fractal-server 2.15.6__tar.gz → 2.15.7__tar.gz

{fractal_server-2.15.6 → fractal_server-2.15.7}/PKG-INFO

@@ -1,19 +1,20 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.15.6
+Version: 2.15.7
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin
 Author-email: tommaso.comparin@exact-lab.it
-Requires-Python: >=3.11,<3.13
+Requires-Python: >=3.11,<3.14
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
 Requires-Dist: cryptography (>=45.0.3,<45.1.0)
 Requires-Dist: fabric (>=3.2.2,<3.3.0)
-Requires-Dist: fastapi (>=0.115.0,<0.116.0)
+Requires-Dist: fastapi (>=0.116.0,<0.117.0)
 Requires-Dist: fastapi-users[oauth] (>=14,<15)
 Requires-Dist: gunicorn (>=23.0,<24.0)
 Requires-Dist: packaging (>=25.0.0,<26.0.0)

fractal_server-2.15.7/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.15.7"

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/app/routes/api/v2/_aux_functions_history.py

@@ -102,8 +102,9 @@ async def _verify_workflow_and_dataset_access(
     Verify user access to a dataset/workflow pair.
 
     Args:
+        project_id:
+        workflow_id:
         dataset_id:
-        workflow_task_id:
         user_id:
         db:
     """
@@ -148,7 +149,7 @@ async def get_wftask_check_owner(
     Args:
         project_id:
         dataset_id:
-        workflow_task_id:
+        workflowtask_id:
         user_id:
         db:
     """

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/app/routes/api/v2/_aux_functions_tasks.py

@@ -231,11 +231,14 @@ async def _get_collection_task_group_activity_status_message(
     )
     task_group_activity_list = res.scalars().all()
     if len(task_group_activity_list) > 1:
-        msg = (
-            "\nWarning: "
+        msg_short = (
             "Expected only one TaskGroupActivityV2 associated to TaskGroup "
             f"{task_group_id}, found {len(task_group_activity_list)} "
             f"(IDs: {[tga.id for tga in task_group_activity_list]})."
+        )
+        logger.error(f"UnreachableBranchError: {msg_short}")
+        msg = (
+            f"\nWarning: {msg_short}\n"
             "Warning: this should have not happened, please contact an admin."
         )
     elif len(task_group_activity_list) == 1:
@@ -268,13 +271,16 @@ async def _verify_non_duplication_user_constraint(
     if duplicate:
         user = await db.get(UserOAuth, user_id)
         if len(duplicate) > 1:
+            error_msg = (
+                f"User '{user.email}' already owns {len(duplicate)} task "
+                f"groups with name='{pkg_name}' and {version=} "
+                f"(IDs: {[group.id for group in duplicate]})."
+            )
+            logger.error(f"UnreachableBranchError: {error_msg}")
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
                 detail=(
-                    "Invalid state:\n"
-                    f"User '{user.email}' already owns {len(duplicate)} task "
-                    f"groups with name='{pkg_name}' and {version=} "
-                    f"(IDs: {[group.id for group in duplicate]}).\n"
+                    f"Invalid state: {error_msg}\n"
                     "This should have not happened: please contact an admin."
                 ),
             )
@@ -310,13 +316,16 @@ async def _verify_non_duplication_group_constraint(
     if duplicate:
         user_group = await db.get(UserGroup, user_group_id)
         if len(duplicate) > 1:
+            error_msg = (
+                f"UserGroup '{user_group.name}' already owns "
+                f"{len(duplicate)} task groups with name='{pkg_name}' and "
+                f"{version=} (IDs: {[group.id for group in duplicate]}).\n"
+            )
+            logger.error(error_msg)
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
                 detail=(
-                    "Invalid state:\n"
-                    f"UserGroup '{user_group.name}' already owns "
-                    f"{len(duplicate)} task groups with name='{pkg_name}' and "
-                    f"{version=} (IDs: {[group.id for group in duplicate]}).\n"
+                    f"Invalid state:\n{error_msg}"
                     "This should have not happened: please contact an admin."
                 ),
             )

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/app/runner/executors/base_runner.py

@@ -91,14 +91,15 @@ class BaseRunner:
             workflow_task_order:
             workflow_task_id:
             task_name:
-            parameters:
-                Dictionary of parameters. Must include `zarr_urls` key.
+            list_parameters:
+                List of dictionaries of parameters (each one must include
+                `zarr_urls` key).
             history_unit_ids:
                 Database IDs of the corresponding `HistoryUnit` entries.
+            list_task_files: `TaskFiles` objects.
             task_type: Task type.
-            task_files: `TaskFiles` object.
             config: Runner-specific parameters.
-            user_id
+            user_id:
         """
         raise NotImplementedError()
 

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/app/runner/executors/slurm_common/_slurm_config.py

@@ -213,7 +213,7 @@ class SlurmConfig(BaseModel):
     `SlurmConfig` attributes (e.g. `mem_per_task_MB`), which are not meant to
     be part of the `FRACTAL_SLURM_CONFIG_FILE` JSON file (details on the
     expected file content are defined in
-    [`SlurmConfigFile`](./#fractal_server.app.runner._slurm._slurm_config.SlurmConfigFile)).
+    [`SlurmConfigFile`](#fractal_server.app.runner._slurm._slurm_config.SlurmConfigFile)).
 
     Part of the attributes map directly to some of the SLURM attributes (see
     https://slurm.schedmd.com/sbatch.html), e.g. `partition`. Other attributes

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/app/runner/executors/slurm_ssh/tar_commands.py

@@ -7,7 +7,7 @@ from pathlib import Path
 def get_tar_compression_cmd(
     subfolder_path: Path,
     filelist_path: Path | None,
-) -> tuple[str, str]:
+) -> str:
     """
     Prepare command to compress e.g. `/path/dir` into `/path/dir.tar.gz`.
 
@@ -17,7 +17,6 @@ def get_tar_compression_cmd(
     Args:
         subfolder_path: Absolute path to the folder to compress.
         filelist_path: If set, to be used in the `--files-from` option.
-        expected_tarfile: If set, it should match to the returned one.
 
     Returns:
         tar command

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/app/runner/v2/runner_functions.py

@@ -32,6 +32,7 @@ from fractal_server.app.runner.v2.task_interface import (
 )
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
 from fractal_server.app.schemas.v2 import TaskType
+from fractal_server.exceptions import UnreachableBranchError
 from fractal_server.logger import set_logger
 
 __all__ = [
@@ -349,11 +350,11 @@ def run_v2_task_parallel(
     for ind in range(len(list_function_kwargs)):
         if ind not in results.keys() and ind not in exceptions.keys():
             error_msg = (
-                f"Invalid branch: {ind=} is not in `results.keys()` "
+                f"UnreachableBranchError: {ind=} is not in `results.keys()` "
                 "nor in `exceptions.keys()`."
             )
             logger.error(error_msg)
-            raise RuntimeError(error_msg)
+            raise UnreachableBranchError(error_msg)
         outcome[ind] = _process_task_output(
             result=results.get(ind, None),
             exception=exceptions.get(ind, None),
@@ -567,13 +568,12 @@ def run_v2_task_compound(
     failure = False
     for ind in range(len(list_function_kwargs)):
         if ind not in results.keys() and ind not in exceptions.keys():
-            # NOTE: see issue 2484
             error_msg = (
-                f"Invalid branch: {ind=} is not in `results.keys()` "
+                f"UnreachableBranchError: {ind=} is not in `results.keys()` "
                 "nor in `exceptions.keys()`."
             )
             logger.error(error_msg)
-            raise RuntimeError(error_msg)
+            raise UnreachableBranchError(error_msg)
         compute_outcomes[ind] = _process_task_output(
             result=results.get(ind, None),
             exception=exceptions.get(ind, None),

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/app/schemas/v2/task_collection.py

@@ -49,7 +49,9 @@ class TaskCollectPipV2(BaseModel):
     package: NonEmptyStr | None = None
     package_version: NonEmptyStr | None = None
     package_extras: NonEmptyStr | None = None
-    python_version: Literal["3.9", "3.10", "3.11", "3.12"] | None = None
+    python_version: Literal[
+        "3.9", "3.10", "3.11", "3.12", "3.13"
+    ] | None = None
     pinned_package_versions: DictStrStr | None = None
 
     @field_validator(

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/config.py

@@ -405,7 +405,7 @@ class Settings(BaseSettings):
     """
 
     FRACTAL_TASKS_PYTHON_DEFAULT_VERSION: None | (
-        Literal["3.9", "3.10", "3.11", "3.12"]
+        Literal["3.9", "3.10", "3.11", "3.12", "3.13"]
     ) = None
     """
     Default Python version to be used for task collection. Defaults to the
@@ -437,6 +437,11 @@ class Settings(BaseSettings):
     Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.12.
     """
 
+    FRACTAL_TASKS_PYTHON_3_13: str | None = None
+    """
+    Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.13.
+    """
+
     @model_validator(mode="before")
     @classmethod
     def check_tasks_python(cls, values):
@@ -450,7 +455,7 @@ class Settings(BaseSettings):
             `FRACTAL_TASKS_PYTHON_X_Y` (and unset all others).
         """
         # `FRACTAL_TASKS_PYTHON_X_Y` variables can only be absolute paths
-        for version in ["3_9", "3_10", "3_11", "3_12"]:
+        for version in ["3_9", "3_10", "3_11", "3_12", "3_13"]:
             key = f"FRACTAL_TASKS_PYTHON_{version}"
             value = values.get(key)
             if value is not None and not Path(value).is_absolute():
@@ -490,7 +495,7 @@ class Settings(BaseSettings):
             )
 
             # Unset all existing interpreters variable
-            for _version in ["3_9", "3_10", "3_11", "3_12"]:
+            for _version in ["3_9", "3_10", "3_11", "3_12", "3_13"]:
                 key = f"FRACTAL_TASKS_PYTHON_{_version}"
                 if _version == current_version:
                     values[key] = sys.executable

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/tasks/v2/ssh/_utils.py

@@ -69,7 +69,7 @@ def _customize_and_run_template(
     )
 
     # Execute script remotely
-    bash = "bash --login " if login_shell else "bash"
+    bash = "bash --login" if login_shell else "bash"
     cmd = f"{bash} {script_path_remote}"
     logger.debug(f"Now run '{cmd}' over SSH.")
     stdout = fractal_ssh.run_command(cmd=cmd)

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/tasks/v2/utils_pixi.py

@@ -56,8 +56,8 @@ def simplify_pyproject_toml(
 
     Args:
         original_toml_string: Original `pyproject.toml` contents
-        environment: Name of the pixi environment to use (e.g. `default`).
-        target_platform: Name of the platform (e.g. `linux-64`)
+        pixi_environment: Name of the pixi environment to use (e.g. `default`).
+        pixi_platform: Name of the platform (e.g. `linux-64`)
 
     Returns:
         New `pyproject.toml` contents
@@ -78,6 +78,10 @@ def simplify_pyproject_toml(
         pixi_data["workspace"]["platforms"] = [pixi_platform]
     except KeyError:
         logger.info("KeyError for workspace/platforms - skip.")
+    try:
+        pixi_data["project"]["platforms"] = [pixi_platform]
+    except KeyError:
+        logger.info("KeyError for project/platforms - skip.")
 
     # Keep a single environment (or skip, if not set)
     try:

{fractal_server-2.15.6 → fractal_server-2.15.7}/fractal_server/tasks/v2/utils_python_interpreter.py

@@ -21,7 +21,7 @@ def get_python_interpreter_v2(
         interpreter: string representing the python executable or its path
     """
 
-    if python_version not in ["3.9", "3.10", "3.11", "3.12"]:
+    if python_version not in ["3.9", "3.10", "3.11", "3.12", "3.13"]:
         raise ValueError(f"Invalid {python_version=}.")
 
     settings = Inject(get_settings)

{fractal_server-2.15.6 → fractal_server-2.15.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.15.6"
+version = "2.15.7"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -10,10 +10,10 @@ authors = [
 ]
 readme = "README.md"
 license = "BSD-3-Clause"
-requires-python = ">=3.11,<3.13"
+requires-python = ">=3.11,<3.14"
 dependencies = [
     "python-dotenv >=1.1.0,<1.2.0",
-    "fastapi >= 0.115.0, <0.116.0",
+    "fastapi >= 0.116.0, <0.117.0",
     "sqlmodel == 0.0.24",
     "sqlalchemy[asyncio] >=2.0.23,<2.1",
     "fastapi-users[oauth] >=14,<15",
@@ -69,22 +69,22 @@ coverage = {extras = ["toml"], version = "7.5.*"}
 pytest-docker = {version = "3.1.*"}
 mypy = "^1.9"
 pytest-subprocess = "^1.5"
-pyyaml="^6.0.1"
 a2wsgi = "^1.10.0"
 jinja2 = "^3.1.3"
+pyyaml=">=6.0.0"
 
 [tool.poetry.group.docs]
 optional = true
 
 [tool.poetry.group.docs.dependencies]
-mkdocs="1.5.3"
-mkdocstrings = { extras = ["python"], version = "0.25.2" }
-mkdocs-material="9.5.17"
+mkdocs="1.6.1"
+mkdocstrings = { extras = ["python"], version = "0.30.0" }
+mkdocs-material="9.6.15"
 mkdocs-gen-files="0.5.0"
-mkdocs-literate-nav="0.6.1"
-mkdocs-section-index="0.3.8"
-mkdocs-render-swagger-plugin="0.1.1"
-pyyaml="^6.0.1"
+mkdocs-literate-nav="0.6.2"
+mkdocs-section-index="0.3.10"
+mkdocs-render-swagger-plugin="0.1.2"
+pyyaml=">=6.0.0"
 
 [tool.pytest.ini_options]
 asyncio_mode = "auto"
@@ -95,7 +95,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos"]
 
 [tool.bumpver]
-current_version = "2.15.6"
+current_version = "2.15.7"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.15.6/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.15.6"