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Format pyproject.toml file with pyproject-fmt using pre-commit #232

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Sep 26, 2024
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4 changes: 4 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,10 @@ repos:
rev: 1.8.0
hooks:
- id: poetry-check
- repo: https://github.com/tox-dev/pyproject-fmt
rev: "2.2.4"
hooks:
- id: pyproject-fmt
- repo: https://github.com/codespell-project/codespell
rev: v2.2.6
hooks:
Expand Down
63 changes: 32 additions & 31 deletions pyproject.toml
Original file line number Diff line number Diff line change
@@ -1,40 +1,33 @@
[build-system]
build-backend = "poetry_dynamic_versioning.backend"
requires = [ "poetry-core>=1", "poetry-dynamic-versioning>=1,<2" ]

[tool.poetry]
name = "CytoTable"
# note: version data is maintained by poetry-dynamic-versioning (do not edit)
version = "0.0.0"
description = "Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools."
authors = ["Cytomining Community"]
authors = [ "Cytomining Community" ]
license = "BSD-3-Clause License"
packages = [{include = "cytotable"}]
packages = [ { include = "cytotable" } ]
readme = "readme.md"
repository = "https://github.com/cytomining/CytoTable"
documentation = "https://cytomining.github.io/CytoTable/"
keywords = ["python", "cellprofiler","single-cell-analysis", "way-lab"]

[tool.poetry-dynamic-versioning]
enable = true
style = "pep440"
vcs = "git"

[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
build-backend = "poetry_dynamic_versioning.backend"

[tool.setuptools_scm]
keywords = [ "python", "cellprofiler", "single-cell-analysis", "way-lab" ]

[tool.poetry.dependencies]
python = ">=3.8,<3.13"
pyarrow = ">=13.0.0"
cloudpathlib = {extras = ["all", "s3"], version = "^0.18.0"}
cloudpathlib = { extras = [ "all", "s3" ], version = "^0.18.0" }
duckdb = ">=0.8.0,!=0.10.0,>=0.10.1"
parsl = ">=2023.9.25"
numpy = [
{version = "<=1.24.4", python = "<3.12"},
{version = ">=1.26.0", python = ">=3.12"}
{ version = "<=1.24.4", python = "<3.12" },
{ version = ">=1.26.0", python = ">=3.12" },
]
scipy = [
{version = "<1.12.0", python = "<3.9"},
{version = "^1.12.0", python = ">=3.9"}
{ version = "<1.12.0", python = "<3.9" },
{ version = "^1.12.0", python = ">=3.9" },
]

[tool.poetry.group.dev.dependencies]
Expand All @@ -46,29 +39,37 @@ sphinxcontrib-mermaid = "^0.9.0"
cytominer-database = "^0.3.4"
pycytominer = "^1.1.0"
dunamai = "^1.19.0"
botocore = "^1.34.133" # added to help avoid dependency reolution issues
botocore = "^1.34.133" # added to help avoid dependency reolution issues

[tool.vulture]
min_confidence = 80
paths = ["cytotable"]
sort_by_size = true
verbose = true
[tool.poetry-dynamic-versioning]
enable = true
style = "pep440"
vcs = "git"

[tool.setuptools_scm]
root = "."

[tool.isort]
profile = "black"

[tool.bandit]
exclude_dirs = ["tests"]
skips = ["B608"]

[tool.codespell]
ignore-words=".codespell-ignore"
ignore-words = ".codespell-ignore"

[tool.pytest.ini_options]
filterwarnings = [
"ignore::DeprecationWarning:pkg_resources",
"ignore::DeprecationWarning:cytominer_database",
]
markers = [
"large_data_tests: tests which involve the use of large data.",
"large_data_tests: tests which involve the use of large data.",
]

[tool.vulture]
min_confidence = 80
paths = [ "cytotable" ]
sort_by_size = true
verbose = true

[tool.bandit]
exclude_dirs = [ "tests" ]
skips = [ "B608" ]