liminal-orm 1.0.5__tar.gz → 1.0.6__tar.gz

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 1.0.5
+Version: 1.0.6
 Summary: An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync.
 Home-page: https://github.com/dynotx/liminal-orm
 Author: DynoTx Open Source
@@ -14,6 +14,7 @@ Requires-Dist: benchling-sdk (>=1.8.0)
 Requires-Dist: bs4 (>=0.0.2,<0.0.3)
 Requires-Dist: lxml (>=5.3.0,<6.0.0)
 Requires-Dist: pandas (>=1.5.3)
+Requires-Dist: psycopg2-binary (>=2.9.10,<3.0.0)
 Requires-Dist: pydantic (>=2,<=2.7)
 Requires-Dist: requests (>=2.32.3,<3.0.0)
 Requires-Dist: rich (>=13.9.2,<14.0.0)
@@ -27,7 +28,12 @@ Description-Content-Type: text/markdown
 
 # [Liminal ORM](#liminal-orm)
 
-Liminal ORM<sup>1</sup> is an open-source Python package that builds on [Benchling's](https://www.benchling.com/) LIMS<sup>2</sup> platform and provides a simple, code-first approach for synchronizing and managing your Benchling schemas. Check out the [**full documentation here**](https://dynotx.github.io/liminal-orm/)!
+[![PyPI version](https://img.shields.io/pypi/v/liminal-orm.svg)](https://pypi.org/project/liminal-orm/)
+[![License](https://img.shields.io/github/license/dynotx/liminal-orm)](https://github.com/dynotx/liminal-orm/blob/main/LICENSE.md)
+[![CI](https://github.com/dynotx/liminal-orm/actions/workflows/liminal.yml/badge.svg)](https://github.com/dynotx/liminal-orm/actions/workflows/liminal.yml)
+[![Downloads](https://static.pepy.tech/personalized-badge/liminal-orm?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads)](https://pepy.tech/project/liminal-orm)
+
+Liminal ORM<sup>1</sup> is an open-source Python package that builds on [Benchling's](https://www.benchling.com/) LIMS<sup>2</sup> platform and provides a simple, code-first approach for synchronizing and managing your Benchling schemas. Check out the [**full documentation here**](https://dynotx.github.io/liminal-orm/) and join our [**Slack community here**](https://join.slack.com/t/liminalorm/shared_invite/zt-2ujrp07s3-bctook4e~cAjn1LgOLVY~Q)!
 
 Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalchemy/sqlalchemy) along with a schema migration service inspired by [Alembic](https://alembic.sqlalchemy.org/en/latest/). This allows you to define your Benchling schemas in code and create a *single source of truth* that synchronizes between your upstream Benchling tenant(s) and downstream dependencies. By creating a standard interface and through using one-line CLI<sup>3</sup> commands, Liminal enables a code-first approach for managing Benchling tenants and accessing Benchling data. With the schemas defined in code, you can also take advantage of the additional capabilities that the Liminal toolkit provides. This includes:
 
@@ -38,10 +44,10 @@ Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalche
 - CI/CD integration with GitHub Actions to ensure that your Benchling schemas and code are always in sync.
 - And more based on community contributions/feedback :)
 
-Benchling is an industry standard cloud platform for life sciences R&D. Liminal builds on top of Benchling's platform and assumes that you already have a Benchling tenant set up and have (or have access to) an admin user account. If not, learn more about getting started with Benchling [here](https://www.benchling.com/explore-benchling)!
-
 If you are a Benchling user, try out Liminal by following the [**Quick Start Guide**](https://dynotx.github.io/liminal-orm/getting-started/prerequisites/)! Reach out in the [Discussions](https://github.com/dynotx/liminal-orm/discussions) forum with any questions or to simply introduce yourself! If there is something blocking you from using Liminal or you're having trouble setting Liminal up, please share in [Issues](https://github.com/dynotx/liminal-orm/issues) or reach out directly (contact information below). You can expect responses within 48 hours :)
 
+Benchling is an industry standard cloud platform for life sciences R&D. Liminal builds on top of Benchling's platform and assumes that you already have a Benchling tenant set up and have (or have access to) an admin user account. If not, learn more about getting started with Benchling [here](https://www.benchling.com/explore-benchling)!
+
 Nirmit Damania is the creator and current maintainer of Liminal (I post Liminal updates to [Discussions](https://github.com/dynotx/liminal-orm/discussions) and my [LinkedIn](https://www.linkedin.com/in/nirmit-damania/)). Most importantly, **you** have the ability to influence the future of Liminal! Any feedback, positive or negative, is highly encouraged and will be used to steer the direction of Liminal. Refer to the [Contributing guide](https://github.com/dynotx/liminal-orm/blob/main/CONTRIBUTING.md) to learn more about how you can contribute to Liminal.
 
 ⭐️ Leave a star on the repo to spread the word!

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/README.md

@@ -1,6 +1,11 @@
 # [Liminal ORM](#liminal-orm)
 
-Liminal ORM<sup>1</sup> is an open-source Python package that builds on [Benchling's](https://www.benchling.com/) LIMS<sup>2</sup> platform and provides a simple, code-first approach for synchronizing and managing your Benchling schemas. Check out the [**full documentation here**](https://dynotx.github.io/liminal-orm/)!
+[![PyPI version](https://img.shields.io/pypi/v/liminal-orm.svg)](https://pypi.org/project/liminal-orm/)
+[![License](https://img.shields.io/github/license/dynotx/liminal-orm)](https://github.com/dynotx/liminal-orm/blob/main/LICENSE.md)
+[![CI](https://github.com/dynotx/liminal-orm/actions/workflows/liminal.yml/badge.svg)](https://github.com/dynotx/liminal-orm/actions/workflows/liminal.yml)
+[![Downloads](https://static.pepy.tech/personalized-badge/liminal-orm?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads)](https://pepy.tech/project/liminal-orm)
+
+Liminal ORM<sup>1</sup> is an open-source Python package that builds on [Benchling's](https://www.benchling.com/) LIMS<sup>2</sup> platform and provides a simple, code-first approach for synchronizing and managing your Benchling schemas. Check out the [**full documentation here**](https://dynotx.github.io/liminal-orm/) and join our [**Slack community here**](https://join.slack.com/t/liminalorm/shared_invite/zt-2ujrp07s3-bctook4e~cAjn1LgOLVY~Q)!
 
 Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalchemy/sqlalchemy) along with a schema migration service inspired by [Alembic](https://alembic.sqlalchemy.org/en/latest/). This allows you to define your Benchling schemas in code and create a *single source of truth* that synchronizes between your upstream Benchling tenant(s) and downstream dependencies. By creating a standard interface and through using one-line CLI<sup>3</sup> commands, Liminal enables a code-first approach for managing Benchling tenants and accessing Benchling data. With the schemas defined in code, you can also take advantage of the additional capabilities that the Liminal toolkit provides. This includes:
 
@@ -11,10 +16,10 @@ Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalche
 - CI/CD integration with GitHub Actions to ensure that your Benchling schemas and code are always in sync.
 - And more based on community contributions/feedback :)
 
-Benchling is an industry standard cloud platform for life sciences R&D. Liminal builds on top of Benchling's platform and assumes that you already have a Benchling tenant set up and have (or have access to) an admin user account. If not, learn more about getting started with Benchling [here](https://www.benchling.com/explore-benchling)!
-
 If you are a Benchling user, try out Liminal by following the [**Quick Start Guide**](https://dynotx.github.io/liminal-orm/getting-started/prerequisites/)! Reach out in the [Discussions](https://github.com/dynotx/liminal-orm/discussions) forum with any questions or to simply introduce yourself! If there is something blocking you from using Liminal or you're having trouble setting Liminal up, please share in [Issues](https://github.com/dynotx/liminal-orm/issues) or reach out directly (contact information below). You can expect responses within 48 hours :)
 
+Benchling is an industry standard cloud platform for life sciences R&D. Liminal builds on top of Benchling's platform and assumes that you already have a Benchling tenant set up and have (or have access to) an admin user account. If not, learn more about getting started with Benchling [here](https://www.benchling.com/explore-benchling)!
+
 Nirmit Damania is the creator and current maintainer of Liminal (I post Liminal updates to [Discussions](https://github.com/dynotx/liminal-orm/discussions) and my [LinkedIn](https://www.linkedin.com/in/nirmit-damania/)). Most importantly, **you** have the ability to influence the future of Liminal! Any feedback, positive or negative, is highly encouraged and will be used to steer the direction of Liminal. Refer to the [Contributing guide](https://github.com/dynotx/liminal-orm/blob/main/CONTRIBUTING.md) to learn more about how you can contribute to Liminal.
 
 ⭐️ Leave a star on the repo to spread the word!

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/liminal/base/properties/base_schema_properties.py

@@ -97,3 +97,12 @@ class BaseSchemaProperties(BaseModel):
         if not isinstance(other, BaseSchemaProperties):
             return False
         return self.model_dump() == other.model_dump()
+
+    def __str__(self) -> str:
+        return ", ".join(
+            [f"{k}={v}" for k, v in self.model_dump(exclude_unset=True).items()]
+        )
+
+    def __repr__(self) -> str:
+        """Generates a string representation of the class so that it can be executed."""
+        return f"{self.__class__.__name__}({', '.join([f'{k}={v.__repr__()}' for k, v in self.model_dump(exclude_defaults=True).items()])})"

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/liminal/cli/cli.py

@@ -79,7 +79,10 @@ def generate_files(
         ..., help="Benchling tenant (or alias) to connect to."
     ),
     write_path: Path = typer.Option(
-        Path("."), help="The path to write the generated files to."
+        Path("."),
+        "-p",
+        "--write-path",
+        help="The path to write the generated files to.",
     ),
 ) -> None:
     current_revision_id, benchling_connection = read_local_env_file(

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/liminal/connection/benchling_service.py

@@ -9,7 +9,12 @@ from bs4 import BeautifulSoup
 from sqlalchemy import create_engine
 from sqlalchemy.engine import Engine
 from sqlalchemy.orm import Session, configure_mappers
-from tenacity import retry, retry_if_exception_type, stop_after_attempt
+from tenacity import (
+    retry,
+    retry_if_exception_type,
+    stop_after_attempt,
+    wait_exponential,
+)
 
 from liminal.connection.benchling_connection import BenchlingConnection
 
@@ -144,6 +149,7 @@ class BenchlingService(Benchling):
     @retry(
         stop=stop_after_attempt(3),
         retry=retry_if_exception_type(ValueError),
+        wait=wait_exponential(multiplier=1, min=1, max=8),
         reraise=True,
     )
     def autogenerate_auth(

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/liminal/entity_schemas/generate_files.py

@@ -106,14 +106,14 @@ def generate_all_entity_schema_files(
             ):
                 if not col.is_multi:
                     relationship_strings.append(
-                        f"""{tab}single_relationship("{wh_name_to_classname[col.entity_link]}", {col_name})"""
+                        f"""{tab}{col_name}_entity = single_relationship("{wh_name_to_classname[col.entity_link]}", {col_name})"""
                     )
                     import_strings.append(
                         "from liminal.orm.relationship import single_relationship"
                     )
                 else:
                     relationship_strings.append(
-                        f"""{tab}multi_relationship("{wh_name_to_classname[col.entity_link]}", "{classname}", "{col_name}")"""
+                        f"""{tab}{col_name}_entities = multi_relationship("{wh_name_to_classname[col.entity_link]}", "{classname}", "{col_name}")"""
                     )
                     import_strings.append(
                         "from liminal.orm.relationship import multi_relationship"

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/liminal/entity_schemas/operations.py

@@ -195,10 +195,10 @@ class UpdateEntitySchema(BaseOperation):
         return update_tag_schema(benchling_service, tag_schema.id, update.model_dump())
 
     def describe_operation(self) -> str:
-        return f"Updating properties for entity schema {self.wh_schema_name}: {repr(self.update_props)}."
+        return f"Updating properties for entity schema {self.wh_schema_name}: {str(self.update_props)}."
 
     def describe(self) -> str:
-        return f"Schema properties for {self.wh_schema_name} are different in code versus Benchling: {repr(self.update_props)}."
+        return f"Schema properties for {self.wh_schema_name} are different in code versus Benchling: {str(self.update_props)}."
 
     def _validate(self, benchling_service: BenchlingService) -> TagSchemaModel:
         all_schemas = TagSchemaModel.get_all_json(benchling_service)
@@ -485,11 +485,7 @@ class UpdateEntitySchemaField(BaseOperation):
         # Only if changing name of field
         if self.update_props.name:
             existing_new_field = next(
-                (
-                    f
-                    for f in tag_schema.allFields
-                    if f.systemName == self.update_props.name
-                ),
+                (f for f in tag_schema.allFields if f.name == self.update_props.name),
                 None,
             )
             if existing_new_field:

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/liminal/entity_schemas/tag_schema_models.py

@@ -59,6 +59,7 @@ class CreateTagSchemaFieldModel(BaseModel):
     systemName: str
     name: str
     requiredLink: FieldRequiredLinkShortModel | None = None
+    tooltipText: str | None = None
 
     @classmethod
     def from_props(
@@ -121,6 +122,7 @@ class CreateTagSchemaFieldModel(BaseModel):
                 folderItemType=folder_item_type,
                 tagSchema=tagSchema,
             ),
+            tooltipText=new_props.tooltip,
         )
 
 

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/liminal/orm/column.py

@@ -82,7 +82,7 @@ class Column(SqlColumn):
         super().__init__(
             self.sqlalchemy_type,
             foreign_key,
-            nullable=not properties.required,
+            nullable=not required,
             info={"benchling_properties": properties},
             **kwargs,
         )
@@ -107,3 +107,7 @@ class Column(SqlColumn):
                 f"Could not set benchling properties for column {column.name}. Please check that the column has a valid benchling properties set."
             )
         return Column(**properties.model_dump())
+
+    def _constructor(self, *args: Any, **kwargs: Any) -> SqlColumn:
+        """Returns a new instance of the SqlAlchemy Column class."""
+        return SqlColumn(*args, **kwargs)

{liminal_orm-1.0.5 → liminal_orm-1.0.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "liminal-orm"
-version = "1.0.5"
+version = "1.0.6"
 description = "An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync."
 authors = ["DynoTx Open Source <opensource@dynotx.com>"]
 readme = "README.md"
@@ -24,6 +24,7 @@ sqlalchemy = "<2" # TODO: We need to assess this upgrade
 tenacity = ">=8,<10"
 typer = "^0.12.5"
 lxml = "^5.3.0"
+psycopg2-binary = "^2.9.10"
 
 [tool.poetry.group.dev.dependencies]
 ipykernel = "^6.29.5"