edc-vitals 1.0.0__tar.gz → 1.1.0__tar.gz

{edc_vitals-1.0.0 → edc_vitals-1.1.0}/.pre-commit-config.yaml

@@ -3,20 +3,20 @@ exclude: tests/etc/user-*
 
 repos:
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.8.2
+    rev: 1.8.3
     hooks:
       - id: bandit
         args:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
         language_version: python3.12
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
+    rev: 7.2.0
     hooks:
       - id: flake8
         args:
@@ -45,7 +45,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.35.1
+    rev: v1.37.0
     hooks:
       - id: yamllint
         args:

edc_vitals-1.1.0/AUTHORS

@@ -0,0 +1,2 @@
+Erik van Widenfelt <ew2789@gmail.com>
+Jonathan Willitts (GitHub: https://github.com/JonathanWillitts)

{edc_vitals-1.0.0 → edc_vitals-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: edc-vitals
-Version: 1.0.0
+Version: 1.1.0
 Summary: Classes for BP, weight, etc for clinicedc/edc projects
 Home-page: https://github.com/clinicedc/edc-vitals
 Author: Erik van Widenfelt
@@ -19,6 +19,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
+Dynamic: license-file
 
 
 |pypi| |actions| |codecov| |downloads|

edc_vitals-1.1.0/edc_vitals/calculators/__init__.py

@@ -0,0 +1 @@
+from .bmi import BMI, CalculatorError, calculate_bmi

edc_vitals-1.1.0/edc_vitals/calculators/bmi.py

@@ -0,0 +1,69 @@
+from dateutil.relativedelta import relativedelta
+from edc_utils import age, get_utcnow
+from edc_utils.round_up import round_half_away_from_zero
+
+__all__ = ["calculate_bmi", "BMI", "CalculatorError"]
+
+
+class CalculatorError(Exception):
+    pass
+
+
+class BMI:
+    """Calculate BMI, raise if not adult."""
+
+    def __init__(
+        self,
+        weight_kg=None,
+        height_cm=None,
+        lower_bmi_value=None,
+        upper_bmi_value=None,
+        dob=None,
+        report_datetime=None,
+        **kwargs,
+    ):
+        if not weight_kg or not height_cm:
+            raise CalculatorError(f"Unable to calculate BMI. Got {weight_kg}kg, {height_cm}cm")
+        if age(dob, report_datetime).years < 18:
+            raise CalculatorError("Unable to calculate BMI. Got age<18")
+        self.lower = float(lower_bmi_value or 5.0)
+        self.upper = float(upper_bmi_value or 75.0)
+        self.weight = float(weight_kg)
+        self.height = float(height_cm) / 100.0
+        self.raw_bmi_value = self.weight / (self.height**2)
+        if not (self.lower <= self.raw_bmi_value <= self.upper):
+            raise CalculatorError(
+                "BMI value is absurd. "
+                f"Using {self.weight}kg, {self.height}m. Got {self.value}."
+            )
+
+    @property
+    def value(self):
+        return round_half_away_from_zero(self.raw_bmi_value, 4)
+
+
+def calculate_bmi(
+    weight_kg=None,
+    height_cm=None,
+    lower_bmi_value=None,
+    upper_bmi_value=None,
+    dob=None,
+    report_datetime=None,
+    **kwargs,
+):
+    """Returns a BMI instance or None.
+
+    Assumes adult dob (18) if dob not provided."""
+    bmi = None
+    if height_cm and weight_kg:
+        report_datetime = report_datetime or get_utcnow()
+        bmi = BMI(
+            weight_kg=weight_kg,
+            height_cm=height_cm,
+            lower_bmi_value=lower_bmi_value,
+            upper_bmi_value=upper_bmi_value,
+            dob=dob or report_datetime - relativedelta(years=18),
+            report_datetime=report_datetime,
+            **kwargs,
+        )
+    return bmi

edc_vitals-1.1.0/edc_vitals/form_validators/__init__.py

@@ -0,0 +1,5 @@
+from .blood_pressure_form_validator_mixin import BloodPressureFormValidatorMixin
+from .bmi_form_validator_mixin import BmiFormValidatorMixin
+from .weight_height_with_bmi_form_validator_mixin import (
+    WeightHeightBmiFormValidatorMixin,
+)

edc_vitals-1.1.0/edc_vitals/form_validators/bmi_form_validator_mixin.py

@@ -0,0 +1,19 @@
+from django import forms
+
+from ..calculators import CalculatorError, calculate_bmi
+
+__all__ = ["BmiFormValidatorMixin"]
+
+
+class BmiFormValidatorMixin:
+    def validate_bmi(self, **kwargs):
+        try:
+            bmi = calculate_bmi(
+                height_cm=self.cleaned_data.get("height"),
+                weight_kg=self.cleaned_data.get("weight"),
+                **self.cleaned_data,
+                **kwargs,
+            )
+        except CalculatorError as e:
+            raise forms.ValidationError(e)
+        return bmi

edc_vitals-1.0.0/edc_vitals/form_validators/weight_height_bmi_form_validator_mixin.py → edc_vitals-1.1.0/edc_vitals/form_validators/weight_height_with_bmi_form_validator_mixin.py

@@ -1,5 +1,6 @@
 from django import forms
-from edc_reportable import CalculatorError, calculate_bmi
+
+from ..calculators import CalculatorError, calculate_bmi
 
 
 class WeightHeightBmiFormValidatorMixin:

{edc_vitals-1.0.0 → edc_vitals-1.1.0}/edc_vitals/model_mixins/weight_height_bmi_model_mixin.py

@@ -1,6 +1,6 @@
 from django.db import models
-from edc_reportable import calculate_bmi
 
+from ..calculators import calculate_bmi
 from ..models import HeightField, WeightField
 
 

edc_vitals-1.1.0/edc_vitals/tests/tests/test_calculators.py

@@ -0,0 +1,77 @@
+from dateutil.relativedelta import relativedelta
+from django import forms
+from django.test import TestCase, tag
+from edc_constants.constants import BLACK, MALE
+from edc_form_validators import FormValidator
+from edc_utils import get_utcnow
+from edc_utils.round_up import round_half_away_from_zero
+
+from edc_vitals.calculators import BMI, CalculatorError, calculate_bmi
+from edc_vitals.form_validators import BmiFormValidatorMixin
+
+
+class TestCalculators(TestCase):
+    @tag("1")
+    def test_bmi_calculator(self):
+        dob = get_utcnow() - relativedelta(years=25)
+        self.assertRaises(CalculatorError, BMI, weight_kg=56, height_cm=None)
+        try:
+            calculate_bmi(weight_kg=56, height_cm=None, dob=dob)
+        except CalculatorError:
+            self.fail("CalculatorError unexpectedly raised ")
+
+        for func in [BMI, calculate_bmi]:
+            with self.subTest(func=func):
+                self.assertRaises(
+                    CalculatorError,
+                    func,
+                    weight_kg=56,
+                    height_cm=1.50,
+                    dob=dob,
+                    report_datetime=get_utcnow(),
+                )
+                try:
+                    bmi = func(
+                        weight_kg=56, height_cm=150, dob=dob, report_datetime=get_utcnow()
+                    )
+                except CalculatorError as e:
+                    self.fail(f"CalculatorError unexpectedly raises. Got {e}")
+                else:
+                    self.assertEqual(round_half_away_from_zero(bmi.value, 2), 24.89)
+
+    @tag("1")
+    def test_bmi_form_validator(self):
+        data = dict(
+            gender=MALE,
+            ethnicity=BLACK,
+            age_in_years=30,
+        )
+
+        class BmiFormValidator(BmiFormValidatorMixin, FormValidator):
+            pass
+
+        # not enough data
+        form_validator = BmiFormValidator(cleaned_data=data)
+        bmi = form_validator.validate_bmi()
+        self.assertIsNone(bmi)
+
+        # calculates
+        data.update(
+            weight=56,
+            height=150,
+            dob=get_utcnow() - relativedelta(years=30),
+            report_datetime=get_utcnow(),
+        )
+        form_validator = BmiFormValidator(cleaned_data=data)
+        bmi = form_validator.validate_bmi()
+        self.assertEqual(bmi.value, 24.8889)
+
+        # calculation error
+        data.update(
+            weight=56,
+            height=1.5,
+            dob=get_utcnow() - relativedelta(years=25),
+            report_datetime=get_utcnow(),
+        )
+        form_validator = BmiFormValidator(cleaned_data=data)
+        self.assertRaises(forms.ValidationError, form_validator.validate_bmi)

{edc_vitals-1.0.0 → edc_vitals-1.1.0}/edc_vitals/tests/tests/test_weight_height_bmi.py

@@ -3,11 +3,10 @@ from decimal import Decimal
 from dateutil.relativedelta import relativedelta
 from django import forms
 from django.test import TestCase
+from edc_reportable.forms import WeightHeightBmiFormValidatorMixin
 from edc_utils import get_utcnow
 from edc_utils.round_up import round_half_away_from_zero
 
-from edc_vitals.form_validators import WeightHeightBmiFormValidatorMixin
-
 from ..models import WeightHeightBmi
 
 

{edc_vitals-1.0.0 → edc_vitals-1.1.0}/edc_vitals.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: edc-vitals
-Version: 1.0.0
+Version: 1.1.0
 Summary: Classes for BP, weight, etc for clinicedc/edc projects
 Home-page: https://github.com/clinicedc/edc-vitals
 Author: Erik van Widenfelt
@@ -19,6 +19,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
+Dynamic: license-file
 
 
 |pypi| |actions| |codecov| |downloads|

{edc_vitals-1.0.0 → edc_vitals-1.1.0}/edc_vitals.egg-info/SOURCES.txt

@@ -22,9 +22,12 @@ edc_vitals.egg-info/SOURCES.txt
 edc_vitals.egg-info/dependency_links.txt
 edc_vitals.egg-info/not-zip-safe
 edc_vitals.egg-info/top_level.txt
+edc_vitals/calculators/__init__.py
+edc_vitals/calculators/bmi.py
 edc_vitals/form_validators/__init__.py
 edc_vitals/form_validators/blood_pressure_form_validator_mixin.py
-edc_vitals/form_validators/weight_height_bmi_form_validator_mixin.py
+edc_vitals/form_validators/bmi_form_validator_mixin.py
+edc_vitals/form_validators/weight_height_with_bmi_form_validator_mixin.py
 edc_vitals/migrations/__init__.py
 edc_vitals/model_mixins/__init__.py
 edc_vitals/model_mixins/blood_pressure_model_mixin.py
@@ -52,6 +55,7 @@ edc_vitals/tests/etc/user-salt-local.key
 edc_vitals/tests/etc/user-salt-restricted.key
 edc_vitals/tests/tests/__init__.py
 edc_vitals/tests/tests/test_blood_pressure.py
+edc_vitals/tests/tests/test_calculators.py
 edc_vitals/tests/tests/test_heart_rate.py
 edc_vitals/tests/tests/test_respiratory_rate.py
 edc_vitals/tests/tests/test_temperature.py

{edc_vitals-1.0.0 → edc_vitals-1.1.0}/pyproject.toml

@@ -13,7 +13,7 @@ extend-exclude = '''^(.*\/)*\b(migrations)\b($|\/.*$)'''
 [tool.isort]
 profile = "black"
 py_version = "312"
-skip = [".tox", ".eggs", "migrations"]
+skip = [".tox", ".eggs", "migrations", "_version.py"]
 
 [tool.coverage.run]
 parallel = false
@@ -84,6 +84,5 @@ commands =
     python --version
     pip --version
     pip freeze
-    pre-commit autoupdate
     pre-commit run --all-files
 """

edc_vitals-1.0.0/AUTHORS

@@ -1 +0,0 @@
-Erik van Widenfelt <ew2789@gmail.com>

edc_vitals-1.0.0/edc_vitals/form_validators/__init__.py

@@ -1,2 +0,0 @@
-from .blood_pressure_form_validator_mixin import BloodPressureFormValidatorMixin
-from .weight_height_bmi_form_validator_mixin import WeightHeightBmiFormValidatorMixin