From 4488833798eaf3d49c2fcd9fd17a72639531df27 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Tue, 9 Apr 2024 15:15:02 -0400 Subject: [PATCH] WIP: minor updates to get working with snakemake>=8.0 The required changes are pretty minimal, just a couple things that have been moved around. I also updated the pyproject since snakemake 8 requires at least python 3.11. NOTE: Still doesn't pass quality checks (pyright stubs), other typing stuff. My local tests were also intermittently failing, but seemed to be going over the runtime. --- poetry.lock | 1851 ++++++++++++++++++----------------- pyproject.toml | 24 +- snakebids/app.py | 4 +- snakebids/tests/test_app.py | 4 +- 4 files changed, 964 insertions(+), 919 deletions(-) diff --git a/poetry.lock b/poetry.lock index 873560ba..2738dbd5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,20 +1,22 @@ -# This file is automatically @generated by Poetry 1.6.1 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" +version = "0.7.16" +description = "A light, configurable Sphinx theme" +category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.9" files = [ - {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, - {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] [[package]] name = "annotated-types" version = "0.6.0" 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-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] -[package.dependencies] -typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} - [[package]] 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 = [ @@ -36,10 +36,23 @@ files = [ {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, ] +[[package]] +name = "argparse-dataclass" +version = "2.0.0" +description = "Declarative CLIs with argparse and dataclasses" +category = "main" +optional = false +python-versions = ">=3.8" +files = [ + {file = "argparse_dataclass-2.0.0-py3-none-any.whl", hash = "sha256:3ffc8852a88d9d98d1364b4441a712491320afb91fb56049afd8a51d74bb52d2"}, + {file = "argparse_dataclass-2.0.0.tar.gz", hash = "sha256:09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f"}, +] + [[package]] name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -53,12 +66,13 @@ 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 = [ @@ -70,6 +84,7 @@ files = [ name = "attrs" version = "23.2.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -89,6 +104,7 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p name = "babel" version = "2.14.0" description = "Internationalization utilities" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -96,9 +112,6 @@ files = [ {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, ] -[package.dependencies] -pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} - 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pathlib-compatible object wrapper for zip files" -optional = false -python-versions = ">=3.8" -files = [ - {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, -] - -[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] - [metadata] lock-version = "2.0" -python-versions = ">=3.8,<4.0" -content-hash = "757f6259ffdcf629d6d88520124a8444a71298186e65a02e86536f8703203dea" +python-versions = ">=3.11,<4.0" +content-hash = "83f4c45dba26cf530605641ce8eeba127051e7bc064a9b35812737d0b4b5a7b9" diff --git a/pyproject.toml b/pyproject.toml index 31ff332b..ae27ac06 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,14 +31,11 @@ patterns = [ [tool.poetry.dependencies] # upper cap imposed by pytest-split -python = ">=3.8,<4.0" +python = ">=3.11,<4.0" # core dep with high breakage potential given plans for redesign, so # keep upper limit pybids = ">=0.16.0,<0.17" -snakemake = [ - { version = ">=5.28.0,<8", python = ">=3.8" }, - { version = ">=7.18.2,<8", python = ">=3.11" }, -] +snakemake = ">=8.0.0" typing-extensions = ">=3.10.0" attrs = ">=21.2.0" boutiques = "^0.5.25" @@ -51,19 +48,12 @@ importlib-resources = ">=5.12.0" # Below are non-direct dependencies (i.e. dependencies of other depenencies) # specified to ensure a version with a pre-built wheel is installed depending # on the python version being used. -numpy = [ - { version = "<=1.24.4", python = "<3.9" }, - { version = ">=1.23.2", python = ">=3.11" }, -] +numpy = ">=1.23.2" + # Use minimum of 1.10.0 because of security vulnerability -scipy = [ - { version = ">=1.10.0,<=1.10.1", python = "<3.9" }, - { version = ">=1.10.0", python = ">=3.9" }, -] -pandas = [ - { version = "<=2.0.3", python = "<3.9" }, - { version = ">=2.1.1", python = ">=3.12" }, -] +scipy = ">=1.10.0" +pandas = ">=2.1.1" + # minimum 8.2.0 to use post-copy mesages copier = ">=8.2.0" jinja2-time = ">=0.2.0" diff --git a/snakebids/app.py b/snakebids/app.py index 2d22d288..9998db85 100644 --- a/snakebids/app.py +++ b/snakebids/app.py @@ -12,7 +12,7 @@ import attr import boutiques.creator as bc # type: ignore import snakemake -from snakemake.io import load_configfile +from snakemake.common.configfile import load_configfile from snakebids.cli import ( SnakebidsArgs, @@ -247,7 +247,7 @@ def run_snakemake(self) -> None: # Run snakemake (passing any leftover args from argparse) # Filter any blank strings before submitting - snakemake.main( # type: ignore + snakemake.cli.main( # type: ignore [ *filter( None, diff --git a/snakebids/tests/test_app.py b/snakebids/tests/test_app.py index b451f092..7256b19e 100644 --- a/snakebids/tests/test_app.py +++ b/snakebids/tests/test_app.py @@ -9,7 +9,7 @@ import hypothesis.strategies as st import pytest -import snakemake +import snakemake.cli from hypothesis import HealthCheck, assume, example, given, settings from pytest_mock.plugin import MockerFixture @@ -122,7 +122,7 @@ def io_mocks(self, mocker: MockerFixture): "write_output_mode": mocker.patch.object(sn_app, "write_output_mode"), "prepare_output": mocker.patch.object(sn_app, "prepare_bidsapp_output"), "write_config": mocker.patch.object(sn_app, "write_config"), - "snakemake": mocker.patch.object(snakemake, "main"), + "snakemake": mocker.patch.object(snakemake.cli, "main"), } @given(