Fractal-server

* Review structure of dataset history (\803):
* Re-define structure for `history` property of `Dataset.meta`;
* Introduce `"api/v1/project/{project_id}/dataset/{dataset_id}/status/"` endpoint;
* Introduce `"api/v1/project/{project_id}/dataset/{dataset_id}/export_history/"` endpoint;
* Move legacy history to `Dataset.meta["HISTORY_LEGACY"]`.
* Make `first_task_index` and `last_task_index` properties of `ApplyWorkflow` required (\803).
* Add `docs_info` and `docs_link` to Task model (\814)
* Accept `TaskUpdate.version=None` in task-patch endpoint (\818).
* Store a copy of the `Workflow` into the optional column `ApplyWorkflow.workflow_dump` at the time of submission (\804, \834).
* Prevent execution of multiple jobs with the same output dataset (\801).
* Transform non-absolute `FRACTAL_TASKS_DIR` into absolute paths, relative to the current working directory (\825).
* Error handling:
* Raise an appropriate error if a task command is not executable (\800).
* Improve handling of errors raised in `get_slurm_config` (\800).
* Documentation:
* Clarify documentation about `SlurmConfig` (\798).
* Update documentation configuration and GitHub actions (\811).
* Tests:
* Move `tests/test_common.py` into `fractal-common` repository (\808).
* Switch to `docker compose` v2 and unpin `pyyaml` version (\816).

* Support execution of a workflow subset (\784).
* Fix internal server error for invalid `task_id` in `create_workflowtask` endpoint (\782).
* Improve logging in background task collection (\776).
* Handle failures in `submit_workflow` without raising errors (\787).
* Simplify internal function for execution of a list of task (\780).
* Exclude `common/tests` and other git-related files from build (\795).
* Remove development dependencies `Pillow` and `pytest-mock` (\795).
* Remove obsolete folders from `tests/data` folder (\795).

* Pin Pydantic to v1 (\779).

* Add sqlalchemy naming convention for DB constraints, and add `render_as_batch=True` to `do_run_migrations` (\757).
* Fix bug in job-stop endpoint, due to missing default for `FractalSlurmExecutor.wait_thread.shutdown_file` (\768, \769).
* Fix bug upon inserting a task with `meta=None` into a Workflow (\772).

* Fix return value of stop-job endpoint (\764).
* Expose new GET `WorkflowTask` endpoint (\762).
* Clean up API modules (\762):
* Split workflow/workflowtask modules;
* Split tasks/task-collection modules.

* Refactor user model:
* Switch from UUID4 to int for IDs (\660, \684).
* Fix many-to-many relationship between users and project (\660).
* Rename `Project.user_member_list` into `Project.user_list` (\660).
* Add `username` column (\704).
* Update endpoints (see also [1.2->1.3 upgrade info](../internals/version_upgrades/upgrade_1_2_5_to_1_3_0/) in the documentation):
* Review endpoint URLs (\669).
* Remove foreign keys from payloads (\669).
* Update `Task` models, task collection and task-related endpoints:
* Add `version` and `owner` columns to `Task` model (\704).
* Set `Task.version` during task collection (\719).
* Set `Task.owner` as part of create-task endpoint (\704).
* For custom tasks, prepend `owner` to user-provided `source` (\725).
* Remove `default_args` from `Tasks` model and from manifest tasks (\707).
* Add `args_schema` and `args_schema_version` to `Task` model (\707).
* Expose `args_schema` and `args_schema_version` in task POST/PATCH endpoints (\749).
* Make `Task.source` task-specific rather than package-specific (\719).
* Make `Task.source` unique (\725).
* Update `_TaskCollectPip` methods, attributes and properties (\719).
* Remove private/public options for task collection (\704).
* Improve error message for missing package manifest (\704).
* Improve behavior when task-collection folder already exists (\704).
* Expose `pinned_package_version` for tasks collection (\744).
* Restrict Task editing to superusers and task owners (\733).
* Implement `delete_task` endpoint (\745).
* Update `Workflow` and `WorkflowTask` endpoints:
* Always merge new `WorkflowTask.args` with defaults from `Task.args_schema`, in `update_workflowtask` endpoint (\759).
* Remove `WorkflowTask.overridden_meta` property and on-the-fly overriding of `meta` (\752).
* Add warning when exporting workflows which include custom tasks (\728).
* When importing a workflow, only use tasks' `source` values, instead of `(source,name)` pairs (\719).
* Job execution:
* Add `FractalSlurmExecutor.shutdown` and corresponding endpoint (\631, \691, \696).
* In `FractalSlurmExecutor`, make `working_dir*` attributes required (\679).
* Remove `ApplyWorkflow.overwrite_input` column (\684, \694).
* Make `output_dataset_id` a required argument of apply-workflow endpoint (\681).
* Improve error message related to out-of-space disk (\699).
* Include timestamp in job working directory, to avoid name clashes (\756).
* Other updates to endpoints and database:
* Add `ApplyWorkflow.end_timestamp` column (\687, \684).
* Prevent deletion of a `Workflow`/`Dataset` in relationship with existing `ApplyWorkflow` (\703).
* Add project-name uniqueness constraint in project-edit endpoint (\689).
* Other updates to internal logic:
* Drop `WorkflowTask.arguments` property and `WorkflowTask.assemble_args` method (\742).
* Add test for collection of tasks packages with tasks in a subpackage (\743).
* Expose `FRACTAL_CORS_ALLOW_ORIGIN` environment variable (\688).
* Expose `FRACTAL_DEFAULT_ADMIN_USERNAME` environment variable (\751).
* Package and repository:
* Remove `fastapi-users-db-sqlmodel` dependency (\660).
* Make coverage measure more accurate (\676) and improve coverage (\678).
* Require pydantic version to be `>=1.10.8` (\711, \713).
* Include multiple `fractal-common` updates (\705, \719).
* Add test equivalent to `alembic check` (\722).
* Update `poetry.lock` to address security alerts (\723).
* Remove `sqlmodel` from `fractal-common`, and declare database models with multiple inheritance (\710).
* Make email generation more robust in `MockCurrentUser` (\730).
* Update `poetry.lock` to `cryptography=41`, to address security alert (\739).
* Add `greenlet` as a direct dependency (\748).
* Removed tests for `IntegrityError` (\754).