Fractal-server

Warning: updating to this version requires changes to the configuration variable

* Updates to SLURM interface:
* Remove `sudo`-requiring `ls` calls from `FractalFileWaitThread.check` (\885);
* Change default of `FRACTAL_SLURM_POLL_INTERVAL` to 5 seconds (\885);
* Rename `FRACTAL_SLURM_OUTPUT_FILE_GRACE_TIME` configuration variables into `FRACTAL_SLURM_ERROR_HANDLING_INTERVAL` (\885);
* Remove `FRACTAL_SLURM_KILLWAIT_INTERVAL` variable and corresponding logic (\885);
* Remove `_multiple_paths_exist_as_user` helper function (\885);
* Review type hints and default values of SLURM-related configuration variables (\885).
* Dependencies:
* Update `fastapi` to version `^0.103.0` (\877);
* Update `fastapi-users` to version `^12.1.0` (\877).

* Make updated-metadata collection robust for metadiff files consisting of a single `null` value (\879).
* Automate procedure for publishing package to PyPI (\881).

* Backend runner:
* Add aggregation logic for parallel-task updated metadata (\852);
* Make updated-metadata collection robust for missing files (\852, \863).
* Database interface:
* API:
* Prevent user from bypassing workflow-name constraint via the PATCH endpoint (\867).
* Handle error upon task collection, when tasks exist in the database but not on-disk (\874).
* Add `_check_project_exists` helper function (\872).
* Configuration variables:
* Remove `DEPLOYMENT_TYPE` variable and update `alive` endpoint (\875);
* Introduce `Settings.check_db` method, and call it during inline/offline migrations (\855);
* Introduce `Settings.check_runner` method (\875);
* Fail if `FRACTAL_BACKEND_RUNNER` is `"local"` and `FRACTAL_LOCAL_CONFIG_FILE` is set but missing on-disk (\875);
* Clean up `Settings.check` method and improve its coverage (\875);
* Package, repository, documentation:
* Change `fractal_server.common` from being a git-submodule to being a regular folder (\859).
* Pin documentation dependencies (\865).
* Split `app/models/project.py` into two modules for dataset and project (\871).
* Revamp documentation on database interface and on the corresponding configuration variables (\855).

* Oauth2-related updates (\822):
* Update configuration of OAuth2 clients, to support OIDC/GitHub/Google;
* Merge `SQLModelBaseOAuthAccount` and `OAuthAccount` models;
* Update `UserOAuth.oauth_accounts` relationship and fix `list_users` endpoint accordingly;
* Introduce dummy `UserManager.on_after_login` method;
* Rename `OAuthClient` into `OAuthClientConfig`;
* Revamp users-related parts of documentation.

* Update `output_dataset.meta` also when workflow execution fails (\843).
* Improve error message for unknown errors in job execution (\843).
* Fix log message incorrectly marked as "error" (\846).

* 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).