fix import linter

.pre-commit-config.yaml

@@ -20,6 +20,12 @@ repos:
     -   id: yamlfmt
         args: [--mapping, '4', --sequence, '4', --offset, '0']
 
+-   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.12.0
+    hooks:
+    -   id: pretty-format-toml
+        args: [--autofix, --indent, '4']
+
 -   repo: https://github.com/asottile/pyupgrade
     rev: v3.15.1
     hooks:

pyproject.toml

@@ -3,23 +3,9 @@ build-backend = "hatchling.build"
 requires = ["hatchling", "hatch-vcs"]
 
 [project]
-name = "bidsmreye"
-description = "bids app using deepMReye to decode eye motion for fMRI time series data"
-readme = "README.md"
-requires-python = ">=3.9.0"
-license = { file="LICENSE" }
 authors = [
-  { name = "Remi Gau", email = "[email protected]" },
+    {name = "Remi Gau", email = "[email protected]"}
 ]
-keywords = [
-    "BIDS",
-    "brain imaging data structure",
-    "neuroimaging",
-    "automated pipeline",
-    "MRI",
-    "Eyetracking",
-    "Machine learning",
-    ]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
@@ -30,7 +16,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
-    "Topic :: Scientific/Engineering :: Image Processing",
+    "Topic :: Scientific/Engineering :: Image Processing"
 ]
 dependencies = [
     "attrs",
@@ -44,9 +30,24 @@ dependencies = [
     "tomli; python_version < '3.11'",
     "keras<3.0.0"
 ]
+description = "bids app using deepMReye to decode eye motion for fMRI time series data"
 dynamic = ["version"]
+keywords = [
+    "BIDS",
+    "brain imaging data structure",
+    "neuroimaging",
+    "automated pipeline",
+    "MRI",
+    "Eyetracking",
+    "Machine learning"
+]
+license = {file = "LICENSE"}
+name = "bidsmreye"
+readme = "README.md"
+requires-python = ">=3.9.0"
 
 [project.optional-dependencies]
+dev = ["bidsmreye[doc,test,style]"]
 # also stored in docs/requirements.txt
 # to speed up readthedocs build
 doc = [
@@ -56,9 +57,10 @@ doc = [
     "sphinx",
     "sphinx-argparse",
     "sphinx-copybutton",
-    "sphinx-rtd-theme",
+    "sphinx-rtd-theme"
 ]
-style =[
+docs = ["bidsmreye[doc]"]
+style = [
     "black",
     "codespell",
     "flake8",
@@ -67,24 +69,30 @@ style =[
     'types-all',
     'pandas-stubs',
     "pre-commit",
-    "sourcery",
+    "sourcery"
 ]
 test = [
     "pytest",
-    "pytest-cov",
+    "pytest-cov"
 ]
-dev = ["bidsmreye[doc,test,style]"]
-docs = ["bidsmreye[doc]"]
 tests = ["bidsmreye[test]"]
 
-[project.urls]
-Homepage = "https://github.com/cpp-lln-lab/bidsMReye"
-"Bug Tracker" = "https://github.com/cpp-lln-lab/bidsMReye/issues"
-
 [project.scripts]
 bidsmreye = "bidsmreye.bidsmreye:cli"
 bidsmreye_model = "bidsmreye.download:cli"
 
+[project.urls]
+"Bug Tracker" = "https://github.com/cpp-lln-lab/bidsMReye/issues"
+Homepage = "https://github.com/cpp-lln-lab/bidsMReye"
+
+[tool.black]
+line-length = 90
+
+[tool.codespell]
+builtin = "clear,rare"
+ignore-words-list = "fo,slite"
+skip = "*.svg,*.eps,.git,env,*build,.mypy*,outputs,.mypy_cache,moae_fmriprep,bidsmreye/templates/CITATION.bib"
+
 [tool.hatch.build.hooks.vcs]
 version-file = "bidsmreye/_version.py"
 
@@ -94,44 +102,49 @@ packages = ["bidsmreye"]
 [tool.hatch.version]
 source = "vcs"
 
-[tool.black]
-line-length = 90
-
-[tool.codespell]
-skip = "*.svg,*.eps,.git,env,*build,.mypy*,outputs,.mypy_cache,moae_fmriprep,bidsmreye/templates/CITATION.bib"
-builtin = "clear,rare"
-ignore-words-list = "fo,slite"
+[tool.importlinter]
+ignore_imports = [
+    "bidsmreye._version"
+]
+root_package = "bidsmreye"
 
-[tool.vulture]
-min_confidence = 70
-paths = ["bidsmreye"]
-sort_by_size = true
+[[tool.importlinter.contracts]]
+containers = "bidsmreye"
+layers = [
+    "bidsmreye",
+    "prepare_data | generalize | download",
+    "quality_control",
+    "visualize",
+    "bids_utils",
+    "methods",
+    "utils",
+    "configuration",
+    "logging",
+    "defaults"
+]
+name = "Layered architecture"
+type = "layers"
 
 [tool.mypy]
-exclude = ['tests/']
-plugins = "pydantic.mypy"
 check_untyped_defs = true
 disallow_any_generics = true
 disallow_incomplete_defs = true
 disallow_untyped_defs = true
+exclude = ['tests/']
 no_implicit_optional = true
+plugins = "pydantic.mypy"
 warn_redundant_casts = true
 warn_unused_ignores = true
 
-[tool.pydantic-mypy]
-init_forbid_extra = true
-init_typed = true
-warn_required_dynamic_aliases = true
-warn_untyped_fields = true
-
 [[tool.mypy.overrides]]
+ignore_errors = true
 module = [
     'bids.*',
     "bidsmreye._version"
 ]
-ignore_errors = true
 
 [[tool.mypy.overrides]]
+ignore_missing_imports = true
 module = [
     'attrs.*',
     "bidsmreye._version",
@@ -142,15 +155,25 @@ module = [
     'plotly.*',
     'pooch.*',
     'rich.*',
-    'scipy.*',
+    'scipy.*'
 ]
-ignore_missing_imports = true
+
+[tool.pydantic-mypy]
+init_forbid_extra = true
+init_typed = true
+warn_required_dynamic_aliases = true
+warn_untyped_fields = true
 
 [tool.pytest.ini_options]
 addopts = "--cov bidsmreye -ra --strict-config --strict-markers --doctest-modules --showlocals -s -vv --durations=0"
 doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
 junit_family = "xunit2"
+log_cli_level = "INFO"
 minversion = "6.0"
-xfail_strict = true
 testpaths = ["tests"]
-log_cli_level = "INFO"
+xfail_strict = true
+
+[tool.vulture]
+min_confidence = 70
+paths = ["bidsmreye"]
+sort_by_size = true