY,155
 linkml/generators/pydanticgen/templates/imports.py.jinja,sha256=d1XFna2eOpkH8cgJML3vXwqGcocczvOcrbg6jjd4kP0,945
-linkml/generators/pydanticgen/templates/module.py.jinja,sha256=gYauXrq8ML3ieaN_DFGB9yj9VfZV2yHG5LRQUzWy4VA,622
-linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=Yo4dubQal-HwEoJKztQkLYM5qCz1I8na2oaDlXuEpwU,532
-linkml/generators/pythongen.py,sha256=CiLmc964siGeJWZC_bOffsqrSnJ5qzn7Eu961C47xgo,52850
-linkml/generators/rdfgen.py,sha256=eQi3XXjWk6xliTLncQ4G0VYzGCJwCU_FFG-O7tA8DSA,2959
+linkml/generators/pydanticgen/templates/module.py.jinja,sha256=NLCYn4wgwVBCs8trV2hNq0_BkZgfIIS6zQTmjzFDJCQ,568
+linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=BhXRGrT7HIweVHEE3Z7ZUtFFV8kP1dmRKJfu53jZBBQ,441
+linkml/generators/pythongen.py,sha256=Ti654YxzTwZRXap-vT5T7iP3NYWox0yFqdp4oHV8tNs,53289
+linkml/generators/rdfgen.py,sha256=OT8oS8MPUVf5UK3OKvRWgAh9iQiWwdyWJSA69PncOw4,2969
 linkml/generators/shacl/__init__.py,sha256=O-M-wndKw8rMW-U8X3QCNHal-ErXP6uXZqxiQSa77l4,108
 linkml/generators/shacl/ifabsent_processor.py,sha256=kV9BGA2ZPXLRfaFuW0o4jpkATvGggvrqpAo9c1UqWNE,2193
 linkml/generators/shacl/shacl_data_type.py,sha256=BT3C9tdFyBQnuucPN7YQiFAKEa9yuzy-Q26X6dmOXgo,1827
-linkml/generators/shaclgen.py,sha256=kgJ3VaVM0_7XBr5cvqgob6wjEarNINZzpC4FK61sC9M,13157
-linkml/generators/shexgen.py,sha256=MhB1HidCREMCJcDGBqutFQ0gWKKz7aSVw-0s-IHUMm4,9930
-linkml/generators/sparqlgen.py,sha256=c7x8GFChKWprBx4rToSnu9qN8OleWTCenVUdZ8XSTWM,6138
+linkml/generators/shaclgen.py,sha256=9fp7qsKhMpplDHNIBIwfFLguYubjOEUn9th_Fvtg8zA,13283
+linkml/generators/shexgen.py,sha256=-GFdapDEAUXAjsXdTI7ZlS39YfuvaxfzPkdqUNM19qI,9941
+linkml/generators/sparqlgen.py,sha256=ULvWokNGPADq1qDENoFeRYg3FmjdTh4-Vq-eYjsAEK4,6151
 linkml/generators/sqlalchemy/__init__.py,sha256=mb9AC1rIFkSiNZhhG0TAk45ol9PjS1XvsrvCjgfVUpQ,249
 linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBikMI5HuNgEhl_PIeWM-B-c2B0W9KUBH4QTg,2542
 linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py,sha256=u4ZpponG1h6XROrOHGOf_0H2e6xL1_s8twAOA-gx94A,1622
-linkml/generators/sqlalchemygen.py,sha256=boXn_tlkbZ_a5TJYoXvdlKzABNwD-Jn5ld9IAbtzWm4,9286
-linkml/generators/sqltablegen.py,sha256=87057FJi9EUVPXOjRfHuSqY0lKmepXRNQsose2fGts4,12343
-linkml/generators/sssomgen.py,sha256=yur3q7so9uwIELWZaZRzkJwNbz_ppBL7IQki9XLIM3k,6879
+linkml/generators/sqlalchemygen.py,sha256=qTyT0s1FhQnCvcgjEsC4OaTWhkgHBAGxcHnxEoF9DmI,9297
+linkml/generators/sqltablegen.py,sha256=nKjUMhd05JaWaME_DjP7AV2DDUulsKpcu7IidhD3PLo,12359
+linkml/generators/sssomgen.py,sha256=zrZy0WL9fF5bk-XAcB-MZYZkhHhqVRHt2rGBUtfqnLY,6891
 linkml/generators/string_template.md,sha256=kRcfic6entgIaJdpSg6GF3jcjC9wbKsCVM6wVT2qipc,1788
-linkml/generators/summarygen.py,sha256=HUO13GmfFzhAzKtL3nFypR-_I_IFIHqQoE6WMW05mpo,3069
-linkml/generators/terminusdbgen.py,sha256=_q5R0OPCkLCHNTQ9AMtCL2hYaO-wReDjzITvj2doaU0,4626
-linkml/generators/typescriptgen.py,sha256=80Ph4RfzDoA1TRCkKaLWlh0NsCNvhakJ2RrNfMqcMmY,8577
-linkml/generators/yamlgen.py,sha256=PKssrY5VHpdbOU54PVwLVLbsRqHwoOgOImlMb6DVcXM,1614
-linkml/generators/yumlgen.py,sha256=xmMCHPDg-x1vhqc4M-_YmU49-yFan_mjZkve4vCVBaU,12197
+linkml/generators/summarygen.py,sha256=C9r34928QtVMaXTbdch-mRPB5L0jDTGmTnVmtrKrR-0,3083
+linkml/generators/terminusdbgen.py,sha256=ItJ-HTMkkX22Ex1-UjJZmtEtE2fn6UdjAxDtn20RXV8,4713
+linkml/generators/typescriptgen.py,sha256=y8l1A1hAyuiRmXw0CyPXfamBKWpi7ag_lspfr8bnIds,8594
+linkml/generators/yamlgen.py,sha256=38zdh5T4tObFhCHgbUbKbc0UuFh1TmmsWBkWM9gcvsI,1625
+linkml/generators/yumlgen.py,sha256=Bg1MGlhCCQoswB19mFKh8xB0UcL9MQGHlUrAVGZSWkc,12208
 linkml/linter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/linter/cli.py,sha256=BpQiETcRfQlZsI1-JALyU9wXPgPOm_KE_n11p0iJaC8,4494
+linkml/linter/cli.py,sha256=tXJ3vwjohCnj4EApEJXvXUSI3NLJ3fI3u6tJVxbgLQg,4505
 linkml/linter/config/datamodel/.linkmllint.yaml,sha256=40rNhcL35FXQSjlVBMWnyPgplwEUqFT_sJmeZqUzxMw,292
 linkml/linter/config/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/linter/config/datamodel/config.py,sha256=WyIBA1damYcW0JI6zLxbFwcHOtSdw0prSADlJdz3zG0,17202
@@ -94,32 +100,32 @@ linkml/linter/rules.py,sha256=Eg_-lIX1KPsCp3PHdPcBiHmSS5qAVZkHbw5LURfkfXk,11481
 linkml/reporting/__init__.py,sha256=Jo0V_nyEcnWhMukMW-bqW9dlbgCfaRlWm3CO-XzgU84,92
 linkml/reporting/model.py,sha256=-10yNfk8wuRC48ZI-akrWvtlJ9a6RYWET2TzlZV3XXo,8622
 linkml/transformers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/transformers/logical_model_transformer.py,sha256=z-1nyD0d8LYJeAPWRn29p-S4Hgmvjocfcj0VrHTAs2c,26703
+linkml/transformers/logical_model_transformer.py,sha256=rPeBYzQdLtcEKPe1kwkOWce4N7HZvFaULDrEGKbB-qI,29838
 linkml/transformers/model_transformer.py,sha256=tK_MpRDI-q2qfe8KHT6qJHP8ZruKjYx1FcM-Fnjse-E,678
 linkml/transformers/relmodel_transformer.py,sha256=aiSI2xaqRz4f0Z_0WFaBP5bknzX0pTnvxsR5mESFysg,18857
 linkml/transformers/schema_renamer.py,sha256=DYRbgL9j41M9FdbHYLY3u4YIdDM98laD3cv_lHcgWHQ,5275
 linkml/utils/__init__.py,sha256=Pkyv-Gfb8QoJdInRdJuuUz1Igfe0sT9t8Gv3V_fyTXc,92
 linkml/utils/cli_utils.py,sha256=MdVbox1qr6kDUHUCWAmFhV-D6ebs_nn8vVwB8KDQfew,742
-linkml/utils/converter.py,sha256=snAF-pgZBSi4ANiaKXxqtZk5w3qonJjTfI4X5OVLmUE,6283
+linkml/utils/converter.py,sha256=vMpJLNFDxZR3yUGMiBCassDC-vvTb2oTq_3NYSLgErk,6297
 linkml/utils/datautils.py,sha256=QlbzwXykh5Fphfe5KxPo6_ekXfniLbHiEGJtLWjUrvY,3742
 linkml/utils/datavalidator.py,sha256=kBdWaVi8IZT1bOwEJgJYx-wZAb_PTBObB9nHpYORfKA,472
 linkml/utils/deprecation.py,sha256=onhB82qjIkKzyUOTO9WDqN6QF3I2cJoyBrbm66vHmgM,8088
-linkml/utils/execute_tutorial.py,sha256=T4kHTSyz3ItJGEUZxVjR-3yLVKnOr5Ix4NMGE47-IuE,6912
+linkml/utils/execute_tutorial.py,sha256=KGmSnaz6joIAShnrD24n8kD6URe6CBoSUYsDOTg7qCg,7039
 linkml/utils/generator.py,sha256=nAZTBFDKAZ2Asi6f54-GSOZoP03jQKgbYCW82KA34Z4,39100
 linkml/utils/helpers.py,sha256=yR8n4zFA5wPcYC7xzRuNF3wO16vG80v6j7DM3qTNmIc,447
 linkml/utils/ifabsent_functions.py,sha256=IkcBcmRYu8sllx7_mTCqu4aHfTxX2AnQoccZ1KOODds,5843
-linkml/utils/logictools.py,sha256=GSmBiobC49TcQjE08RtXEE3JwJEOV7eEREio25uJiFs,21184
+linkml/utils/logictools.py,sha256=BGtcoqr_Rsu08Ywa6lNiL881uZzQmNWk1p4FEIVKYe0,23641
 linkml/utils/mergeutils.py,sha256=QVm2iQB4v_L2rSvPBsPe9C865R03BgV3TzlPoTTTwWQ,9044
 linkml/utils/rawloader.py,sha256=nUB8Gfn8yEVwyo6bx0TtB2mBGkilC-fybi0xvQ73Gks,4417
-linkml/utils/schema_builder.py,sha256=4qhrur8O0xRZnPm7H1h2BZmTkut5R4q-IE_1KKiHy_c,9937
-linkml/utils/schema_fixer.py,sha256=Uz8M3AOQ_BputJr1f6lbfk1iyvmANUNG80-0B3BQKJ8,16761
+linkml/utils/schema_builder.py,sha256=LwaLeo65IQBHcmRD1kIxnjI1idFZyZsgfPACPow1_JY,9983
+linkml/utils/schema_fixer.py,sha256=dzAkID_hO8VNrSpO9Jbz_GLJQAoRju13cZ3fnY03ZX8,16771
 linkml/utils/schemaloader.py,sha256=dWZO044p_UcUWnrd8HZ-NsbLXQ9cA6c8HKfNI9-qH2A,47388
 linkml/utils/schemasynopsis.py,sha256=j7sNt6j-E3rmf-1qEo351Kth2kltt6crQV-dxJAGCUE,18414
-linkml/utils/sqlutils.py,sha256=Cwoaz44MLcvAGUEBshT4jtn0Z3w7jVOp85zGkd6FTHY,17071
+linkml/utils/sqlutils.py,sha256=Ddm6nsUd3oqLEWwZj7yakpyhRCO92Vvfl2MobiFaaXo,17083
 linkml/utils/typereferences.py,sha256=8Yfuz9-HAwOPoJLbIcO_sY9zf32hvPRzGeSOzECfMWA,2232
 linkml/utils/validation.py,sha256=eLw1-d8x3N1V14bSc6H_mJJXo59ryKvvUIBcOJ1dVMw,1438
 linkml/validator/__init__.py,sha256=u0CeorIw50Qqwa60-lIFsJXg-sOdfo90hqvLpyvvwo4,4993
-linkml/validator/cli.py,sha256=uVe_tbBzsK-4BNboE5zRyohS_dEs5Nl1gbhklrzOEpw,7605
+linkml/validator/cli.py,sha256=-7_hU787d321z_4pJeUs9dQsM76xpXie9dS-552c7Xs,7683
 linkml/validator/loaders/__init__.py,sha256=FjUqEfBHeT5PEMBEZ9XwpclyQOysr4OCI1M0w_MYPVc,1165
 linkml/validator/loaders/delimited_file_loader.py,sha256=fdh61ZMPTfH29_DM93f5dY0jLP7KQPNh_QAHZppsdNw,2616
 linkml/validator/loaders/json_loader.py,sha256=Qy42naS2clb0fNXbUushckRu5AIX32b3UFUL6KMhxDE,809
@@ -136,15 +142,15 @@ linkml/validator/report.py,sha256=LwFpmJ74Cvsi2CuEDhm1a8nn9x1VI3Z98DbkUZVhKMA,89
 linkml/validator/validation_context.py,sha256=Pmccq-LQ9iEeLyZhamp3mKjjtwp4ji1hIe5TT05AUT4,2732
 linkml/validator/validator.py,sha256=BFgfKdu9Nad2dc9XTpmz9daQTj_FTcvo6mBq3e8fhJs,5649
 linkml/validators/__init__.py,sha256=43W3J5NPKhwa3ZFHLRYsJMocwQKWGYCF9Ki9r0ccGbc,202
-linkml/validators/jsonschemavalidator.py,sha256=_ku7MQGqA6KplbHMiyzDRqgRwwXGloobhLptuXqLCp4,7951
-linkml/validators/sparqlvalidator.py,sha256=JowuZ5KxmWkldgWIXAb8DJi7YCPm8x3it0QkgM4lSi0,4612
+linkml/validators/jsonschemavalidator.py,sha256=LVhBF3Fp4Ltjeaov36duoODxXVXwKqe07SrohH_uzhg,7968
+linkml/validators/sparqlvalidator.py,sha256=KU4Vj-B3i_0Fde0Sn89oqkOVxt1UGW3uI4F6YNoJMTQ,4625
 linkml/workspaces/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/workspaces/datamodel/workspaces.py,sha256=4HdkqweGNfMPqnB1_Onc9DcTfkhoagTRcqruh08nRoI,14905
 linkml/workspaces/datamodel/workspaces.yaml,sha256=EjVrwPpeRZqJRjuGyyDRxxFzuv55SiLIXPBRUG6HStU,4233
-linkml/workspaces/example_runner.py,sha256=hDk2RGxRE5-WYNriWknugtbm3Mhn8bFcAcXGMlkYxVk,11705
-linkml-1.8.1.dist-info/entry_points.txt,sha256=7haDkIbyC7ZLhm5z-e3BhrLJpY2xoW1yuD8Y7QPNtVg,2093
-linkml-1.8.1.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.8.1.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.8.1.dist-info/METADATA,sha256=-Nk6qRvku2ysnCvxuObK_ILTulyQzPAKyvbbUbzSSfk,3724
-linkml-1.8.1.dist-info/RECORD,,
+linkml/workspaces/example_runner.py,sha256=qrn3EALJsHpyzQXo2npg5oTmMNQTrCjaNIAuMV0P5c8,11720
+linkml-1.8.2.dist-info/entry_points.txt,sha256=jvnPJ8UTca4_L-Dh8OdUm5td8I3ZFlKRhMPjqRLtaSg,2084
+linkml-1.8.2.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
+linkml-1.8.2.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.8.2.dist-info/METADATA,sha256=rdL9CvP5g68hZnKnQcInhtIMvcI2Ip5wqBdII0le-nY,3731
+linkml-1.8.2.dist-info/RECORD,,

{linkml-1.8.1.dist-info → linkml-1.8.2.dist-info}/entry_points.txt

@@ -18,7 +18,6 @@ gen-owl=linkml.generators.owlgen:cli
 gen-plantuml=linkml.generators.plantumlgen:cli
 gen-prefix-map=linkml.generators.prefixmapgen:cli
 gen-project=linkml.generators.projectgen:cli
-gen-prolog=linkml.generators.lpgen:cli
 gen-proto=linkml.generators.protogen:cli
 gen-py-classes=linkml.generators.pythongen:cli
 gen-pydantic=linkml.generators.pydanticgen:cli
@@ -36,6 +35,7 @@ gen-terminusdb=linkml.generators.terminusdbgen:cli
 gen-typescript=linkml.generators.typescriptgen:cli
 gen-yaml=linkml.generators.yamlgen:cli
 gen-yuml=linkml.generators.yumlgen:cli
+linkml=linkml.cli.main:linkml
 linkml-convert=linkml.utils.converter:cli
 linkml-jsonschema-validate=linkml.validators.jsonschemavalidator:cli
 linkml-lint=linkml.linter.cli:main