[FIX] pin keras and fix make file (#197)

* fix some bugs

* use import linter

* do not use pkg resource

* do not treat warnings as errors

* drop python 3.8

* fix import linter

.github/workflows/test_and_coverage.yml

@@ -18,7 +18,7 @@ jobs:
         strategy:
             matrix:
                 os: [ubuntu-latest, macOS-latest] # windows-latest: do not work. antspyx is not available for windows
-                python-version: ['3.8', '3.9', '3.10', '3.11']
+                python-version: ['3.9', '3.10', '3.11']
                 exclude:
                 -   os: macOS-latest # anstpyx install is messed up with macOS and python 3.9
                     python-version: '3.9'

.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:
@@ -31,13 +37,25 @@ repos:
     hooks:
     -   id: flynt
 
+-   repo: https://github.com/seddonym/import-linter
+    rev: v2.0
+    hooks:
+    -   id: import-linter
+
 -   repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
     -   id: isort
         args: [--profile, black]
 
--   repo: https://github.com/psf/black
+-   repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.16.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies:
+        -   black==24.2.0
+
+-   repo: https://github.com/psf/black-pre-commit-mirror
     rev: 24.2.0
     hooks:
     -   id: black
@@ -70,3 +88,7 @@ repos:
         exclude: tests_.*.py|version.*.py|setup.py     # ignore tests and versioneer related code
         args: [--verbose]
         additional_dependencies: [flake8-docstrings]
+
+
+ci:
+    autoupdate_commit_msg: 'chore: update pre-commit hooks'

CITATION.cff

@@ -20,20 +20,25 @@ identifiers:
     value: "10.5281/zenodo.7493322"
 
 contact:
-  - affiliation: "Université catholique de Louvain"
-    email: remi.gau@uclouvain.be
+  - affiliation: "McGill university"
+    email: remi.gau2@mcgill.ca
     family-names: Gau
     given-names: Rémi
 
 authors:
   - family-names: "Gau"
     given-names: "Rémi"
     orcid: "https://orcid.org/0000-0002-1535-9767"
-    affiliation: "Université catholique de Louvain"
+    affiliation: "McGill university"
 
   - family-names: "Cabee"
     given-names: "Pauline"
 
+  - family-names: "Yang"
+    given-names: "Ying"
+    orcid: "https://orcid.org/0000-0002-4157-2975"
+    affiliation: "Université catholique de Louvain"
+
 license: GPL-3.0
 
 keywords:

Makefile

@@ -69,8 +69,8 @@ dist: clean ## builds source and wheel package
 clean-models: ## remove pretrained models
 	rm -fr models/
 
-models: ## gets all pretrained models from OSF
-	bidsmreye_model --model_name all
+models:
+	bidsmreye_model --model_name 1to6
 models/dataset1_guided_fixations.h5:
 	bidsmreye_model
 models/dataset2_pursuit.h5:

bidsmreye/download.py

@@ -5,13 +5,14 @@
 import argparse
 import sys
 import warnings
+from importlib import resources
 from pathlib import Path
 from typing import IO, Any
 
-import pkg_resources
 import pooch
 import rich
 
+import bidsmreye
 from bidsmreye.defaults import available_models, default_model
 from bidsmreye.logging import bidsmreye_log
 
@@ -98,8 +99,9 @@ def download(
         base_url="https://osf.io/download/",
         registry=None,
     )
-    registry_file = pkg_resources.resource_stream("bidsmreye", "models/registry.txt")
-    POOCH.load_registry(registry_file)
+    source = resources.files(bidsmreye).joinpath("models/registry.txt")
+    with resources.as_file(source) as registry_file:
+        POOCH.load_registry(registry_file)
 
     output_file = output_dir.joinpath(f"dataset_{model_name}")
 

pyproject.toml

@@ -3,50 +3,51 @@ 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 = ">=3.8.0"
-license = { file="LICENSE" }
 authors = [
-  { name = "Remi Gau", email = "remi.gau@gmail.com" },
+    {name = "Remi Gau", email = "remi.gau@gmail.com"}
 ]
-keywords = [
-    "BIDS",
-    "brain imaging data structure",
-    "neuroimaging",
-    "automated pipeline",
-    "MRI",
-    "Eyetracking",
-    "Machine learning",
-    ]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
     "Operating System :: Unix",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "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",
-    "chevron",
-    "deepmreye",
+    "chevron>=0.14.0",
+    "deepmreye>=0.2.1",
     "kaleido",
     "pooch>=1.6.0",
     "pybids",
     "rich",
     "tqdm",
-    "tomli; python_version < '3.11'"
+    "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",
@@ -142,9 +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 -vv"
+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"
+testpaths = ["tests"]
+xfail_strict = true
+
+[tool.vulture]
+min_confidence = 70
+paths = ["bidsmreye"]
+sort_by_size = true