332 remove bmds 2.7 (#6)

* bmds3 collapse changes

* dueling formatters

* fixup gitlab actions?

---------

Co-authored-by: Andy Shapiro <[email protected]>

.github/workflows/main.yml

@@ -21,12 +21,12 @@ jobs:
     steps:
     - name: Checkout bmds-server
       uses: actions/checkout@v3
-    - name: Checkout bmds@next
+    - name: Checkout bmds@main
       uses: actions/checkout@v3
       with:
         repository: USEPA/bmds-private
         path: venv
-        ref: next
+        ref: main
         token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
@@ -55,8 +55,7 @@ jobs:
         export "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/lib"
         sudo cp vendor/libnlopt.so /usr/local/lib/libnlopt.so.0
         sudo ln -s /lib/x86_64-linux-gnu/libgsl.so /usr/local/lib/libgsl.so.25
-        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bin/BMDS330/libDRBMD.so"
-        echo $BMD_DLL
+        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so"
         ldd $BMD_DLL
     - name: lint
       run: |
@@ -141,12 +140,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Checkout bmds@next
+    - name: Checkout bmds@main
       uses: actions/checkout@v3
       with:
         repository: USEPA/bmds-private
         path: venv
-        ref: next
+        ref: main
         token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
@@ -176,8 +175,7 @@ jobs:
         export "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/lib"
         sudo cp vendor/libnlopt.so /usr/local/lib/libnlopt.so.0
         sudo ln -s /lib/x86_64-linux-gnu/libgsl.so /usr/local/lib/libgsl.so.25
-        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bin/BMDS330/libDRBMD.so"
-        echo $BMD_DLL
+        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so"
         ldd $BMD_DLL
     # https://github.community/t/how-to-retry-a-failed-step-in-github-actions-workflow/125880
     - name: run integration tests

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
 

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/Dockerfile

@@ -42,5 +42,5 @@ USER app
 
 ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
-RUN ldd /usr/local/lib/python3.11/site-packages/bmds/bmdscore.cpython-311-x86_64-linux-gnu.so && \
+RUN ldd /usr/local/lib/python3.11/site-packages/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so && \
     python /app/test.py

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