fractal-server 2.7.1__py3-none-any.whl → 2.8.1__py3-none-any.whl

fractal_server/tasks/v2/utils_package_names.py

@@ -0,0 +1,77 @@
+import re
+
+from fractal_server.logger import get_logger
+
+
+def _parse_wheel_filename(wheel_filename: str) -> dict[str, str]:
+    """
+    Extract distribution and version from a wheel filename.
+
+    The structure of a wheel filename is fixed, and it must start with
+    `{distribution}-{version}` (see
+    https://packaging.python.org/en/latest/specifications/binary-distribution-format
+    ).
+
+    Note that we transform exceptions in `ValueError`s, since this function is
+    also used within Pydantic validators.
+    """
+    if "/" in wheel_filename:
+        raise ValueError(
+            "[_parse_wheel_filename] Input must be a filename, not a full "
+            f"path (given: {wheel_filename})."
+        )
+    try:
+        parts = wheel_filename.split("-")
+        return dict(distribution=parts[0], version=parts[1])
+    except Exception as e:
+        raise ValueError(
+            f"Invalid {wheel_filename=}. Original error: {str(e)}."
+        )
+
+
+def normalize_package_name(name: str) -> str:
+    """
+    Implement PyPa specifications for package-name normalization
+
+    The name should be lowercased with all runs of the characters `.`, `-`,
+    or `_` replaced with a single `-` character. This can be implemented in
+    Python with the re module.
+    (https://packaging.python.org/en/latest/specifications/name-normalization)
+
+    Args:
+        name: The non-normalized package name.
+
+    Returns:
+        The normalized package name.
+    """
+    return re.sub(r"[-_.]+", "-", name).lower()
+
+
+def compare_package_names(
+    *,
+    pkg_name_pip_show: str,
+    pkg_name_task_group: str,
+    logger_name: str,
+) -> None:
+    """
+    Compare the package names from `pip show` and from the db.
+    """
+    logger = get_logger(logger_name)
+
+    if pkg_name_pip_show == pkg_name_task_group:
+        return
+
+    logger.warning(
+        f"Package name mismatch: "
+        f"{pkg_name_task_group=}, {pkg_name_pip_show=}."
+    )
+    normalized_pkg_name_pip = normalize_package_name(pkg_name_pip_show)
+    normalized_pkg_name_taskgroup = normalize_package_name(pkg_name_task_group)
+    if normalized_pkg_name_pip != normalized_pkg_name_taskgroup:
+        error_msg = (
+            f"Package name mismatch persists, after normalization: "
+            f"{pkg_name_task_group=}, "
+            f"{pkg_name_pip_show=}."
+        )
+        logger.error(error_msg)
+        raise ValueError(error_msg)

fractal_server/tasks/v2/{utils.py → utils_python_interpreter.py}

@@ -31,29 +31,3 @@ def get_python_interpreter_v2(
     if value is None:
         raise ValueError(f"Requested {python_version=}, but {key}={value}.")
     return value
-
-
-def _parse_wheel_filename(wheel_filename: str) -> dict[str, str]:
-    """
-    Extract distribution and version from a wheel filename.
-
-    The structure of a wheel filename is fixed, and it must start with
-    `{distribution}-{version}` (see
-    https://packaging.python.org/en/latest/specifications/binary-distribution-format
-    ).
-
-    Note that we transform exceptions in `ValueError`s, since this function is
-    also used within Pydantic validators.
-    """
-    if "/" in wheel_filename:
-        raise ValueError(
-            "[_parse_wheel_filename] Input must be a filename, not a full "
-            f"path (given: {wheel_filename})."
-        )
-    try:
-        parts = wheel_filename.split("-")
-        return dict(distribution=parts[0], version=parts[1])
-    except Exception as e:
-        raise ValueError(
-            f"Invalid {wheel_filename=}. Original error: {str(e)}."
-        )

fractal_server/tasks/v2/utils_templates.py

@@ -0,0 +1,59 @@
+from pathlib import Path
+
+TEMPLATES_DIR = Path(__file__).parent / "templates"
+
+
+def customize_template(
+    *,
+    template_name: str,
+    replacements: list[tuple[str, str]],
+    script_path: str,
+) -> str:
+    """
+    Customize a bash-script template and write it to disk.
+
+    Args:
+        template_filename:
+        templates_folder:
+        replacements:
+    """
+    # Read template
+    template_path = TEMPLATES_DIR / template_name
+    with template_path.open("r") as f:
+        template_data = f.read()
+    # Customize template
+    script_data = template_data
+    for old_new in replacements:
+        script_data = script_data.replace(old_new[0], old_new[1])
+    # Write script locally
+    with open(script_path, "w") as f:
+        f.write(script_data)
+
+
+def parse_script_5_stdout(stdout: str) -> dict[str, str]:
+    """
+    Parse standard output of template 5.
+    """
+    searches = [
+        ("Python interpreter:", "python_bin"),
+        ("Package name:", "package_name"),
+        ("Package version:", "package_version"),
+        ("Package parent folder:", "package_root_parent"),
+        ("Manifest absolute path:", "manifest_path"),
+    ]
+    stdout_lines = stdout.splitlines()
+    attributes = dict()
+    for search, attribute_name in searches:
+        matching_lines = [_line for _line in stdout_lines if search in _line]
+        if len(matching_lines) == 0:
+            raise ValueError(f"String '{search}' not found in stdout.")
+        elif len(matching_lines) > 1:
+            raise ValueError(
+                f"String '{search}' found too many times "
+                f"({len(matching_lines)})."
+            )
+        else:
+            actual_line = matching_lines[0]
+            attribute_value = actual_line.split(search)[-1].strip(" ")
+            attributes[attribute_name] = attribute_value
+    return attributes

fractal_server/utils.py

@@ -14,13 +14,15 @@ This module provides general purpose utilities that are not specific to any
 subsystem.
 """
 import asyncio
+import shlex
+import subprocess  # nosec
 from datetime import datetime
 from datetime import timezone
 from pathlib import Path
-from shlex import split as shlex_split
 from typing import Optional
 
 from .logger import get_logger
+from .string_tools import validate_cmd
 
 
 def get_timestamp() -> datetime:
@@ -30,7 +32,7 @@ def get_timestamp() -> datetime:
     return datetime.now(tz=timezone.utc)
 
 
-async def execute_command(
+async def execute_command_async(
     *,
     command: str,
     cwd: Optional[Path] = None,
@@ -56,7 +58,7 @@ async def execute_command(
         RuntimeError: if the process exited with non-zero status. The error
             string is set to the `stderr` of the process.
     """
-    command_split = shlex_split(command)
+    command_split = shlex.split(command)
     cmd, *args = command_split
 
     logger = get_logger(logger_name)
@@ -75,3 +77,46 @@ async def execute_command(
     if proc.returncode != 0:
         raise RuntimeError(stderr.decode("utf-8"))
     return stdout.decode("utf-8")
+
+
+def execute_command_sync(
+    *,
+    command: str,
+    logger_name: Optional[str] = None,
+    allow_char: Optional[str] = None,
+) -> str:
+    """
+    Execute arbitrary command
+
+    If the command returns a return code different from zero, a `RuntimeError`
+    is raised.
+
+    Arguments:
+        command: Command to be executed.
+        logger_name: Name of the logger.
+        allow_char: Argument propagated to `validate_cmd`.
+    """
+    logger = get_logger(logger_name)
+    logger.debug(f"START subprocess call to '{command}'")
+    validate_cmd(command=command, allow_char=allow_char)
+    res = subprocess.run(  # nosec
+        shlex.split(command),
+        capture_output=True,
+        encoding="utf-8",
+    )
+    returncode = res.returncode
+    stdout = res.stdout
+    stderr = res.stderr
+    logger.debug(f"{returncode=}")
+    logger.debug(f"{stdout=}")
+    logger.debug(f"{stderr=}")
+    if res.returncode != 0:
+        logger.debug(f"ERROR in subprocess call to '{command}'")
+        raise RuntimeError(
+            f"Command {command} failed.\n"
+            f"returncode={res.returncode}\n"
+            f"{stdout=}\n"
+            f"{stderr=}\n"
+        )
+    logger.debug(f"END   subprocess call to '{command}'")
+    return stdout

{fractal_server-2.7.1.dist-info → fractal_server-2.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.7.1
+Version: 2.8.1
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -37,15 +37,20 @@ Description-Content-Type: text/markdown
 
 # Fractal Server
 
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/16e9cf11-d47d-4db8-a9b1-f5349e4175b7" alt="Fractal server" width="400">
+</p>
+
 [![PyPI version](https://img.shields.io/pypi/v/fractal-server?color=gree)](https://pypi.org/project/fractal-server/)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![CI Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml?query=branch%3Amain)
 [![Coverage](https://raw.githubusercontent.com/fractal-analytics-platform/fractal-server/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/python-coverage-comment-action-data/htmlcov/index.html)
-[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![Documentation Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/documentation.yaml/badge.svg)](https://fractal-analytics-platform.github.io/fractal-server)
 [![Benchmarks](https://img.shields.io/badge/Benchmarks-Done-blue)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/benchmark-api/benchmarks/bench.html)
 
 [Fractal](https://fractal-analytics-platform.github.io/) is a framework developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.
 
-![Fractal_overview](https://github.com/user-attachments/assets/286122d9-08cf-48e8-996d-3cf53e0a81c6)
+![Fractal_overview](https://github.com/user-attachments/assets/666c8797-2594-4b8e-b1d2-b43fca66d1df)
 
 This is the server component of the fractal analytics platform.
 Find more information about Fractal in general and the other repositories at
@@ -58,14 +63,12 @@ See https://fractal-analytics-platform.github.io/fractal-server.
 
 # Contributors and license
 
-Unless otherwise stated in each individual module, all Fractal components are
-released according to a BSD 3-Clause License, and Copyright is with Friedrich
-Miescher Institute for Biomedical Research and University of Zurich.
+Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it).
+
+Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.
 
 The SLURM compatibility layer is based on
 [`clusterfutures`](https://github.com/sampsyo/clusterfutures), by
 [@sampsyo](https://github.com/sampsyo) and collaborators, and it is released
 under the terms of the MIT license.
 
-Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it/).
-

{fractal_server-2.7.1.dist-info → fractal_server-2.8.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=e5_mOoPeW4Rbnylz3g2qQviWIKwVN-scjNbLROol4Xc,22
+fractal_server/__init__.py,sha256=_UadKzwkiZjaRG8tsoM0cHEnXlBYpVpNzh9Ld4g5XDg,22
 fractal_server/__main__.py,sha256=dEkCfzLLQrIlxsGC-HBfoR-RBMWnJDgNrxYTyzmE9c0,6146
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -7,7 +7,7 @@ fractal_server/app/models/__init__.py,sha256=aG7mf1zZbsgzDSp7GHEcZhdjHfW3TGPOLCI
 fractal_server/app/models/linkusergroup.py,sha256=LWTUfhH2uAnn_4moK7QdRUIHWtpw-hPZuW-5jClv_OE,610
 fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
 fractal_server/app/models/security.py,sha256=2npjgRKBZ7OAnhAXNbYxjtuOsSm1P4kak__qfk2SpeM,3770
-fractal_server/app/models/user_settings.py,sha256=0YXCAwoAVGqI2irRLdXgr9-JS0STtHhSaoFENigAnrk,1312
+fractal_server/app/models/user_settings.py,sha256=3LodhERbRz3ajjmCnZiU1TOitduKu_9Lyv_Rgdnyusw,1350
 fractal_server/app/models/v1/__init__.py,sha256=hUI7dEbPaiZGN0IbHW4RSmSicyvtn_xeuevoX7zvUwI,466
 fractal_server/app/models/v1/dataset.py,sha256=99GDgt7njx8yYQApkImqp_7bHA5HH3ElvbR6Oyj9kVI,2017
 fractal_server/app/models/v1/job.py,sha256=QLGXcWdVRHaUHQNDapYYlLpEfw4K7QyD8TmcwhrWw2o,3304
@@ -20,7 +20,7 @@ fractal_server/app/models/v2/collection_state.py,sha256=Yx18ZbywjraOdlHFyRVlb3VP
 fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0SRvqS2iOQU,1455
 fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb2-y550,1535
 fractal_server/app/models/v2/project.py,sha256=rAHoh5KfYwIaW7rTX0_O0jvWmxEvfo1BafvmcXuSSRk,786
-fractal_server/app/models/v2/task.py,sha256=YIqPCQY4y0DbgWpDxYkZNApElFoHMEz_9GIP1nEGvUI,3295
+fractal_server/app/models/v2/task.py,sha256=NmDGtSX5kGahAnsvFG__QEpyXCKxO9-E2Y_1lK6kKM8,3712
 fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
 fractal_server/app/models/v2/workflowtask.py,sha256=iDuJYk8kp4PNqGmbKRtGI7y-QsbjkNd_gDsbMzL4i-g,1274
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -43,16 +43,17 @@ fractal_server/app/routes/api/v1/workflow.py,sha256=2T93DuEnSshaDCue-JPmjuvGCtbk
 fractal_server/app/routes/api/v1/workflowtask.py,sha256=OYYConwJbmNULDw5I3T-UbSJKrbbBiAHbbBeVcpoFKQ,5785
 fractal_server/app/routes/api/v2/__init__.py,sha256=jybEV-vrknPoQvbgKJl0QQvHDPHOJXbDUG5vatHeis4,1963
 fractal_server/app/routes/api/v2/_aux_functions.py,sha256=mb4R_qqFxeW0LAis2QJIIfVx8Sydv1jTYaRIMsMxnIk,11720
+fractal_server/app/routes/api/v2/_aux_functions_task_collection.py,sha256=MtUoI0XWHuPSousDeH2IC2WU--AUKQVup6Q6AbHiNUA,4102
 fractal_server/app/routes/api/v2/_aux_functions_tasks.py,sha256=IVzSb7J4ls5qp1HI8WcjRLIq6nx3ffcMI3vUi_aM_gc,10565
-fractal_server/app/routes/api/v2/dataset.py,sha256=Eilf_BAGjicIhqUiVwI86jlW45ineA5sVzxXW4b2GoQ,8329
+fractal_server/app/routes/api/v2/dataset.py,sha256=Y6uZz--YSEGgnPYu05rZ9sr1Ug08bNl2v1h3VeApBe8,9441
 fractal_server/app/routes/api/v2/images.py,sha256=JR1rR6qEs81nacjriOXAOBQjAbCXF4Ew7M7mkWdxBU0,7920
 fractal_server/app/routes/api/v2/job.py,sha256=Bga2Kz1OjvDIdxZObWaaXVhNIhC_5JKhKRjEH2_ayEE,5157
 fractal_server/app/routes/api/v2/project.py,sha256=eWYFJ7F2ZYQcpi-_n-rhPF-Q4gJhzYBsVGYFhHZZXAE,6653
 fractal_server/app/routes/api/v2/status.py,sha256=6N9DSZ4iFqbZImorWfEAPoyoFUgEruo4Hweqo0x0xXU,6435
 fractal_server/app/routes/api/v2/submit.py,sha256=tq-NGnUlpIcm_MRN47rJRHkRcIJ5HiL4Wj1wItJy3o8,8185
-fractal_server/app/routes/api/v2/task.py,sha256=hrYuVT6XDb3eFFUkQJrAf0O9eMDlE4bi0v5iJyQ5J5E,7293
-fractal_server/app/routes/api/v2/task_collection.py,sha256=URtHWrUy83v17uJyIciILYPuZXbGRryw-xO2FC5J9PQ,11581
-fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=kWctxgNi20uwsfHx9l_mwhI50OIxWRESjU9UiCDVVFU,6217
+fractal_server/app/routes/api/v2/task.py,sha256=K0ik33t7vL8BAK5S7fqyJDNdRK4stGqb_73bSa8tvPE,7159
+fractal_server/app/routes/api/v2/task_collection.py,sha256=aCOg9zhRtGfJvRpukS_mSah19jhGEqXaE8hUDOMIZUs,10479
+fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=CTxRy0ghYZahlS6WNr6qRFa0xfAQbbU6xZh6F9VykAY,6212
 fractal_server/app/routes/api/v2/task_group.py,sha256=P32EUYbtGThexSWe5zI9WUFrgoOMof035fJBILTNnfQ,5580
 fractal_server/app/routes/api/v2/workflow.py,sha256=PyvkrUHHzFGUGZE5X0VW5u3DPQA7wtXXNcEpG7-N66I,8687
 fractal_server/app/routes/api/v2/workflow_import.py,sha256=rD26vZ-ztjehvglrERixTeHtXuzepAtgAuPiKRNz84Q,10981
@@ -131,10 +132,10 @@ fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=1fWvQ6YZUUnDhO
 fractal_server/app/runner/v2/task_interface.py,sha256=hT3p-bRGsLNAR_dNv_PYFoqzIF_EQtSsGwl38j1haYA,1824
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
 fractal_server/app/schemas/__init__.py,sha256=stURAU_t3AOBaH0HSUbV-GKhlPKngnnIMoqWc3orFyI,135
-fractal_server/app/schemas/_validators.py,sha256=XKEGEHxp3H6YSJewtFWXe_2Nh7SDdNtAXmlEmJO6Vb0,3606
+fractal_server/app/schemas/_validators.py,sha256=3YBteFMxrEE9DOYlIHvIMsUOWTPSHEZlDL7dUQzBQjs,3616
 fractal_server/app/schemas/user.py,sha256=aUD8YAcfYTEO06TEUoTx4heVrXFiX7E2Mb8D2--4FsA,2130
 fractal_server/app/schemas/user_group.py,sha256=YwJvYgj-PI66LWy38CEd_FIZPsBV1_2N5zJPGFcFvBw,2143
-fractal_server/app/schemas/user_settings.py,sha256=UEST1MSmd9w2YypCji3SONSFlJcr2u4uG3bTczZy_Pk,3102
+fractal_server/app/schemas/user_settings.py,sha256=TalISeEfCrtN8LgqbLx1Q8ZPoeiZnbksg5NYAVzkIqY,3527
 fractal_server/app/schemas/v1/__init__.py,sha256=CrBGgBhoemCvmZ70ZUchM-jfVAICnoa7AjZBAtL2UB0,1852
 fractal_server/app/schemas/v1/applyworkflow.py,sha256=uuIh7fHlHEL4yLqL-dePI6-nfCsqgBYATmht7w_KITw,4302
 fractal_server/app/schemas/v1/dataset.py,sha256=n71lNUO3JLy2K3IM9BZM2Fk1EnKQOTU7pm2s2rJ1FGY,3444
@@ -146,14 +147,14 @@ fractal_server/app/schemas/v1/task.py,sha256=7BxOZ_qoRQ8n3YbQpDvB7VMcxB5fSYQmR5R
 fractal_server/app/schemas/v1/task_collection.py,sha256=uvq9bcMaGD_qHsh7YtcpoSAkVAbw12eY4DocIO3MKOg,3057
 fractal_server/app/schemas/v1/workflow.py,sha256=tuOs5E5Q_ozA8if7YPZ07cQjzqB_QMkBS4u92qo4Ro0,4618
 fractal_server/app/schemas/v2/__init__.py,sha256=97y6QY0I4322CPXQCt3WO3QBWhVkmFgwLn8y2ZwWNR0,2382
-fractal_server/app/schemas/v2/dataset.py,sha256=865ia13E9mWu1DaYyppKW2csNYglaInrScrprdVYX7A,2552
+fractal_server/app/schemas/v2/dataset.py,sha256=Jipcj9LiOOipAeM2Ew113wuNQ6CrbC1nf3KwnNApBco,2638
 fractal_server/app/schemas/v2/dumps.py,sha256=s6dg-pHZFui6t2Ktm0SMxjKDN-v-ZqBHz9iTsBQF3eU,1712
 fractal_server/app/schemas/v2/job.py,sha256=oYSLYkQ0HL83QyjEGIaggtZ117FndzFlONMKWd9sTXM,3270
 fractal_server/app/schemas/v2/manifest.py,sha256=Uqtd7DbyOkf9bxBOKkU7Sv7nToBIFGUcfjY7rd5iO7c,6981
 fractal_server/app/schemas/v2/project.py,sha256=UXEA0UUUe0bFFOVLLmVtvDFLBO5vmD1JVI7EeTIcwDo,756
 fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
 fractal_server/app/schemas/v2/task.py,sha256=FFAbYwDlqowB8gVMdjFVPVHvAM0T89PYLixUth49xfQ,6870
-fractal_server/app/schemas/v2/task_collection.py,sha256=Ddw_7QaQ93kdEIwWQvzLQDu03gho_OHdhah3n0ioK3M,6296
+fractal_server/app/schemas/v2/task_collection.py,sha256=56VWGwOZcgmfZ1bKz-_MSSO8HYwtMAKNBL5tfeQc7uQ,7000
 fractal_server/app/schemas/v2/task_group.py,sha256=oWy7NNsw8Co85qpLyK8FPNTgpAMvx0ZuXjIOVZuLEpM,2466
 fractal_server/app/schemas/v2/workflow.py,sha256=HSNQSrBRdoBzh8Igr76FUWCAWvVzykrqmUv1vGv-8og,2026
 fractal_server/app/schemas/v2/workflowtask.py,sha256=vDdMktYbHeYBgB5OuWSv6wRPRXWqvetkeqQ7IC5YtfA,5751
@@ -174,6 +175,7 @@ fractal_server/migrations/naming_convention.py,sha256=htbKrVdetx3pklowb_9Cdo5Rqe
 fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
 fractal_server/migrations/versions/034a469ec2eb_task_groups.py,sha256=vrPhC8hfFu1c4HmLHNZyCuqEfecFD8-bWc49bXMNes0,6199
 fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py,sha256=-BSS9AFTPcu3gYC-sYbawSy4MWQQx8TfMb5BW5EBKmQ,1450
+fractal_server/migrations/versions/19eca0dd47a9_user_settings_project_dir.py,sha256=Q1Gj1cJ0UrdLBJ5AXfFK9QpxTtmcv-4Z3NEGDnxOme4,961
 fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
 fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py,sha256=Mob8McGYAcmgvrseyyYOa54E6Gsgr-4SiGdC-r9O4_A,1157
 fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py,sha256=5ROUgcoZOdjf8kMt6cxuvPhzHmV6xaCxvZEbhUEyZM4,3271
@@ -198,33 +200,34 @@ fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.p
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
 fractal_server/ssh/_fabric.py,sha256=Pha-gRVUImj1cMsxulrJzaQa6Z60CmMYRAS4o22FcP0,19506
-fractal_server/string_tools.py,sha256=Z4qcleqXSG6RCG4hqS1emm0U-Bvv0sgTm_T87ZdYn7M,2395
+fractal_server/string_tools.py,sha256=XtMNsr5R7GmgzmFi68zkKMedHs8vjGoVMMCXqWhIk9k,2568
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
-fractal_server/tasks/utils.py,sha256=8sbVCxvgfuzGxEhSfnLWRv36Rx4ZUwR7IAPP1TXfJFM,2178
+fractal_server/tasks/utils.py,sha256=lJeaGX0xw4uE_dQGMnFAvmz03gUVh_nv8m47yuwFcKc,1340
 fractal_server/tasks/v1/_TaskCollectPip.py,sha256=ARq5AoHYXH0hziEsb-nFAqbsLA-VIddXOdXL38O6_zA,3746
 fractal_server/tasks/v1/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/tasks/v1/background_operations.py,sha256=zYhqAP3-hedHxF9AMHFf8Y1znoFvC7Lq1qhqJPNROfk,11781
-fractal_server/tasks/v1/endpoint_operations.py,sha256=YyMU1Y3Xt7D9WOKqaMLuwEoIaAqQP2Klz3I-ypAgOLI,5077
+fractal_server/tasks/v1/background_operations.py,sha256=0Zm8TT_RV0BxJCXbruYJCu1eXOkEcHpqnWn_BEe7huw,11829
+fractal_server/tasks/v1/endpoint_operations.py,sha256=NQYvgh-_qEI9YhsLiulfOFPDacCd-rgl3cCbPbkJUA0,5103
 fractal_server/tasks/v1/get_collection_data.py,sha256=5C22jp356rCH5IIC0J57wOu-DCC_kp3B6p68JooN7IM,508
-fractal_server/tasks/v1/utils.py,sha256=J9oKys-82OehBxOon5wWl3CxjVBgYWeVEEyWGVFnreI,1759
+fractal_server/tasks/v1/utils.py,sha256=HYFyNAyZofmf--mVgdwGC5TJpGShIWIDaS01yRr4HxM,1771
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/tasks/v2/_venv_pip.py,sha256=EaauUkFIk4wa79B4OudhV8CYOzgWftTdfz8u4bEdjgo,6555
-fractal_server/tasks/v2/background_operations.py,sha256=jWmg_XkBmcXQfPKJu_eu0wtDL4sMp1QP2bIZ9QtMj_Y,15411
-fractal_server/tasks/v2/background_operations_ssh.py,sha256=_G0rOohkkHLGcvCQyfoMObnII-sxVwrLDW2PKz8IfCQ,13631
+fractal_server/tasks/v2/collection_local.py,sha256=pRGF2NYIc5hwwNZOruyb7RSChWytRMxC2e8WSeMuYMI,13615
+fractal_server/tasks/v2/collection_ssh.py,sha256=Yv8TgUK0yqiRjVo1mHXLbYV2NpTWE_nPzBFGdCPJX0E,13437
 fractal_server/tasks/v2/database_operations.py,sha256=6r56yyFPnEBrXl6ncmO6D76znzISQCFZqCYcD-Ummd4,1213
-fractal_server/tasks/v2/endpoint_operations.py,sha256=MtUoI0XWHuPSousDeH2IC2WU--AUKQVup6Q6AbHiNUA,4102
-fractal_server/tasks/v2/templates/_1_create_venv.sh,sha256=7tt-B6n8KRN-pannZ0enE6XSxyq-hKRYRGY63CvtINI,1151
-fractal_server/tasks/v2/templates/_2_preliminary_pip_operations.sh,sha256=NwkfDtNeT4YjUsqZuK4uN71bTe-wHIn2wmNhflimRo8,595
-fractal_server/tasks/v2/templates/_3_pip_install.sh,sha256=T9sabeB9iQzVZpLfuLkKGz9EpfHkUrJHKWO4HNij6yM,595
+fractal_server/tasks/v2/templates/_1_create_venv.sh,sha256=bfpX3GJtrns1ogidyQHmYaAZjVdQLG-YYazc2GR4z5w,967
+fractal_server/tasks/v2/templates/_2_preliminary_pip_operations.sh,sha256=nRDvTbGljCmJdzfRJz_w-RptyyJoeAtIMiP7NCwVNnU,625
+fractal_server/tasks/v2/templates/_3_pip_install.sh,sha256=nTw8mGmZEVGc-WGDaIK3WVSsJRDuIS8X2l1T3gl34OM,1371
 fractal_server/tasks/v2/templates/_4_pip_freeze.sh,sha256=qHdDKu1svXi1VQKGePciEJK4_uEKuwAvwaDCcGxSvNk,274
-fractal_server/tasks/v2/templates/_5_pip_show.sh,sha256=GrJ19uHYQxANEy9JaeNJZVTquY9c8Ww9eCdnC7eLVr0,1754
-fractal_server/tasks/v2/utils.py,sha256=MnY6MhcxDRo4rPuXo2tQ252eWEPZF3OlCGe-p5MrG9U,1846
+fractal_server/tasks/v2/templates/_5_pip_show.sh,sha256=OdPKVUu3gU0N9ygLoRWvW5rBe8_HO4YCCNX8ulsy9-M,1754
+fractal_server/tasks/v2/utils_background.py,sha256=Q88PtbeyfYXfxupTU9d71EcNRurxKwCjuunXN567SC0,6569
+fractal_server/tasks/v2/utils_package_names.py,sha256=RDg__xrvQs4ieeVzmVdMcEh95vGQYrv9Hfal-5EDBM8,2393
+fractal_server/tasks/v2/utils_python_interpreter.py,sha256=-EWh3Y3VqHLDOWUO_wG_wknqmGqKAD0O2KTLhNjrZaI,948
+fractal_server/tasks/v2/utils_templates.py,sha256=61uz9WSb4BDe6JUyJGiasw8BjVrPAmtc8pnNSJ51yS4,1840
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
-fractal_server/utils.py,sha256=jrlCBPmC7F0ptBVcDac-EbZNsdYTLbHfX9oxkXthS5Q,2193
+fractal_server/utils.py,sha256=BTvNYA8xG-2K42x_hhsKmxrludbSvUbPpbWPq-Dousg,3481
 fractal_server/zip_tools.py,sha256=xYpzBshysD2nmxkD5WLYqMzPYUcCRM3kYy-7n9bJL-U,4426
-fractal_server-2.7.1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.7.1.dist-info/METADATA,sha256=L3ZYv96IVgdninD7rHRXpJ6M7HqL_zh2KMG86cqHtlE,4303
-fractal_server-2.7.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.7.1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.7.1.dist-info/RECORD,,
+fractal_server-2.8.1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.8.1.dist-info/METADATA,sha256=Kg5Q0Ww6lgtblwriHrTueIpkYnal0gCmO9F3JMvf7jc,4588
+fractal_server-2.8.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.8.1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.8.1.dist-info/RECORD,,

fractal_server/tasks/v2/_venv_pip.py

@@ -1,198 +0,0 @@
-from pathlib import Path
-from typing import Optional
-
-from ..utils import COLLECTION_FREEZE_FILENAME
-from fractal_server.app.models.v2 import TaskGroupV2
-from fractal_server.config import get_settings
-from fractal_server.logger import get_logger
-from fractal_server.syringe import Inject
-from fractal_server.tasks.v2.utils import get_python_interpreter_v2
-from fractal_server.utils import execute_command
-
-
-async def _init_venv_v2(
-    *,
-    venv_path: Path,
-    python_version: Optional[str] = None,
-    logger_name: str,
-) -> Path:
-    """
-    Set a virtual environment at `path/venv`
-
-    Args:
-        path : Path
-            path to the venv actual directory (not its parent).
-        python_version : default=None
-            Python version the virtual environment will be based upon
-
-    Returns:
-        python_bin : Path
-            path to python interpreter
-    """
-    logger = get_logger(logger_name)
-    logger.debug(f"[_init_venv_v2] {venv_path=}")
-    interpreter = get_python_interpreter_v2(python_version=python_version)
-    logger.debug(f"[_init_venv_v2] {interpreter=}")
-    await execute_command(
-        command=f"{interpreter} -m venv {venv_path}",
-        logger_name=logger_name,
-    )
-    python_bin = venv_path / "bin/python"
-    logger.debug(f"[_init_venv_v2] {python_bin=}")
-    return python_bin
-
-
-async def _pip_install(
-    task_group: TaskGroupV2,
-    logger_name: str,
-) -> Path:
-    """
-    Install package in venv
-
-    Args:
-        venv_path:
-        task_pkg:
-        logger_name:
-
-    Returns:
-        The location of the package.
-    """
-    settings = Inject(get_settings)
-
-    logger = get_logger(logger_name)
-
-    python_bin = Path(task_group.venv_path) / "bin/python"
-    pip_install_str = task_group.pip_install_string
-    logger.info(f"{pip_install_str=}")
-
-    await execute_command(
-        cwd=Path(task_group.venv_path),
-        command=(
-            f"{python_bin} -m pip install --upgrade "
-            f"'pip<={settings.FRACTAL_MAX_PIP_VERSION}'"
-        ),
-        logger_name=logger_name,
-    )
-    await execute_command(
-        cwd=Path(task_group.venv_path),
-        command=f"{python_bin} -m pip install setuptools",
-        logger_name=logger_name,
-    )
-    await execute_command(
-        cwd=Path(task_group.venv_path),
-        command=f"{python_bin} -m pip install {pip_install_str}",
-        logger_name=logger_name,
-    )
-
-    if task_group.pinned_package_versions:
-        for (
-            pinned_pkg_name,
-            pinned_pkg_version,
-        ) in task_group.pinned_package_versions.items():
-            logger.debug(
-                "Specific version required: "
-                f"{pinned_pkg_name}=={pinned_pkg_version}"
-            )
-            logger.debug(
-                "Preliminary check: verify that "
-                f"{pinned_pkg_name} is already installed"
-            )
-            stdout_show = await execute_command(
-                cwd=Path(task_group.venv_path),
-                command=f"{python_bin} -m pip show {pinned_pkg_name}",
-                logger_name=logger_name,
-            )
-            current_version = next(
-                line.split()[-1]
-                for line in stdout_show.split("\n")
-                if line.startswith("Version:")
-            )
-            if current_version != pinned_pkg_version:
-                logger.debug(
-                    f"Currently installed version of {pinned_pkg_name} "
-                    f"({current_version}) differs from pinned version "
-                    f"({pinned_pkg_version}); "
-                    f"install version {pinned_pkg_version}."
-                )
-                await execute_command(
-                    cwd=Path(task_group.venv_path),
-                    command=(
-                        f"{python_bin} -m pip install "
-                        f"{pinned_pkg_name}=={pinned_pkg_version}"
-                    ),
-                    logger_name=logger_name,
-                )
-            else:
-                logger.debug(
-                    f"Currently installed version of {pinned_pkg_name} "
-                    f"({current_version}) already matches the pinned version."
-                )
-
-    # Extract package installation path from `pip show`
-    stdout_show = await execute_command(
-        cwd=Path(task_group.venv_path),
-        command=f"{python_bin} -m pip show {task_group.pkg_name}",
-        logger_name=logger_name,
-    )
-
-    location = Path(
-        next(
-            line.split()[-1]
-            for line in stdout_show.split("\n")
-            if line.startswith("Location:")
-        )
-    )
-
-    # NOTE
-    # https://packaging.python.org/en/latest/specifications/recording-installed-packages/
-    # This directory is named as {name}-{version}.dist-info, with name and
-    # version fields corresponding to Core metadata specifications. Both
-    # fields must be normalized (see the name normalization specification and
-    # the version normalization specification), and replace dash (-)
-    # characters with underscore (_) characters, so the .dist-info directory
-    # always has exactly one dash (-) character in its stem, separating the
-    # name and version fields.
-    package_root = location / (task_group.pkg_name.replace("-", "_"))
-    logger.debug(f"[_pip install] {location=}")
-    logger.debug(f"[_pip install] {task_group.pkg_name=}")
-    logger.debug(f"[_pip install] {package_root=}")
-
-    # Run `pip freeze --all` and store its output
-    stdout_freeze = await execute_command(
-        cwd=Path(task_group.venv_path),
-        command=f"{python_bin} -m pip freeze --all",
-        logger_name=logger_name,
-    )
-    with (Path(task_group.path) / COLLECTION_FREEZE_FILENAME).open("w") as f:
-        f.write(stdout_freeze)
-
-    return package_root
-
-
-async def _create_venv_install_package_pip(
-    *,
-    task_group: TaskGroupV2,
-    logger_name: str,
-) -> tuple[Path, Path]:
-    """
-    Create venv and install package
-
-    Args:
-        path: the directory in which to create the environment
-        task_pkg: object containing the different metadata required to install
-            the package
-
-    Returns:
-        python_bin: path to venv's python interpreter
-        package_root: the location of the package manifest
-    """
-    python_bin = await _init_venv_v2(
-        venv_path=Path(task_group.venv_path),
-        python_version=task_group.python_version,
-        logger_name=logger_name,
-    )
-    package_root = await _pip_install(
-        task_group=task_group,
-        logger_name=logger_name,
-    )
-    return python_bin, package_root