diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4a079703..0013e92f 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,7 +9,7 @@ version: 2 build: os: ubuntu-20.04 tools: - python: "3.9" + python: "3.8" # You can also specify other tool versions: # nodejs: "16" # rust: "1.55" diff --git a/doc/source/api.rst b/doc/source/api.rst index aa80526f..a157ce66 100644 --- a/doc/source/api.rst +++ b/doc/source/api.rst @@ -1,5 +1,5 @@ API -================ +=== This page is the reference for the functions in OSL. @@ -162,9 +162,11 @@ Utility functions for running an OSL Preprocessing pipeline. GLM -****** +*** + GLM Base ++++++++ + Modality specific wrappers for glmtools. .. currentmodule:: osl.glm.glm_base @@ -193,7 +195,7 @@ Modality specific wrappers for glmtools. SensorClusterPerm.get_sig_clusters GLM Epochs -++++++++++++++++++++++++ +++++++++++ .. currentmodule:: osl.glm.glm_epochs @@ -227,7 +229,7 @@ GLM Epochs GLM Spectrum -++++++++++++++++++++++++ +++++++++++++ GLM-Spectrum classes and functions designed to work with GLM-Spectra computed from MNE format sensorspace data @@ -284,11 +286,13 @@ GLM-Spectrum classes and functions designed to work with GLM-Spectra computed fr RHINO -******************** +***** + Tools for Coregistration and forward modeling Coregistration ++++++++++++++ + Deep-level RHINO functions used by wrappers .. currentmodule:: osl.source_recon.rhino.coreg @@ -309,6 +313,7 @@ Deep-level RHINO functions used by wrappers Forward modeling ++++++++++++++++ + Deep-level RHINO functions used by wrappers .. currentmodule:: osl.source_recon.rhino.forward_model @@ -324,7 +329,8 @@ Deep-level RHINO functions used by wrappers FSL-utils -+++++++++++ ++++++++++ + Deep-level RHINO functions used by wrappers .. currentmodule:: osl.source_recon.rhino.fsl_utils @@ -342,7 +348,8 @@ Deep-level RHINO functions used by wrappers Polhemus -+++++++++++ +++++++++ + Deep-level RHINO functions used by wrappers .. currentmodule:: osl.source_recon.rhino.polhemus @@ -358,7 +365,8 @@ Deep-level RHINO functions used by wrappers Surfaces -+++++++++++ +++++++++ + Deep-level RHINO functions used by wrappers .. currentmodule:: osl.source_recon.rhino.surfaces @@ -378,7 +386,8 @@ Deep-level RHINO functions used by wrappers Utils -+++++++++++ ++++++ + Deep-level RHINO functions used by wrappers .. currentmodule:: osl.source_recon.rhino.utils @@ -448,7 +457,7 @@ Deep-level RHINO functions used by wrappers Source Reconstruction -********************** +********************* Pipeline Functions ++++++++++++++++++ @@ -467,6 +476,7 @@ Primary user-level functions for running OSL coregistration and source_recon fun Wrappers ++++++++ + Primary wrapper functions to use in a source_recon configuration .. currentmodule:: osl.source_recon.wrappers @@ -499,6 +509,7 @@ Primary wrapper functions to use in a source_recon configuration Beamforming +++++++++++ + Second-level beamforming functions used by wrappers .. currentmodule:: osl.source_recon.beamforming @@ -533,9 +544,9 @@ Second-level beamforming functions used by wrappers _prepare_beamformer_input - Sign-flipping +++++++++++++ + Second-level sign-flipping functions used by wrappers .. currentmodule:: osl.source_recon.sign_flipping @@ -566,6 +577,7 @@ Second-level sign-flipping functions used by wrappers Utils +++++ + Utility functions for running an OSL Source Recon pipeline. .. currentmodule:: osl.source_recon.batch @@ -580,6 +592,7 @@ Utility functions for running an OSL Source Recon pipeline. Parcellation ************ + Second-level Parcellation functions used by wrappers .. currentmodule:: osl.source_recon.parcellation.parcellation @@ -620,6 +633,7 @@ Second-level Parcellation functions used by wrappers Nifti Utils ++++++++++++ + Second-level Parcellation functions used by wrappers .. currentmodule:: osl.source_recon.parcellation.nii @@ -638,9 +652,11 @@ Second-level Parcellation functions used by wrappers Report ****** + Sensor level ++++++++++++ -.. currentmodule:: osl.report.raw_report + +.. currentmodule:: osl.report.preproc_report .. autosummary:: :toctree: stubs @@ -656,6 +672,7 @@ Sensor level Source level ++++++++++++ + .. currentmodule:: osl.report.src_report .. autosummary:: @@ -685,7 +702,7 @@ File handling Logger -++++++++++++ +++++++ .. currentmodule:: osl.utils.logger @@ -735,4 +752,4 @@ OPM Utilities convert_notts - correct_mri \ No newline at end of file + correct_mri diff --git a/doc/source/conf.py b/doc/source/conf.py index 66dfab65..1ca4efd4 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -6,14 +6,18 @@ # -- Path setup -------------------------------------------------------------- +import os +import sys +import inspect + +__location__ = os.path.join( + os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe())) +) + # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) - +sys.path.insert(0, os.path.join(__location__, "../..")) # -- Project information ----------------------------------------------------- diff --git a/requirements.txt b/requirements.txt index 53dd28db..2c078455 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,36 +1,33 @@ -numpy~=1.22.2 -scipy~=1.8.0 -matplotlib~=3.5.0 -mne==1.0.0 -scikit-learn~=0.0 -fslpy +numpy~=1.23.5 +scipy~=1.10.1 +matplotlib~=3.7.1 +mne==1.3.1 +scikit-learn~=1.2.2 +fslpy~=3.11.3 sails>=1.4.0 glmtools>=0.2.1 -tabulate~=0.8.9 -pyyaml>=5.1 -neurokit2 -jinja2-3.0.3 -file-tree -pymatreader +tabulate~=0.9.0 +pyyaml~=6.0 +neurokit2~=0.2.3 +jinja2~=3.1.2 +pandas~=1.5.3 +nilearn~=0.10.2 +nibabel~=5.0.1 +opencv-python~=4.7.0.72 +numba~=0.56.4 +parse~=1.19.0 +dask~=2023.3.2 +distributed~=2023.3.2 + # Docs -sphinx==4.0.2 +sphinx numpydoc sphinx_gallery pydata-sphinx-theme + # Dev -setuptools>=41.0.1 +setuptools pytest pytest-cov coverage flake8 - -#yaml~=0.2.5 # killing the docs build for some reason -h5py~=3.6.0 -anamnesis~=1.0.3 -pandas~=1.3.5 -nilearn~=0.9.0 -nibabel~=3.2.2 -#scikit-learn~=1.0.2 -opencv-python~=4.5.5.62 -open3d==0.9.0.0 -numba~=0.53.1