Who-validation

docker-compose.yml

@@ -3,7 +3,11 @@ services:
     build: .
     container_name: rcpchgrowth-dev
     volumes:
+      # Mount the entire project directory for live development
       - .:/app
+      # Prevent overwriting installed packages and cache directories
+      - /usr/local/lib/python3.12/site-packages
+      - /app/.pytest_cache
     working_dir: /app
     environment:
       - PYTHONPATH=/app

rcpchgrowth/__init__.py

@@ -14,25 +14,3 @@
 from .trisomy_21_aap import select_reference_data_for_trisomy_21_aap
 from .turner import select_reference_data_for_turner
 from .uk_who import select_reference_data_for_uk_who_chart
-
-# Version
-try:
-    from importlib import metadata as _md
-    __version__ = _md.version("rcpchgrowth")
-except Exception:
-    import pathlib, sys
-    _root = pathlib.Path(__file__).resolve().parent.parent
-    _pyproj = _root / "pyproject.toml"
-    _ver = "0.0.0+unknown"
-    if _pyproj.is_file():
-        try:
-            if sys.version_info >= (3, 11):
-                import tomllib
-            else:
-                import tomli as tomllib  # type: ignore
-            with _pyproj.open("rb") as f:
-                _data = tomllib.load(f)
-            _ver = _data.get("project", {}).get("version", _ver)
-        except Exception:
-            pass
-    __version__ = _ver

rcpchgrowth/cdc.py

@@ -26,6 +26,7 @@
 
 # load the reference data
 data_directory = resources.files("rcpchgrowth.data_tables")
+who_data_directory = Path(data_directory, "who/pre_2025")
 
 # data_path = Path(data_directory,"fenton", "fenton.json")  # 23 weeks to 50 weeks - currently not in the code base
 # with open(data_path) as json_file:
@@ -45,7 +46,7 @@
 # public functions
 
 data_path = Path(
-    data_directory, "who_infants.json")  # 2 weeks to 2 years
+    who_data_directory, "who_infants.json")  # 2 weeks to 2 years
 with open(data_path) as json_file:
     WHO_INFANTS_DATA = json.load(json_file)
     json_file.close()

rcpchgrowth/constants/reference_constants.py

@@ -35,8 +35,8 @@
 WHO_REFERENCES = [WHO_2006_INFANT, WHO_2006_CHILD, WHO_2007_CHILD] # WHO references
 
 WHO_2006_REFERENCE_LOWER_THRESHOLD = ((42 * 7) - (40 * 7)) / 365.25  # 42 weeks as decimal age  # 2 weeks as decimal age
-WHO_2006_REFERENCE_UPPER_THRESHOLD = 5.0  # 5 years as decimal age
-WHO_2007_REFERENCE_LOWER_THRESHOLD = 5.0  # 5 years as decimal age
+WHO_2006_REFERENCE_UPPER_THRESHOLD = 1856/365.25  # 5 years and one month just under as decimal age
+WHO_2007_REFERENCE_LOWER_THRESHOLD = (61/30.4375)/365.25  # 5 years and one month as decimal age (61 mths)
 WHO_2007_REFERENCE_UPPER_THRESHOLD = 19.0  # 19 years as decimal age
 
 # 23 weeks is the lowest decimal age available on the UK90 charts

rcpchgrowth/data_tables/bayley_pinneau/bayley_pinneau_boys_advanced.csv

@@ -0,0 +1,43 @@
+SKELETAL AGES 7 THROUGH 11 YEARS,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Skeletal Age,7-0,7-3,7-6,7-9,8-0,8-3,8-6,8-9,9-0,9-3,9-6,9-9,10,10-3,10-6,10-9,11,11-3,11-6,11-9,12-0,12-3,12-6,12-9,13-0,13-3,13-6,13-9,14-0,14-3,14-6,14-9,15-0,15-3,15-6,15-9,16-0,16-3,16-6,16-9,17-0
+% of Mature Height,67,67.6,68.3,68.9,69.6,70.3,70.9,71.5,72,72.8,73.4,74.1,74.7,75.3,75.8,76.3,76.7,77.6,77.8,80,80.9,81.8,82.8,83.9,85,86.3,87.5,89,90.5,91.8,93,94.3,95.8,96.7,97.1,97.6,98,98.3,98.5,98.8,
+Ht. (inches),,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+41,61.2,60.7,60,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+42,62.7,62.1,61.5,61,60.3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+43,64.2,63.6,63,62.4,61.8,61.2,60.6,60.1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+44,65.7,65.1,64.4,63.8,63.2,62.6,62.1,61.5,61.1,60.4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+45,67.2,66.6,65.9,65.3,64.7,64,63.5,62.9,62.5,61.8,61.3,60.7,60.2,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+46,68.7,68,67.3,66.8,66.1,65.4,64.9,64.3,63.9,63.2,62.7,62.1,61.6,61.1,60.7,60.3,60,,,,,,,,,,,,,,,,,,,,,,,,
+47,70.1,69.5,68.8,68.2,67.5,66.9,66.3,65.7,65.3,64.6,64,63.4,62.9,62.4,62,61.6,61.3,60.6,,,,,,,,,,,,,,,,,,,,,,,
+48,71.6,71,70.3,69.7,69,68.3,67.7,67.1,66.7,65.9,65.4,64.8,64.3,63.7,63.3,62.9,62.6,61.9,61.1,60,,,,,,,,,,,,,,,,,,,,,
+49,73.1,72.5,71.7,71.1,70.4,69.7,69.1,68.5,68.1,67.3,66.8,66.1,65.6,65.1,64.6,64.2,63.9,63.1,62.3,61.3,60.6,,,,,,,,,,,,,,,,,,,,
+50,74.6,74,73.2,72.6,71.8,71.1,70.5,69.9,69.4,68.7,68.1,67.5,66.9,66.4,66,65.3,65.2,64.4,63.6,62.5,61.8,61.1,60.4,,,,,,,,,,,,,,,,,,
+51,76.2,75.4,74.7,74,73.3,72.5,71.9,71.3,70.8,70.1,69.5,68.8,68.3,67.7,67.3,66.8,66.5,65.7,64.9,63.8,63,62.3,61.6,60.8,60,,,,,,,,,,,,,,,,
+52,77.6,76.9,76.1,75.5,74.7,74,73.3,72.7,72.2,71.4,70.8,70.2,69.6,69.1,68.6,68.2,67.8,67.3,66.2,66,64.3,63.6,62.8,62,61.2,60.3,,,,,,,,,,,,,,,
+53,79.1,78.4,77.6,76.9,76.2,75.4,74.8,74.1,73.6,72.8,72.2,71.5,71,70.4,69.9,69.5,69.1,68.3,67.4,66.3,65.5,64.8,64,63.2,62.4,61.4,60.6,,,,,,,,,,,,,,
+54,80.6,79.9,79.1,78.4,77.6,76.8,76.2,75.5,75,74.2,73.6,72.9,72.3,71.7,71.2,70.8,70.4,69.6,68.7,67.5,66.7,66,65.2,64.4,63.6,62.9,62.1,60.7,,,,,,,,,,,,,
+55,,,80.5,79.8,79,78.3,77.6,76.9,76.4,75.9,75.2,74.6,73.6,73,72.6,72.1,71.7,70.9,70,68.8,68,67.2,66.4,65.6,64.7,63.9,63,61.8,60.8,,,,,,,,,,,,
+56,,,,,,80.5,79.7,79,78.3,77.8,77.1,76.6,75,74.4,73.9,73.4,73,72.2,71.2,70,69.2,68.5,67.6,66.7,65.9,64.9,64,62.9,61.9,61,60.2,,,,,,,,,,
+57,,,,,,,,80.4,79.7,79.2,78.5,77.8,76.3,75.7,75.2,74.7,74.3,73.5,72.5,71.3,70.5,69.7,68.8,67.9,67.1,66,65.1,64,63,62.1,61.3,60.4,,,,,,,,,
+58,,,,,,,,,80.6,79.7,79,78.3,77.6,77,76.5,76,75.6,74.7,73.8,72.5,71.7,70.9,70,69.1,68.2,67.2,66.3,65.2,64.1,63.2,62.4,61.5,60.5,60,,,,,,,
+59,,,,,,,,,,,80.4,79.6,79,78.4,77.8,77.3,76.9,76,75.1,73.8,72.9,72.1,71.3,70.3,69.4,68.4,67.4,66.3,65.2,64.3,63.4,62.6,61.6,61,60.8,,,,,,
+60,,,,,,,,,,,,,80.3,79.7,79.2,78.6,78.2,76,76.3,75,74.2,73.4,72.5,71.5,70.6,69.5,68.6,67.4,66.3,65.4,64.5,63.6,62.6,62,61.8,60.5,60.2,60,,,
+61,,,,,,,,,,,,,,,80.5,79.9,79.5,76.3,77.6,76.3,75.4,74.6,73.7,72.7,71.8,70.7,69.7,68.6,67.4,66.4,65.6,64.7,63.7,63.1,62.8,61.5,61.2,61,60.9,60.7,60.6
+62,,,,,,,,,,,,,,,,81.3,80.8,77.9,78.9,77.5,76.6,75.8,74.9,73.9,72.9,71.8,70.9,69.7,68.5,67.5,66.7,65.7,64.7,64.1,63.9,62.6,62.2,62.1,61.9,61.7,61.6
+63,,,,,,,,,,,,,,,,,,,80.2,78.8,77.9,77,76.1,75.1,74.1,73,72,70.8,69.6,68.7,67.7,66.8,65.8,65.1,64.9,63.5,63.1,62.9,62.8,62.6,62.6
+64,,,,,,,,,,,,,,,,,,,,80,79.1,78.2,77.3,76.3,75.3,74.2,73.1,71.9,70.7,69.7,68.7,67.9,66.8,66.2,65.9,64.5,64.3,64.1,64,63.8,63.6
+65,,,,,,,,,,,,,,,,,,,,,80.3,79.5,78.5,77.5,76.5,75.3,74.3,73,71.8,70.8,70,68.9,67.8,67.2,66.9,65.6,65.3,65.1,65,64.8,64.6
+66,,,,,,,,,,,,,,,,,,,,,,80.7,79.7,78.7,77.6,76.5,75.4,74.2,72.9,71.9,71,70,68.9,68.3,68,66.6,66.3,66.1,66,65.8,65.7
+67,,,,,,,,,,,,,,,,,,,,,,,80.9,79.9,78.8,77.6,76.6,75.4,74,73,72.2,71.1,70,69.3,69,67.6,67.3,67.1,67,66.8,66.7
+68,,,,,,,,,,,,,,,,,,,,,,,,,80,78.8,77.7,76.4,75.1,74.1,73.1,72.1,71,70.3,70,68.6,68.4,68.2,68,67.8,67.7
+69,,,,,,,,,,,,,,,,,,,,,,,,,,80,78.9,77.8,76.2,75.2,74.2,73.2,72,71.4,71.1,69.7,69.4,69.2,69,68.8,68.7
+70,,,,,,,,,,,,,,,,,,,,,,,,,,,80,78.7,77.3,76.3,75.3,74.2,73.1,72.4,72.1,70.7,70.4,70.2,70,69.8,69.7
+71,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.9,79.6,78.4,77.3,76.3,75.3,74.1,73.4,73.1,71.7,71.4,71.2,71.1,70.8
+72,,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.7,79.5,78.5,77.4,76.2,75.2,74.5,74.2,72.7,72.4,72.2,72.1,71.9
+73,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.6,79.6,78.5,77.2,76.2,75.2,74.5,73.8,73.5,72.7,72.4,72.2
+74,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.6,79.5,78.3,77.2,76.2,75.2,74.5,73.8,73.5,72.7,72.4
+75,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.6,79.5,78.3,77.2,76.2,75.2,74.5,73.8,73.5,72.7
+76,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.4,79.6,78.3,77.3,76.2,75.2,74.5,73.8,73.5
+77,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.4,79.6,78.3,77.3,76.2,75.2,74.5,73.8
+78,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,80.7,79.8,78.9,78.2,77.5,76.8,76.1
+79,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,79.9,79.8,79.3,79.2,78.9,78.8

rcpchgrowth/data_tables/bayley_pinneau/bayley_pinneau_boys_delayed.csv

@@ -0,0 +1,31 @@
+Skeletal Age,6-0,6-3,6-6,6-9,7-0,7-3,7-6,7-9,8-0,8-3,8-6,8-9,9-0,9-3,9-6,9-9,10-0,10-3,10-6,10-9,11-0,11-3,11-6,11-9,12-0,12-3,12-6,12-9,13-0
+% of Mature Height,68,69,70,70.9,71.8,72.8,73.8,74.7,75.6,76.5,77.3,77.9,78.6,79.4,80,80.7,81.2,81.6,81.9,82.1,82.3,82.7,83.2,83.9,84.5,85.2,86,86.9,88
+Mature Height,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Ht. (inches),,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+41,60.3,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+42,61.8,60.9,60,,,,,,,,,,,,,,,,,,,,,,,,,,
+43,63.2,62.3,61.4,60.6,,,,,,,,,,,,,,,,,,,,,,,,,
+44,64.7,63.8,62.9,62.1,61.3,60.4,,,,,,,,,,,,,,,,,,,,,,,
+45,66.2,65.2,64.3,63.5,62.7,61.8,61,60.2,,,,,,,,,,,,,,,,,,,,,
+46,67.6,66.7,65.7,64.9,64.1,63.2,62.3,61.6,60.8,,,,,,,,,,,,,,,,,,,,
+47,69.1,68.1,67.1,66.3,65.5,64.6,63.7,62.9,62.2,60.1,,,,,,,,,,,,,,,,,,,
+48,70.6,69.6,68.6,67.7,66.9,65.9,65,64.3,63.5,61.4,60.8,60.3,,,,,,,,,,,,,,,,,
+49,72.1,71,70,69.1,68.3,67.3,66.4,65.6,64.8,62.7,62.1,61.6,61.1,60.5,60,,,,,,,,,,,,,,
+50,73.5,72.5,71.4,70.5,69.6,68.7,67.8,66.9,66.1,64.1,63.4,62.9,62.3,61.7,61.3,60.7,60.3,60,,,,,,,,,,,
+51,75,73.9,72.9,71.9,71,70.1,69.3,68.5,67.5,65.4,64.7,64.2,63.6,63,62.5,62,61.6,61.3,61.1,60.9,60.8,60.5,60.1,,,,,,
+52,76.5,75.4,74.3,73.3,72.4,71.4,70.5,69.8,68.8,66.7,66,65.5,64.9,64.2,63.8,63.2,62.8,62.5,62.3,62.1,62,61.7,61.3,60.8,60.4,,,,
+53,77.9,76.8,75.7,74.8,73.8,72.8,71.8,71,70.1,68,67.3,66.8,66.2,65.5,65,64.4,64,63.7,63.5,63.3,63.2,62.9,62.5,62,61.5,61,60.5,,
+54,79.4,78.3,77.1,76.2,75.2,74.2,73.2,72.3,71.4,69.3,68.6,68,67.4,66.8,66.3,65.7,65.3,65,64.7,64.4,64.1,64.1,63.7,63.2,62.7,62.2,61.6,61,60.2
+55,80.9,79.7,78.6,77.6,76.6,75.5,74.5,73.6,72.8,70.6,69.9,69.3,68.7,68,67.5,66.9,66.5,66.2,65.9,65.8,65.6,65.3,64.9,64.4,63.9,63.4,62.8,62.1,61.4
+56,,,80,79,78,76.9,75.9,75,74.1,71.9,71.2,70.6,70,69.3,68.8,68.2,67.7,67.4,67.2,67,66.8,66.5,66.1,65.6,65.1,64.6,64,63.3,62.5
+57,,,,80.4,79.4,78.3,77.2,76.3,75.4,73.2,72.4,71.9,71.2,70.5,70,69.4,69,68.6,68.4,68.2,68,67.7,67.3,66.7,66.3,65.7,65.1,64.4,63.6
+58,,,,,80.8,79.7,78.6,78.8,76.7,74.5,73.7,73.2,72.5,71.8,71.3,70.6,70.2,69.9,69.6,69.4,69.3,68.9,68.5,67.9,67.5,66.9,66.3,65.6,64.8
+59,,,,,,,79.9,79,78,75.8,75,74.5,73.8,73,72.5,72.5,71.4,71.1,71.1,70.8,70.5,70.5,70.1,69.7,69.1,68.6,67.4,67.4,65.9
+60,,,,,,,,80.3,79.4,77.1,77.6,75.7,75.1,74.3,73.8,73.1,72.7,72.3,72,71.9,71.7,71.3,70.9,70.3,69.8,69.2,68.8,68.8,67
+61,,,,,,,,,80.7,78.4,78.1,77,76.3,75.6,75,74.4,73.9,73.5,73.3,73.1,72.9,72.6,72.1,71.5,71,70.4,69.8,69.8,68.2
+62,,,,,,,,,,79.7,78.9,78.3,77.6,76.8,76.3,75.6,75.1,74.8,74.5,74.3,74.1,73.8,73.3,72.7,72.2,71.6,70.9,70.9,69.3
+63,,,,,,,,,,,80.2,79.6,78.9,78.1,77.5,76.8,76.4,76,75.7,75.5,75.3,75,74.5,73.9,73.4,72.8,72.1,72.1,70.5
+64,,,,,,,,,,,,80.9,80.2,79.3,78.8,78.1,77.6,77.2,76.9,76.7,76.5,76.2,75.7,75.1,74.5,73.9,73.3,73.3,71.6
+65,,,,,,,,,,,,,,80.6,80,79.3,78.8,78.4,78.1,78,77.8,77.4,76.9,76.3,75.7,75.1,74.4,74.4,72.7
+66,,,,,,,,,,,,,,,,80.5,80,79.7,79.4,79.2,79,78.6,78.1,77.5,76.9,76.3,75.6,75.6,73.9
+67,,,,,,,,,,,,,,,,,,80.9,80.6,80.4,80.2,79.8,79.3,78.7,78.1,77.5,76.7,76.7,75

rcpchgrowth/data_tables/bayley_pinneau/bayley_pinneau_boys_normal.csv

@@ -0,0 +1,40 @@
+Skeletal Age,7-0,7-3,7-6,7-9,8-0,8-3,8-6,8-9,9-0,9-3,9-6,9-9,10,10-3,10-6,10-9,11,11-3,11-6,11-9,12-0,12-3,12-6,12-9,13-0,13-3,13-6,13-9,14-0,14-3,14-6,14-9,15-0,15-3,15-6,15-9,16-0,16-3,16-6,16-9,17-0,17-3,17-6,17-9,18-0,18-3,18-6
+Mature Height,,,,,,,,,,,,,,,,,,,,,,,,,87.6,89,90.2,91.4,92.7,93.8,94.8,95.8,96.8,97.3,97.6,98,98.2,98.5,98.7,98.9,99.1,99.3,99.4,99.5,99.6,99.8,100
+Ht. (inches),,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+42,60.4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+43,61.9,61.3,60.6,60.1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+44,63.3,62.7,62.1,61.5,60.9,60.2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+45,64.7,64.1,63.5,62.8,62.2,61.6,60.9,60.3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+46,66.2,65.5,64.9,64.2,63.6,62.9,62.2,61.7,61.2,60.4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+47,67.6,67,66.3,65.6,65,64.3,63.6,63,62.5,61.8,61.1,60.5,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+48,69.1,68.4,67.7,67,66.4,65.7,65,64.3,63.8,63.1,62.4,61.8,61.2,60.7,60.4,60,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+49,70.5,69.8,69.1,68.4,67.8,67,66.3,65.7,65.2,64.4,63.7,63.1,62.5,61.9,61.6,61.3,60.9,60.3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+50,71.9,71.2,70.5,69.8,69.2,68.4,67.7,67,66.5,65.7,65,64.4,63.8,63.2,62.9,62.5,62.2,61.6,61.1,60.5,,,,,,,,,,,,,,,,,,,,,,,,,,,
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