first commit

.vscode/settings.json

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+{
+    "python.pythonPath": "/Users/SimonChapman/.pyenv/versions/rcpchgrowth-cli/bin/python"
+}

cli/__main__.py

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+import click
+from datetime import datetime
+from rcpchgrowth import date_calculations
+from rcpchgrowth import centile_bands
+from rcpchgrowth.centile_bands import centile_band_for_centile
+from rcpchgrowth.global_functions import centile, measurement_from_sds, sds_for_measurement
+
+@click.group()
+def cli():
+    pass
+
+@click.command()
+@click.argument('birth_date')
+@click.argument('observation_date')
+@click.argument('gestation_weeks')
+@click.argument('gestation_days')
+@click.option('--adjustment', '-a')
+def age_calculation(birth_date: datetime, observation_date: datetime, gestation_weeks=40, gestation_days=0, adjustment=False):
+    decimal_age=0
+    calendar_age=""
+    if adjustment:
+        decimal_age=date_calculations.corrected_decimal_age(
+            birth_date=birth_date,
+            observation_date=observation_date,
+            gestation_weeks=gestation_weeks,
+            gestation_days=gestation_days)
+        calendar_age=date_calculations.chronological_calendar_age(
+            birth_date=birth_date, 
+            observation_date=observation_date)
+    else:
+        decimal_age=date_calculations.chronological_decimal_age(
+            birth_date=birth_date,
+            observation_date=observation_date
+        )
+        calendar_age=date_calculations.chronological_calendar_age(
+            birth_date=birth_date, 
+            observation_date=observation_date)
+    click.echo(f"{decimal_age} y, \n {calendar_age}")
+
+@click.command()
+@click.argument('reference')
+@click.argument('decimal_age')
+@click.argument('measurement_method')
+@click.argument('observation_value')
+@click.argument('sex')
+def sds(reference: str, decimal_age: float, measurement_method: str, observation_value: float, sex: str):
+    result = sds_for_measurement(
+        reference=reference,
+        age=decimal_age,
+        measurement_method=measurement_method,
+        observation_value=observation_value,
+        sex=sex
+    )
+    cent = centile(result)
+    click.echo(f"SDS: {result}\n Centile: {cent}\n ")
+
+@click.command()
+@click.argument('reference')
+@click.argument('decimal_age')
+@click.argument('sex')
+@click.argument('measurement_method')
+@click.argument('sds')
+def measurement(reference: str, decimal_age: float, sex:str, measurement_method: str, sds: float):
+    result = measurement_from_sds(
+        reference, 
+        requested_sds=sds,
+        measurement_method=measurement_method,
+        sex=sex,
+        age=decimal_age
+    )
+    suffix="cm"
+    if measurement_method=="weight":
+        suffix="kg"
+    elif measurement_method=="bmi":
+        suffix="kg/m2"
+    click.echo(f"SDS {sds}\n {measurement_method}: {result} {suffix}")
+
+
+cli.add_command(age_calculation)
+cli.add_command(sds)
+cli.add_command(measurement)
+
+if __name__ == 'main':
+    cli()

python-version

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+rcpchgrowth-cli

requirements.txt

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+attrs==20.3.0
+click==7.1.2
+iniconfig==1.1.1
+marshmallow==3.11.1
+numpy==1.20.2
+packaging==20.9
+pluggy==0.13.1
+py==1.10.0
+pyparsing==2.4.7
+pytest==6.2.3
+python-dateutil==2.8.1
+rcpchgrowth==2.1.11
+scipy==1.6.2
+six==1.15.0
+toml==0.10.2

setup.py

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+from setuptools import setup, find_packages
+
+with open('requirements.txt') as f:
+    requirements = f.readlines()
+
+long_description = 'Calculate SDS and centiles using \
+      UK-WHO, Down and Turner reference data. \
+          This is official RCPCH software.'
+
+setup(
+        name ='rcpchgrowth-python-cli',
+        version ='1.0.0',
+        author ='Simon Chapman',
+        author_email ='[email protected]',
+        url ='https://github.com/rcpch/rcpchgrowth-python-cli',
+        description ='Command Line Interface for RCPCHGrowth.',
+        long_description = long_description,
+        long_description_content_type ="text/markdown",
+        packages = find_packages(),
+        entry_points ={
+            'console_scripts': [
+                'rcpchgrowth-cli = cli:main'
+            ]
+        },
+        classifiers =(
+            "Programming Language :: Python :: 3",
+            'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
+            "Operating System :: OS Independent",
+        ),
+        keywords ='RCPCHGrowth UK-WHO Down Turner',
+        install_requires = requirements,
+        zip_safe = False
+)