Updates

.github/workflows/backend.yml

@@ -21,23 +21,18 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v5
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.13"
+          version: "0.12.19"
+
+      - name: Install system dependencies
+        run: apt-get update && apt-get install -y --no-install-recommends ca-certificates python3
 
       - name: Install dependencies
-        run: |
-          apt-get update && apt-get install -y curl python3.13-dev libpq-dev gcc
-          python -m pip install --upgrade pip
-          curl -sSL https://install.python-poetry.org | python3 -
-          export PATH="/github/home/.local/bin:$PATH"
-          echo "$HOME/.local/bin" >> $GITHUB_PATH # allow poetry to be used in next step
-          poetry env use python3.13
-          poetry install --no-interaction --no-root
+        run: uv sync --locked --no-build --no-python-downloads --python /usr/bin/python3
         working-directory: ./src/backend
 
       - name: Run tests
-        run: |
-          poetry run pytest ./tests
+        run: uv run --no-sync pytest ./tests
         working-directory: ./src/backend

.github/workflows/frontend.yml

@@ -18,13 +18,18 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v5
 
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '26.10.0'
+
       - name: Setup pnpm
         uses: pnpm/action-setup@v4
         with:
-          version: 8
+          version: 12.8.1
 
       - name: Install dependencies
-        run: pnpm install
+        run: pnpm install --frozen-lockfile
         working-directory: ./src/frontend/acc
 
       - name: Lint

.gitignore

@@ -2,6 +2,7 @@ __pycache__
 .idea
 /.mypy_cache/
 **/venv
+**/.venv
 .vscode
 .devcontainer
-build/
+build/

docs/backend/README.md

@@ -8,7 +8,7 @@
 - [services](./services/)
 
 # Environment variables
-- `ACC_DB_URL` - PostgreSQL database connection string.
+- `ACC_DB_URL` - PostgreSQL database connection string using Psycopg 3: `postgresql+psycopg://user:password@host:5432/database`. Custom environment overrides must use this driver scheme too.
 - `ACC_DATA_DIR` - Directory for storing uploaded files and calculation results.
 - `ACC_EXAMPLES_DIR` - Directory for storing precalculated examples.
 - `ACC_LOG_DIR` - Directory for storing logs.
@@ -23,4 +23,4 @@
 - `OIDC_REDIRECT_URL` - Redirect URL after successful Life Science auth.
 - `OIDC_DISCOVERY_URL` - URL for fetching OIDC Life Science infomation (auth endpoint, ...).
 - `OIDC_CLIENT_ID` - Client ID of the registered Life Science Application.
-- `OIDC_CLIENT_SECRET` - Client secret of the registered Life Science Application.
+- `OIDC_CLIENT_SECRET` - Client secret of the registered Life Science Application.

docs/backend/db/README.md

@@ -15,13 +15,13 @@ Migrations are handled by `alembic`, with related code being located [here](../.
 ### Creating a new migration
 ```bash
 $ cd src/backend/app
-$ poetry run alembic revision --autogenerate -m "<migration name>"
+$ uv run --no-sync alembic revision --autogenerate -m "<migration name>"
 ```
 
 ### Running migrations
 ```bash
 $ cd src/backend/app
-$ poetry run alembic upgrade head
+$ uv run --no-sync alembic upgrade head
 ```
 
 ## Updating the database schema

src/backend/Dockerfile

@@ -2,27 +2,21 @@ FROM chargefw2-base:acc
 
 USER root
 
-ENV POETRY_HOME=/opt/poetry
-ENV POETRY_VIRTUALENVS_CREATE=false
-ENV PATH="/opt/poetry/bin:$PATH"
+COPY --from=ghcr.io/astral-sh/uv:0.12.19 /uv /usr/local/bin/uv
+
+ENV UV_PYTHON_DOWNLOADS=never
+ENV UV_PROJECT_ENVIRONMENT=/opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     ca-certificates \
-    curl \
-    gcc \
-    python3-dev \
-    libpq-dev && \
+    python3 && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
-# Install Poetry
-RUN curl -sSL https://install.python-poetry.org | python3 - && \
-    poetry config virtualenvs.create false
-
-
 WORKDIR /acc
-COPY poetry.lock pyproject.toml ./
-RUN poetry install --no-interaction --no-ansi --no-root
+COPY uv.lock pyproject.toml ./
+RUN uv sync --locked --no-cache --no-build --python /usr/bin/python3
 
 COPY ./app /acc/app
 COPY ./entrypoint.sh /acc/

src/backend/README.md

@@ -26,20 +26,28 @@ $ cmake .. -DCMAKE_INSTALL_PREFIX=<WHERE-TO-INSTALL> -DPYTHON_MODULE=ON
 All required environment variables are located in the [.env file](./app/.env) except `OIDC_CLIENT_ID` and `OIDC_CLIENT_SECRET` (required for Life Science auth, can be ignored for local setup). All used environment variables are described in [docs](../../docs/backend/README.md). How to obtain the abovementioned environment variables is also mentioned [here](../../docs/backend/life-science/README.md). 
 
 ### Installing dependencies
-ACC III uses [Poetry](https://python-poetry.org/) for depencency management.
+ACC III uses [uv](https://docs.astral.sh/uv/) for dependency management. Docker and CI use uv 0.12.19.
 
-#### Install Poetry
+#### Install uv
 ```bash
-$ curl -sSL https://install.python-poetry.org | python3 -
+$ curl -LsSf https://astral.sh/uv/0.12.19/install.sh | sh
 ```
 
 #### Install project dependencies
-*Note:* Poetry will automatically create a virtual environment inside the project before the installation. Configured [here](./poetry.toml).
+uv creates a `.venv` in the backend directory and installs the versions recorded in `uv.lock`. Use Python 3.13 or newer, matching the Python version used to build your ChargeFW2 bindings. Docker uses Ubuntu's Python and does not download another interpreter.
 
 ```bash
-$ poetry install
+$ uv sync --locked --no-python-downloads --python python3
 ```
 
+For API tests using Starlette's `TestClient`, enable the optional `api-test` group:
+
+```bash
+$ uv sync --locked --group api-test --no-python-downloads --python python3
+```
+
+This supplies `httpx2` for `TestClient` without changing the application's `httpx` client. The group is not installed in production images. Use `uv run --no-sync` after syncing to retain the optional test dependencies.
+
 ### Startup
 We firstly need to start the database. Easiest way is by using an official postgresql docker image. Connection string is located in the `.env` file.
 ```bash
@@ -53,13 +61,14 @@ $ cd app
 
 After the database is ready, we need to run migrations:
 ```bash
-$ poetry run alembic upgrade head
+$ uv run --no-sync alembic upgrade head
 ```
 
-API can now be started just by running the main file:
+Prepare the shared example files once, then start the API workers. Run these commands in order:
 
 ```bash
-$ poetry run gunicorn --workers 4 --worker-class uvicorn.workers.UvicornWorker main:web_app
+$ uv run --no-sync python main.py
+$ uv run --no-sync gunicorn --workers 4 --worker-class uvicorn_worker.UvicornWorker main:web_app
 ```
 
 API runs by default on `--bind 127.0.0.1:8000`. Documentation (Swagger) is available on `/docs`. Alternatively you can use Redoc available on `/redoc`.

src/backend/app/.env

@@ -1,6 +1,6 @@
 PYTHONPATH="/opt/chargefw2/lib"
 
-ACC_DB_URL="postgresql://postgres:postgres@localhost:5432/postgres"
+ACC_DB_URL="postgresql+psycopg://postgres:postgres@localhost:5432/postgres"
 ACC_DATA_DIR="/home/acc/data"
 ACC_EXAMPLES_DIR="/home/acc/examples"
 ACC_LOG_DIR="/var/log/acc"

src/backend/app/api/v1/routes/charges.py

@@ -386,7 +386,7 @@ async def calculate_charges(
         if available_b <= 0:
             quota_mb = quota_b / 1024 / 1024
             raise BadRequestError(
-                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
                 detail="Unable to calculate charges. Quota exceeded. "
                 + f"Maximum storage space is {quota_mb} MB.",
             )
@@ -440,7 +440,7 @@ async def calculate_charges(
         if total_size > io_service.max_file_size:
             max_file_size_mb = io_service.max_file_size / 1024 / 1024
             raise BadRequestError(
-                status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+                status_code=status.HTTP_413_CONTENT_TOO_LARGE,
                 detail="Unable to calculate charges. Calculation is too large. "
                 + f"Maximum allowed size is {max_file_size_mb} MB.",
             )
@@ -576,7 +576,7 @@ async def setup(
         if available_b <= 0:
             quota_mb = quota_b / 1024 / 1024
             raise BadRequestError(
-                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
                 detail="Unable to set up calculation. Quota would be exceeded. "
                 + f"Maximum storage space is {quota_mb} MB.",
             )
@@ -589,7 +589,7 @@ async def setup(
     if total_size > io_service.max_file_size:
         max_file_size_mb = io_service.max_file_size / 1024 / 1024
         raise BadRequestError(
-            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+            status_code=status.HTTP_413_CONTENT_TOO_LARGE,
             detail="Unable to set up calculation. Calculation is too large. "
             + f"Maximum allowed size is {max_file_size_mb} MB.",
         )

src/backend/app/db/repositories/calculation_set_repository.py

@@ -106,7 +106,7 @@ def store(self, session: Session, calculation_set: CalculationSet) -> None:
     def _paginate(
         self, session: Session, statement: Select, page: int, page_size: int
     ) -> PagedList[CalculationSet]:
-        total_statement = select(func.count()).select_from(statement)
+        total_statement = select(func.count()).select_from(statement.subquery())
         items_statement = statement.limit(page_size).offset((page - 1) * page_size)
 
         total_count = (session.execute(total_statement)).unique().scalar()

src/backend/app/main.py

@@ -40,7 +40,8 @@ def move_example_files() -> None:
 def create_app() -> FastAPI:
     """Creates FastAPI apps with routers and middleware."""
 
-    move_example_files()
+    if not load_dotenv():
+        raise EnvironmentError("Could not load environment variables.")
 
     # Create DI container
     container = Container()
@@ -49,6 +50,8 @@ def create_app() -> FastAPI:
         title="Atomic Charge Calculator III API",
         root_path="/api",
         swagger_ui_parameters={"syntaxHighlight": False},
+        # Preserve the existing logging setup without automatic telemetry exporters.
+        telemetry={"tracing": False, "metrics": False, "logs": False, "auto_configure": False},
     )
 
     container.wire()
@@ -78,4 +81,7 @@ def create_app() -> FastAPI:
     return app
 
 
-web_app = create_app()
+if __name__ == "__main__":
+    move_example_files()
+else:
+    web_app = create_app()

src/backend/app/services/calculation_storage.py

@@ -271,37 +271,6 @@ def filter_existing_calculations(
             self.logger.error(f"Error filtering existing calculations: {traceback.format_exc()}")
             raise e
 
-    def get_calculation_results(self, computation_id: str) -> list[CalculationResultDto]:
-        """Get calculation results from database."""
-
-        try:
-            self.logger.info(f"Getting calculation results for computation {computation_id}.")
-            with self.session_manager.session() as session:
-                calculation_set = self.set_repository.get(session, computation_id)
-
-                if not calculation_set:
-                    return []
-
-                result = [
-                    CalculationResultDto(
-                        config=CalculationConfigDto.model_validate(config),
-                        calculations=[
-                            CalculationDto.model_validate(calculation)
-                            for calculation in calculation_set.calculations
-                            if calculation.config == config
-                        ],
-                    )
-                    for config in calculation_set.configs
-                ]
-
-                return result
-
-        except Exception as e:
-            self.logger.error(
-                f"Error getting calculation results for computation {computation_id}: {traceback.format_exc()}"
-            )
-            raise e
-
     def delete_calculation_set(self, computation_id: str) -> None:
         """Delete calculation set from database."""
 

src/backend/app/services/io.py

@@ -602,7 +602,7 @@ def ensure_upload_files_sizes_valid(self, files: list[UploadFile]) -> None:
         if any((file.size or 0) > self.max_file_size for file in files):
             max_file_size_mb = self.max_file_size / 1024 / 1024
             raise BadRequestError(
-                status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+                status_code=status.HTTP_413_CONTENT_TOO_LARGE,
                 detail="Unable to upload files. One or more files are too large. "
                 + f"Maximum allowed size is {max_file_size_mb} MB.",
             )
@@ -612,7 +612,7 @@ def ensure_upload_files_sizes_valid(self, files: list[UploadFile]) -> None:
         if upload_size_b > self.max_upload_size:
             max_upload_size_mb = self.max_upload_size / 1024 / 1024
             raise BadRequestError(
-                status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
+                status_code=status.HTTP_413_CONTENT_TOO_LARGE,
                 detail="Unable to upload files. Maximum upload size exceeded. "
                 + f"Maximum upload size is {max_upload_size_mb} MB.",
             )
@@ -633,7 +633,7 @@ def ensure_quota_not_exceeded(
             if upload_size_b > available_b:
                 quota_mb = quota_b / 1024 / 1024
                 raise BadRequestError(
-                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                    status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
                     detail="Unable to upload files. Quota exceeded. "
                     + f"Maximum storage space is {quota_mb} MB.",
                 )

src/backend/app/services/oidc.py

@@ -3,12 +3,10 @@
 import os
 
 import httpx
-
+import jwt
 from cachetools import TTLCache
 from dotenv import load_dotenv
-
-from jose import JWTError, jwt
-
+from jwt.exceptions import PyJWTError
 from services.logging.base import LoggerBase
 
 
@@ -102,13 +100,13 @@ async def verify_token(self, token: str) -> dict | None:
 
             payload = jwt.decode(
                 token,
-                rsa_key,
+                jwt.PyJWK.from_dict(rsa_key, algorithm="RS256").key,
                 algorithms=["RS256"],
                 audience=self.client_id,
                 issuer=config["issuer"],
             )
             return payload
-        except JWTError as e:
+        except PyJWTError as e:
             self.logger.warn(f"Invalid token: {str(e)}")
             return None
         except Exception as e:

src/backend/entrypoint.sh

@@ -8,8 +8,11 @@ cd /acc/app
 # run database migrations
 alembic upgrade head
 
+# Prepare shared examples once, before workers import the application.
+python main.py || exit $?
+
 # use gunicorn with 4 workers
-# uvicorn.workers.UvicornWorker is used for async processing
+# uvicorn_worker.UvicornWorker is used for async processing
 # setting timeout to 1 hour for long lasting computations
 # running on port 8000
-exec gunicorn --workers 4 --worker-class uvicorn.workers.UvicornWorker --timeout 6000 --bind 0.0.0.0:8000 main:web_app
+exec gunicorn --workers 4 --worker-class uvicorn_worker.UvicornWorker --timeout 6000 --bind 0.0.0.0:8000 main:web_app