Merge pull request #20 from rcpch/18-python-version-upgrade-3.11

Python Version upgrade, Dockerisation, GitHub Actions testing, repo tidy.

.github/pull_request_template.md

@@ -0,0 +1,19 @@
+### Overview
+
+Please describe the purpose of this PR here.
+
+### Code changes
+
+Please describe the changes you made here.
+
+### Documentation changes (done or required as a result of this PR)
+
+Please describe any changes to documentation here.
+
+### Related Issues
+
+List any issues related to this PR here.
+
+### Mentions
+
+@mentions of the person or team responsible for reviewing proposed changes.

.github/workflows/auto-add-issues-to-project.yml

@@ -0,0 +1,20 @@
+name: Adds new Issues automatically to the dGC Project on GitHub
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add issue or PR to project automatically
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+        with:
+          project-url: https://github.com/orgs/rcpch/projects/5 #dGC Project
+          github-token: ${{ secrets.AUTO_ADD_TO_PROJECT_TOKEN }}
+

.github/workflows/run-pytest-on-push-and-all-prs.yml

@@ -0,0 +1,41 @@
+name: Run Pytest on pushes to main branches or PRs to any branch
+
+on:
+  pull_request:
+    branches:
+      - "*"
+  push:
+    branches:
+      - development
+      - staging
+      - live
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+    # Runs tests on multiple python versions across the range we support
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4 # latest as at March 2024
+
+    - name: Set up Python version ${{ matrix.python-version }}
+      uses: actions/setup-python@v5 # latest as at March 2024
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Display Python version
+      run: python -c "import sys; print(sys.version)"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel
+        pip install -r requirements.txt
+
+    - name: Run pytest
+      run: |
+        pytest

.gitignore

@@ -130,3 +130,6 @@ dmypy.json
 
 .vscode
 .pytest/cache
+
+# MacOS DS_Store files
+.DS_Store

CITATION.cff

@@ -6,11 +6,12 @@ authors:
     orcid: "https://orcid.org/0000-0001-9897-2040"
   - family-names: "Baw"
     given-names: "Marcus"
+    orcid: "https://orcid.org/0000-0003-4369-8659"
   - family-names: "Cole"
     given-names: "Tim"
     orcid: "https://orcid.org/0000-0001-5711-8200"
 title: "rcpchgrowth"
 version: 3.1.17
 doi: 10.5281/zenodo.6301089
 date-released: 2022-05-14
-url: "https://github.com/rcpch/rcpchgrowth-python"
+url: "https://github.com/rcpch/rcpchgrowth-python"

Dockerfile

@@ -0,0 +1,7 @@
+FROM python:3.12-bookworm
+
+COPY requirements.txt .
+
+RUN pip install -r requirements.txt
+
+COPY . .

docker-compose.yml

@@ -0,0 +1,12 @@
+# NOTE The below is the Docker Compose specification version NOT the Python version:
+version: '3.8'
+
+services:
+  rcpchgrowth-python:
+    build: .
+    volumes:
+      - .:/app
+    tty: true  # Allocate a pseudo-TTY
+    stdin_open: true  # Keep stdin open
+    command: |
+      cd app; pytest

rcpchgrowth/constants/validation_constants.py

@@ -8,7 +8,7 @@
 MAXIMUM_HEIGHT_CM = 300
 # The smallest baby was report by the BBC on 9/8/2021 (https://www.bbc.co.uk/news/world-asia-58141756.amp)
 # to have a length of just 24cm and was born at 25 weeks gestation, discharged at 13 mths of age (chronological)
-# from Singapore's National University Hospital 
+# from Singapore's National University Hospital
 # The tallest person for whom there is irrefutable evidence is
 # Robert Pershing Wadlow who was 2.72m (8 ft 11.1 in) tall at his death in 1940
 # https://en.wikipedia.org/wiki/Robert_Wadlow
@@ -18,7 +18,7 @@
 MAXIMUM_WEIGHT_KG = 500
 # The smallest baby was report by the BBC on 9/8/2021 (https://www.bbc.co.uk/news/world-asia-58141756.amp)
 # to weigh just 212g and was born at 25 weeks gestation, discharged at 13 mths of age (chronological)
-# from Singapore's National University Hospital 
+# from Singapore's National University Hospital
 # The heaviest man according to google is Jon Brower Minnoch (US)
 # who had suffered from obesity since childhood. In September 1976,
 # he measured 185 cm (6 ft 1 in) tall and weighed 442 kg (974 lb; 69 st 9 lb)
@@ -41,6 +41,13 @@
 
 # GESTATION CONSTANTS
 MINIMUM_GESTATION_WEEKS = 22
-MINIMUM_GESTATION_WEEKS_ERROR = f'It is very unlikely that a gestational age of less than {MINIMUM_GESTATION_WEEKS} weeks is correct'
+MINIMUM_GESTATION_WEEKS_ERROR = f"It is very unlikely that a gestational age of less than {MINIMUM_GESTATION_WEEKS} weeks is correct"
 MAXIMUM_GESTATION_WEEKS = 44
-MAXIMUM_GESTATION_WEEKS_ERROR = f'It is very unlikely that a gestational age of more than {MAXIMUM_GESTATION_WEEKS} weeks is correct'
+MAXIMUM_GESTATION_WEEKS_ERROR = f"It is very unlikely that a gestational age of more than {MAXIMUM_GESTATION_WEEKS} weeks is correct"
+
+# PARENTAL HEIGHT CONSTANTS
+MINIMUM_PARENTAL_HEIGHT_CM = 50
+# the shortest man in the world was 54.6 cm Chandra Bahadur Dangi
+# the shortest woman in the world is Jyoti Kishanji Amge at 62.8 cm
+# lower limit to paternal and maternal height here therefore set arbitrarily at 50 cm
+# (this constant was added from the API server `schemas/request_validation_classes.py`)

rcpchgrowth/dynamic_growth.py

@@ -6,6 +6,7 @@
 
 # from scipy.interpolate import UnivariateSpline
 # import matplotlib.pyplot as plt
+# TODO #21 - do the above lines need to be commented out?
 
 # rcpchgrowth local imports
 from rcpchgrowth.constants.reference_constants import FEMALE, MALE, UK_WHO, WEIGHT
@@ -14,13 +15,13 @@
 """
 These functions are experimental
 Height, weight, BMI or OFC in terms of SDS / Centile are snapshots in time and tell
-us actually very little about growth, which is a dynamic measure. In order to make 
+us actually very little about growth, which is a dynamic measure. In order to make
 predictions, we need to look at change in parameter measured over time (velocity)
 which requires 2 measurements over a known time interval, or change in velocity (acceleration/deceleration)
-which requires three measurements. 
+which requires three measurements.
 
 From these measurements predictions can be made about speed of growth, or rate of slowing (catch down)
-or acceleration (catch up). The normative data against which to compare the index child are 
+or acceleration (catch up). The normative data against which to compare the index child are
 thrive lines, generated here.
 
 """
@@ -134,7 +135,7 @@ def nine_centiles(sex: str):
     t=[centile * 0.5 for centile in range(24)]
     requested_sd_scores=[-2.67, -2.0, -1.33, -0.67, 0, 0.67, 1.33, 2.0, 2.67]
     final_array=[]
-    
+
     for index, requested_sd_score in enumerate(requested_sd_scores):
         return_ages_array=[]
         return_m_array=[]
@@ -186,7 +187,7 @@ def create_thrive_line(t: list, z1: float, sex: str, target_centile: float = 5.0
     cycle_sds=[z1]
     return_ages=[t[0]]
     z2=0.0
-    
+
     for index in range(len(t)):
         observation_value=None
         # loop through the list of ages which are ordered and evenly spaced a month apart
@@ -202,7 +203,7 @@ def create_thrive_line(t: list, z1: float, sex: str, target_centile: float = 5.0
             # this is the last item in the list
             t2 = t1
             z2=z_current
-        
+
         # convert z2 to a measurement and add to the list against t2 in years
         observation_value = measurement_from_sds(
             reference=UK_WHO,
@@ -215,18 +216,18 @@ def create_thrive_line(t: list, z1: float, sex: str, target_centile: float = 5.0
         cycle_sds.append(z2)
         return_ages.append(t2/12)
         return_observation_values.append(observation_value)
-        
+
     return {
-        "zs": cycle_sds, 
-        "ages": return_ages, 
+        "zs": cycle_sds,
+        "ages": return_ages,
         "observation_values": return_observation_values
     }
 
 def create_thrive_lines(target_centile: float, sex: str):
     # Creates thrive lines for weights in the under 1s
-    # Each thrive line requires a starting SDS and list of ages against 
+    # Each thrive line requires a starting SDS and list of ages against
     # which the lines are plotted.
-    # The centile_target refers to the velocity centile cut off at which 
+    # The centile_target refers to the velocity centile cut off at which
     # the line is drawn.
 
     time_blocks = [i for i in range(12)]
@@ -235,11 +236,11 @@ def create_thrive_lines(target_centile: float, sex: str):
     for index, centile_line in enumerate(centile_lines):
         # these are the 9 centile lines
         plt.plot(centile_line["ages"], centile_line["observation_values"], linestyle='--' if index % 2==0 else '-' , color="grey", linewidth=0.5)
-        
+
     z=-25
     while z <= 25:
         thrive_line = create_thrive_line(
-            t=time_blocks, 
+            t=time_blocks,
             z1=z,
             sex=sex,
             target_centile=target_centile)
@@ -283,17 +284,17 @@ def create_thrive_lines(target_centile: float, sex: str):
                 measurements.append(thrive_line['observation_values'][counter])
                 ages.append(thrive_line['ages'][counter])
             counter += 1
-        
+
     #     x, y = ages, measurements
     #     # smoothed_measurements = UnivariateSpline(x,y) smoothed_measurements(x)
     #     if len(x) > 0 and len(y) > 0:
     #         plt.plot(x, y, color="green", linestyle='--', dashes=(15,2.5), linewidth=1.0)
-        
+
     # plt.title('Thrive Lines', fontsize=16)
     # plt.show()
 
 def return_correlation(t1, t2, time_interval: Literal["weeks", "months"]):
-    # import the reference - the index of each row and column 
+    # import the reference - the index of each row and column
     # relates to the number of weeks or months
 
     cwd = os.path.dirname(__file__)  # current location
@@ -310,20 +311,20 @@ def return_correlation(t1, t2, time_interval: Literal["weeks", "months"]):
     with open(final_file_path, mode="r") as json_file:
         data=json.load(json_file)
         json_file.close()
-    
+
     lowerIndexT1 = math.floor(t1)
     upperIndexT1 = lowerIndexT1+1
     lowerIndexT2 = math.floor(t2)
     upperIndexT2 = lowerIndexT2+1
-    
+
     lowerT1lowerT2 = data[lowerIndexT1][str(lowerIndexT2)]
     lowerT1upperT2 = data[lowerIndexT1][str(upperIndexT2)]
     upperT1lowerT2 = data[upperIndexT1][str(lowerIndexT2)]
     upperT1upperT2 = data[upperIndexT1][str(upperIndexT2)]
 
     correlation = bilinear_interpolation(
-            x=t1, 
-            y=t2, 
+            x=t1,
+            y=t2,
             points=[
                 (lowerIndexT1, lowerIndexT2, lowerT1lowerT2),
                 (lowerIndexT1, upperIndexT2, lowerT1upperT2),

requirements.txt

@@ -3,4 +3,4 @@ pytest
 python-dateutil
 scipy
 matplotlib
-setuptools
+setuptools

s/down

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -v  # Enable verbose mode
+set -e  # Exit on error
+
+# scripts may need to be made executable on some platforms before they can be run
+# chmod +x <filename> is the command to do this on unixy systems
+
+# shuts down the Docker Compose setup but does not destroy containers or images
+docker compose down

s/rebuild

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -v  # Enable verbose mode
+set -e  # Exit on error
+
+# scripts may need to be made executable on some platforms before they can be run
+# chmod +x <filename> is the command to do this on unixy systems
+
+s/remove-containers-and-images
+s/up

s/remove-containers-and-images

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -v  # Enable verbose mode
+set -e  # Exit on error
+
+# scripts may need to be made executable on some platforms before they can be run
+# chmod +x <filename> is the command to do this on unixy systems
+
+# shuts down the Docker Compose setup AND deletes containers and images (but not volumes)
+docker compose down --rmi local # removes the container and local images