Merge branch 'live' into 18-python-version-upgrade-3.11

.bumpversion.cfg

@@ -1,8 +1,8 @@
 [bumpversion]
-current_version = 3.2.0
+current_version = 4.0.0
 tag = False
 commit = True
 
 [bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
+search = version="{current_version}"
+replace = version="{new_version}"

.github/workflows/python-publish.yml

@@ -9,30 +9,29 @@ on:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.8.3'
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-        pip install -r requirements.txt
-    - name: Run pytest
-      run: |
-        pytest
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+          pip install -r requirements.txt
+      - name: Run pytest
+        run: |
+          pytest
 
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

rcpchgrowth/fictional_child.py

@@ -1,5 +1,5 @@
 # core imports
-from datetime import datetime, timedelta
+from datetime import date, timedelta
 import random
 import math
 
@@ -47,7 +47,7 @@ def generate_fictional_child_data(
   The development of growth references and growth charts, T J Cole, Ann Hum Biol. 2012 Sep; 39(5): 382–394.
   Wikipedia: https://en.wikipedia.org/wiki/Philippe_Gu%C3%A9neau_de_Montbeillard
   """
-  birth_date = datetime(1759, 4, 11)  # YYYY m d
+  birth_date = date(1759, 4, 11)  # YYYY m d
   observation_date = birth_date + timedelta(days=start_chronological_age*365.25)
 
   # set the counters

rcpchgrowth/measurement.py

@@ -553,14 +553,14 @@ def __create_measurement_object(
             if corrected_centile_value > 99 or corrected_centile_value < 1:
                 corrected_centile_value = round(corrected_centile_value, 1)
             else:
-                corrected_centile_value = int(corrected_centile_value)
+                corrected_centile_value = round(corrected_centile_value, 1)
 
         if chronological_centile_value:
             if chronological_centile_value > 99 or chronological_centile_value < 1:
                 chronological_centile_value = round(
                     chronological_centile_value, 1)
             else:
-                chronological_centile_value = int(chronological_centile_value)
+                chronological_centile_value = round(chronological_centile_value, 1)
 
         measurement_calculated_values = {
             "corrected_sds": corrected_sds_value,

rcpchgrowth/trisomy_21.py

@@ -1,5 +1,6 @@
 import json
-import pkg_resources
+from importlib import resources
+from pathlib import Path
 from .constants import *
 # from .global_functions import z_score, cubic_interpolation, linear_interpolation, centile, measurement_for_z, nearest_lowest_index, fetch_lms
 # import timeit #see below, comment back in if timing functions in this module
@@ -18,10 +19,13 @@
 reference: reference data
 """
 
-#load the reference data
+# load the reference data
+data_directory = resources.files("rcpchgrowth.data_tables")
 
-TRISOMY_21_DATA = pkg_resources.resource_filename(__name__, "/data_tables/trisomy_21.json")
-with open(TRISOMY_21_DATA) as json_file:
+
+
+data_path = Path(data_directory, "trisomy_21.json")
+with open(data_path) as json_file:
             TRISOMY_21_DATA = json.load(json_file)
             json_file.close()
 

rcpchgrowth/turner.py

@@ -1,5 +1,6 @@
 import json
-import pkg_resources
+from importlib import resources
+from pathlib import Path
 from .constants import *
 # import timeit #see below, comment back in if timing functions in this module
 
@@ -17,10 +18,11 @@
 reference: reference data
 """
 
-#load the reference data
+# load the reference data
+data_directory = resources.files("rcpchgrowth.data_tables")
 
-TURNER_DATA = pkg_resources.resource_filename(__name__, "/data_tables/turner.json")
-with open(TURNER_DATA) as json_file:
+data_path = Path(data_directory, "turner.json")
+with open(data_path) as json_file:
             TURNER_DATA = json.load(json_file)
             json_file.close()
 

rcpchgrowth/uk_who.py

@@ -4,7 +4,8 @@
 
 # standard imports
 import json
-import pkg_resources
+from importlib import resources
+from pathlib import Path
 
 # rcpch imports
 from .constants import *
@@ -24,34 +25,35 @@
 """
 
 # load the reference data
+data_directory = resources.files("rcpchgrowth.data_tables")
 
-UK90_PRETERM_DATA = pkg_resources.resource_filename(
-    __name__, "/data_tables/uk90_preterm.json")  # 23 - 42 weeks gestation
-with open(UK90_PRETERM_DATA) as json_file:
+data_path = Path(
+    data_directory, "uk90_preterm.json")  # 23 - 42 weeks gestation
+with open(data_path) as json_file:
     UK90_PRETERM_DATA = json.load(json_file)
     json_file.close()
 
-UK90_TERM_DATA = pkg_resources.resource_filename(
-    __name__, "/data_tables/uk90_term.json")  # 37-42 weeks gestation
-with open(UK90_TERM_DATA) as json_file:
+data_path = Path(
+    data_directory, "uk90_term.json")  # 37-42 weeks gestation
+with open(data_path) as json_file:
     UK90_TERM_DATA = json.load(json_file)
     json_file.close()
 
-WHO_INFANTS_DATA = pkg_resources.resource_filename(
-    __name__, "/data_tables/who_infants.json")  # 2 weeks to 2 years
-with open(WHO_INFANTS_DATA) as json_file:
+data_path = Path(
+    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()
 
-WHO_CHILD_DATA = pkg_resources.resource_filename(
-    __name__, "/data_tables/who_children.json")  # 2 years to 4 years
-with open(WHO_CHILD_DATA) as json_file:
+data_path = Path(
+    data_directory, "who_children.json")  # 2 years to 4 years
+with open(data_path) as json_file:
     WHO_CHILD_DATA = json.load(json_file)
     json_file.close()
 
-UK90_CHILD_DATA = pkg_resources.resource_filename(
-    __name__, "/data_tables/uk90_child.json")  # 4 years to 20 years
-with open(UK90_CHILD_DATA) as json_file:
+data_path = Path(
+    data_directory, "uk90_child.json")  # 4 years to 20 years
+with open(data_path) as json_file:
     UK90_CHILD_DATA = json.load(json_file)
     json_file.close()
 

setup.py

@@ -1,46 +1,34 @@
-from setuptools import _install_setup_requires, setup, find_packages
+from setuptools import setup, find_packages
 from os import path
 
 here = path.abspath(path.dirname(__file__))
 
-with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+with open(path.join(here, "README.md"), encoding="utf-8") as f:
     long_description = f.read()
 
 setup(
-    name='rcpchgrowth',
-    version='3.2.0',
-    description='SDS and Centile calculations for UK Growth Data',
-    long_description="https://github.com/rcpch/digital-growth-charts/blob/master/README.md",
-    url='https://github.com/rcpch/digital-growth-charts/blob/master/README.md',
-    author='@eatyourpeas, @marcusbaw @statist7 RCPCH',
-
-    author_email='[email protected]',
+    name="rcpchgrowth",
+    version="4.0.0",
+    description="SDS and Centile calculations for UK Growth Data",
+    long_description=long_description,
+    url="https://github.com/rcpch/digital-growth-charts/blob/master/README.md",
+    author="@eatyourpeas, @marcusbaw, @statist7, RCPCH Incubator",
+    author_email="[email protected]",
     classifiers=[
-        'Development Status :: 3 - Alpha',
-        'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3 :: Only',
-        'Topic :: Scientific/Engineering :: Medical Science Apps.'
+        "Development Status :: 5 - Production/Stable",
+        "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3 :: Only",
+        "Topic :: Scientific/Engineering :: Medical Science Apps.",
     ],
-    keywords='growth charts anthropometry SDS Centile',  
-
-    packages=find_packages(),  
-    python_requires='>=3.5, <3.9',
-    install_requires=[
-        'python-dateutil',
-        "scipy",
-        'six',
-        'pytest',
-        'click'
-    ],  
-    extras_require={  
-        'dev': ['check-manifest'],
-        'test': ['coverage'],
-    },
+    keywords="growth charts, anthropometry, SDS, centile, UK-WHO, UK90, Trisomy 21, Turner",
+    packages=find_packages(),
+    python_requires=">3.8",
+    install_requires=["python-dateutil", "scipy"],
     include_package_data=True,
-    project_urls={  
-        'Bug Reports': 'https://github.com/rcpch/digital-growth-charts/issues',
-        'API management': 'https://dev.rcpch.ac.uk',
-        'Source': 'https://github.com/rcpch/digital-growth-charts',
+    project_urls={
+        "Bug Reports": "https://github.com/rcpch/rcpchgrowth-python/issues",
+        "API management": "https://dev.rcpch.ac.uk",
+        "Source": "https://github.com/rcpch/rcpchgrowth-python",
     },
 )