bmds3 collapse changes

bmds_server/analysis/executor.py

@@ -3,11 +3,10 @@
 from typing import NamedTuple, Self
 
 import bmds
-from bmds.bmds3.constants import DistType
-from bmds.bmds3.models.multi_tumor import Multitumor, MultitumorBase
-from bmds.bmds3.sessions import BmdsSession
-from bmds.bmds3.types.nested_dichotomous import IntralitterCorrelation, LitterSpecificCovariate
-from bmds.constants import ModelClass
+from bmds.constants import DistType, ModelClass
+from bmds.models.multi_tumor import Multitumor, MultitumorBase
+from bmds.sessions import BmdsSession
+from bmds.types.nested_dichotomous import IntralitterCorrelation, LitterSpecificCovariate
 
 from .schema import AnalysisSessionSchema
 from .transforms import (

bmds_server/analysis/models.py

@@ -8,10 +8,10 @@
 import bmds
 import pandas as pd
 import reversion
-from bmds.bmds3.batch import BatchBase, BmdsSessionBatch, MultitumorBatch
-from bmds.bmds3.recommender.recommender import RecommenderSettings
-from bmds.bmds3.types.sessions import VersionSchema
+from bmds.batch import BatchBase, BmdsSessionBatch, MultitumorBatch
 from bmds.constants import ModelClass
+from bmds.recommender.recommender import RecommenderSettings
+from bmds.types.sessions import VersionSchema
 from django.conf import settings
 from django.core.cache import cache
 from django.core.exceptions import ValidationError

bmds_server/analysis/reporting/docx.py

@@ -5,9 +5,8 @@
 
 import docx
 from bmds import __version__
-from bmds.bmds3.reporting import write_setting_p
 from bmds.datasets.transforms.polyk import PolyKAdjustment
-from bmds.reporting.styling import Report
+from bmds.reporting.styling import Report, write_setting_p
 from django.conf import settings
 from django.utils.timezone import now
 
@@ -58,14 +57,20 @@ def build_docx(
 
     bmds_version = analysis.get_bmds_version()
     if bmds_version:
-        write_setting_p(report, "BMDS version: ", f"{bmds_version.pretty} ({bmds_version.dll})")
+        write_setting_p(
+            report, "BMDS version: ", f"{bmds_version.pretty} ({bmds_version.dll})"
+        )
 
     write_setting_p(report, "BMDS Online version: ", str(settings.COMMIT))
 
     if not analysis.is_finished:
-        report.document.add_paragraph("Execution is incomplete; no report could be generated")
+        report.document.add_paragraph(
+            "Execution is incomplete; no report could be generated"
+        )
     elif analysis.has_errors:
-        report.document.add_paragraph("Execution generated errors; no report can be generated")
+        report.document.add_paragraph(
+            "Execution generated errors; no report can be generated"
+        )
     else:
         batch = analysis.to_batch()
         batch.to_docx(

bmds_server/analysis/reporting/excel.py

@@ -3,8 +3,8 @@
 from typing import Any
 
 import pandas as pd
-from bmds.bmds3.sessions import BmdsSession
 from bmds.constants import Dtype
+from bmds.sessions import BmdsSession
 
 from ..executor import AnalysisSession, MultiTumorSession
 

bmds_server/analysis/schema.py

@@ -2,8 +2,8 @@
 from io import StringIO
 
 import pandas as pd
-from bmds.bmds3.types.sessions import VersionSchema
 from bmds.datasets.transforms.polyk import PolyKAdjustment
+from bmds.types.sessions import VersionSchema
 from pydantic import BaseModel, Field, field_validator
 from rest_framework.schemas.openapi import SchemaGenerator
 

bmds_server/analysis/transforms.py

@@ -2,11 +2,11 @@
 from enum import StrEnum
 
 import bmds
-from bmds.bmds3.types.continuous import ContinuousModelSettings
-from bmds.bmds3.types.dichotomous import DichotomousModelSettings
-from bmds.bmds3.types.nested_dichotomous import NestedDichotomousModelSettings
-from bmds.bmds3.types.priors import PriorClass
 from bmds.constants import Dtype
+from bmds.types.continuous import ContinuousModelSettings
+from bmds.types.dichotomous import DichotomousModelSettings
+from bmds.types.nested_dichotomous import NestedDichotomousModelSettings
+from bmds.types.priors import PriorClass
 
 from .validators.datasets import AdverseDirection
 

bmds_server/analysis/validators/__init__.py

@@ -1,4 +1,4 @@
-from bmds.bmds3.recommender import RecommenderSettings
+from bmds.recommender import RecommenderSettings
 
 from ...common.validation import pydantic_validate
 from .datasets import validate_datasets

bmds_server/analysis/validators/options.py

@@ -1,10 +1,10 @@
 from typing import Any
 
 import bmds
-from bmds.bmds3.constants import DistType
-from bmds.bmds3.types.continuous import ContinuousRiskType
-from bmds.bmds3.types.dichotomous import DichotomousRiskType
-from bmds.bmds3.types.nested_dichotomous import LitterSpecificCovariate
+from bmds.constants import DistType
+from bmds.types.continuous import ContinuousRiskType
+from bmds.types.dichotomous import DichotomousRiskType
+from bmds.types.nested_dichotomous import LitterSpecificCovariate
 from django.conf import settings
 from django.core.exceptions import ValidationError
 from pydantic import BaseModel, Field

bmds_server/analysis/validators/selectors.py

@@ -1,4 +1,4 @@
-from bmds.bmds3.selected import SelectedModelSchema
+from bmds.selected import SelectedModelSchema
 from pydantic import BaseModel
 
 

compose/app/test.py

@@ -1,5 +1,5 @@
 import bmds
-from bmds.bmds3.models.dichotomous import Logistic
+from bmds.models.dichotomous import Logistic
 
 dataset = bmds.DichotomousDataset(
     doses=[0, 50, 100, 150, 200], ns=[100, 100, 100, 100, 100], incidences=[0, 5, 30, 65, 90]

tests/analysis/test_api.py

@@ -4,7 +4,7 @@
 import docx
 import pandas as pd
 import pytest
-from bmds.bmds3.recommender import RecommenderSettings
+from bmds.recommender import RecommenderSettings
 from django.urls import reverse
 from rest_framework.test import APIClient
 

tests/analysis/test_executor.py

@@ -1,7 +1,7 @@
 from copy import deepcopy
 
-from bmds.bmds3.constants import ContinuousModelIds, DichotomousModelIds
-from bmds.bmds3.types.priors import PriorClass
+from bmds.constants import ContinuousModelIds, DichotomousModelIds
+from bmds.types.priors import PriorClass
 
 from bmds_server.analysis.executor import AnalysisSession
 

tests/analysis/test_transforms.py

@@ -1,8 +1,8 @@
 import bmds
 import pytest
-from bmds.bmds3.types.continuous import ContinuousRiskType
-from bmds.bmds3.types.dichotomous import DichotomousRiskType
 from bmds.constants import M_Exponential, M_ExponentialM3, M_ExponentialM5
+from bmds.types.continuous import ContinuousRiskType
+from bmds.types.dichotomous import DichotomousRiskType
 
 from bmds_server.analysis import transforms
 

tests/conftest.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 import pytest
-from bmds.bmds3.recommender import RecommenderSettings
+from bmds.recommender import RecommenderSettings
 from django.core.management import call_command
 
 
@@ -38,7 +38,9 @@ def vcr_config():
 
 @pytest.fixture(scope="module")
 def vcr_cassette_dir(request):
-    cassette_dir = Path(__file__).parent.absolute() / "cassettes" / request.module.__name__
+    cassette_dir = (
+        Path(__file__).parent.absolute() / "cassettes" / request.module.__name__
+    )
     return str(cassette_dir)