Merge pull request #26 from linkml/dynamic-build

Adding dynamic build

.github/workflows/pypi-publish.yaml

@@ -1,36 +1,39 @@
 name: Publish Python Package
 
 on:
-  workflow_dispatch:
   release:
     types: [created]
 
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
-    # needs: [test]
-    environment: release
-    permissions:
-      id-token: write
+
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3.1.0
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
-          cache: pip
-          cache-dependency-path: '**/pyproject.toml'
 
       - name: Install Poetry
-        run: pip install poetry poetry-dynamic-versioning
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.3.2
 
-      - name: Install dependencies
-        run: poetry install --no-interaction
+      - name: Add dynamic versioning plugin
+        run: poetry self add "poetry-dynamic-versioning[plugin]"
+
+      # - name: Install dependencies
+      #   run: poetry install --no-interaction
 
       - name: Build source and wheel archives
-        run: poetry build
+        run: |
+          poetry build
 
-      - name: Publish
-        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "linkml-map"
-version = "0.1.0"
-description = ""
+version = "0.0.0"
+description = "a framework for specifying and executing mappings between data models"
 authors = ["cmungall <cjm@berkeleybop.org>"]
 readme = "README.md"
 
@@ -10,7 +10,7 @@ python = "^3.9"
 linkml-runtime = ">=1.7.2"
 asteval = "^0.9.29"
 deepdiff = "^6.7.1"
-pydantic = "^2.5.3"
+pydantic = ">=2.0.0"
 ucumvert = "^0.1.1"
 
 [tool.poetry.dev-dependencies]
@@ -22,6 +22,11 @@ mknotebooks = "^0.8.0"
 mkdocs-windmill = "*"
 tox = "*"
 
+[tool.poetry-dynamic-versioning]
+enable = true
+vcs = "git"
+style = "pep440"
+
 [tool.poetry.scripts]
 linkml-map = "linkml_map.cli.cli:main"
 
@@ -42,8 +47,8 @@ graphviz = "^0.20.1"
 duckdb = "^0.10.1"
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
+build-backend = "poetry_dynamic_versioning.backend"
 
 [tool.black]
 line-length = 100

src/linkml_map/compiler/sql_compiler.py

@@ -114,6 +114,10 @@ def create_ddl(self, schemaview: SchemaView) -> str:
             ddl.append(");")
         return "\n".join(ddl)
 
+    def create_target_ddl(self, specification: TransformationSpecification) -> str:
+        target_sv = self.derived_target_schemaview(specification)
+        return self.create_ddl(target_sv)
+
     def sql_type(self, slot: SlotDefinition, schemaview: SchemaView) -> str:
         """
         Map LinkML types to DuckDB SQL types.

src/linkml_map/datamodel/transformer_model.py

@@ -1,18 +1,14 @@
 from __future__ import annotations
 
-import re
-import sys
-from datetime import date, datetime
-from decimal import Decimal
 from enum import Enum
-from typing import Any, Dict, List, Literal, Optional, Union
+from typing import Any, Dict, List, Optional
 
 from pydantic.version import VERSION as PYDANTIC_VERSION
 
 if int(PYDANTIC_VERSION[0]) >= 2:
-    from pydantic import BaseModel, ConfigDict, Field, field_validator
+    from pydantic import BaseModel, ConfigDict, Field
 else:
-    from pydantic import BaseModel, Field, validator
+    from pydantic import BaseModel, Field
 
 metamodel_version = "None"
 version = "None"

tests/input/examples/flattening/model/denormalized_model.py

@@ -7,33 +7,20 @@
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 
 import dataclasses
-import re
-import sys
 from dataclasses import dataclass
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
-from jsonasobj2 import JsonObj, as_dict
-from linkml_runtime.linkml_model.meta import (
-    EnumDefinition,
-    PermissibleValue,
-    PvFormulaOptions,
-)
-from linkml_runtime.linkml_model.types import String
+from jsonasobj2 import as_dict
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.utils.dataclass_extensions_376 import (
     dataclasses_init_fn_with_kwargs,
 )
-from linkml_runtime.utils.enumerations import EnumDefinitionImpl
-from linkml_runtime.utils.formatutils import camelcase, sfx, underscore
-from linkml_runtime.utils.metamodelcore import bnode, empty_dict, empty_list
+from linkml_runtime.utils.metamodelcore import empty_list
 from linkml_runtime.utils.slot import Slot
 from linkml_runtime.utils.yamlutils import (
     YAMLRoot,
-    extended_float,
-    extended_int,
-    extended_str,
 )
-from rdflib import Namespace, URIRef
+from rdflib import URIRef
 
 metamodel_version = "1.7.0"
 version = None

tests/input/examples/flattening/model/normalized_model.py

@@ -7,33 +7,21 @@
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 
 import dataclasses
-import re
-import sys
 from dataclasses import dataclass
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
-from jsonasobj2 import JsonObj, as_dict
-from linkml_runtime.linkml_model.meta import (
-    EnumDefinition,
-    PermissibleValue,
-    PvFormulaOptions,
-)
-from linkml_runtime.linkml_model.types import String
+from jsonasobj2 import as_dict
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.utils.dataclass_extensions_376 import (
     dataclasses_init_fn_with_kwargs,
 )
-from linkml_runtime.utils.enumerations import EnumDefinitionImpl
-from linkml_runtime.utils.formatutils import camelcase, sfx, underscore
-from linkml_runtime.utils.metamodelcore import bnode, empty_dict, empty_list
+from linkml_runtime.utils.metamodelcore import empty_dict, empty_list
 from linkml_runtime.utils.slot import Slot
 from linkml_runtime.utils.yamlutils import (
     YAMLRoot,
-    extended_float,
-    extended_int,
     extended_str,
 )
-from rdflib import Namespace, URIRef
+from rdflib import URIRef
 
 metamodel_version = "1.7.0"
 version = None

tests/input/examples/personinfo_basic/model/agent_model.py

@@ -8,38 +8,31 @@
 
 import dataclasses
 import re
-import sys
 from dataclasses import dataclass
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
-from jsonasobj2 import JsonObj, as_dict
+from jsonasobj2 import as_dict
 from linkml_runtime.linkml_model.meta import (
     EnumDefinition,
     PermissibleValue,
-    PvFormulaOptions,
 )
-from linkml_runtime.linkml_model.types import Boolean, Date, Float, String
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.utils.dataclass_extensions_376 import (
     dataclasses_init_fn_with_kwargs,
 )
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
-from linkml_runtime.utils.formatutils import camelcase, sfx, underscore
 from linkml_runtime.utils.metamodelcore import (
     Bool,
     XSDDate,
-    bnode,
     empty_dict,
     empty_list,
 )
 from linkml_runtime.utils.slot import Slot
 from linkml_runtime.utils.yamlutils import (
     YAMLRoot,
-    extended_float,
-    extended_int,
     extended_str,
 )
-from rdflib import Namespace, URIRef
+from rdflib import URIRef
 
 metamodel_version = "1.7.0"
 version = None

tests/input/examples/personinfo_basic/model/personinfo_model.py

@@ -8,38 +8,31 @@
 
 import dataclasses
 import re
-import sys
 from dataclasses import dataclass
 from typing import Any, ClassVar, Dict, List, Optional, Union
 
-from jsonasobj2 import JsonObj, as_dict
+from jsonasobj2 import as_dict
 from linkml_runtime.linkml_model.meta import (
     EnumDefinition,
     PermissibleValue,
-    PvFormulaOptions,
 )
-from linkml_runtime.linkml_model.types import Boolean, Date, Float, Integer, String
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.utils.dataclass_extensions_376 import (
     dataclasses_init_fn_with_kwargs,
 )
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
-from linkml_runtime.utils.formatutils import camelcase, sfx, underscore
 from linkml_runtime.utils.metamodelcore import (
     Bool,
     XSDDate,
-    bnode,
     empty_dict,
     empty_list,
 )
 from linkml_runtime.utils.slot import Slot
 from linkml_runtime.utils.yamlutils import (
     YAMLRoot,
-    extended_float,
-    extended_int,
     extended_str,
 )
-from rdflib import Namespace, URIRef
+from rdflib import URIRef
 
 metamodel_version = "1.7.0"
 version = None