FIX name the data properly

Accept the weird loacal configuration and embrace neurolibre competible
set up.

- update repo2data requirements
- Makefile to grab data with repo2data
- update all the relevant path

Makefile

@@ -1,27 +1,22 @@
-.PHONY: help atlas data book all
+.PHONY: help data book all
 
 PYTHON ?= python
 
-all: atlas data book figures
+all: data book figures
 
 help:
 	@echo "Please use 'make <target>' where <target> is one of:"
-	@echo "  atlas				to download atlases for analysis"
-	@echo "  data				to download data needed for jupyter book"
+	@echo "  data				to download data needed for jupyter book with repo2data"
 	@echo "  book				to compile the jupyter book"
 	@echo "  figures			to make all manuscript figures"
 	@echo "  all				to run 'atlas', templateflow, and 'book'"
 
-atlas:
-	@echo "Download the original atlases..."
-	if [ ! -d inputs/custome_templateflow ]; then wget -c -O custome_templateflow.tar.gz "https://zenodo.org/record/7362211/files/custome_templateflow.tar.gz?download=1" && mkdir -p inputs && tar xf custome_templateflow.tar.gz -C inputs && rm custome_templateflow.tar.gz; fi
-
 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
+	cd content/notebooks &&	repo2data -r ../../binder/data_requirement.json && cd ../..
 
 book:
 	jb build content --all
 
-figures: inputs/denoise-metrics
+figures: inputs/fmriprep-denoise-benchmark/denoise-metrics
 	$(PYTHON) scripts/make_manuscript_figures.py

binder/data_requirement.json

@@ -1,3 +1,5 @@
-{ "src": "10.5281/zenodo.7764979",
-  "dst": "..",
-  "projectName": "inputs"}
+{ 
+    "src": "10.5281/zenodo.7764979",
+    "dst": "../inputs",
+    "projectName": "fmriprep-denoise-benchmark"
+}

fmriprep_denoise/visualization/utils.py

@@ -47,7 +47,8 @@ def repo2data_path():
 
 def get_data_root():
     """Get motion metric data path root."""
-    default_path = Path(__file__).parents[2] / "inputs"
+    default_path = Path(__file__).parents[2] / \
+        "inputs" / "fmriprep-denoise-benchmark"
     if not (default_path / "data_requirement.json").exists():
         default_path = repo2data_path()
     return default_path

scripts/make_manuscript_figures.py

@@ -25,7 +25,8 @@
 
 
 if __name__ == "__main__":
-    path_root = Path(__file__).parents[1] / "inputs" / "denoise-metrics"
+    path_root = Path(__file__).parents[1] / "inputs" / \
+        "fmriprep-denoise-benchmark" / "denoise-metrics"
     strategy_order = list(utils.GRID_LOCATION.values())
 
     # mean fd