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Overhaul snakebids create #336

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merged 8 commits into from
Oct 18, 2023
+1,726 −734
Merged

Overhaul snakebids create #336

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780f9aa
Fix newline encoding issue in zip_list print
pvandyken Sep 15, 2023
1062113
Fix 'bids_dirs' typo in tests
pvandyken Sep 15, 2023
420624c
Overhaul of snakebids create
pvandyken Aug 24, 2023
70f198c
Address comments from PR
pvandyken Sep 22, 2023
58cd9bd
Automatically calculate template snakebids version
pvandyken Sep 22, 2023
d7d9be2
Opt out of docker tests
pvandyken Sep 23, 2023
3b6032f
Refactor build backends
pvandyken Sep 23, 2023
b3f69e2
Fix spelling mistake
pvandyken Oct 18, 2023
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171 changes: 31 additions & 140 deletions poetry.lock
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35 changes: 20 additions & 15 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,7 @@ authors = [
"Jason Kai <[email protected]>",
]
license = "MIT"
packages = [
{ include = "snakebids" }
]
packages = [{ include = "snakebids" }]
exclude = ["snakebids/tests/**"]

[tool.poetry-dynamic-versioning]
Expand All @@ -26,12 +24,11 @@ bump = true

[tool.poetry-dynamic-versioning.substitution]
files = [
'snakebids/project_template/cookiecutter.json',
'snakebids/__init__.py'
'snakebids/__init__.py',
]
patterns = [
"(^\\s+\"snakebids_version\":\\s*\")[^'\"]*(\")",
"(^__version__\\s*(?::.*?)?=\\s*['\"])[^'\"]*(['\"])"
"(^__version__\\s*(?::.*?)?=\\s*['\"])[^'\"]*(['\"])",
]

[tool.poetry.dependencies]
Expand All @@ -42,7 +39,6 @@ snakemake = [
{ version = ">=7.18.2", python = ">=3.11" },
]
PyYAML = "^6"
cookiecutter = "^2.1.1"
typing-extensions = ">=3.10.0"
attrs = ">=21.2.0,<24"
boutiques = "^0.5.25"
Expand All @@ -57,15 +53,18 @@ importlib-resources = ">=5.12.0,<7"
# on the python version being used.
numpy = [
{ version = "<=1.24.4", python = "<3.9" },
{ version = ">=1.23.2", python = ">=3.11" }
{ version = ">=1.23.2", python = ">=3.11" },
]
# 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" }
{ version = ">=1.10.0", python = ">=3.9" },
]
# minimum 8.2.0 to use post-copy mesages
copier = ">=8.2.0"
jinja2-time = ">=0.2.0"
# minimum 2.31.0 because of security vulnerability
requests = ">=2.31.0"

[tool.poetry.group.dev.dependencies]
black = "^23.1.0"
Expand All @@ -88,6 +87,7 @@ ruff = "^0.0.285"
pytest-xdist = "^3.3.1"
pytest-split = "^0.8.1"
tomli = "^2.0.1"
requests-mock = "^1.11.0"

[tool.poetry.scripts]
snakebids = "snakebids.admin:main"
Expand All @@ -113,13 +113,18 @@ expr = "platform.python_version()"

[tool.poe.tasks.build-container]
args = [{ name = "container_id", positional = true, required = true }]
uses = { VERSION = "_get_version"}
uses = { VERSION = "_get_version" }
cmd = """
docker build 'containers/${container_id}' \
--tag 'snakebids/${container_id}:${VERSION}' \
--build-arg="PYTHON_VERSION=${VERSION}"
"""

[tool.pytest.ini_options]
markers = [
"docker: marks tests as requiring docker (deselect with '-m \"not docker\"')",
]

[tool.isort]
profile = "black"
multi_line_output = 3
Expand All @@ -133,11 +138,11 @@ reportImportCycles = false

[tool.ruff]
select = [
"E", # pycodestyle error
"F", # pyflakes
"PL", # pylint
"RUF", # ruff
"UP", #pyupgrade
"E", # pycodestyle error
"F", # pyflakes
"PL", # pylint
"RUF", # ruff
"UP", #pyupgrade
"T100", # debugger
]
ignore = ["PLR0913"]
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2 changes: 1 addition & 1 deletion snakebids/admin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ def gen_parser() -> argparse.ArgumentParser:


def main() -> None:
"""Invoke snakebids cli."""
"""Invoke Snakebids cli."""

parser = gen_parser()
args = parser.parse_args()
Expand Down
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