fractal-server 2.15.3__tar.gz → 2.15.5__tar.gz

{fractal_server-2.15.3 → fractal_server-2.15.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.15.3
+Version: 2.15.5
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin
@@ -23,6 +23,7 @@ Requires-Dist: pydantic-settings (>=2.7.0)
 Requires-Dist: python-dotenv (>=1.1.0,<1.2.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
 Requires-Dist: sqlmodel (==0.0.24)
+Requires-Dist: tomli_w (>=1.2.0,<1.3.0)
 Requires-Dist: uvicorn (>=0.29.0,<0.35.0)
 Requires-Dist: uvicorn-worker (==0.3.0)
 Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server

fractal_server-2.15.5/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.15.5"

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/models/v2/project.py

@@ -12,7 +12,6 @@ from fractal_server.utils import get_timestamp
 
 
 class ProjectV2(SQLModel, table=True):
-
     id: int | None = Field(default=None, primary_key=True)
     name: str
     timestamp_created: datetime = Field(

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/models/v2/task_group.py

@@ -107,7 +107,6 @@ class TaskGroupV2(SQLModel, table=True):
 
 
 class TaskGroupActivityV2(SQLModel, table=True):
-
     id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id")
     taskgroupv2_id: int | None = Field(

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/models/v2/workflow.py

@@ -12,7 +12,6 @@ from .workflowtask import WorkflowTaskV2
 
 
 class WorkflowV2(SQLModel, table=True):
-
     id: int | None = Field(default=None, primary_key=True)
     name: str
     project_id: int = Field(foreign_key="projectv2.id", ondelete="CASCADE")

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/admin/v2/accounting.py

@@ -82,7 +82,6 @@ async def query_accounting_slurm(
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> JSONResponse:
-
     stm = select(AccountingRecordSlurm.slurm_job_ids)
     if query.user_id is not None:
         stm = stm.where(AccountingRecordSlurm.user_id == query.user_id)

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/admin/v2/job.py

@@ -12,12 +12,15 @@ from sqlmodel import select
 from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
+from fractal_server.app.models.v2 import HistoryRun
+from fractal_server.app.models.v2 import HistoryUnit
 from fractal_server.app.models.v2 import JobV2
 from fractal_server.app.models.v2 import ProjectV2
 from fractal_server.app.routes.auth import current_active_superuser
 from fractal_server.app.routes.aux._job import _write_shutdown_file
 from fractal_server.app.routes.aux._runner import _check_shutdown_is_supported
 from fractal_server.app.runner.filenames import WORKFLOW_LOG_FILENAME
+from fractal_server.app.schemas.v2 import HistoryUnitStatus
 from fractal_server.app.schemas.v2 import JobReadV2
 from fractal_server.app.schemas.v2 import JobStatusTypeV2
 from fractal_server.app.schemas.v2 import JobUpdateV2
@@ -111,7 +114,6 @@ async def view_single_job(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> JobReadV2:
-
     job = await db.get(JobV2, job_id)
     if not job:
         raise HTTPException(
@@ -149,6 +151,11 @@ async def update_job(
             status_code=status.HTTP_404_NOT_FOUND,
             detail=f"Job {job_id} not found",
         )
+    if job.status != JobStatusTypeV2.SUBMITTED:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=f"Job {job_id} has status {job.status=} != 'submitted'.",
+        )
 
     if job_update.status != JobStatusTypeV2.FAILED:
         raise HTTPException(
@@ -165,6 +172,25 @@ async def update_job(
         f"{job.log or ''}\nThis job was manually marked as "
         f"'{JobStatusTypeV2.FAILED}' by an admin ({timestamp.isoformat()}).",
     )
+
+    res = await db.execute(
+        select(HistoryRun)
+        .where(HistoryRun.job_id == job_id)
+        .order_by(HistoryRun.timestamp_started.desc())
+        .limit(1)
+    )
+    latest_run = res.scalar_one_or_none()
+    if latest_run is not None:
+        setattr(latest_run, "status", HistoryUnitStatus.FAILED)
+        res = await db.execute(
+            select(HistoryUnit).where(
+                HistoryUnit.history_run_id == latest_run.id
+            )
+        )
+        history_units = res.scalars().all()
+        for history_unit in history_units:
+            setattr(history_unit, "status", HistoryUnitStatus.FAILED)
+
     await db.commit()
     await db.refresh(job)
     await db.close()

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/admin/v2/task.py

@@ -20,7 +20,6 @@ router = APIRouter()
 
 
 class TaskV2Minimal(BaseModel):
-
     id: int
     name: str
     type: str
@@ -32,13 +31,11 @@ class TaskV2Minimal(BaseModel):
 
 
 class ProjectUser(BaseModel):
-
     id: int
     email: EmailStr
 
 
 class TaskV2Relationship(BaseModel):
-
     workflow_id: int
     workflow_name: str
     project_id: int
@@ -47,7 +44,6 @@ class TaskV2Relationship(BaseModel):
 
 
 class TaskV2Info(BaseModel):
-
     task: TaskV2Minimal
     relationships: list[TaskV2Relationship]
 

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/admin/v2/task_group.py

@@ -43,7 +43,6 @@ async def get_task_group_activity_list(
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupActivityV2Read]:
-
     stm = select(TaskGroupActivityV2)
     if task_group_activity_id is not None:
         stm = stm.where(TaskGroupActivityV2.id == task_group_activity_id)
@@ -73,7 +72,6 @@ async def query_task_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:
-
     task_group = await db.get(TaskGroupV2, task_group_id)
     if task_group is None:
         raise HTTPException(
@@ -96,7 +94,6 @@ async def query_task_group_list(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupReadV2]:
-
     stm = select(TaskGroupV2)
 
     if user_group_id is not None and private is True:

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/_aux_functions.py

@@ -333,7 +333,6 @@ async def _workflow_has_submitted_job(
     workflow_id: int,
     db: AsyncSession,
 ) -> bool:
-
     res = await db.execute(
         select(JobV2.id)
         .where(JobV2.status == JobStatusTypeV2.SUBMITTED)

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/_aux_functions_tasks.py

@@ -224,7 +224,6 @@ async def _get_collection_task_group_activity_status_message(
     task_group_id: int,
     db: AsyncSession,
 ) -> str:
-
     res = await db.execute(
         select(TaskGroupActivityV2)
         .where(TaskGroupActivityV2.taskgroupv2_id == task_group_id)

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/history.py

@@ -71,7 +71,6 @@ async def get_workflow_tasks_statuses(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> JSONResponse:
-
     # Access control
     workflow = await _get_workflow_check_owner(
         project_id=project_id,
@@ -335,7 +334,6 @@ async def get_history_images(
     db: AsyncSession = Depends(get_async_db),
     pagination: PaginationRequest = Depends(get_pagination_params),
 ) -> ImagePage:
-
     # Access control and object retrieval
     wftask = await get_wftask_check_owner(
         project_id=project_id,

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/images.py

@@ -31,7 +31,6 @@ router = APIRouter()
 
 
 class ImagePage(PaginationResponse[SingleImage]):
-
     attributes: dict[str, list[ImageAttributeValue]]
     types: list[str]
 
@@ -64,7 +63,6 @@ async def post_new_image(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> Response:
-
     output = await _get_dataset_check_owner(
         project_id=project_id, dataset_id=dataset_id, user_id=user.id, db=db
     )
@@ -117,7 +115,6 @@ async def query_dataset_images(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> ImagePage:
-
     page = pagination.page
     page_size = pagination.page_size
 
@@ -131,7 +128,6 @@ async def query_dataset_images(
     types = aggregate_types(images)
 
     if query is not None:
-
         if query.zarr_url is not None:
             image = next(
                 (
@@ -190,7 +186,6 @@ async def delete_dataset_images(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> Response:
-
     output = await _get_dataset_check_owner(
         project_id=project_id, dataset_id=dataset_id, user_id=user.id, db=db
     )

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/pre_submission_checks.py

@@ -96,7 +96,6 @@ async def check_non_processed_images(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> JSONResponse:
-
     db_workflow_task, db_workflow = await _get_workflow_task_check_owner(
         project_id=project_id,
         workflow_task_id=workflowtask_id,

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/submit.py

@@ -57,7 +57,6 @@ async def apply_workflow(
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> JobReadV2 | None:
-
     # Remove non-submitted V2 jobs from the app state when the list grows
     # beyond a threshold
     settings = Inject(get_settings)

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/task_collection_custom.py

@@ -47,7 +47,6 @@ async def collect_task_custom(
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskReadV2]:
-
     settings = Inject(get_settings)
 
     # Validate query parameters related to user-group ownership
@@ -97,7 +96,6 @@ async def collect_task_custom(
                 )
 
     if task_collect.package_root is None:
-
         package_name_underscore = task_collect.package_name.replace("-", "_")
         # Note that python_command is then used as part of a subprocess.run
         # statement: be careful with mixing `'` and `"`.

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/task_collection_pixi.py

@@ -89,7 +89,6 @@ async def collect_task_pixi(
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupActivityV2Read:
-
     settings = Inject(get_settings)
     # Check if Pixi is available
     if settings.pixi is None:

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/task_group.py

@@ -72,7 +72,6 @@ async def get_task_group_activity_list(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupActivityV2Read]:
-
     stm = select(TaskGroupActivityV2).where(
         TaskGroupActivityV2.user_id == user.id
     )
@@ -105,7 +104,6 @@ async def get_task_group_activity(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupActivityV2Read:
-
     activity = await db.get(TaskGroupActivityV2, task_group_activity_id)
 
     if activity is None:

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/task_group_lifecycle.py

@@ -115,7 +115,6 @@ async def deactivate_task_group(
     # Submit background task
     settings = Inject(get_settings)
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-
         # Validate user settings (backend-specific)
         user_settings = await validate_user_settings(
             user=user, backend=settings.FRACTAL_RUNNER_BACKEND, db=db
@@ -242,7 +241,6 @@ async def reactivate_task_group(
     # Submit background task
     settings = Inject(get_settings)
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-
         # Validate user settings (backend-specific)
         user_settings = await validate_user_settings(
             user=user, backend=settings.FRACTAL_RUNNER_BACKEND, db=db

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/task_version_update.py

@@ -78,7 +78,6 @@ async def get_workflow_version_update_candidates(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[list[TaskVersionRead]]:
-
     workflow = await _get_workflow_check_owner(
         project_id=project_id,
         workflow_id=workflow_id,
@@ -181,7 +180,6 @@ async def replace_workflowtask(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> WorkflowTaskReadV2:
-
     # Get objects from database
     workflow_task, workflow = await _get_workflow_task_check_owner(
         project_id=project_id,

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/api/v2/workflow.py

@@ -147,7 +147,6 @@ async def update_workflow(
 
     for key, value in patch.model_dump(exclude_unset=True).items():
         if key == "reordered_workflowtask_ids":
-
             if await _workflow_has_submitted_job(
                 workflow_id=workflow_id, db=db
             ):
@@ -329,7 +328,6 @@ async def get_workflow_type_filters(
 
     response_items = []
     for wftask in workflow.task_list:
-
         # Compute input_type_filters, based on wftask and task manifest
         input_type_filters = merge_type_filters(
             wftask_type_filters=wftask.type_filters,

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/auth/group.py

@@ -39,7 +39,6 @@ async def get_list_user_groups(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[UserGroupRead]:
-
     # Get all groups
     stm_all_groups = select(UserGroup)
     res = await db.execute(stm_all_groups)
@@ -88,7 +87,6 @@ async def create_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-
     # Check that name is not already in use
     existing_name_str = select(UserGroup).where(
         UserGroup.name == group_create.name
@@ -121,7 +119,6 @@ async def update_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-
     group = await _usergroup_or_404(group_id, db)
 
     # Patch `viewer_paths`
@@ -143,7 +140,6 @@ async def delete_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> Response:
-
     group = await _usergroup_or_404(group_id, db)
 
     if group.name == FRACTAL_DEFAULT_GROUP_NAME:
@@ -219,7 +215,6 @@ async def remove_user_from_group(
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-
     # Check that user and group exist
     await _usergroup_or_404(group_id, db)
     user = await _user_or_404(user_id, db)

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/routes/pagination.py

@@ -11,7 +11,6 @@ T = TypeVar("T")
 
 
 class PaginationRequest(BaseModel):
-
     page: int = Field(ge=1)
     page_size: int | None = Field(ge=1)
 
@@ -38,7 +37,6 @@ def get_pagination_params(
 
 
 class PaginationResponse(BaseModel, Generic[T]):
-
     current_page: int = Field(ge=1)
     page_size: int = Field(ge=0)
     total_count: int = Field(ge=0)

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/runner/executors/local/runner.py

@@ -28,7 +28,6 @@ def run_single_task(
     parameters: dict[str, Any],
     task_files: TaskFiles,
 ):
-
     # Write args.json file
     with open(task_files.args_file_local, "w") as f:
         json.dump(parameters, f)
@@ -169,7 +168,6 @@ class LocalRunner(BaseRunner):
         exceptions: dict[int, BaseException] = {}
 
         try:
-
             self.validate_multisubmit_parameters(
                 list_parameters=list_parameters,
                 task_type=task_type,
@@ -208,7 +206,6 @@ class LocalRunner(BaseRunner):
 
         # Execute tasks, in chunks of size `parallel_tasks_per_job`
         for ind_chunk in range(0, n_elements, parallel_tasks_per_job):
-
             list_parameters_chunk = list_parameters[
                 ind_chunk : ind_chunk + parallel_tasks_per_job
             ]

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/runner/v2/db_tools.py

@@ -50,7 +50,6 @@ def bulk_update_status_of_history_unit(
     status: HistoryUnitStatus,
     db_sync: Session,
 ) -> None:
-
     len_history_unit_ids = len(history_unit_ids)
     logger.debug(
         f"[bulk_update_status_of_history_unit] {len_history_unit_ids=}."

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/runner/v2/merge_outputs.py

@@ -3,7 +3,6 @@ from fractal_server.app.runner.v2.task_interface import TaskOutput
 
 
 def merge_outputs(task_outputs: list[TaskOutput]) -> TaskOutput:
-
     if len(task_outputs) == 0:
         return TaskOutput()
 
@@ -11,7 +10,6 @@ def merge_outputs(task_outputs: list[TaskOutput]) -> TaskOutput:
     final_image_list_removals = []
 
     for task_output in task_outputs:
-
         final_image_list_updates.extend(task_output.image_list_updates)
         final_image_list_removals.extend(task_output.image_list_removals)
 

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/runner/v2/runner.py

@@ -415,7 +415,6 @@ def execute_tasks_v2(
             # Write current dataset images into the database.
             db_dataset = db.get(DatasetV2, dataset.id)
             if ENRICH_IMAGES_WITH_STATUS:
-
                 db_dataset.images = _remove_status_from_attributes(tmp_images)
             else:
                 db_dataset.images = tmp_images

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/runner/v2/task_interface.py

@@ -11,7 +11,6 @@ from fractal_server.types import ZarrUrlStr
 
 
 class TaskOutput(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     image_list_updates: list[SingleImageTaskOutput] = Field(
@@ -40,7 +39,6 @@ class TaskOutput(BaseModel):
 
 
 class InitArgsModel(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     zarr_url: ZarrUrlStr
@@ -48,14 +46,13 @@ class InitArgsModel(BaseModel):
 
 
 class InitTaskOutput(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     parallelization_list: list[InitArgsModel] = Field(default_factory=list)
 
 
 def _cast_and_validate_TaskOutput(
-    task_output: dict[str, Any]
+    task_output: dict[str, Any],
 ) -> TaskOutput | None:
     try:
         validated_task_output = TaskOutput(**task_output)

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/schemas/v2/accounting.py

@@ -6,7 +6,6 @@ from pydantic.types import AwareDatetime
 
 
 class AccountingRecordRead(BaseModel):
-
     id: int
     user_id: int
     timestamp: AwareDatetime

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/schemas/v2/project.py

@@ -9,14 +9,12 @@ from fractal_server.types import NonEmptyStr
 
 
 class ProjectCreateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
 class ProjectReadV2(BaseModel):
-
     id: int
     name: str
     timestamp_created: AwareDatetime
@@ -27,7 +25,6 @@ class ProjectReadV2(BaseModel):
 
 
 class ProjectUpdateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/app/schemas/v2/workflow.py

@@ -17,14 +17,12 @@ from fractal_server.types import NonEmptyStr
 
 
 class WorkflowCreateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
 class WorkflowReadV2(BaseModel):
-
     id: int
     name: str
     project_id: int
@@ -42,7 +40,6 @@ class WorkflowReadV2WithWarnings(WorkflowReadV2):
 
 
 class WorkflowUpdateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/config.py

@@ -95,10 +95,11 @@ class PixiSettings(BaseModel):
     PIXI_CONCURRENT_SOLVES: int = 4
     PIXI_CONCURRENT_DOWNLOADS: int = 4
     TOKIO_WORKER_THREADS: int = 2
+    DEFAULT_ENVIRONMENT: str = "default"
+    DEFAULT_PLATFORM: str = "linux-64"
 
     @model_validator(mode="after")
     def check_pixi_settings(self):
-
         if self.default_version not in self.versions:
             raise ValueError(
                 f"Default version '{self.default_version}' not in "
@@ -108,7 +109,6 @@ class PixiSettings(BaseModel):
         pixi_base_dir = Path(self.versions[self.default_version]).parent
 
         for key, value in self.versions.items():
-
             pixi_path = Path(value)
 
             if pixi_path.parent != pixi_base_dir:

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/data_migrations/2_14_10.py

@@ -15,7 +15,6 @@ def fix_db():
     logger.info("START execution of fix_db function")
 
     with next(get_sync_db()) as db:
-
         stm = select(HistoryRun).order_by(HistoryRun.id)
         history_runs = db.execute(stm).scalars().all()
 

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/main.py

@@ -83,7 +83,6 @@ async def lifespan(app: FastAPI):
     settings = Inject(get_settings)
 
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-
         from fractal_server.ssh._fabric import FractalSSHList
 
         app.state.fractal_ssh_list = FractalSSHList()

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/migrations/versions/1eac13a26c83_drop_v1_tables.py

@@ -33,7 +33,6 @@ TABLES_V1 = [
 
 
 def upgrade() -> None:
-
     logger = logging.getLogger("alembic.runtime.migration")
 
     target_metadata = SQLModel.metadata

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py

@@ -18,7 +18,6 @@ depends_on = None
 
 
 def upgrade() -> None:
-
     with op.batch_alter_table("workflowtaskv2") as batch_op:
         batch_op.alter_column(
             "task_id", existing_type=sa.INTEGER(), nullable=False

{fractal_server-2.15.3 → fractal_server-2.15.5}/fractal_server/tasks/v2/local/_utils.py

@@ -1,11 +1,18 @@
 from pathlib import Path
 
+from ..utils_pixi import simplify_pyproject_toml
 from fractal_server.app.schemas.v2 import TaskCreateV2
+from fractal_server.config import get_settings
 from fractal_server.logger import get_logger
+from fractal_server.logger import set_logger
+from fractal_server.syringe import Inject
 from fractal_server.tasks.v2.utils_templates import customize_template
 from fractal_server.utils import execute_command_sync
 
 
+logger = set_logger(__name__)
+
+
 def _customize_and_run_template(
     template_filename: str,
     replacements: list[tuple[str, str]],
@@ -69,3 +76,28 @@ def check_task_files_exist(task_list: list[TaskCreateV2]) -> None:
                     f"Task `{_task.name}` has `command_parallel` "
                     f"pointing to missing file `{_task_path}`."
                 )
+
+
+def edit_pyproject_toml_in_place_local(pyproject_toml_path: Path) -> None:
+    """
+    Wrapper of `simplify_pyproject_toml`, with I/O.
+    """
+
+    # Read `pyproject.toml`
+    with pyproject_toml_path.open() as f:
+        pyproject_contents = f.read()
+
+    # Simplify contents
+    settings = Inject(get_settings)
+    new_pyproject_contents = simplify_pyproject_toml(
+        original_toml_string=pyproject_contents,
+        pixi_environment=settings.pixi.DEFAULT_ENVIRONMENT,
+        pixi_platform=settings.pixi.DEFAULT_PLATFORM,
+    )
+    # Write new `pyproject.toml`
+    with pyproject_toml_path.open("w") as f:
+        f.write(new_pyproject_contents)
+    logger.debug(
+        f"Replaced local {pyproject_toml_path.as_posix()} "
+        "with simplified version."
+    )