Merge pull request #204 from nismod/fix/python-deps

Fix/python deps

backend/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10
+FROM python:3.12
 
 WORKDIR /code
 

backend/Pipfile

@@ -4,25 +4,25 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-fastapi = "*"
-geoalchemy2 = "*"
-uvicorn = "*"
-fastapi-pagination = "*"
+backend = { editable = true, path = "." }
+fastapi = "~=0.115"
+fastapi-pagination = "~=0.12"
+geoalchemy2 = "~=0.16"
 setuptools = "*"
-backend = {editable = true, path = "."}
-psycopg2-binary = "*"
+uvicorn = "~=0.32"
+psycopg2-binary = "~=2.9"
+pydantic = "~=2.9"
 
 [dev-packages]
 black = "*"
 geopandas = "*"
 pandas = "*"
 pyarrow = "*"
-pygeos = "*"
 shapely = "*"
 snakefmt = "*"
 snakemake = "*"
 tqdm = "*"
 ujson = "*"
 
 [requires]
-python_version = "3.10"
+python_version = "3.12"

backend/backend/app/internal/attribute_access.py

@@ -55,7 +55,7 @@ def add_adaptation_value_query(
         adaptation_protection_level=dimensions.adaptation_protection_level,
     )
 
-    value: Column | ColumnOperators = None
+    value: Column | ColumnOperators | None = None
 
     if field == "cost_benefit_ratio":
         cost_benefit_params: schemas.AdaptationCostBenefitRatioParameters = field_params
@@ -78,7 +78,7 @@ class DataGroupConfig:
     add_value_query: Callable[
         [Query, schemas.DataDimensions, str, schemas.DataParameters | None], Query
     ]
-    field_parameters_schemas: dict[str, schemas.DataParameters] = None
+    field_parameters_schemas: dict[str, schemas.DataParameters] | None = None
 
 
 DATA_GROUP_CONFIGS: dict[str, DataGroupConfig] = {
@@ -136,7 +136,7 @@ def add_value_query(
     field_group: str,
     field_dimensions: schemas.DataDimensions,
     field: str,
-    field_params: schemas.DataParameters = None,
+    field_params: schemas.DataParameters | None = None,
 ):
     data_group_config = DATA_GROUP_CONFIGS.get(field_group)
 

backend/backend/app/routers/features.py

@@ -1,4 +1,7 @@
-from fastapi import APIRouter, Depends
+from typing import Optional
+
+import sqlalchemy.exc
+from fastapi import APIRouter, Depends, HTTPException
 from fastapi_pagination import Page, Params
 from fastapi_pagination.ext.sqlalchemy import paginate
 from sqlalchemy import desc
@@ -20,12 +23,18 @@
 
 @router.get("/{feature_id}", response_model=schemas.FeatureOut)
 def read_feature(feature_id: int, db: Session = Depends(get_db)):
-    feature = db.query(models.Feature).filter(models.Feature.id == feature_id).one()
+    try:
+        feature = db.query(models.Feature).filter(models.Feature.id == feature_id).one()
+    except sqlalchemy.exc.NoResultFound:
+        raise HTTPException(status_code=404, detail="Feature not found")
     return feature
 
 
 def get_layer_spec(
-    layer: str = None, sector: str = None, subsector: str = None, asset_type: str = None
+    layer: Optional[str] = None,
+    sector: Optional[str] = None,
+    subsector: Optional[str] = None,
+    asset_type: Optional[str] = None,
 ):
     return schemas.LayerSpec(
         layer_name=layer,

backend/backend/app/schemas.py

@@ -1,14 +1,14 @@
 from enum import Enum
-from typing import Any, Generic, Literal, TypeVar
-from pydantic import BaseModel, conint, validator
-from pydantic.generics import GenericModel
+from typing import Generic, Optional, TypeVar
+from typing_extensions import Annotated
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
 
 class FeatureBase(BaseModel):
     id: int
     string_id: str
     layer: str
-    sublayer: str | None
+    sublayer: Optional[str] = None
     properties: dict
 
 
@@ -34,7 +34,7 @@ class DataParameters(BaseModel):
 class ExpectedDamagesDimensions(DataDimensions):
     hazard: str
     rcp: str
-    epoch: str
+    epoch: str | int
     protection_standard: int
 
 
@@ -48,15 +48,14 @@ class ExpectedDamagesVariables(DataVariables):
 
 
 class ExpectedDamage(ExpectedDamagesDimensions, ExpectedDamagesVariables):
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 # Return Period Damages
 class ReturnPeriodDamagesDimensions(DataDimensions):
     hazard: str
     rcp: str
-    epoch: str
+    epoch: str | int
     rp: int
 
 
@@ -71,8 +70,7 @@ class ReturnPeriodDamagesVariables(DataVariables):
 
 
 class ReturnPeriodDamage(ReturnPeriodDamagesDimensions, ReturnPeriodDamagesVariables):
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 # NPV Damages
@@ -91,8 +89,7 @@ class NPVDamagesVariables(DataVariables):
 
 
 class NPVDamage(NPVDamagesDimensions, NPVDamagesVariables):
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 # Adaptation Options
@@ -117,10 +114,10 @@ class AdaptationVariables(DataVariables):
 
 
 class AdaptationCostBenefitRatioParameters(DataParameters):
-    eael_days: conint(ge=1, le=30)
+    eael_days: Annotated[int, Field(ge=1, le=30)]
 
-    @validator('eael_days')
-    def fix_eael_days(cls, eael_days) -> float:
+    @field_validator("eael_days")
+    def fix_eael_days(cls, eael_days: int) -> float:
         """
         The data for `AdaptationCostBenefit.avoided_eael_mean` is erroneous and
         should be modified in the meantime. This validator adds a fudge factor
@@ -132,14 +129,12 @@ def fix_eael_days(cls, eael_days) -> float:
 
 
 class Adaptation(AdaptationDimensions, AdaptationVariables):
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 # Features
 class FeatureOutBase(FeatureBase):
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 class FeatureOut(FeatureOutBase):
@@ -162,15 +157,14 @@ class LayerSpec(BaseModel):
 SortFieldT = TypeVar("SortFieldT")
 
 
-class FeatureListItemOut(GenericModel, Generic[SortFieldT]):
+class FeatureListItemOut(BaseModel, Generic[SortFieldT]):
     id: int
     string_id: str
     layer: str
     bbox_wkt: str
     value: SortFieldT
 
-    class Config:
-        orm_mode = True
+    model_config = ConfigDict(from_attributes=True)
 
 
 # Feature Attributes Lookups

backend/requirements.txt

@@ -2,27 +2,26 @@
 # These requirements were autogenerated by pipenv
 # To regenerate from the project's Pipfile, run:
 #
-#    pipenv lock --requirements
+#    sed -i '7,$ d' requirements.txt; pipenv requirements >> requirements.txt
 #
-
 -i https://pypi.org/simple
+annotated-types==0.7.0; python_version >= '3.8'
+anyio==4.6.2.post1; python_version >= '3.9'
 -e .
-anyio==3.5.0; python_full_version >= '3.6.2'
-asgiref==3.5.0; python_version >= '3.7'
-click==8.1.2; python_version >= '3.7'
-fastapi-pagination==0.9.3
-fastapi==0.75.2
-geoalchemy2==0.11.1
-greenlet==1.1.2; python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))
-h11==0.13.0; python_version >= '3.6'
-idna==3.3; python_version >= '3.5'
-packaging==21.3; python_version >= '3.6'
-psycopg2==2.9.3
-pydantic==1.9.0; python_full_version >= '3.6.1'
-pyparsing==3.0.8; python_full_version >= '3.6.8'
-setuptools==62.1.0
-sniffio==1.2.0; python_version >= '3.5'
-sqlalchemy==1.4.36; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-starlette==0.17.1; python_version >= '3.6'
-typing-extensions==4.2.0; python_version >= '3.7'
-uvicorn==0.17.6
+click==8.1.7; python_version >= '3.7'
+fastapi==0.115.5; python_version >= '3.8'
+fastapi-pagination==0.12.32; python_version >= '3.8' and python_version < '4.0'
+geoalchemy2==0.16.0; python_version >= '3.7'
+greenlet==3.1.1; python_version >= '3.7'
+h11==0.14.0; python_version >= '3.7'
+idna==3.10; python_version >= '3.6'
+packaging==24.2; python_version >= '3.8'
+psycopg2-binary==2.9.10; python_version >= '3.8'
+pydantic==2.9.2; python_version >= '3.8'
+pydantic-core==2.23.4; python_version >= '3.8'
+setuptools==75.5.0; python_version >= '3.9'
+sniffio==1.3.1; python_version >= '3.7'
+sqlalchemy==2.0.36; python_version >= '3.7'
+starlette==0.41.3; python_version >= '3.8'
+typing-extensions==4.12.2; python_version >= '3.8'
+uvicorn==0.32.0; python_version >= '3.8'

deploy/README.md

@@ -207,18 +207,18 @@ Build and publish all images:
 
 ```bash
 # Build images locally
-docker compose -f docker-compose-prod.yaml build
+docker compose -f docker-compose.prod.yml build
 
 # Push to GitHub container registry
 docker push ghcr.io/nismod/jsrat-frontend:0.1
-docker push ghcr.io/nismod/jsrat-backend:0.1
+docker push ghcr.io/nismod/jsrat-backend:0.2
 docker push ghcr.io/nismod/jsrat-vector-tileserver:0.1
 docker push ghcr.io/nismod/jsrat-raster-tileserver:0.1
 ```
 
 ```bash
 docker push ghcr.io/nismod/jsrat-frontend:0.1
-docker push ghcr.io/nismod/jsrat-backend:0.1
+docker push ghcr.io/nismod/jsrat-backend:0.2
 docker push ghcr.io/nismod/jsrat-vector-tileserver:0.1
 docker push ghcr.io/nismod/jsrat-raster-tileserver:0.1
 ```
@@ -228,12 +228,12 @@ docker push ghcr.io/nismod/jsrat-raster-tileserver:0.1
 Update a specific image, then build and push:
 
 ```bash
-# Edit the image version in `docker-compose.prod.yaml`
+# Edit the image version in `docker-compose.prod.yml`
 # in this example it's on line 33:
 #     image: ghcr.io/nismod/jsrat-frontend:0.1
 
 # Build
-docker compose -f docker-compose.prod.yaml build frontend
+docker compose -f docker-compose.prod.yml build frontend
 
 # Push
 docker push ghcr.io/nismod/jsrat-frontend:0.1

docker-compose.dev.yml

@@ -1,5 +1,4 @@
 # Development environment - includes database, hard-coded env vars
-version: '3.9'
 volumes:
   postgis-data:
 
@@ -34,7 +33,7 @@ services:
       - "traefik.http.services.frontend.loadbalancer.server.port=80"
 
   backend:
-    image: ghcr.io/nismod/jsrat-backend:0.1
+    image: ghcr.io/nismod/jsrat-backend:0.2
     build: ./backend
     ports:
       - 8888:80
@@ -117,5 +116,5 @@ services:
         "ingest",
         "/data/{type}__rp_{rp}__rcp_{rcp}__epoch_{epoch}__conf_{confidence}.tif",
         "-o",
-        "/data/terracotta.sqlite"
+        "/data/terracotta.sqlite",
       ]

docker-compose.prod.yml

@@ -1,6 +1,4 @@
 # Production environment
-version: "3.9"
-
 services:
   frontend:
     image: ghcr.io/nismod/jsrat-frontend:0.1
@@ -9,7 +7,7 @@ services:
       - "3000:80"
 
   backend:
-    image: ghcr.io/nismod/jsrat-backend:0.1
+    image: ghcr.io/nismod/jsrat-backend:0.2
     build: ./backend
     ports:
       - "3001:80"

docker-compose.stage.yml

@@ -8,7 +8,7 @@ services:
       - "3000:80"
 
   backend:
-    image: ghcr.io/nismod/jsrat-backend:0.1
+    image: ghcr.io/nismod/jsrat-backend:0.2
     platform: linux/amd64
     build: ./backend
     ports: