Fractal-server

> **WARNINGs**:
>
> 1. This update requires running a fix-db script, available at https://raw.githubusercontent.com/fractal-analytics-platform/fractal-server/1.4.2/scripts/fix_db/current.py.
> 2. Starting from this version, non-verified users have limited access to `/api/v1/` endpoints. Before the upgrade, all existing users must be manually set to verified.

* API:
* Prevent access to `GET/PATCH` task endpoints for non-verified users (\1114).
* Prevent access to task-collection and workflow-apply endpoints for non-verified users (\1099).
* Make first-admin-user verified (\1110).
* Add the automatic setting of `ApplyWorkflow.end_timestamp` when patching `ApplyWorkflow.status` via `PATCH /admin/job/{job_id}` (\1121).
* Change `ProjectDump.timestamp_created` type from `datetime` to `str` (\1120).
* Change `_DatasetHistoryItem.workflowtask` type into `WorkflowTaskDump` (\1139).
* Change status code of stop-job endpoints to 202 (\1151).
* API (internal):
* Implement cascade operations explicitly, in `DELETE` endpoints for datasets, workflows and projects (\1130).
* Update `GET /project/{project_id}/workflow/{workflow_id}/job/` to avoid using `Workflow.job_list` (\1130).
* Remove obsolete sync-database dependency from apply-workflow endpoint (\1144).
* Database:
* Add `ApplyWorkflow.project_dump` column (\1070).
* Provide more meaningful names to fix-db scripts (\1107).
* Add `Project.timestamp_created` column, with timezone-aware default (\1102, \1131).
* Remove `Dataset.list_jobs_input` and `Dataset.list_jobs_output` relationships (\1130).
* Remove `Workflow.job_list` (\1130).
* Runner:
* In SLURM backend, use `slurm_account` (as received from apply-workflow endpoint) with top priority (\1145).
* Forbid setting of SLURM account from `WorkflowTask.meta` or as part of `worker_init` variable (\1145).
* Include more info in error message upon `sbatch` failure (\1142).
* Replace `sbatch` `--chdir` option with `-D`, to support also slurm versions before 17.11 (\1159).
* Testing:
* Extended systematic testing of database models (\1078).
* Review `MockCurrentUser` fixture, to handle different kinds of users (\1099).
* Remove `persist` from `MockCurrentUser` (\1098).
* Update `migrations.yml` GitHub Action to use up-to-date database and also test fix-db script (\1101).
* Add more schema-based validation to fix-db current script (\1107).
* Update `.dict()` to `.model_dump()` for `SQLModel` objects, to fix some `DeprecationWarnings`(\1133).
* Small improvement in schema coverage (\1125).
* Add unit test for `security` module (\1036).
* Dependencies:
* Update `sqlmodel` to version 0.0.14 (\1124).
* Benchmarks:
* Add automatic benchmark system for API's performances (\1123)
* App (internal):
* Move `_create_first_user` from `main` to `security` module, and allow it to create multiple regular users (\1036).

* API:
* Add `GET /admin/job/{job_id}/stop/` and `GET /admin/job/{job_id}/download/` endpoints (\1059).
* Use `DatasetDump` and `WorkflowDump` models for "dump" attributes of `ApplyWorkflowRead` (\1049, \1082).
* Add `slurm_accounts` to `User` schemas and add `slurm_account` to `ApplyWorkflow` schemas (\1067).
* Prevent providing a `package_version` for task collection from a `.whl` local package (\1069).
* Add `DatasetRead.project` and `WorkflowRead.project` attributes (\1082).
* Database:
* Make `ApplyWorkflow.workflow_dump` column non-nullable (\1049).
* Add `UserOAuth.slurm_accounts` and `ApplyWorkflow.slurm_account` columns (\1067).
* Add script for adding `ApplyWorkflow.user_email` (\1058).
* Add `Dataset.project` and `Workflow.project` relationships (\1082).
* Avoid using `Project` relationships `dataset_list` or `workflow_list` within some `GET` endpoints (\1082).
* Fully remove `Project` relationships `dataset_list`, `workflow_list` and `job_list` (\1091).
* Testing:
* Only use ubuntu-22.04 in GitHub actions (\1061).
* Improve unit testing of database models (\1082).
* Dependencies:
* Pin `bcrypt` to 4.0.1 to avoid warning in passlib (\1060).
* Runner:
* Set SLURM-job working directory to `job.working_dir_user` through `--chdir` option (\1064).

> directly.

* Make `Dataset.resource_list` an `ordering_list`, ordered by `Resource.id` (\951).
* Expose `redirect_url` for OAuth clients (\953).
* Expose JSON Schema for the `ManifestV1` Pydantic model (\942).
* Improve delete-resource endpoint (\943).
* Dependencies:
* Upgrade sqlmodel to 0.0.11 (\949).
* Testing:
* Fix bug in local tests with Docker/SLURM (\948).

> **WARNING**: This version introduces a change that is then reverted in 1.4.0,
> namely it sets the `ApplyWorkflow.status` type to `Enum`, when used with

* Configure sqlite WAL to avoid "database is locked" errors (\860).
* Dependencies:
* Add `sqlalchemy[asyncio]` extra, and do not directly require `greenlet` (\895).
* Fix `cloudpickle`-version definition in `pyproject.toml` (\937).
* Remove obsolete `sqlalchemy_utils` dependency (\939).
* Testing:
* Use ubuntu-22 for GitHub CI (\909).
* Run GitHub CI both with SQLite and Postgres (\915).
* Disable `postgres` service in GitHub action when running tests with SQLite (\931).
* Make `test_commands.py` tests stateless, also when running with Postgres (\917).
* Documentation:
* Add information about minimal supported SQLite version (\916).

* Project creation:
* Do not automatically create a dataset upon project creation (\897).
* Remove `ProjectCreate.default_dataset_name` attribute (\897).
* Dataset history:
* Create a new (**non-nullable**) history column in `Dataset` table (\898, \901).
* Deprecate history handling in `/project/{project_id}/job/{job_id}` endpoint (\898).
* Deprecate `HISTORY_LEGACY` (\898).
* Testing:
* Remove obsolete fixture `slurm_config` (\903).