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feat: negative control + NIFTI Writer #76

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df23c47
feat: implement negative control strategies and region handling in im…
jjjermiah Dec 4, 2024
456d366
feat: enhance image processing with improved negative control strateg…
jjjermiah Dec 5, 2024
84ab96e
feat: notebooks
jjjermiah Dec 5, 2024
a590083
feat: add NIFTI file writing capabilities and update Ruff configuration
jjjermiah Dec 5, 2024
9c562b7
feat: implement NIFTI file reading capabilities and update NIFTIWrite…
jjjermiah Dec 5, 2024
03f846f
feat: refactor NegativeControlManager to improve strategy handling an…
jjjermiah Dec 6, 2024
341c037
feat: working neg_control script
jjjermiah Dec 6, 2024
8d58b58
feat: update patient ID logging in neg_control_example script and upg…
jjjermiah Dec 6, 2024
cef1b79
feat: enhance logging in neg_control_example script, improve NIFTIWri…
jjjermiah Dec 7, 2024
6ba5c08
feat: sort ROI names before displaying in roi_names script
jjjermiah Dec 9, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci-cd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ jobs:
locked: false

- name: Run Ruff
run: pixi run lint
run: pixi run qc

################################################################################################
# Semantic-Release: Run semantic-release to automate versioning and publishing
Expand Down
74 changes: 35 additions & 39 deletions config/ruff.toml
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Original file line number Diff line number Diff line change
@@ -1,27 +1,46 @@
cache-dir = "~/.cache/ruff"

# iteratively adding files to the include list
include = [
# "src/readii/loaders.py",
# "src/readii/feature_extraction.py"
"src/readii/loaders.py",
"src/readii/feature_extraction.py",
"src/readii/negative_controls_refactor/**/*.py",
"src/readii/io/**/*.py",
]


# extend-exclude is used to exclude directories from the flake8 checks
extend-exclude = [
"docs/*",
"tests/*",
".pixi/",
"src/readii/image_processing.py",
"src/readii/metadata.py",
"src/readii/negative_controls.py",
"src/readii/pipeline.py",]
"src/readii/pipeline.py",
]

# Same as Black.
line-length = 100


[lint]
# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default.
# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
# McCabe complexity (`C901`) by default.

# [lint] # commented for now, will iterate on this later
# select = [
# "E",
# "F",
# "W", # flake8
# "C", # mccabe
# # "N", # pep8-naming
# "ANN", # flake8-annotations
# "BLE", # flake8-blind-except
# "B", # flake8-bugbear
# "A", # flake8-builtins
# # "G", # flake8-logging-format
# "ERA", # eradicate
# "RUF", # Ruff-specific rules
# "TCH", # flake8-type-checking
# ]
# ignore = ["ANN101"]


select = [
###########################################################################
Expand Down Expand Up @@ -65,6 +84,9 @@ select = [
# Provide clear and explanatory error messages
# https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
"EM",
# Check for McCabe complexity
# https://docs.astral.sh/ruff/rules/complex-structure/
"C",

###########################################################################
# STANDARDS & STYLE
Expand All @@ -83,13 +105,14 @@ select = [

# Pydocstyle
# https://docs.astral.sh/ruff/rules/#pydocstyle-d
# "D",
"D",
]

# Readii uses a lot of camelcase so ignoring pep-8 conventions.
# https://docs.astral.sh/ruff/rules/#pep8-naming-n
# "N",

ignore = [
# allow self to not need type annotations
"ANN101",
# Allow too many arguments for functions
"PLR0913",
# Public Module Docstrings
Expand All @@ -103,7 +126,6 @@ ignore = [
known-first-party = ["readii"]
force-wrap-aliases = true
combine-as-imports = true
lines-after-imports = 1
relative-imports-order = "closest-to-furthest"

[lint.mccabe]
Expand All @@ -120,33 +142,7 @@ convention = "numpy"


[format]

quote-style = "double"
indent-style = "tab"
docstring-code-format = true
docstring-code-line-length = 20


# [lint] # commented for now, will iterate on this later
# select = [
# "E",
# "F",
# "W", # flake8
# "C", # mccabe
# "I", # isort
# "D", # pydocstyle
# # "N", # pep8-naming
# "ANN", # flake8-annotations
# "BLE", # flake8-blind-except
# "B", # flake8-bugbear
# "A", # flake8-builtins
# # "G", # flake8-logging-format
# "ERA", # eradicate
# "RUF", # Ruff-specific rules
# "TCH", # flake8-type-checking
# ]
# ignore = ["ANN101"]

# Readii uses a lot of camelcase so ignoring pep-8 conventions.
# https://docs.astral.sh/ruff/rules/#pep8-naming-n
# "N",
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