bump versions and fix issues

docs/spelling_wordlist.txt

@@ -82,6 +82,7 @@ extraEnvFrom
 filesystem
 FilterFlights
 findable
+formatter
 Fortran
 gapped
 git-lfs
@@ -166,6 +167,7 @@ online
 OpenID
 openssl
 papermill
+parallelize
 param
 parameterizable
 parametrization

pyproject.toml

@@ -50,117 +50,119 @@ Changelog = "https://github.com/swissdatasciencecenter/renku-python/blob/master/
 
 [tool.poetry.dependencies]
 python = ">=3.8.1,<3.12"
-attrs = "~23"
+attrs = "^23.1.0"
 bashlex = "^0.16"
 calamus = "^0.4"
-click = "~8.1"
+click = "~8.1.7"
 click-option-group = "^0.5.2"
 click-plugins = "~1.1.1"
-coverage = { version = "~7.3", extras=["toml"], optional = true }
-cryptography = "^41"
+coverage = { version = "^6.0", extras=["toml"], optional = true }
+cryptography = "^41.0.7"
 cwl-utils = "^0.27"
-cwltool = "~3.1"
-deal = "~4.24"
-deepdiff = "~6.7"
-deepmerge = "~1.1"
-docker = "^5"
-gitpython = "~3.1"
+cwltool = "==3.1.20230601100705"
+deal = "~4.24.3"
+deepdiff = "~6.7.1"
+deepmerge = "~1.1.0"
+docker = "^5.0.3"
+gitpython = "~3.1.40"
 grandalf = "^0.8"
-humanize = "~4.9"
-importlib-resources = "~5.12"
-inject = "~4.3"
-jinja2 = "~3.1"
+humanize = "~4.9.0"
+importlib-resources = "~5.12.0"
+inject = "~4.3.1"
+jinja2 = "~3.1.2"
 networkx = "~3.1"
-packaging = "^23"
+packaging = "^23.2"
 pathspec = "^0.11"
 patool = "~1.12"
-pluggy = "~1.3"
-portalocker = "~2.7"
+pluggy = "~1.3.0"
+portalocker = "~2.7.0"
 poetry-dynamic-versioning = "^0.21"
-psutil = "~5.9"
-pydantic = "~2.5"
-pyjwt = "~2.4"
+psutil = "~5.9.6"
+pydantic = "~2.5.2"
+pyjwt = "~2.4.0"
 pyld = "~2.0.3"
 pyshacl = "^0.25"
-python-dateutil = "~2.8"
-python-gitlab = "~4.2"
-pyyaml = "~6.0"
-rdflib = "^6"
-requests = "~2.31"
-rich = "^13"
-shellingham = "~1.5.1"
+python-dateutil = "~2.8.2"
+python-gitlab = "~4.2.0"
+pyyaml = "~6.0.1"
+rdflib = "^6.3.2"
+requests = "~2.31.0"
+rich = "^13.7.0"
+shellingham = "~1.5.4"
 tabulate = "^0.9"
-toil = "~5.12"
-tqdm = "~4.66"
-werkzeug = "~3.0"
+toil = "~5.12.0"
+tqdm = "~4.66.1"
+werkzeug = "~3.0.1"
 yagup = "^0.1"
-yaspin = "~2.5"
+yaspin = "~2.5.0"
 "zc.relation" = "~2.0"
-zodb = "~5.8"
+zodb = "~5.8.1"
 zstandard = "^0.22"
 
 # service dependencies:
-apispec = { version = "~6.3", optional = true }
-apispec-oneofschema = { version = "^3", optional = true}
+apispec = { version = "~6.3.0", optional = true }
+apispec-oneofschema = { version = "^3.0.0", optional = true}
 apispec-webframeworks = { version = "^0.5", optional = true }
 circus = { version = "^0.18", optional = true }
-flask = { version = "^2", optional = true }
+flask = { version = "^2.3.3", optional = true }
 gunicorn = { version = "*", optional = true }
-marshmallow = { version = "~3.19", optional = true }
+marshmallow = { version = "~3.19.0", optional = true }
 marshmallow-oneofschema = { version = "^3.0.1", optional = true }
-pillow = { version = "^10", optional = true }
+pillow = { version = "^10.1.0", optional = true }
 python-dotenv = { version = "^0.20", optional = true }
-redis = { version = "~5.0", optional = true }
-rq = { version = "~1.15", optional = true }
-sentry-sdk = { version = "~1.38", extras = ["flask"],  optional = true }
+redis = { version = "~5.0.1", optional = true }
+rq = { version = "~1.15.1", optional = true }
+sentry-sdk = { version = "~1.38.0", extras = ["flask"],  optional = true }
 walrus = { version = "^0.9", optional = true }
 prometheus-flask-exporter = "^0.23"
+filetype = "^1.2.0"
+orjson = "^3.9.10"
 
 [tool.poetry.group.dev.dependencies]
-black = "~23.1"
-flake8 = "^6"
+black = "~23.1.0"
+flake8 = "^6.1.0"
 Flake8-pyproject = "==1.2.2"
-isort = "^5"
-mypy = "^1.2.0"
+isort = "^5.12.0"
+mypy = "^1.7.1"
 poetry-lock-package = "^0.5"
-pre-commit = "^3"
-types-PyYAML = "~6.0"
-types-python-dateutil = "^2.8.10"
-types-redis = "~4.0"
-types-requests = "~2.30"
+pre-commit = "^3.5.0"
+types-PyYAML = "~6.0.12.12"
+types-python-dateutil = "^2.8.19.14"
+types-redis = "~4.0.6"
+types-requests = "~2.30.0.0"
 types-tabulate = "^0.9"
 
 [tool.poetry.group.tests]
 optional = true
 
 [tool.poetry.group.tests.dependencies]
-coverage = { version = ">=4.5.3,<7.4", extras=["toml"] }
-fakeredis = { version = ">=1.4.1,<2.11.2", extras = ["lua"]}
-flaky = "==3.7.0"
-pexpect = "<4.9.0,>=4.8.0"
-pydocstyle = "<6.1.2,>=4.0.1"
-pyte = ">=0.8.0,<0.9.0"
-pytest = ">=4.0.0,<7.1.4"
-pytest-black = "<0.3.13,>=0.3.10"
-pytest-cache = "==1.0"
-pytest-cov = "<3.1.0,>=2.5.1"
-pytest-flake8 = ">=1.0.6,<1.1.2"
-pytest-lazy-fixture = ">=0.6.3,<0.7.0"
-pytest-mock = ">=3.2.0,<3.11.0"
-pytest-pep8 = "==1.0.6"
-pytest-recording = "==0.13.0"
-pytest-timeout = "==2.1.0"
-pytest-xdist = ">=1.34.0,<3.4.0"
-responses = ">=0.22.0,<0.24.0"
+coverage = { version = "^6.0", extras=["toml"] }
+fakeredis = { version = "~2.20", extras = ["lua"]}
+flaky = "~3.7.0"
+pexpect = "~4.9"
+pydocstyle = "~6.3"
+pyte = "^0.8"
+pytest = "~7.4"
+pytest-black = "^0.3"
+pytest-cache = "~1.0"
+pytest-cov = "~4.1"
+pytest-flake8 = "~1.1"
+pytest-lazy-fixture = "^0.6"
+pytest-mock = "~3.12"
+pytest-pep8 = "~1.0"
+pytest-recording = "^0.13"
+pytest-timeout = "~2.2"
+pytest-xdist = "~3.5"
+responses = "^0.24"
 
 [tool.poetry.group.docs]
 optional = true
 
 [tool.poetry.group.docs.dependencies]
 plantweb = ">=1.2.1,<1.3.0"
-renku-sphinx-theme = ">=0.2.0"
+renku-sphinx-theme = "^0.4"
 sphinx-click = "^4.3.0"
-sphinx-rtd-theme = "<1.1,>=0.5.0"
+sphinx-rtd-theme = "~1.3"
 sphinx-tabs = "==3.4.1"
 sphinxcontrib-spelling = ">=7,<9"
 
@@ -238,7 +240,7 @@ pattern = """(?x)                                          (?# ignore whitespace
 """
 
 [tool.pytest.ini_options]
-addopts = "--doctest-glob=\"*.rst\" --doctest-modules --cov --cov-report=term-missing --ignore=docs/cheatsheet/"
+addopts = "--doctest-glob=\"*.rst\" --doctest-modules --cov --cov-report=term-missing --ignore=docs/cheatsheet/ --tb=line"
 doctest_optionflags = "ALLOW_UNICODE"
 flake8-ignore = ["*.py", "E121", "E126", "E203", "E226", "E231", "W503", "W504", "docs/conf.py", "docs/cheatsheet/conf.py", "ALL"]
 flake8-max-line-length = 120
@@ -290,6 +292,7 @@ module = [
     "circus",
     "fakeredis",
     "flaky",
+    "filetype.*",
     "grandalf.*",
     "gunicorn.*",
     "humanize",

renku/command/clone.py

@@ -19,13 +19,13 @@
 from typing import Any, Dict, Optional, Union
 
 from git.remote import RemoteProgress
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder.command import Command
 from renku.domain_model.project_context import project_context
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _project_clone(
     url: str,
     path: Optional[Union[str, Path]] = None,

renku/command/config.py

@@ -17,7 +17,7 @@
 
 from typing import Dict, Optional
 
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder.command import Command
 from renku.core import errors
@@ -41,7 +41,7 @@ def _split_section_and_key(key):
     return "renku", key
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _update_multiple_config(
     values: Dict[str, Optional[str]], global_only: bool = False, commit_message: Optional[str] = None
 ):
@@ -70,7 +70,7 @@ def update_multiple_config():
     )
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _update_config(
     key: str,
     *,
@@ -111,7 +111,7 @@ def update_config():
     )
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _read_config(key: Optional[str], config_filter: ConfigFilter = ConfigFilter.ALL, as_string: bool = True):
     """Read configuration.
 

renku/command/doctor.py

@@ -17,7 +17,7 @@
 
 import traceback
 
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder.command import Command
 from renku.command.util import ERROR
@@ -29,7 +29,7 @@
 """
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _doctor_check(fix: bool, force: bool):
     """Check your system and repository for potential problems.
 

renku/command/graph.py

@@ -18,7 +18,7 @@
 import json
 from typing import Dict, List, Optional, Set, Union
 
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder.command import Command, inject
 from renku.command.schema.activity import ActivitySchema, WorkflowFileActivityCollectionSchema
@@ -54,7 +54,7 @@ def export_graph_command():
     return Command().command(export_graph).with_database(write=False).require_migration()
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def export_graph(
     format: str = "json-ld", revision_or_range: Optional[str] = None, strict: bool = False
 ) -> GraphViewModel:

renku/command/log.py

@@ -17,7 +17,7 @@
 
 from typing import List
 
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder import Command, inject
 from renku.command.view_model.log import LogViewModel
@@ -32,7 +32,7 @@ def log_command():
 
 
 @inject.autoparams("activity_gateway", "dataset_gateway")
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _log(
     activity_gateway: IActivityGateway,
     dataset_gateway: IDatasetGateway,

renku/command/mergetool.py

@@ -17,7 +17,7 @@
 
 from pathlib import Path
 
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder.command import Command
 from renku.domain_model.project_context import project_context
@@ -28,7 +28,7 @@ def mergetool_command():
     return Command().command(_mergetool).require_migration().with_database()
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _mergetool(local: Path, remote: Path, base: Path) -> None:
     """Merge renku metadata files.
 
@@ -49,7 +49,7 @@ def mergetool_install_command():
     return Command().command(setup_mergetool)
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def setup_mergetool(with_attributes: bool = True):
     """Setup renku custom mergetool."""
     repository = project_context.repository

renku/command/migrate.py

@@ -18,7 +18,7 @@
 from dataclasses import dataclass
 from typing import List, Optional, Tuple, Union
 
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder.command import Command
 from renku.core.errors import MinimumVersionError
@@ -294,7 +294,7 @@ def _check_project():
     return status | SUPPORTED_RENKU_PROJECT
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _check_immutable_template_files(paths: List[str]):
     """Check paths and return a list of those that are marked immutable in the project template.
 

renku/command/move.py

@@ -19,7 +19,7 @@
 from pathlib import Path
 from typing import List, Optional
 
-from pydantic import validate_arguments
+from pydantic import ConfigDict, validate_call
 
 from renku.command.command_builder import inject
 from renku.command.command_builder.command import Command
@@ -39,7 +39,7 @@ def move_command():
     return Command().command(_move).require_migration().require_clean().with_database(write=True).with_commit()
 
 
-@validate_arguments(config=dict(arbitrary_types_allowed=True))
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def _move(sources: List[str], destination: str, force: bool, verbose: bool, to_dataset: Optional[str]):
     """Move files and check repository for potential problems.