migrate to Django 5.0.0 (#959)

* update requirements.txt

* add changes from django-upgrade

* fix for assuming HTTPS in URL Field

* fix one more django warning

* add extra unrelated change from #962

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>

hawc/apps/animal/managers.py

@@ -1,4 +1,3 @@
-from copy import deepcopy
 from typing import Any
 
 import numpy as np
@@ -20,13 +19,12 @@ class ExperimentManager(BaseManager):
     assessment_relation = "study__assessment"
 
     def get_type_choices(self, assessment_id: int):
-        choices = deepcopy(constants.ExperimentType.choices)
         types = set(
             self.model.objects.filter(study__assessment_id=assessment_id)
             .values_list("type", flat=True)
             .distinct()
         )
-        return [c for c in choices if c[0] in types]
+        return [c for c in constants.ExperimentType.choices if c[0] in types]
 
 
 class AnimalGroupManager(BaseManager):

hawc/apps/animal/models.py

@@ -48,7 +48,7 @@ class Experiment(models.Model):
     )
     type = models.CharField(
         max_length=2,
-        choices=constants.ExperimentType.choices,
+        choices=constants.ExperimentType,
         help_text="Type of study being performed; be as specific as possible",
     )
     has_multiple_generations = models.BooleanField(default=False)
@@ -84,7 +84,7 @@ class Experiment(models.Model):
     purity_available = models.BooleanField(default=True, verbose_name="Chemical purity available?")
     purity_qualifier = models.CharField(
         max_length=1,
-        choices=constants.PurityQualifier.choices,
+        choices=constants.PurityQualifier,
         blank=True,
         default=constants.PurityQualifier.NA,
     )
@@ -220,7 +220,7 @@ class AnimalGroup(models.Model):
         help_text="When adding a new strain, put the stock in parenthesis, e.g., "
         + '"Sprague-Dawley (Harlan)."',
     )
-    sex = models.CharField(max_length=1, choices=constants.Sex.choices)
+    sex = models.CharField(max_length=1, choices=constants.Sex)
     animal_source = models.CharField(
         max_length=128, help_text="Source from where animals were acquired", blank=True
     )
@@ -250,7 +250,7 @@ class AnimalGroup(models.Model):
     )
     siblings = models.ForeignKey("self", blank=True, null=True, on_delete=models.SET_NULL)
     generation = models.CharField(
-        blank=True, default="", max_length=2, choices=constants.Generation.choices
+        blank=True, default="", max_length=2, choices=constants.Generation
     )
     parents = models.ManyToManyField("self", related_name="children", symmetrical=False, blank=True)
     dosing_regime = models.ForeignKey(
@@ -381,7 +381,7 @@ class DosingRegime(models.Model):
     )
     route_of_exposure = models.CharField(
         max_length=2,
-        choices=constants.RouteExposure.choices,
+        choices=constants.RouteExposure,
         help_text="Primary route of exposure. If multiple primary-exposures, describe in notes-field below",
     )
     duration_exposure = models.FloatField(
@@ -429,7 +429,7 @@ class DosingRegime(models.Model):
     negative_control = models.CharField(
         max_length=2,
         default=constants.NegativeControl.VT,
-        choices=constants.NegativeControl.choices,
+        choices=constants.NegativeControl,
         help_text="Description of negative-controls used",
     )
     description = models.TextField(
@@ -626,7 +626,7 @@ class Endpoint(BaseEndpoint):
     )
     litter_effects = models.CharField(
         max_length=2,
-        choices=constants.LitterEffect.choices,
+        choices=constants.LitterEffect,
         default=constants.LitterEffect.NA,
         help_text='Type of controls used for litter-effects. The "No" response '
         + "will be infrequently used. More typically the information will be "
@@ -645,7 +645,7 @@ class Endpoint(BaseEndpoint):
         "optional, should be recorded if the same effect was measured multiple times.",
     )
     observation_time_units = models.PositiveSmallIntegerField(
-        default=constants.ObservationTimeUnits.NR, choices=constants.ObservationTimeUnits.choices
+        default=constants.ObservationTimeUnits.NR, choices=constants.ObservationTimeUnits
     )
     observation_time_text = models.CharField(
         max_length=64,
@@ -660,7 +660,7 @@ class Endpoint(BaseEndpoint):
         '1 and Text, p.24")',
     )
     expected_adversity_direction = models.PositiveSmallIntegerField(
-        choices=constants.AdverseDirection.choices,
+        choices=constants.AdverseDirection,
         default=constants.AdverseDirection.NR,
         verbose_name="Expected response adversity direction",
         help_text="Response direction which would be considered adverse",
@@ -673,12 +673,12 @@ class Endpoint(BaseEndpoint):
     )
     data_type = models.CharField(
         max_length=2,
-        choices=constants.DataType.choices,
+        choices=constants.DataType,
         default=constants.DataType.CONTINUOUS,
         verbose_name="Dataset type",
     )
     variance_type = models.PositiveSmallIntegerField(
-        default=constants.VarianceType.SD, choices=constants.VarianceType.choices
+        default=constants.VarianceType.SD, choices=constants.VarianceType
     )
     confidence_interval = models.FloatField(
         blank=True,
@@ -706,7 +706,7 @@ class Endpoint(BaseEndpoint):
         help_text="Response values were estimated using a digital ruler or other methods",
     )
     monotonicity = models.PositiveSmallIntegerField(
-        default=constants.Monotonicity.NR, choices=constants.Monotonicity.choices
+        default=constants.Monotonicity.NR, choices=constants.Monotonicity
     )
     statistical_test = models.CharField(
         max_length=256,
@@ -718,7 +718,7 @@ class Endpoint(BaseEndpoint):
         null=True, blank=True, help_text="Numerical result for trend-test, if available"
     )
     trend_result = models.PositiveSmallIntegerField(
-        default=constants.TrendResult.NR, choices=constants.TrendResult.choices
+        default=constants.TrendResult.NR, choices=constants.TrendResult
     )
     diagnostic = models.TextField(
         verbose_name="Diagnostic (as reported)",
@@ -1359,7 +1359,7 @@ class EndpointGroup(ConfidenceIntervalsMixin, models.Model):
         null=True,
         blank=True,
         default=None,
-        choices=constants.TreatmentEffect.choices,
+        choices=constants.TreatmentEffect,
         help_text="Expert judgement based report of treatment related effects (add direction if known). Use when statistical analysis not available. In results comments, indicate whether it was author judgment or assessment team judgement",
     )
 

hawc/apps/assessment/models.py

@@ -259,13 +259,13 @@ def get_rob_name_default():
     )
     noel_name = models.PositiveSmallIntegerField(
         default=get_noel_name_default,
-        choices=constants.NoelName.choices,
+        choices=constants.NoelName,
         verbose_name="NEL/NOEL/NOAEL name",
         help_text="What term should be used to refer to NEL/NOEL/NOAEL and LEL/LOEL/LOAEL?",
     )
     rob_name = models.PositiveSmallIntegerField(
         default=get_rob_name_default,
-        choices=constants.RobName.choices,
+        choices=constants.RobName,
         verbose_name="Risk of bias/Study evaluation name",
         help_text="What term should be used to refer to risk of bias/study evaluation questions?",
     )
@@ -288,7 +288,7 @@ def get_rob_name_default():
         needed.""",
     )
     epi_version = models.PositiveSmallIntegerField(
-        choices=constants.EpiVersion.choices,
+        choices=constants.EpiVersion,
         default=constants.EpiVersion.V2,
         verbose_name="Epidemiology schema version",
         help_text="Data extraction schema version used for epidemiology studies",
@@ -515,7 +515,7 @@ class AssessmentDetail(models.Model):
         help_text="If part of a product line, the name of the project type",
     )
     project_status = models.PositiveSmallIntegerField(
-        choices=constants.Status.choices,
+        choices=constants.Status,
         default=constants.Status.SCOPING,
         help_text="High-level project management milestones for this assessment",
     )
@@ -527,7 +527,7 @@ class AssessmentDetail(models.Model):
     )
     peer_review_status = models.PositiveSmallIntegerField(
         verbose_name="Peer Review Status",
-        choices=constants.PeerReviewType.choices,
+        choices=constants.PeerReviewType,
         help_text="Define the current status of peer review of this assessment, if any",
         default=constants.PeerReviewType.NONE,
     )
@@ -582,7 +582,7 @@ class AssessmentValue(models.Model):
 
     assessment = models.ForeignKey(Assessment, models.CASCADE, related_name="values")
     evaluation_type = models.PositiveSmallIntegerField(
-        choices=constants.EvaluationType.choices,
+        choices=constants.EvaluationType,
         default=constants.EvaluationType.CANCER,
         help_text="Substance evaluation conducted",
     )
@@ -592,7 +592,7 @@ class AssessmentValue(models.Model):
         help_text="Identify the health system of concern (e.g., Hepatic, Nervous, Reproductive)",
     )
     value_type = models.PositiveSmallIntegerField(
-        choices=constants.ValueType.choices,
+        choices=constants.ValueType,
         help_text="Type of derived value",
     )
     value = models.FloatField(
@@ -640,7 +640,7 @@ class AssessmentValue(models.Model):
     uncertainty = models.IntegerField(
         blank=True,
         null=True,
-        choices=constants.UncertaintyChoices.choices,
+        choices=constants.UncertaintyChoices,
         verbose_name="Uncertainty factor",
         help_text="Composite uncertainty factor applied to POD to derive the final value",
     )
@@ -1121,10 +1121,10 @@ class Job(models.Model):
         Assessment, blank=True, null=True, on_delete=models.CASCADE, related_name="jobs"
     )
     status = models.PositiveSmallIntegerField(
-        choices=constants.JobStatus.choices, default=constants.JobStatus.PENDING, editable=False
+        choices=constants.JobStatus, default=constants.JobStatus.PENDING, editable=False
     )
     job = models.PositiveSmallIntegerField(
-        choices=constants.JobType.choices, default=constants.JobType.TEST
+        choices=constants.JobType, default=constants.JobType.TEST
     )
 
     kwargs = models.JSONField(default=dict, blank=True, null=True)
@@ -1268,7 +1268,7 @@ class ContentTypeChoices(models.IntegerChoices):
 
 
 class Content(models.Model):
-    content_type = models.PositiveIntegerField(choices=ContentTypeChoices.choices, unique=True)
+    content_type = models.PositiveIntegerField(choices=ContentTypeChoices, unique=True)
     template = models.TextField()
     created = models.DateTimeField(auto_now_add=True)
     last_updated = models.DateTimeField(auto_now=True)

hawc/apps/bmd/models.py

@@ -17,7 +17,7 @@ class AssessmentSettings(models.Model):
     )
     version = models.CharField(
         max_length=10,
-        choices=constants.BmdsVersion.choices,
+        choices=constants.BmdsVersion,
         default=constants.BmdsVersion.BMDS330,
         help_text="Select the BMDS version to be used for dose-response modeling. Version 2 is no longer supported for execution; but results will be available for any version after execution is complete.",
     )
@@ -56,7 +56,7 @@ class Session(models.Model):
     dose_units = models.ForeignKey(
         "assessment.DoseUnits", on_delete=models.CASCADE, related_name="bmd_sessions"
     )
-    version = models.CharField(max_length=10, choices=constants.BmdsVersion.choices)
+    version = models.CharField(max_length=10, choices=constants.BmdsVersion)
     inputs = models.JSONField(default=dict)
     outputs = models.JSONField(default=dict)
     errors = models.JSONField(default=dict)

hawc/apps/eco/models.py

@@ -24,7 +24,7 @@ def __str__(self):
 
 class NestedTerm(MP_Node):
     name = models.CharField(max_length=128)
-    type = models.CharField(choices=TypeChoices.choices, max_length=2, default="CE")
+    type = models.CharField(choices=TypeChoices, max_length=2, default="CE")
     created = models.DateTimeField(auto_now_add=True)
     last_updated = models.DateTimeField(auto_now=True)
     notes = models.TextField(blank=True)
@@ -66,7 +66,7 @@ def as_dataframe(cls) -> pd.DataFrame:
 
 
 class Vocab(models.Model):
-    category = models.IntegerField(choices=VocabCategories.choices)
+    category = models.IntegerField(choices=VocabCategories)
     value = models.CharField(max_length=128)
     parent = models.ForeignKey(
         "self",
@@ -408,7 +408,7 @@ class Result(models.Model):
         default=0,
     )
     relationship_direction = models.IntegerField(
-        choices=ChangeTrajectory.choices,
+        choices=ChangeTrajectory,
         verbose_name="Direction of relationship",
         help_text="Direction of cause and effect relationship",
     )