feat: Weight percentiles report #512 (#708)

* feat: weight percentiles report
https://github.com/babybuddy/babybuddy/issues/512

* fix: formatting on weight percentile graph to extend out only 1 day more than the last weigh in date
https://github.com/babybuddy/babybuddy/pull/708#discussion_r1332335789

* feat: pre-commit lint with black hook
tested and stops the python commit if formatting is bad. then it runs black and fixes the formatting, resulting in a new git change to add/commit again

---------

Co-authored-by: Christopher Charbonneau Wells <10456740+cdubz@users.noreply.github.com>

.devcontainer.json

@@ -4,8 +4,16 @@
       "extensions": [
         "bbenoist.Nix",
         "ms-python.python",
-        "batisteo.vscode-django"
+        "batisteo.vscode-django",
-      ]
+        "ms-python.black-formatter"
+      ],
+      "settings": {
+        "[python]": {
+          "editor": {
+            "defaultFormatter": "ms-python.black-formatter"
+          }
+        }
+      }
     }
   },
   "image": "ghcr.io/cachix/devenv:latest",

core/migrations/0030_weightpercentile_weightpercentile_unique_age_sex.py

@@ -0,0 +1,92 @@
+# Generated by Django 4.2.5 on 2023-09-20 10:56
+
+from django.db import migrations, models, transaction
+from django.utils import dateparse
+import csv
+
+
+def add_to_ORM(WeightPercentile: models.Model, alias, filepath: str, sex: str):
+    with open(filepath) as csvfile:
+        weight_reader = csv.DictReader(csvfile)
+        data_list = []
+        for row in weight_reader:
+            data_list.append(
+                WeightPercentile(
+                    age_in_days=dateparse.parse_duration(f'P{row["Age"]}D'),
+                    sex=sex,
+                    p3_weight=row["P3"],
+                    p15_weight=row["P15"],
+                    p50_weight=row["P50"],
+                    p85_weight=row["P85"],
+                    p97_weight=row["P97"],
+                )
+            )
+        WeightPercentile.objects.using(alias).bulk_create(data_list, batch_size=50)
+
+
+def insert_weight_percentiles(apps, schema_editor):
+    WeightPercentile: models.Model = apps.get_model("core", "WeightPercentile")
+    db_alias = schema_editor.connection.alias
+    with transaction.atomic():
+        add_to_ORM(
+            WeightPercentile,
+            db_alias,
+            "core/migrations/weight_percentile_boys.csv",
+            "boy",
+        )
+    with transaction.atomic():
+        add_to_ORM(
+            WeightPercentile,
+            db_alias,
+            "core/migrations/weight_percentile_girls.csv",
+            "girl",
+        )
+
+
+def remove_weight_percentiles(apps, schema_editor):
+    WeightPercentile: models.Model = apps.get_model("core", "WeightPercentile")
+    db_alias = schema_editor.connection.alias
+    with transaction.atomic():
+        WeightPercentile.objects.using(db_alias).all().delete()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("core", "0029_alter_pumping_options_remove_pumping_time_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="WeightPercentile",
+            fields=[
+                (
+                    "id",
+                    models.AutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("age_in_days", models.DurationField()),
+                ("p3_weight", models.FloatField()),
+                ("p15_weight", models.FloatField()),
+                ("p50_weight", models.FloatField()),
+                ("p85_weight", models.FloatField()),
+                ("p97_weight", models.FloatField()),
+                (
+                    "sex",
+                    models.CharField(
+                        choices=[("girl", "Girl"), ("boy", "Boy")], max_length=255
+                    ),
+                ),
+            ],
+        ),
+        migrations.AddConstraint(
+            model_name="weightpercentile",
+            constraint=models.UniqueConstraint(
+                fields=("age_in_days", "sex"), name="unique_age_sex"
+            ),
+        ),
+        migrations.RunPython(insert_weight_percentiles, remove_weight_percentiles),
+    ]

core/models.py

@@ -699,3 +699,31 @@ class Weight(models.Model):
 
     def clean(self):
         validate_date(self.date, "date")
+
+
+class WeightPercentile(models.Model):
+    model_name = "weight percentile"
+    age_in_days = models.DurationField(null=False)
+    p3_weight = models.FloatField(null=False)
+    p15_weight = models.FloatField(null=False)
+    p50_weight = models.FloatField(null=False)
+    p85_weight = models.FloatField(null=False)
+    p97_weight = models.FloatField(null=False)
+    sex = models.CharField(
+        null=False,
+        max_length=255,
+        choices=[
+            ("girl", _("Girl")),
+            ("boy", _("Boy")),
+        ],
+    )
+
+    class Meta:
+        constraints = [
+            models.UniqueConstraint(
+                fields=["age_in_days", "sex"], name="unique_age_sex"
+            )
+        ]
+
+    def __str__(self):
+        return f"Sex: {self.sex}, Age: {self.age_in_days} days, p3: {self.p3_weight} kg, p15: {self.p15_weight} kg, p50: {self.p50_weight} kg, p85: {self.p85_weight} kg, p97: {self.p97_weight} kg"

devenv.nix

@@ -9,6 +9,7 @@
     pkgs.pipenv
     pkgs.nodejs_18
     pkgs.nodePackages.gulp
+    pkgs.sqlite
   ];
 
   # https://devenv.sh/scripts/
@@ -29,14 +30,21 @@
 
   devcontainer = {
     enable = true;
+    settings.customizations.vscode.settings."[python]".editor.defaultFormatter = "ms-python.black-formatter";
     settings.customizations.vscode.extensions = [
       "bbenoist.Nix"
       "ms-python.python"
       "batisteo.vscode-django"
+      "ms-python.black-formatter"
     ];
   };
 
   # services.nginx.enable = true;
 
+  pre-commit.hooks = {
+    # format Python code 
+    black.enable = true;
+  };
+
   # See full reference at https://devenv.sh/reference/options/
 }

reports/graphs/weight_change.py

@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
+from datetime import datetime, timedelta
 from django.utils.translation import gettext as _
+from django.db.models.manager import BaseManager
 
 import plotly.offline as plotly
 import plotly.graph_objs as go
@@ -7,28 +9,99 @@ import plotly.graph_objs as go
 from reports import utils
 
 
-def weight_change(objects):
+def weight_change(
+    actual_weights: BaseManager, percentile_weights: BaseManager, birthday: datetime
+):
     """
     Create a graph showing weight over time.
-    :param objects: a QuerySet of Weight instances.
+    :param actual_weights: a QuerySet of Weight instances.
+    :param percentile_weights: a QuerySet of Weight Percentile instances.
+    :param birthday: a datetime of the child's birthday
     :returns: a tuple of the the graph's html and javascript.
     """
-    objects = objects.order_by("-date")
+    actual_weights = actual_weights.order_by("-date")
 
-    trace = go.Scatter(
+    weighing_dates: list[datetime] = list(actual_weights.values_list("date", flat=True))
+    measured_weights = list(actual_weights.values_list("weight", flat=True))
+
+    actual_weights_trace = go.Scatter(
         name=_("Weight"),
-        x=list(objects.values_list("date", flat=True)),
+        x=weighing_dates,
-        y=list(objects.values_list("weight", flat=True)),
+        y=measured_weights,
         fill="tozeroy",
+        mode="lines+markers",
     )
 
+    if percentile_weights:
+        dates = list(
+            map(
+                lambda timedelta: birthday + timedelta,
+                percentile_weights.values_list("age_in_days", flat=True),
+            )
+        )
+
+        # reduce percentile data xrange to end 1 day after last weigh in for formatting purposes
+        # https://github.com/babybuddy/babybuddy/pull/708#discussion_r1332335789
+        last_date_for_percentiles = max(weighing_dates) + timedelta(days=2)
+        dates = dates[: dates.index(last_date_for_percentiles)]
+
+        percentile_weight_3_trace = go.Scatter(
+            name=_("P3"),
+            x=dates,
+            y=list(percentile_weights.values_list("p3_weight", flat=True)),
+            line={"color": "red"},
+        )
+        percentile_weight_15_trace = go.Scatter(
+            name=_("P15"),
+            x=dates,
+            y=list(percentile_weights.values_list("p15_weight", flat=True)),
+            line={"color": "orange"},
+        )
+        percentile_weight_50_trace = go.Scatter(
+            name=_("P50"),
+            x=dates,
+            y=list(percentile_weights.values_list("p50_weight", flat=True)),
+            line={"color": "green"},
+        )
+        percentile_weight_85_trace = go.Scatter(
+            name=_("P85"),
+            x=dates,
+            y=list(percentile_weights.values_list("p85_weight", flat=True)),
+            line={"color": "orange"},
+        )
+        percentile_weight_97_trace = go.Scatter(
+            name=_("P97"),
+            x=dates,
+            y=list(percentile_weights.values_list("p97_weight", flat=True)),
+            line={"color": "red"},
+        )
+
+    data = [
+        actual_weights_trace,
+    ]
     layout_args = utils.default_graph_layout_options()
     layout_args["barmode"] = "stack"
     layout_args["title"] = _("<b>Weight</b>")
     layout_args["xaxis"]["title"] = _("Date")
     layout_args["xaxis"]["rangeselector"] = utils.rangeselector_date()
     layout_args["yaxis"]["title"] = _("Weight")
+    if percentile_weights:
+        # zoom in on the relevant dates
+        layout_args["xaxis"]["range"] = [
+            birthday,
+            max(weighing_dates) + timedelta(days=1),
+        ]
+        layout_args["yaxis"]["range"] = [0, max(measured_weights) * 1.5]
+        data.extend(
+            [
+                percentile_weight_97_trace,
+                percentile_weight_85_trace,
+                percentile_weight_50_trace,
+                percentile_weight_15_trace,
+                percentile_weight_3_trace,
+            ]
+        )
 
-    fig = go.Figure({"data": [trace], "layout": go.Layout(**layout_args)})
+    fig = go.Figure({"data": data, "layout": go.Layout(**layout_args)})
     output = plotly.plot(fig, output_type="div", include_plotlyjs=False)
     return utils.split_graph_output(output)

reports/templates/reports/report_list.html

@@ -30,6 +30,8 @@
             <a href="{% url 'reports:report-temperature-change-child' object.slug %}" class="list-group-item list-group-item-action">{% trans "Temperature" %}</a>
             <a href="{% url 'reports:report-tummy-time-duration-child' object.slug %}" class="list-group-item list-group-item-action">{% trans "Tummy Time Durations (Sum)" %}</a>
             <a href="{% url 'reports:report-weight-change-child' object.slug %}" class="list-group-item list-group-item-action">{% trans "Weight" %}</a>
+            <a href="{% url 'reports:report-weight-change-child-sex' object.slug 'boy' %}" class="list-group-item list-group-item-action">{% trans "WHO Weight Percentiles for Boys in kg" %}</a>
+            <a href="{% url 'reports:report-weight-change-child-sex' object.slug 'girl' %}" class="list-group-item list-group-item-action">{% trans "WHO Weight Percentiles for Girls in kg" %}</a>
         </div>
     </div>
 {% endblock %}

reports/urls.py

@@ -81,4 +81,9 @@ urlpatterns = [
         views.WeightChangeChildReport.as_view(),
         name="report-weight-change-child",
     ),
+    path(
+        "children/<str:slug>/reports/weight/<sex>/",
+        views.WeightChangeChildReport.as_view(),
+        name="report-weight-change-child-sex",
+    ),
 ]

reports/views.py

@@ -295,7 +295,13 @@ class WeightChangeChildReport(PermissionRequiredMixin, DetailView):
     def get_context_data(self, **kwargs):
         context = super(WeightChangeChildReport, self).get_context_data(**kwargs)
         child = context["object"]
-        objects = models.Weight.objects.filter(child=child)
+        birthday = child.birth_date
-        if objects:
+        actual_weights = models.Weight.objects.filter(child=child)
-            context["html"], context["js"] = graphs.weight_change(objects)
+        percentile_weights = models.WeightPercentile.objects.filter(
+            sex=self.kwargs.get("sex")
+        )
+        if actual_weights:
+            context["html"], context["js"] = graphs.weight_change(
+                actual_weights, percentile_weights, birthday
+            )
         return context