Merge branch 'main' into smri_files

.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"

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
+    correct_mri

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 -----------------------------------------------------
 

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