liminal-orm 4.7.0a1__tar.gz → 5.1.0__tar.gz

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/.gitignore

@@ -19,4 +19,5 @@ site/
 # for local testing
 test_liminal/
 
-.history
+.history/
+.cursor/

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: liminal-orm
-Version: 4.7.0a1
+Version: 5.1.0
 Summary: An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync.
 Project-URL: Homepage, https://github.com/dynotx/liminal-orm
 Project-URL: Repository, https://github.com/dynotx/liminal-orm
@@ -15,9 +15,7 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Python: <3.14,>=3.10
 Requires-Dist: benchling-sdk<2,>=1.21.2
-Requires-Dist: bs4<0.0.3,>=0.0.2
 Requires-Dist: click<8.2.0,>=8.0.0
-Requires-Dist: lxml<6,>=5.3.0
 Requires-Dist: numpy<2,>=1.23.5; python_version < '3.12'
 Requires-Dist: numpy<2,>=1.26; python_version == '3.12'
 Requires-Dist: numpy<3,>=2.1; python_version == '3.13'
@@ -25,14 +23,11 @@ Requires-Dist: pandas<3,>=1.5.3; python_version == '3.10'
 Requires-Dist: pandas<4,>=1.5.3; python_version == '3.11'
 Requires-Dist: pandas<4,>=2.2.3; python_version == '3.13'
 Requires-Dist: pandas<4,>=2.2; python_version == '3.12'
-Requires-Dist: playwright>=1.58.0
 Requires-Dist: psycopg2-binary<3,>=2.9.10
 Requires-Dist: pydantic<=2.13,>=2
-Requires-Dist: requests<3,>=2.32.3
 Requires-Dist: rich<14,>=13.9.2
 Requires-Dist: sqlalchemy<2,>=1.4.53
 Requires-Dist: tenacity<10,>=8
-Requires-Dist: tornado==6.5.0
 Requires-Dist: typer<0.13,>=0.12.5
 Description-Content-Type: text/markdown
 

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/base/base_operation.py

@@ -9,20 +9,21 @@ Order of operations based on order class var:
     2. UpdateDropdownName
     3. UnarchiveDropdown
     4. CreateDropdownOption
-    5. UpdateDropdownOption
-    6. ArchiveDropdownOption
-    7. ReorderDropdownOptions
-    8. CreateSchema
-    9. UnarchiveSchema
-    10. CreateField
-    11. UpdateEntitySchemaNameTemplate
-    12. UpdateSchema
-    13. UnarchiveField
-    14. UpdateField
-    15. ArchiveField
-    16. ReorderFields
-    17. ArchiveSchema
-    18. ArchiveDropdown
+    5. UnarchiveDropdownOption
+    6. UpdateDropdownOption
+    7. ArchiveDropdownOption
+    8. ReorderDropdownOptions
+    9. CreateEntitySchema
+    10. UnarchiveEntitySchema
+    11. CreateEntitySchemaField
+    12. UpdateEntitySchemaNameTemplate
+    13. UpdateEntitySchema
+    14. UnarchiveEntitySchemaField
+    15. UpdateEntitySchemaField
+    16. ArchiveEntitySchemaField
+    17. ReorderEntitySchemaFields
+    18. ArchiveEntitySchema
+    19. ArchiveDropdown
 """
 
 

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/base/name_template_parts.py

@@ -3,6 +3,6 @@ import warnings
 from liminal.orm.name_template_parts import *  # noqa: F403
 
 warnings.warn(
-    "Importing from 'liminal.base.name_template_parts' is deprecated. Please import from 'liminal.orm.name_template_parts' instead. This will be removed in v5.",
+    "Importing from 'liminal.base.name_template_parts' is deprecated. Please import from 'liminal.orm.name_template_parts' instead. This will be removed in v6.",
     FutureWarning,
 )

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/base/properties/base_field_properties.py

@@ -56,6 +56,23 @@ class BaseFieldProperties(BaseModel):
         super().__init__(**data)
         self._archived = data.get("_archived", None)
 
+    @staticmethod
+    def unsupported_field_properties(
+        field_type: BenchlingFieldType, has_entity_link: bool
+    ) -> set[str]:
+        """Returns the properties that Benchling does not support for the given field type."""
+        unsupported: set[str] = set()
+        non_multi_types = BenchlingFieldType.get_non_multi_select_types()
+        if field_type in non_multi_types:
+            unsupported.add("is_multi")
+        if not (has_entity_link and field_type == BenchlingFieldType.ENTITY_LINK):
+            unsupported.add("parent_link")
+        if field_type not in BenchlingFieldType.get_number_field_types():
+            unsupported.add("unit_name")
+        if field_type != BenchlingFieldType.DECIMAL:
+            unsupported.add("decimal_places")
+        return unsupported
+
     def set_archived(self, value: bool) -> BaseFieldProperties:
         self._archived = value
         return self

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/cli/cli.py

@@ -1,12 +1,16 @@
 #!/usr/bin/env python
+import json
 from pathlib import Path
+import sys
 from typing import Any
+
 import typer
 from rich import print
 from typer.core import TyperGroup
 
 from liminal.cli.controller import (
     autogenerate_revision_file,
+    diff_benchling_tenant,
     downgrade_benchling_tenant,
     generate_all_files,
     upgrade_benchling_tenant,
@@ -67,8 +71,6 @@ connection = BenchlingConnection(
     api_client_id="my-secret-api-client-id",
     api_client_secret="my-secret-api-client-secret",
     warehouse_connection_string="...",
-    internal_api_admin_email="my-secret-internal-api-admin-email",
-    internal_api_admin_password="my-secret-internal-api-admin-password",
     config_flags=TenantConfigFlags(...)
 )
 """
@@ -119,7 +121,7 @@ def generate_files(
     ),
 ) -> None:
     benchling_connection = read_local_liminal_dir(LIMINAL_DIR_PATH, benchling_tenant)
-    benchling_service = BenchlingService(benchling_connection, use_internal_api=True)
+    benchling_service = BenchlingService(benchling_connection)
     if not write_path.exists():
         write_path.mkdir()
         print(f"[green]Created directory: {write_path}")
@@ -147,20 +149,101 @@ def current(
     ),
 ) -> None:
     benchling_connection = read_local_liminal_dir(LIMINAL_DIR_PATH, benchling_tenant)
-    benchling_service = BenchlingService(benchling_connection, use_internal_api=True)
+    benchling_service = BenchlingService(benchling_connection)
     remote_revision_id = benchling_service.get_remote_revision_id()
     print(f"[blue]Current remote revision_id: {remote_revision_id}.")
 
 
 @app.command(
     name="head",
-    help="Returns the local heads, or the latest revision_id, in your linear revision timeline.",
+    help="Returns the local heads, or the latest revision_id, in your linear revision timeline. Pass --reset to delete the local head revision file.",
 )
-def head() -> None:
+def head(
+    reset: bool = typer.Option(
+        False,
+        "-r",
+        "--reset",
+        help="Deletes the local head revision file, making its down_revision the new head. Only use this for revisions that have not been applied to any tenant.",
+    ),
+) -> None:
     revision_timeline = RevisionsTimeline(VERSIONS_DIR_PATH)
+    if reset:
+        latest_revision = revision_timeline.get_latest_revision()
+        file_path = VERSIONS_DIR_PATH / latest_revision.revision_file_name
+        print(
+            f"[bold yellow]Delete local head revision file {latest_revision.id} ({file_path})?[/bold yellow]"
+        )
+        typer.confirm("Confirm", abort=True)
+        revision_timeline.delete_latest_revision()
+        print(f"[dim]Deleted revision file {file_path}.")
     print(f"[blue]{revision_timeline.get_latest_revision().id}: (head)[/blue]")
 
 
+@app.command(
+    name="diff",
+    help="Compares the locally defined dropdowns and entity schemas to the given Benchling tenant. Exit codes: 0=in sync, 1=error, 2=differences found.",
+)
+def diff(
+    benchling_tenant: str = typer.Argument(
+        ..., help="Benchling tenant (or alias) to connect to."
+    ),
+    dropdowns_flag: bool = typer.Option(
+        False,
+        "-d",
+        "--dropdowns",
+        help="Only compare dropdowns.",
+    ),
+    entity_schemas_flag: bool = typer.Option(
+        False,
+        "-es",
+        "--entity-schemas",
+        help="Only compare entity schemas.",
+    ),
+    json_output: bool = typer.Option(
+        False,
+        "--json",
+        help="Write a machine-readable comparison report to stdout.",
+    ),
+) -> None:
+    benchling_connection = read_local_liminal_dir(LIMINAL_DIR_PATH, benchling_tenant)
+    benchling_service = BenchlingService(benchling_connection)
+    if not dropdowns_flag and not entity_schemas_flag:
+        dropdowns_flag = True
+        entity_schemas_flag = True
+    report = diff_benchling_tenant(
+        benchling_service, dropdowns_flag, entity_schemas_flag
+    )
+    if json_output:
+        typer.echo(json.dumps(report, sort_keys=True))
+    else:
+        for key, label in (
+            ("dropdowns", "Dropdowns"),
+            ("entity_schemas", "Entity schemas"),
+        ):
+            section = report[key]
+            if not section["compared"]:
+                continue
+            if section["in_sync"]:
+                print(f"[bold green]{label} are in sync for {report['tenant']} tenant.")
+                continue
+            print(
+                f"[bold yellow]{label}: {len(section['differences'])} difference(s) for {report['tenant']} tenant."
+            )
+            for index, difference in enumerate(section["differences"], start=1):
+                print(f"  {index}. {difference['description']}")
+
+        if report["in_sync"]:
+            print(
+                f"[bold green]No differences found. {report['tenant']} is in sync with code."
+            )
+        else:
+            print(
+                f"[bold yellow]{report['total_differences']} total difference(s) found between code and {report['tenant']}. Run `liminal revision {report['tenant']} '<description>'` to generate a revision file that resolves them."
+            )
+    if not report["in_sync"]:
+        raise typer.Exit(code=2)
+
+
 @app.command(
     name="revision",
     help="Generates a revision file with a list of operations to bring the given Benchling tenant up to date with the locally defined schemas. Writes revision file to liminal/versions/.",
@@ -180,7 +263,7 @@ def revision(
     ),
 ) -> None:
     benchling_connection = read_local_liminal_dir(LIMINAL_DIR_PATH, benchling_tenant)
-    benchling_service = BenchlingService(benchling_connection, use_internal_api=True)
+    benchling_service = BenchlingService(benchling_connection)
     revisions_timeline = RevisionsTimeline(VERSIONS_DIR_PATH)
     is_init_revision = revisions_timeline.is_only_init_revision()
     if is_init_revision:
@@ -214,7 +297,7 @@ def autogenerate(
     ),
 ) -> None:
     raise DeprecationWarning(
-        "CLI command `liminal autogenerate ...` is deprecated and will be removed in v5. Please use `liminal revision ...` instead."
+        "CLI command `liminal autogenerate ...` is deprecated and will be removed in v6. Please use `liminal revision ...` instead."
     )
 
 
@@ -233,7 +316,7 @@ def upgrade(
     ),
 ) -> None:
     benchling_connection = read_local_liminal_dir(LIMINAL_DIR_PATH, benchling_tenant)
-    benchling_service = BenchlingService(benchling_connection, use_internal_api=True)
+    benchling_service = BenchlingService(benchling_connection)
     current_revision_id = benchling_service.get_remote_revision_id()
     revisions_timeline = RevisionsTimeline(VERSIONS_DIR_PATH)
     upgrade_revision_id = upgrade_benchling_tenant(
@@ -261,7 +344,7 @@ def downgrade(
     ),
 ) -> None:
     benchling_connection = read_local_liminal_dir(LIMINAL_DIR_PATH, benchling_tenant)
-    benchling_service = BenchlingService(benchling_connection, use_internal_api=True)
+    benchling_service = BenchlingService(benchling_connection)
     current_revision_id = benchling_service.get_remote_revision_id()
     revisions_timeline = RevisionsTimeline(VERSIONS_DIR_PATH)
     downgrade_revision_id = downgrade_benchling_tenant(
@@ -301,7 +384,7 @@ def live_test(
             "Only one of --entity-schema-migration or --dropdown-migration can be set."
         )
     benchling_connection = read_local_liminal_dir(LIMINAL_DIR_PATH, benchling_tenant)
-    benchling_service = BenchlingService(benchling_connection, use_internal_api=True)
+    benchling_service = BenchlingService(benchling_connection)
     if test_entity_schema_migration:
         mock_entity_schema_full_migration(
             benchling_service, "test_dont_touch", dry_run=not execute
@@ -312,5 +395,5 @@ def live_test(
         )
 
 
-print("Starting Liminal CLI...")
+print("Starting Liminal CLI...", file=sys.stderr)
 app()

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/cli/controller.py

@@ -1,9 +1,13 @@
 from pathlib import Path
+from typing import Any
 
 from rich import print
 
+from liminal.base.compare_operation import CompareOperation
 from liminal.connection.benchling_service import BenchlingService
+from liminal.dropdowns.compare import compare_dropdowns
 from liminal.dropdowns.generate_files import generate_all_dropdown_files
+from liminal.entity_schemas.compare import compare_entity_schemas
 from liminal.entity_schemas.generate_files import generate_all_entity_schema_files
 from liminal.migrate.components import execute_operations, get_full_migration_operations
 from liminal.migrate.revisions_timeline import RevisionsTimeline
@@ -45,6 +49,68 @@ def generate_all_files(
         generate_all_results_schema_files(benchling_service, write_path, overwrite)
 
 
+def diff_benchling_tenant(
+    benchling_service: BenchlingService,
+    dropdowns_flag: bool = True,
+    entity_schemas_flag: bool = True,
+) -> dict[str, Any]:
+    """Compares locally defined schemas to a Benchling tenant.
+
+    This is read-only and does not make any changes to the Benchling tenant or
+    write any files.
+
+    Parameters
+    ----------
+    benchling_service : BenchlingService
+        The Benchling service object that is connected to a specified Benchling tenant.
+    dropdowns_flag : bool
+        Whether to compare dropdowns.
+    entity_schemas_flag : bool
+        Whether to compare entity schemas.
+
+    Returns
+    -------
+    dict[str, Any]
+        A machine-readable report of the comparison.
+    """
+    tenant = benchling_service.benchling_tenant
+    sections: dict[str, dict[str, list[CompareOperation]] | None] = {
+        "dropdowns": None,
+        "entity_schemas": None,
+    }
+    if dropdowns_flag:
+        sections["dropdowns"] = compare_dropdowns(benchling_service)
+    if entity_schemas_flag:
+        sections["entity_schemas"] = compare_entity_schemas(benchling_service)
+
+    report: dict[str, Any] = {"tenant": tenant, "total_differences": 0}
+    for section_name, comparison in sections.items():
+        compared = comparison is not None
+        differences = [
+            {
+                "name": name,
+                "operation": compare_op.op.__class__.__name__,
+                "description": compare_op.op.describe(),
+            }
+            for name, compare_op in sorted(
+                (
+                    (name, compare_op)
+                    for name, compare_ops in (comparison or {}).items()
+                    for compare_op in compare_ops
+                ),
+                key=lambda difference: difference[1],
+            )
+        ]
+        report[section_name] = {
+            "compared": compared,
+            "in_sync": len(differences) == 0 if compared else None,
+            "differences": differences,
+        }
+        report["total_differences"] += len(differences)
+    report["in_sync"] = report["total_differences"] == 0
+    return report
+
+
 def autogenerate_revision_file(
     benchling_service: BenchlingService,
     revisions_timeline: RevisionsTimeline,
@@ -76,7 +142,7 @@ def autogenerate_revision_file(
         )
     if current_revision_id != revisions_timeline.get_latest_revision().id:
         raise Exception(
-            f"Your target Benchling tenant is currently at revision_id {current_revision_id}, which is not up to date with the local head revision ({revisions_timeline.get_latest_revision().id}). Please upgrade your tenant to the latest revision before generating a new revision."
+            f"Your target Benchling tenant is currently at revision_id {current_revision_id}, which is not up to date with the local head revision ({revisions_timeline.get_latest_revision().id}). Please upgrade your tenant to the latest revision before generating a new revision. If the local head revision should not be applied, run `liminal head --reset` to delete it."
         )
     if compare:
         compare_ops = get_full_migration_operations(benchling_service)

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/cli/live_test_entity_schema_migration.py

@@ -1,5 +1,6 @@
 from liminal.base.base_operation import BaseOperation
 from liminal.base.properties.base_field_properties import BaseFieldProperties
+from liminal.base.properties.base_name_template import BaseNameTemplate
 from liminal.base.properties.base_schema_properties import BaseSchemaProperties
 from liminal.connection.benchling_service import BenchlingService
 from liminal.entity_schemas.operations import (
@@ -12,6 +13,7 @@ from liminal.entity_schemas.operations import (
     UnarchiveEntitySchemaField,
     UpdateEntitySchema,
     UpdateEntitySchemaField,
+    UpdateEntitySchemaNameTemplate,
 )
 from liminal.enums import (
     BenchlingEntityType,
@@ -19,6 +21,7 @@ from liminal.enums import (
     BenchlingNamingStrategy,
 )
 from liminal.migrate.components import execute_operations, execute_operations_dry_run
+from liminal.orm.name_template_parts import FieldPart, SeparatorPart, TextPart
 from liminal.orm.schema_properties import SchemaProperties
 from liminal.utils import generate_random_id
 
@@ -122,6 +125,18 @@ def mock_entity_schema_full_migration(
         ["test_column_1", "test_column_2", "test_column_3", "test_column_4"],
     )
 
+    update_name_template_op = UpdateEntitySchemaNameTemplate(
+        test_model_wh_name,
+        BaseNameTemplate(
+            parts=[
+                TextPart(value="TEST"),
+                SeparatorPart(value="-"),
+                FieldPart(wh_field_name="test_column_1"),
+            ],
+            order_name_parts_by_sequence=False,
+        ),
+    )
+
     archive_entity_schema_op = ArchiveEntitySchema(test_model_wh_name)
     unarchive_entity_schema_op = UnarchiveEntitySchema(test_model_wh_name)
     rearchive_entity_schema_op = ArchiveEntitySchema(test_model_wh_name)
@@ -134,6 +149,7 @@ def mock_entity_schema_full_migration(
         archive_entity_schema_field_op,
         unarchive_entity_schema_field_op,
         reorder_entity_schema_field_op,
+        update_name_template_op,
         archive_entity_schema_op,
         unarchive_entity_schema_op,
         rearchive_entity_schema_op,

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/cli/utils.py

@@ -25,7 +25,7 @@ def read_local_liminal_dir(
     liminal_dir_path: Path, benchling_tenant: str
 ) -> BenchlingConnection:
     """Imports the env.py file from /liminal/env.py and returns the BenchlingConnection object.
-    The BenchlingConnection object is expected to be defined and have connection information for the Benchling API client and internal API.
+    The BenchlingConnection object is expected to be defined and have connection information for the Benchling API client.
     """
     _check_liminal_directory_initialized(liminal_dir_path)
     env_file_path = liminal_dir_path / "env.py"
@@ -36,7 +36,7 @@ def _read_local_env_file(
     env_file_path: Path, benchling_tenant: str
 ) -> BenchlingConnection:
     """Imports the env.py file from the current working directory and returns the BenchlingConnection object.
-    The BenchlingConnection object is expected to be defined and have connection information for the Benchling API client and internal API.
+    The BenchlingConnection object is expected to be defined and have connection information for the Benchling API client.
     """
     module_path = Path.cwd() / env_file_path
     spec = importlib.util.spec_from_file_location(env_file_path.stem, module_path)

{liminal_orm-4.7.0a1 → liminal_orm-5.1.0}/liminal/connection/benchling_connection.py

@@ -1,5 +1,6 @@
 import keyword
 import re
+import warnings
 
 from pydantic import BaseModel, model_validator
 
@@ -37,14 +38,11 @@ class BenchlingConnection(BaseModel):
     warehouse_connection_string: str | None = None
         The connection string for the warehouse.
     internal_api_admin_email: str | None = None
-        The email of the internal API admin. If SSO is not enabled or optional on your Benchling tenant, this email is used to log in to Benchling, and give Liminal the authenticated internal API session cookie.
+        DEPRECATED: Liminal no longer uses Benchling's internal API, so this is ignored. It will be removed in v6.
     internal_api_admin_password: str | None = None
-        The password of the internal API admin. If SSO is not enabled or optional on your Benchling tenant, this password is used to log in to Benchling, and give Liminal the authenticated internal API session cookie.
-    playwright_data_dir: str | None = "~/.liminal/chrome_data/"
-        The directory to store the playwright browser user data. If SSO is enabled and required on your Benchling tenant,
-        Liminal uses playwright so the user can log into Benchling in order to give Liminal the authenticated internal API session cookie.
-        This directory is used to store playwright's persistent context, allowing the user to set up a persistent chrome profile.
-        Set this to None in order to disable playwright's persistent context which enables automatic login.
+        DEPRECATED: Liminal no longer uses Benchling's internal API, so this is ignored. It will be removed in v6.
+    playwright_data_dir: str | None = None
+        DEPRECATED: Liminal no longer uses Playwright to log into Benchling's internal API, so this is ignored. It will be removed in v6.
     fieldsets: bool = False
         Whether your Benchling tenant has access to fieldsets.
     config_flags: TenantConfigFlags = TenantConfigFlags()
@@ -59,7 +57,7 @@ class BenchlingConnection(BaseModel):
     warehouse_connection_string: str | None = None
     internal_api_admin_email: str | None = None
     internal_api_admin_password: str | None = None
-    playwright_data_dir: str | None = "~/.liminal/playwright_chrome_data/"
+    playwright_data_dir: str | None = None
     fieldsets: bool = False
     config_flags: TenantConfigFlags = TenantConfigFlags()
 
@@ -81,3 +79,26 @@ class BenchlingConnection(BaseModel):
 
             values["current_revision_id_var_name"] = var_name
         return values
+
+    @model_validator(mode="after")
+    def warn_deprecated_internal_api_credentials(self) -> "BenchlingConnection":
+        if (
+            self.internal_api_admin_email is not None
+            or self.internal_api_admin_password is not None
+        ):
+            warnings.warn(
+                "Deprecated BenchlingConnection properties set: internal_api_admin_email and internal_api_admin_password. Liminal no longer uses Benchling's internal API, so they are ignored. Remove them from your BenchlingConnection, since they will be removed in v6.",
+                FutureWarning,
+                stacklevel=3,
+            )
+        return self
+
+    @model_validator(mode="after")
+    def warn_deprecated_playwright_data_dir(self) -> "BenchlingConnection":
+        if self.playwright_data_dir is not None:
+            warnings.warn(
+                "Deprecated BenchlingConnection property set: playwright_data_dir. Liminal no longer uses Playwright to log into Benchling, so it is ignored. Remove it from your BenchlingConnection, since it will be removed in v6.",
+                FutureWarning,
+                stacklevel=3,
+            )
+        return self