Merge pull request #41 from biosimulations/simple-slurm-submission

Simple slurm submission

Author: Ezequiel-Valencia

.github/workflows/ci-test.yml

@@ -0,0 +1,52 @@
+name: Main
+
+on:
+  push:
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Run checks
+        run: make check
+
+  tests-and-type-check:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13"]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run All tests
+        run: uv run python -m pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
+
+      - name: Check typing
+        run: uv run mypy
+
+      - name: Upload coverage reports to Codecov with GitHub Action on Python 3.11
+        uses: codecov/codecov-action@v4
+        if: ${{ matrix.python-version == '3.11' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -177,7 +177,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # Abstra
 # Abstra is an AI-powered process automation framework.

.idea/compose-api.iml

@@ -1,6 +1,9 @@
 # Use the official Python image from the Docker Hub
 FROM python:3.13.2-slim-bookworm AS base
 
+ARG APP_GID=10000
+ARG APP_UID=16997
+
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     openssh-client && \
@@ -11,18 +14,23 @@ ENV PYTHONUNBUFFERED=1
 
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
 
+# create user/group
+RUN groupadd -g $APP_GID appgroup && \
+    useradd -m -u $APP_UID -g $APP_GID appuser
+USER appuser
+
 # Change the working directory to the `app` directory
 WORKDIR /app
 
 # Copy the lockfile and `pyproject.toml` into the image
-COPY uv.lock /app/uv.lock
-COPY pyproject.toml /app/pyproject.toml
+COPY --chown=appuser:appgroup uv.lock /app/uv.lock
+COPY --chown=appuser:appgroup pyproject.toml /app/pyproject.toml
 
 # Install dependencies
 RUN uv sync --frozen --no-install-project
 
 # Copy the project into the image
-COPY . /app
+COPY --chown=appuser:appgroup . /app
 
 # Sync the project
 RUN uv sync --frozen
@@ -37,4 +45,4 @@ ENV APP_DIR=/app/app
 ENV ASSETS_DIR=/app/assets
 
 # Command to run the application
-CMD ["uvicorn", "compose_api.api.main:app", "--host", "0.0.0.0", "--port", "8000"]
+CMD ["/bin/bash", "-c", "source .venv/bin/activate && uvicorn compose_api.api.main:app --host 0.0.0.0 --port 8000"]

.idea/inspectionProfiles/profiles_settings.xml

@@ -15,6 +15,13 @@ check: ## Run code quality tools.
 	@echo "🚀 Checking for obsolete dependencies: Running deptry"
 	@uv run deptry .
 
+.PHONY: clients
+clients: ## Run code quality tools.
+	@echo "🚀 Generating OpenAPI Spec"
+	@python3 compose_api/api/openapi_spec.py
+	@echo "🚀 Creating HTTPX Clients"
+	@scripts/generate-api-client.sh
+
 .PHONY: test
 test: ## Test the code with pytest
 	@echo "🚀 Testing code: Running pytest"

.idea/misc.xml

@@ -20,10 +20,16 @@ SLURM_SUBMIT_USER=
 SLURM_SUBMIT_KEY_PATH=
 SLURM_PARTITION=
 SLURM_NODE_LIST=
+SLURM_BUILD_NODE=
 SLURM_QOS=
 SLURM_LOG_BASE_PATH=
 SLURM_SUBMIT_KNOWN_HOSTS=
 
 HPC_IMAGE_BASE_PATH=
 HPC_SIM_BASE_PATH=
 HPC_SIM_CONFIG_FILE=
+SLURM_SBATCH_BASE_PATH=
+
+# The home compose_api dir for crbmapi
+INTERNAL_MOUNT_DIR=/mnt/crbmapi
+NAMESPACE=test

Dockerfile-api

@@ -0,0 +1,174 @@
+from http import HTTPStatus
+from typing import Any, Optional, Union, cast
+
+import httpx
+
+from ...client import AuthenticatedClient, Client
+from ...types import Response, UNSET
+from ... import errors
+
+from ...models.body_analyze_simulation_omex import BodyAnalyzeSimulationOmex
+from ...models.http_validation_error import HTTPValidationError
+from typing import cast
+
+
+def _get_kwargs(
+    *,
+    body: BodyAnalyzeSimulationOmex,
+) -> dict[str, Any]:
+    headers: dict[str, Any] = {}
+
+    _kwargs: dict[str, Any] = {
+        "method": "post",
+        "url": "/core/simulation/analyze",
+    }
+
+    _kwargs["files"] = body.to_multipart()
+
+    _kwargs["headers"] = headers
+    return _kwargs
+
+
+def _parse_response(
+    *, client: Union[AuthenticatedClient, Client], response: httpx.Response
+) -> Optional[Union[HTTPValidationError, str]]:
+    if response.status_code == 200:
+        response_200 = response.text
+        return response_200
+    if response.status_code == 422:
+        response_422 = HTTPValidationError.from_dict(response.json())
+
+        return response_422
+    if client.raise_on_unexpected_status:
+        raise errors.UnexpectedStatus(response.status_code, response.content)
+    else:
+        return None
+
+
+def _build_response(
+    *, client: Union[AuthenticatedClient, Client], response: httpx.Response
+) -> Response[Union[HTTPValidationError, str]]:
+    return Response(
+        status_code=HTTPStatus(response.status_code),
+        content=response.content,
+        headers=response.headers,
+        parsed=_parse_response(client=client, response=response),
+    )
+
+
+def sync_detailed(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyAnalyzeSimulationOmex,
+) -> Response[Union[HTTPValidationError, str]]:
+    """Analyze a process bi-graph,
+        and determine the singularity definition file which would build an environment it can run in.
+
+     Resulting container definition file
+
+    Args:
+        body (BodyAnalyzeSimulationOmex):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Response[Union[HTTPValidationError, str]]
+    """
+
+    kwargs = _get_kwargs(
+        body=body,
+    )
+
+    response = client.get_httpx_client().request(
+        **kwargs,
+    )
+
+    return _build_response(client=client, response=response)
+
+
+def sync(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyAnalyzeSimulationOmex,
+) -> Optional[Union[HTTPValidationError, str]]:
+    """Analyze a process bi-graph,
+        and determine the singularity definition file which would build an environment it can run in.
+
+     Resulting container definition file
+
+    Args:
+        body (BodyAnalyzeSimulationOmex):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Union[HTTPValidationError, str]
+    """
+
+    return sync_detailed(
+        client=client,
+        body=body,
+    ).parsed
+
+
+async def asyncio_detailed(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyAnalyzeSimulationOmex,
+) -> Response[Union[HTTPValidationError, str]]:
+    """Analyze a process bi-graph,
+        and determine the singularity definition file which would build an environment it can run in.
+
+     Resulting container definition file
+
+    Args:
+        body (BodyAnalyzeSimulationOmex):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Response[Union[HTTPValidationError, str]]
+    """
+
+    kwargs = _get_kwargs(
+        body=body,
+    )
+
+    response = await client.get_async_httpx_client().request(**kwargs)
+
+    return _build_response(client=client, response=response)
+
+
+async def asyncio(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyAnalyzeSimulationOmex,
+) -> Optional[Union[HTTPValidationError, str]]:
+    """Analyze a process bi-graph,
+        and determine the singularity definition file which would build an environment it can run in.
+
+     Resulting container definition file
+
+    Args:
+        body (BodyAnalyzeSimulationOmex):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Union[HTTPValidationError, str]
+    """
+
+    return (
+        await asyncio_detailed(
+            client=client,
+            body=body,
+        )
+    ).parsed