FIX repo2data

- remove jupyter book build time limit
- use repo2data directly to source data in the jupyterbook
- adjust README.md accordingly
- remove `make book` target

Makefile

@@ -20,7 +20,7 @@ data:
 	@echo "Download input data to build the report"
 	if [ ! -d inputs/denoise-metrics ]; then wget -c -O denoise-metrics.tar.gz "https://zenodo.org/record/7764979/files/denoise-metrics.tar.gz?download=1" && mkdir -p inputs && tar xf denoise-metrics.tar.gz -C inputs && rm denoise-metrics.tar.gz; fi
 
-book: inputs/denoise-metrics
+book:
 	jb build content --all
 
 figures: inputs/denoise-metrics

README.md

@@ -16,7 +16,6 @@ virtualenv env
 source env/bin/activate
 pip install -r binder/requirements.txt
 pip install .
-make data
 make book
 ```
 

content/_config.yml

@@ -11,7 +11,7 @@ only_build_toc_files: true
 # See https://jupyterbook.org/content/execute.html
 execute:
   execute_notebooks: force
-  timeout: 600
+  timeout: -1
 
 # Define the name of the latex output file for PDF builds
 latex:

content/research_report/results-atlas.md

@@ -23,7 +23,7 @@ from fmriprep_denoise.visualization import figures, utils
 import ipywidgets as widgets
 from ipywidgets import interactive, interact
 
-path_root = utils.get_data_root() / "denoise-metrics"
+path_root = utils.repo2data_path() / "denoise-metrics"
 ```
 
 # Results: atlas level

content/research_report/results-group.md

@@ -22,7 +22,7 @@ import ipywidgets as widgets
 from ipywidgets import interactive
 from fmriprep_denoise.visualization import utils
 
-path_root = utils.get_data_root() / "denoise-metrics"
+path_root = utils.repo2data_path() / "denoise-metrics"
 strategy_order = list(utils.GRID_LOCATION.values())
 group_order = {
     "ds000228": ["adult", "child"],

content/supplementary_materials/ohbm2022abstract.md

@@ -20,7 +20,7 @@ warnings.filterwarnings('ignore')
 from fmriprep_denoise.visualization import figures, utils
 from myst_nb import glue
 
-path_root = utils.get_data_root() / "denoise-metrics"
+path_root = utils.repo2data_path() / "denoise-metrics"
 
 # Load metric data
 dataset = 'ds000228'