diff --git a/poetry.lock b/poetry.lock index 5af5bc9d..46f57530 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -15,6 +16,7 @@ files = [ name = "annotated-types" version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -22,13 +24,11 @@ files = [ {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, ] -[package.dependencies] -typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} - [[package]] name = "anyio" version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -51,6 +51,7 @@ trio = ["trio (>=0.23)"] name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" optional = false python-versions = "*" files = [ @@ -62,6 +63,7 @@ files = [ name = "argparse-dataclass" version = "2.0.0" description = "Declarative CLIs with argparse and dataclasses" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -73,6 +75,7 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -86,12 +89,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "astor" version = "0.8.1" description = "Read/rewrite/write Python ASTs" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" files = [ @@ -103,6 +107,7 @@ files = [ name = "attrs" version = "23.2.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -122,6 +127,7 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p name = "babel" version = "2.15.0" description = "Internationalization utilities" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -129,9 +135,6 @@ files = [ {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, ] -[package.dependencies] -pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} - [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] @@ -139,6 +142,7 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] name = "beautifulsoup4" version = "4.12.3" description = "Screen-scraping library" +category = "dev" optional = false python-versions = ">=3.6.0" files = [ @@ -158,19 +162,48 @@ lxml = ["lxml"] [[package]] name = "bids-validator" -version = "1.14.6" +version = "1.14.7.post0" description = "Validator for the Brain Imaging Data Structure" +category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "bids_validator-1.14.6-py3-none-any.whl", hash = "sha256:e7194193d97bedc6fb173b8606f6d3ed5a467c141f01bca11cd0f38ad1717941"}, - {file = "bids_validator-1.14.6.tar.gz", hash = "sha256:df2b6b5d1aaad61d34ccad0494f2ed73ce3082825ada31954c4e14c2538d485c"}, + {file = "bids_validator-1.14.7.post0-py3-none-any.whl", hash = "sha256:a1ee196eae8e5cf3b3fe9fd1985e03997e3e21a40ea3bcb494ff1e0dcec86a89"}, + {file = "bids_validator-1.14.7.post0.tar.gz", hash = "sha256:e6005a500b75f8a961593fb67d46085107dadb116f59a5c3b524aa0697945b66"}, ] +[package.dependencies] +bidsschematools = ">=0.10" + +[[package]] +name = "bidsschematools" +version = "0.11.3.post3" +description = "Python tools for working with the BIDS schema." +category = "main" +optional = false +python-versions = ">=3.8" +files = [ + {file = "bidsschematools-0.11.3.post3-py3-none-any.whl", hash = "sha256:37bc00f9c31c48dca0bd8bf3825f8f5026b499b22fe6c553843255b7fd8653db"}, + {file = "bidsschematools-0.11.3.post3.tar.gz", hash = "sha256:18630d0045bf83205a76e56eccf379fbd8661d8a7e5d02701bc29005e56429f7"}, +] + +[package.dependencies] +click = "*" +jsonschema = "*" +pyyaml = "*" + +[package.extras] +all = ["codecov", "coverage[toml]", "flake8", "flake8-black", "flake8-isort", "markdown-it-py", "pandas", "pyparsing", "pytest", "pytest-cov", "sphinx (>=1.5.3)", "sphinx-rtd-theme", "tabulate"] +doc = ["sphinx (>=1.5.3)", "sphinx-rtd-theme"] +expressions = ["pyparsing"] +render = ["markdown-it-py", "pandas", "tabulate"] +tests = ["codecov", "coverage[toml]", "flake8", "flake8-black", "flake8-isort", "pytest", "pytest-cov"] + [[package]] name = "boutiques" version = "0.5.26" description = "Schema for describing bash command-line tools" +category = "main" optional = false python-versions = "*" files = [ @@ -190,6 +223,7 @@ all = ["coverage", "docopt", "mock", "nexus-sdk", "oyaml", "pytest", "pytest-run name = "certifi" version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -201,6 +235,7 @@ files = [ name = "cfgv" version = "3.4.0" description = "Validate configuration and produce human readable error messages." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -212,6 +247,7 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -311,6 +347,7 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -325,6 +362,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -336,6 +374,7 @@ files = [ name = "conda-inject" version = "1.3.2" description = "Helper functions for injecting a conda environment into the current python environment (by modifying sys.path, without actually changing the current python environment)." +category = "main" optional = false python-versions = "<4.0,>=3.9" files = [ @@ -350,6 +389,7 @@ pyyaml = ">=6.0,<7.0" name = "configargparse" version = "1.7" description = "A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables." +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -365,6 +405,7 @@ yaml = ["PyYAML"] name = "connection-pool" version = "0.0.3" description = "thread safe connection pool" +category = "main" optional = false python-versions = "*" files = [ @@ -375,6 +416,7 @@ files = [ name = "copier" version = "9.3.1" description = "A library for rendering project templates." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -396,12 +438,12 @@ pydantic = ">=2.4.2" pygments = ">=2.7.1" pyyaml = ">=5.3.1" questionary = ">=1.8.1" -typing-extensions = {version = ">=3.7.4,<5.0.0", markers = "python_version < \"3.9\""} [[package]] name = "coverage" version = "7.5.4" description = "Code coverage measurement for Python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -469,6 +511,7 @@ toml = ["tomli"] name = "datrie" version = "0.8.2" description = "Super-fast, efficiently stored Trie for Python." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -503,6 +546,7 @@ files = [ name = "distlib" version = "0.3.8" description = "Distribution utilities" +category = "dev" optional = false python-versions = "*" files = [ @@ -514,6 +558,7 @@ files = [ name = "docopt" version = "0.6.2" description = "Pythonic argument parser, that will make you smile" +category = "main" optional = false python-versions = "*" files = [ @@ -524,6 +569,7 @@ files = [ name = "docstring-parser" version = "0.16" description = "Parse Python docstrings in reST, Google and Numpydoc format" +category = "dev" optional = false python-versions = ">=3.6,<4.0" files = [ @@ -535,6 +581,7 @@ files = [ name = "docutils" version = "0.20.1" description = "Docutils -- Python Documentation Utilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -546,6 +593,7 @@ files = [ name = "dpath" version = "2.2.0" description = "Filesystem-like pathing and searching for dictionaries" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -557,6 +605,7 @@ files = [ name = "dunamai" version = "1.21.2" description = "Dynamic version generation" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -571,6 +620,7 @@ packaging = ">=20.9" name = "eval-type-backport" version = "0.2.0" description = "Like `typing._eval_type`, but lets older Python versions use newer typing features." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -585,6 +635,7 @@ tests = ["pytest"] name = "exceptiongroup" version = "1.2.1" description = "Backport of PEP 654 (exception groups)" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -599,6 +650,7 @@ test = ["pytest (>=6)"] name = "execnet" version = "2.1.1" description = "execnet: rapid multi-Python deployment" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -613,6 +665,7 @@ testing = ["hatch", "pre-commit", "pytest", "tox"] name = "fastjsonschema" version = "2.20.0" description = "Fastest Python implementation of JSON schema" +category = "main" optional = false python-versions = "*" files = [ @@ -627,6 +680,7 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc name = "filelock" version = "3.15.4" description = "A platform independent file lock." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -643,6 +697,7 @@ typing = ["typing-extensions (>=4.8)"] name = "formulaic" version = "0.5.2" description = "An implementation of Wilkinson formulas." +category = "main" optional = false python-versions = ">=3.7.2" files = [ @@ -652,7 +707,6 @@ files = [ [package.dependencies] astor = ">=0.8" -graphlib-backport = {version = ">=1.0.0", markers = "python_version < \"3.9\""} interface-meta = ">=1.2.0" numpy = ">=1.16.5" pandas = ">=1.0" @@ -664,10 +718,51 @@ wrapt = ">=1.0" arrow = ["pyarrow (>=1)"] calculus = ["sympy (>=1.3,<1.10)"] +[[package]] +name = "fsspec" +version = "2024.6.1" +description = "File-system specification" +category = "main" +optional = false +python-versions = ">=3.8" +files = [ + {file = "fsspec-2024.6.1-py3-none-any.whl", hash = "sha256:3cb443f8bcd2efb31295a5b9fdb02aee81d8452c80d28f97a6d0959e6cee101e"}, + {file = "fsspec-2024.6.1.tar.gz", hash = "sha256:fad7d7e209dd4c1208e3bbfda706620e0da5142bebbd9c384afb95b07e798e49"}, +] + +[package.extras] +abfs = ["adlfs"] +adl = ["adlfs"] +arrow = ["pyarrow (>=1)"] +dask = ["dask", "distributed"] +dev = ["pre-commit", "ruff"] +doc = ["numpydoc", "sphinx", "sphinx-design", "sphinx-rtd-theme", "yarl"] +dropbox = ["dropbox", "dropboxdrivefs", "requests"] +full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"] +fuse = ["fusepy"] +gcs = ["gcsfs"] +git = ["pygit2"] +github = ["requests"] +gs = ["gcsfs"] +gui = ["panel"] +hdfs = ["pyarrow (>=1)"] +http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)"] +libarchive = ["libarchive-c"] +oci = ["ocifs"] +s3 = ["s3fs"] +sftp = ["paramiko"] +smb = ["smbprotocol"] +ssh = ["paramiko"] +test = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "numpy", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "requests"] +test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask-expr", "dask[dataframe,test]", "moto[server] (>4,<5)", "pytest-timeout", "xarray"] +test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard"] +tqdm = ["tqdm"] + [[package]] name = "funcy" version = "2.0" description = "A fancy and practical functional tools" +category = "main" optional = false python-versions = "*" files = [ @@ -679,6 +774,7 @@ files = [ name = "furo" version = "2024.5.6" description = "A clean customisable Sphinx documentation theme." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -696,6 +792,7 @@ sphinx-basic-ng = ">=1.0.0.beta2" name = "gitdb" version = "4.0.11" description = "Git Object Database" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -710,6 +807,7 @@ smmap = ">=3.0.1,<6" name = "gitpython" version = "3.1.43" description = "GitPython is a Python library used to interact with Git repositories" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -724,21 +822,11 @@ gitdb = ">=4.0.1,<5" doc = ["sphinx (==4.3.2)", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "sphinxcontrib-applehelp (>=1.0.2,<=1.0.4)", "sphinxcontrib-devhelp (==1.0.2)", "sphinxcontrib-htmlhelp (>=2.0.0,<=2.0.1)", "sphinxcontrib-qthelp (==1.0.3)", "sphinxcontrib-serializinghtml (==1.1.5)"] test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions"] -[[package]] -name = "graphlib-backport" -version = "1.1.0" -description = "Backport of the Python 3.9 graphlib module for Python 3.6+" -optional = false -python-versions = ">=3.6,<4.0" -files = [ - {file = "graphlib_backport-1.1.0-py3-none-any.whl", hash = "sha256:eccacf9f2126cdf89ce32a6018c88e1ecd3e4898a07568add6e1907a439055ba"}, - {file = "graphlib_backport-1.1.0.tar.gz", hash = "sha256:00a7888b21e5393064a133209cb5d3b3ef0a2096cf023914c9d778dff5644125"}, -] - [[package]] name = "greenlet" version = "3.0.3" description = "Lightweight in-process concurrent programming" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -810,6 +898,7 @@ test = ["objgraph", "psutil"] name = "h11" version = "0.14.0" description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -821,6 +910,7 @@ files = [ name = "humanfriendly" version = "10.0" description = "Human friendly output for text interfaces using Python" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -835,6 +925,7 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve name = "hypothesis" version = "6.105.1" description = "A library for property-based testing" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -868,6 +959,7 @@ zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2024.1)"] name = "identify" version = "2.6.0" description = "File identification library for Python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -882,6 +974,7 @@ license = ["ukkonen"] name = "idna" version = "3.7" description = "Internationalized Domain Names in Applications (IDNA)" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -893,6 +986,7 @@ files = [ name = "imagesize" version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -904,6 +998,7 @@ files = [ name = "immutables" version = "0.20" description = "Immutable Collections" +category = "main" optional = false python-versions = ">=3.8.0" files = [ @@ -957,6 +1052,7 @@ test = ["flake8 (>=5.0,<6.0)", "mypy (>=1.4,<2.0)", "pycodestyle (>=2.9,<3.0)", name = "importlib-metadata" version = "8.0.0" description = "Read metadata from Python packages" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -976,6 +1072,7 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p name = "importlib-resources" version = "6.4.0" description = "Read resources from Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -994,6 +1091,7 @@ testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "p name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1005,6 +1103,7 @@ files = [ name = "interface-meta" version = "1.3.0" description = "`interface_meta` provides a convenient way to expose an extensible API with enforced method signatures and consistent documentation." +category = "main" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -1016,6 +1115,7 @@ files = [ name = "jinja2" version = "3.1.4" description = "A very fast and expressive template engine." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1033,6 +1133,7 @@ i18n = ["Babel (>=2.7)"] name = "jinja2-ansible-filters" version = "1.3.2" description = "A port of Ansible's jinja2 filters without requiring ansible core." +category = "main" optional = false python-versions = "*" files = [ @@ -1051,6 +1152,7 @@ test = ["pytest", "pytest-cov"] name = "jinja2-time" version = "0.2.0" description = "Jinja2 Extension for Dates and Times" +category = "main" optional = false python-versions = "*" files = [ @@ -1066,6 +1168,7 @@ jinja2 = "*" name = "jsonschema" version = "4.23.0" description = "An implementation of JSON Schema validation for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1075,9 +1178,7 @@ files = [ [package.dependencies] attrs = ">=22.2.0" -importlib-resources = {version = ">=1.4.0", 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A base package on which Jupyter projects rely." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1124,6 +1226,7 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout" name = "lazy-loader" version = "0.4" description = "Makes it easy to load subpackages and functions on demand." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1139,24 +1242,11 @@ dev = ["changelist (==0.5)"] lint = ["pre-commit (==3.7.0)"] test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"] -[[package]] -name = "livereload" -version = "2.7.0" -description = "Python LiveReload is an awesome tool for web developers" -optional = false -python-versions = ">=3.7" -files = [ - {file = "livereload-2.7.0-py3-none-any.whl", hash = "sha256:19bee55aff51d5ade6ede0dc709189a0f904d3b906d3ea71641ed548acff3246"}, - {file = "livereload-2.7.0.tar.gz", hash = "sha256:f4ba199ef93248902841e298670eebfe1aa9e148e19b343bc57dbf1b74de0513"}, -] - -[package.dependencies] -tornado = "*" - [[package]] name = "markdown-it-py" version = "3.0.0" description = "Python port of markdown-it. 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+category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3574,6 +3529,7 @@ files = [ name = "typing-extensions" version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3585,6 +3541,7 @@ files = [ name = "tzdata" version = "2024.1" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ @@ -3596,6 +3553,7 @@ files = [ name = "ubelt" version = "1.3.6" description = "A Python utility belt containing simple tools, a stdlib like feel, and extra batteries" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3615,10 +3573,30 @@ tests-strict = ["coverage (==4.3.4)", "coverage (==4.5)", "coverage (==5.3.1)", types = ["autoflake (>=1.4)", "mypy", "yapf (>=0.32.0)"] types-strict = ["autoflake (==1.4)", "mypy", "yapf (==0.32.0)"] +[[package]] +name = "universal-pathlib" +version = "0.2.2" +description = "pathlib api extended to use fsspec backends" +category = "main" +optional = false +python-versions = ">=3.8" +files = [ + {file = "universal_pathlib-0.2.2-py3-none-any.whl", hash = "sha256:9bc176112d593348bb29806a47e409eda78dff8d95391d66dd6f85e443aaa75d"}, + {file = "universal_pathlib-0.2.2.tar.gz", hash = "sha256:6bc215548792ad5db3553708b1c19bafd9e2fa1667dc925ed404c95e52ae2f13"}, +] + +[package.dependencies] +fsspec = ">=2022.1.0" + +[package.extras] +dev = ["adlfs", "aiohttp", "cheroot", "gcsfs", "moto[s3,server] (<5)", "mypy (==1.8.0)", "packaging", "pydantic", "pydantic-settings", "pylint (==2.17.4)", "pytest (==8.0.0)", "pytest-cov (==4.1.0)", "pytest-mock (==3.12.0)", "pytest-sugar (==0.9.7)", "requests", "s3fs", "webdav4[fsspec]", "wsgidav"] +tests = ["mypy (==1.8.0)", "packaging", "pylint (==2.17.4)", "pytest (==8.0.0)", "pytest-cov (==4.1.0)", "pytest-mock (==3.12.0)", "pytest-sugar (==0.9.7)"] + [[package]] name = "urllib3" version = "2.2.2" description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3636,6 +3614,7 @@ zstd = ["zstandard (>=0.18.0)"] name = "uvicorn" version = "0.30.1" description = "The lightning-fast ASGI server." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3655,6 +3634,7 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", name = "virtualenv" version = "20.26.3" description = "Virtual Python Environment builder" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3675,6 +3655,7 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess name = "watchfiles" version = "0.22.0" description = "Simple, modern and high performance file watching and code reload in python." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3762,6 +3743,7 @@ anyio = ">=3.0.0" name = "wcwidth" version = "0.2.13" description = "Measures the displayed width of unicode strings in a terminal" +category = "main" optional = false python-versions = "*" files = [ @@ -3773,6 +3755,7 @@ files = [ name = "websockets" version = "12.0" description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3854,6 +3837,7 @@ files = [ name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3933,6 +3917,7 @@ files = [ name = "yte" version = "1.5.4" description = "A YAML template engine with Python expressions" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3949,6 +3934,7 @@ pyyaml = ">=6.0,<7.0" name = "zipp" version = "3.19.2" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3962,5 +3948,5 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", [metadata] lock-version = "2.0" -python-versions = ">=3.8,<4.0" -content-hash = "54226160563b4a89ec54e25fd3f2ba358794abbd9dde347b1139318441c71fcc" +python-versions = ">=3.9,<4.0" +content-hash = "d3733565c557380df0e540ce369c8b8526ae05a461ba2d6db46ef46bd57a4b6a" diff --git a/pyproject.toml b/pyproject.toml index 8e147a64..810d2170 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,10 +31,10 @@ patterns = [ [tool.poetry.dependencies] # upper cap imposed by pytest-split -python = ">=3.8,<4.0" +python = ">=3.9,<4.0" # core dep with high breakage potential given plans for redesign, so # keep upper limit -pybids = ">=0.16.0,<0.17" +pybids = ">=0.18.1,<0.19" snakemake = [ { version = ">=5.28.0,<8", python = "<3.11" }, { version = ">=7.18.2", python = ">=3.11" }, diff --git a/snakebids/plugins/snakemake.py b/snakebids/plugins/snakemake.py index 30304f6c..97a08c0d 100644 --- a/snakebids/plugins/snakemake.py +++ b/snakebids/plugins/snakemake.py @@ -289,7 +289,7 @@ def finalize_config(self, config: dict[str, Any]): print(err.msg, file=sys.stderr) sys.exit(1) self.cwd = config["output_dir"] - root = Path() + root = "" # uses "" instead of Path() so we drop the leading ./ configfile_path = self.configfile_path or self.snakemake_dir / "snakebids.yaml" if self.configfile_outpath is None: