fixes

Makefile

@@ -3,4 +3,4 @@ remark: package.json
 	npx remark *.md docs/*.md docs/**/*.md --rc-path .remarkrc
 
 package.json:
-	npm install `cat npm-requirements.txt`
+	npm install `cat npm-requirements.txt`

docs/contributing/contributing.md

@@ -31,7 +31,7 @@ If you are unsure where to start, we list some of the possibilities in the secti
 
     ---
 
-    We want to create [boilerplate method sections](https://github.com/Remi-Gau/eCobidas/tree/main/inputs/boilerplate)
+    We want to create boilerplate method sections
     corresponding to a single item or a set of items of the checklist
     to automate methods writing once the checklist is completed.
 

ecobidas/create_schema.py

@@ -141,7 +141,7 @@ def initialize_activity(items: pd.DataFrame, output_dir: str | Path) -> tuple[Ac
         name=activity_name,
         prefLabel=activity_pref_label,
         output_dir=f"{output_dir}/activities/{activity_name}/",
-        messages = []
+        messages=[],
     )
 
     print_info("activity", activity_pref_label, activity.URI)

ecobidas/inputs/data-dictionary.json

@@ -213,4 +213,4 @@
     "Description": "Unique identifier of the item.",
     "RequirementLevel": "optional"
   }
-}
+}

ecobidas/inputs/neurovault/neurovault.tsv

@@ -85,4 +85,4 @@ Group modeling	7	6	Was this a repeated measures design at the group level?			rad
 Group modeling	7	7	If multiple measurements per subject, list method to account for within subject correlation, exact assumptions made about correlation/variance			textarea			group repeated measures method	group_repeated_measures == 1		group repeated measures method	1	3						5ecb4cfd-88ed-4cfb-9368-a5fe30d1e12f
 Group inference	8	1	Type of statistic that is the basis of the inference			select	Z | T | F | X2 | PostProb | Non-parametric Permutations | Monte Carlo Permutations | other		group statistic type	1		group statistic type	1	2	Describe your statistical inference					54fb8092-087f-4a6c-b433-bad80e6a85f2
 Group inference	8	2	Parameters of the null distribution of the test statisic.		Typically degrees of freedom (should be clear from the test statistic what these are).	float			group statistic parameters	1		group statistic parameters	1	1						30c1374b-3087-418e-8ba7-afc5c48f3c12
-Group inference	8	3	Noise smoothness for statistical inference		This is the estimated smoothness used with Random Field Theory or a simulation-based inference method.	float	0		group smoothness fwhm	1		group smoothness fwhm	1	1						9d9b6e18-4ea8-472e-a148-793749f6704a
+Group inference	8	3	Noise smoothness for statistical inference		This is the estimated smoothness used with Random Field Theory or a simulation-based inference method.	float	0		group smoothness fwhm	1		group smoothness fwhm	1	1						9d9b6e18-4ea8-472e-a148-793749f6704a

ecobidas/item.py

@@ -81,7 +81,7 @@ def get_item_info(this_item: dict) -> dict:
         "visibility": visibility,
         "mandatory": mandatory,
         "sub_section": sub_section,
-        "message": message
+        "message": message,
     }
 
 

tests/data/activities/visibility/visibility_schema.jsonld

@@ -158,4 +158,4 @@
             "jsExpression": "multi_2_or_5 < radio_vis"
         }
     ]
-}
+}

tests/inputs/test.tsv

@@ -17,7 +17,7 @@ activity_order	include	activity	activity_pref_label	preamble	item	item_pref_labe
 5	1		Visibility			radio_vis		4	1	1	1	select one or several answer	radio_multiple	1 | 2 | 3 | 4 | 5 | 6
 5	1		Visibility			multi_gt_5		5	1	radio_vis>5	1	should appear for answers greater than 5	text
 5	1		Visibility			multi_lt_2		6	1	radio_vis<=2	1	should appear for answers less than 2	text
-5	1		Visibility			multi_2_or_5		7	1	radio_vis == 2 OR radio_vis == 5	1	should appear for answers 2 or 5	text		multi_2_or_5 < radio_vis,  Radio vis must be greater than Foo. 
+5	1		Visibility			multi_2_or_5		7	1	radio_vis == 2 OR radio_vis == 5	1	should appear for answers 2 or 5	text		multi_2_or_5 < radio_vis,  Radio vis must be greater than Foo.
 5	1		Visibility			select_boolean		8	1	1	1	select one answer	select	preset:boolean
 5	1		Visibility			select_boolean==1		9	1	select_boolean==1	1	this should only show if you selected ‘yes’	text
 5	1		Visibility			select_boolean==0		10	1	select_boolean==0	1	this should only show if you selected ‘no’	text

tests/test_item.py

@@ -93,7 +93,7 @@ def test_get_item_info():
         "mandatory": True,
         "description": "item name",
         "sub_section": "",
-        "message": None
+        "message": None,
     }
 
     assert item_info == expected
@@ -127,7 +127,7 @@ def test_get_item_info_with_name():
         "mandatory": True,
         "description": "desc",
         "sub_section": "",
-        "message": None        
+        "message": None,
     }
 
     assert item_info == expected
@@ -160,7 +160,7 @@ def test_get_item_info_with_only_name():
         "mandatory": True,
         "description": "desc",
         "sub_section": "",
-                "message": None    
+        "message": None,
     }
 
     assert item_info == expected