Html report per subject

.circleci/config.yml

@@ -0,0 +1,50 @@
+# This config was automatically generated from your source code
+# Stacks detected: cicd:github-actions:.github/workflows,deps:python:.,package_manager:poetry:.,test:tox:.
+version: 2.1
+orbs:
+  python: circleci/python@2
+jobs:
+  test-python:
+    # Install dependencies and run tests
+    docker:
+      - image: cimg/python:3.10-node
+    steps:
+      - checkout
+      - python/install-packages:
+          pkg-manager: poetry
+      - run:
+          name: Check
+          command: poetry run tox -e check -v
+      - run:
+          name: docs
+          command: poetry run tox -e docs -v
+      - run:
+          name: flake8
+          command: poetry run tox -e flake8 -v
+      - run:
+          name: tests
+          command: poetry run pytest
+      - run:
+          name: coverage
+          command: poetry run tox -e report -v
+      - store_test_results:
+          path: junit.xml
+  deploy:
+    # This is an example deploy job, not actually used by the workflow
+    docker:
+      - image: cimg/base:stable
+    steps:
+      # Replace this with steps to deploy to users
+      - run:
+          name: deploy
+          command: '#e.g. ./deploy.sh'
+      - run:
+          name: found github actions config
+          command: ':'
+workflows:
+  build-and-test:
+    jobs:
+      - test-python
+    # - deploy:
+    #     requires:
+    #       - test-python

README.rst

@@ -13,7 +13,7 @@ Overview
     * - docs
       - |docs|
     * - tests, CI & coverage
-      - |github-actions| |codecov| |codacy|
+      - |github-actions| |circleci| |codecov| |codacy|
     * - codeclimate
       - |codeclimate-maintainability| |codeclimate-testcoverage|
     * - version
@@ -31,6 +31,10 @@ Overview
     :alt: GitHub Actions Build Status
     :target: https://github.com/GalKepler/keprep/actions
 
+.. |circleci| image:: https://dl.circleci.com/status-badge/img/circleci/J6A3JWLZsHZMCMZ1aCKdXb/AVFefVDaX15sp62PZ8MpA9/tree/main.svg?style=svg
+    :alt: CircleCI Build Status
+    :target: https://dl.circleci.com/status-badge/redirect/circleci/J6A3JWLZsHZMCMZ1aCKdXb/AVFefVDaX15sp62PZ8MpA9/tree/main
+
 .. |codecov| image:: https://codecov.io/github/GalKepler/keprep/graph/badge.svg?token=LO5CH471O4
     :alt: Coverage Status
     :target: https://app.codecov.io/github/GalKepler/keprep

pyproject.toml

@@ -31,6 +31,11 @@ smriprep = "^0.12.1"
 sdcflows = "^2.5.1"
 tox = "^4.16.0"
 doc8 = "^1.1.1"
+flake8-pyproject = "^1.2.3"
+pytest = "^8.3.2"
+nireports = "^23.2.1"
+setuptools = "^72.1.0"
+dipy = "^1.9.0"
 
 [tool.poetry.dev-dependencies]
 coverage = "^7.5.4"  # testing
@@ -88,3 +93,7 @@ source = [
 omit = [
     "tests/*"
 ]
+
+[tool.flake8]
+max-line-length = 88
+per-file-ignores = ["src/keprep/config.py:E501", "src/keprep/workflows/dwi/descriptions/*.py:E501","src/keprep/interfaces/*.py:E501"]

src/keprep/config.py

@@ -254,7 +254,7 @@ class nipype(_Config):
     memory_gb = None
     """Estimation in GB of the RAM this workflow can allocate at any given time."""
     nprocs = os.cpu_count()
-    """Number of processes (compute tasks) that can be run in parallel (multiprocessing only)."""  # noqa: C0301
+    """Number of processes (compute tasks) that can be run in parallel (multiprocessing only)."""  # noqa: E501
     omp_nthreads = None
     """Number of CPUs a single process can access for multithreaded execution."""
     plugin = "MultiProc"
@@ -342,6 +342,8 @@ class execution(_Config):
     """FreeSurfer's subjects directory."""
     layout = None
     """A :py:class:`~keprep.bids.layout.QSIPrepLayout` object, see :py:func:`init`."""
+    reportlets_dir = None
+    """Path to a directory where reportlets will be stored."""
     log_dir = None
     """The path to a directory that contains execution logs."""
     log_level = 25
@@ -424,6 +426,9 @@ def init(cls):
             cls.participant_label = cls.layout.get_subjects()
         else:
             cls.participant_label = list(cls.participant_label)
+        if cls.reportlets_dir is None:
+            cls.reportlets_dir = Path(cls.work_dir) / "reportlets"
+        cls.reportlets_dir.mkdir(exist_ok=True, parents=True)  # type: ignore[union-attr]
 
 
 # These variables are not necessary anymore
@@ -442,6 +447,10 @@ class workflow(_Config):
 
     anat_only = False
     """Execute the anatomical preprocessing only."""
+    dwi2t1w_method = "epireg"
+    """
+    Method to use for DWI-to-T1w coregistration. Either "epireg" (default) or "flirt"
+    """
     dwi2t1w_dof = 6
     """Degrees of freedom of the DWI-to-T1w registration steps."""
     dwi2t1w_init = "register"
@@ -465,6 +474,19 @@ class workflow(_Config):
     skull_strip_t1w = "force"
     """Skip brain extraction of the T1w image (default is ``force``, meaning that
     *KePrep* will run brain extraction of the T1w)."""
+    denoise_method = "dwidenoise"
+    """Image-based denoising method. Either "dwidenoise" (MRtrix), "patch2self" (DIPY)
+    or "none"."""
+    dwi_denoise_window = "auto"
+    """Window size in voxels for image-based denoising, integer or "auto"."""
+    dwi_no_biascorr = False
+    """DEPRECATED: see --b1-biascorrect-stage."""
+    eddy_config = "--fwhm=0 --flm='quadratic' --repol"
+    """Configuration for running Eddy."""
+    hmc_model = "eddy"
+    """Model used to generate target images for hmc."""
+    b0_threshold = 100
+    """any value in the .bval file less than this will be considered a b=0 image."""
 
 
 class loggers:

src/keprep/data/__init__.py

@@ -0,0 +1,14 @@
+"""fMRIPrep data files
+
+.. autofunction:: load
+
+.. automethod:: load.readable
+
+.. automethod:: load.as_path
+
+.. automethod:: load.cached
+"""
+
+from acres import Loader
+
+load = Loader(__package__)