clinicedc 2.0.20__py3-none-any.whl → 2.0.22__py3-none-any.whl

edc_visit_schedule/schedule/schedule.py

@@ -204,7 +204,7 @@ class Schedule:
                 f"See {visit}. Got visit.timepoint={visit.timepoint}."
             )
         visit.base_timepoint = self.base_timepoint
-        self.visits.update({visit.code: visit})
+        self.visits.update(**{visit.code: visit})
         return visit
 
     @property
@@ -235,9 +235,7 @@ class Schedule:
                 visit_codes.append(visit_code)
         return visit_codes
 
-    def subject(
-        self, subject_identifier: str, consent_definition: ConsentDefinition = None
-    ) -> SubjectSchedule:
+    def subject(self, subject_identifier: str) -> SubjectSchedule:
         """Returns a SubjectSchedule instance for this subject.
 
         Note: SubjectSchedule puts a subject on/off schedule by
@@ -292,9 +290,7 @@ class Schedule:
                 f"'{consent_definition.proxy_model}', "
                 f"version='{consent_definition.version}'). "
             )
-        self.subject(
-            subject_identifier, consent_definition=consent_definition
-        ).put_on_schedule(
+        self.subject(subject_identifier).put_on_schedule(
             onschedule_datetime,
             skip_baseline=skip_baseline,
             skip_get_current_site=skip_get_current_site,

edc_visit_schedule/schedule/window.py

@@ -49,7 +49,7 @@ class Window:
             try:
                 self.visits.get(self.visit_code)
             except VisitCollectionError as e:
-                raise ScheduleError(e)
+                raise ScheduleError(e) from e
             if self.is_scheduled_visit or not self.visits.next(self.visit_code):
                 self.raise_for_scheduled_not_in_window()
             else:

edc_visit_schedule/simple_model_validator.py

@@ -1,7 +1,7 @@
 from django.apps import apps as django_apps
 
 
-class InvalidModel(Exception):
+class InvalidModel(Exception):  # noqa: N818
     pass
 
 
@@ -14,11 +14,11 @@ class SimpleModelValidator:
     def __init__(self, model=None, attr=None):
         try:
             app_label, _ = model.split(".")
-        except AttributeError:
-            raise InvalidModel(f"Invalid label lower format for '{attr}'. " f"Got {model}")
+        except AttributeError as e:
+            raise InvalidModel(f"Invalid label lower format for '{attr}'. Got {model}") from e
         else:
             app_labels = [app_config.name for app_config in django_apps.get_app_configs()]
             if app_label not in app_labels:
                 raise InvalidModel(
-                    f"Invalid model. app_label does not exist for " f"'{attr}'. Got {model}"
+                    f"Invalid model. app_label does not exist for '{attr}'. Got {model}"
                 )

edc_visit_schedule/site_visit_schedules.py

@@ -121,9 +121,7 @@ class SiteVisitSchedules:
         visit_schedule, schedule = ret[0]
         return visit_schedule, schedule
 
-    def get_by_onschedule_model(
-        self, onschedule_model: str = None
-    ) -> tuple[VisitSchedule, Schedule]:
+    def get_by_onschedule_model(self, onschedule_model: str) -> tuple[VisitSchedule, Schedule]:
         """Returns a tuple of (visit_schedule, schedule)
         for the given onschedule model.
 
@@ -132,7 +130,7 @@ class SiteVisitSchedules:
         return self.get_by_model(attr="onschedule_model", model=onschedule_model)
 
     def get_by_offschedule_model(
-        self, offschedule_model: str = None
+        self, offschedule_model: str
     ) -> tuple[VisitSchedule, Schedule]:
         """Returns a tuple of visit_schedule, schedule
         for the given offschedule model.
@@ -142,7 +140,7 @@ class SiteVisitSchedules:
         return self.get_by_model(attr="offschedule_model", model=offschedule_model)
 
     def get_by_loss_to_followup_model(
-        self, loss_to_followup_model: str = None
+        self, loss_to_followup_model: str
     ) -> tuple[VisitSchedule, Schedule]:
         """Returns a tuple of visit_schedule, schedule
         for the given loss_to_followup model.
@@ -151,9 +149,7 @@ class SiteVisitSchedules:
         """
         return self.get_by_model(attr="loss_to_followup_model", model=loss_to_followup_model)
 
-    def get_by_model(
-        self, attr: str = None, model: str = None
-    ) -> tuple[VisitSchedule, Schedule]:
+    def get_by_model(self, attr: str, model: str) -> tuple[VisitSchedule, Schedule]:
         ret = []
         model = model.lower()
         for visit_schedule in self.visit_schedules.values():
@@ -178,14 +174,15 @@ class SiteVisitSchedules:
         visit_schedule, schedule = ret[0]
         return visit_schedule, schedule
 
-    def get_by_offstudy_model(self, offstudy_model: str = None) -> list[VisitSchedule]:
+    def get_by_offstudy_model(self, offstudy_model: str) -> list[VisitSchedule]:
         """Returns a list of visit_schedules for the given
         offstudy model.
         """
-        visit_schedules = []
-        for visit_schedule in self.visit_schedules.values():
-            if visit_schedule.offstudy_model == offstudy_model:
-                visit_schedules.append(visit_schedule)
+        visit_schedules = [
+            visit_schedule
+            for visit_schedule in self.visit_schedules.values()
+            if visit_schedule.offstudy_model == offstudy_model
+        ]
         if not visit_schedules:
             raise SiteVisitScheduleError(
                 f"No visit schedules have been defined using the "
@@ -220,7 +217,7 @@ class SiteVisitSchedules:
     @staticmethod
     def get_offstudy_model() -> str:
         offstudy_models = []
-        for _, visit_schedule in site_visit_schedules.get_visit_schedules().items():
+        for visit_schedule in site_visit_schedules.get_visit_schedules().values():
             if visit_schedule.offstudy_model not in offstudy_models:
                 offstudy_models.append(visit_schedule.offstudy_model)
         if len(offstudy_models) > 1:
@@ -236,8 +233,7 @@ class SiteVisitSchedules:
                 "No off study model defined in visit_schedule. "
                 f"Got registered visit_schedules: {visit_schedule_names}."
             )
-        offstudy_model = offstudy_models[0]
-        return offstudy_model
+        return offstudy_models[0]
 
     @property
     def all_post_consent_models(self) -> dict[str, str]:

edc_visit_schedule/subject_schedule.py

@@ -237,13 +237,13 @@ class SubjectSchedule:
                 schedule_name=self.schedule_name,
                 visit_schedule_name=self.visit_schedule_name,
             )
-        except ObjectDoesNotExist:
+        except ObjectDoesNotExist as e:
             raise NotOnScheduleError(
                 "Failed to take subject off schedule. "
                 f"Subject has not been put on schedule "
                 f"'{self.visit_schedule_name}.{self.schedule_name}'. "
                 f"Got '{self.subject_identifier}'."
-            )
+            ) from e
 
         if history_obj:
             self.update_history_or_raise(
@@ -293,7 +293,7 @@ class SubjectSchedule:
                 subject_identifier=self.subject_identifier,
                 schedule_name=self.schedule_name,
                 visit_schedule_name=self.visit_schedule_name,
-                **{f"{related_visit_model_attr}__report_datetime__gt": (offschedule_datetime)},
+                **{f"{related_visit_model_attr}__report_datetime__gt": offschedule_datetime},
             )
         except ObjectDoesNotExist:
             appointments = None
@@ -302,7 +302,7 @@ class SubjectSchedule:
                 subject_identifier=self.subject_identifier,
                 schedule_name=self.schedule_name,
                 visit_schedule_name=self.visit_schedule_name,
-                **{f"{related_visit_model_attr}__report_datetime__gt": (offschedule_datetime)},
+                **{f"{related_visit_model_attr}__report_datetime__gt": offschedule_datetime},
             )
         if appointments:
             raise InvalidOffscheduleDate(
@@ -336,12 +336,12 @@ class SubjectSchedule:
         model_cls = django_apps.get_model(self.registered_subject_model)
         try:
             obj = model_cls.objects.get(subject_identifier=self.subject_identifier)
-        except ObjectDoesNotExist:
+        except ObjectDoesNotExist as e:
             raise UnknownSubjectError(
                 f"Failed to put subject on schedule. Unknown subject. "
                 f"Searched `{self.registered_subject_model}`. "
                 f"Got subject_identifier=`{self.subject_identifier}`."
-            )
+            ) from e
         return obj
 
     @property
@@ -350,11 +350,11 @@ class SubjectSchedule:
             onschedule_obj = self.onschedule_model_cls.objects.get(
                 subject_identifier=self.subject_identifier
             )
-        except ObjectDoesNotExist:
+        except ObjectDoesNotExist as e:
             raise NotOnScheduleError(
                 f"Subject has not been put on a schedule `{self.schedule_name}`. "
                 f"Got subject_identifier=`{self.subject_identifier}`."
-            )
+            ) from e
         return onschedule_obj
 
     def onschedule_or_raise(self, report_datetime=None, compare_as_datetimes=None):

edc_visit_schedule/system_checks.py

@@ -5,7 +5,7 @@ from collections import Counter, defaultdict
 from typing import TYPE_CHECKING
 
 from django.apps import apps as django_apps
-from django.core.checks import Error, Warning
+from django.core.checks import Error, Warning  # noqa: A004
 from django.core.exceptions import ObjectDoesNotExist
 
 from .site_visit_schedules import site_visit_schedules
@@ -55,7 +55,7 @@ def check_subject_schedule_history(app_configs, **kwargs) -> list:
         )
         for obj in subject_schedule_history_cls.objects.all():
             try:
-                obj.onschedule_obj
+                obj.onschedule_obj  # noqa: B018
             except LookupError as e:
                 errors.append(
                     Error(
@@ -201,7 +201,7 @@ def check_multiple_proxies_same_proxy_root(
         if proxies_counter & proxies_sharing_roots_counter == proxies_counter:
             # OK if proxies counter reflects ALL defined proxy shared roots
             del proxy_root_to_child_proxies[proxy_root]
-        elif len(proxies_counter) == 1 and next(iter(proxies_counter.values())) <= 2:
+        elif len(proxies_counter) == 1 and next(iter(proxies_counter.values())) <= 2:  # noqa: PLR2004
             # OK for a single proxy to be defined in two places (CRFs collection + PRNs)
             del proxy_root_to_child_proxies[proxy_root]
         else:

edc_visit_schedule/templatetags/edc_visit_schedule_extras.py

@@ -51,7 +51,7 @@ def subject_schedule_footer_row(
         context.update(
             offschedule_datetime=None,
             onschedule_datetime=onschedule_model_obj.onschedule_datetime,
-            href=mark_safe(href),  # nosec B703, B308
+            href=mark_safe(href),  # nosec B703, B308  # noqa: S308
         )
     elif history_obj.offschedule_datetime:
         # subject is OFF this schedule (offschedule_model_obj)
@@ -71,6 +71,6 @@ def subject_schedule_footer_row(
         context.update(
             offschedule_datetime=history_obj.offschedule_datetime,
             onschedule_datetime=onschedule_model_obj.onschedule_datetime,
-            href=mark_safe(href),  # nosec B703, B308
+            href=mark_safe(href),  # nosec B703, B308  # noqa: S308
         )
     return context

edc_visit_schedule/utils.py

@@ -76,9 +76,7 @@ def raise_if_not_baseline(subject_visit) -> None:
         raise forms.ValidationError("This form is only available for completion at baseline.")
 
 
-def get_onschedule_models(
-    subject_identifier: str = None, report_datetime: datetime = None
-) -> list[str]:
+def get_onschedule_models(subject_identifier: str, report_datetime: datetime) -> list[str]:
     """Returns a list of onschedule models, in label_lower format,
     for this subject and date.
     """
@@ -96,7 +94,7 @@ def get_onschedule_models(
     return onschedule_models
 
 
-def get_offschedule_models(subject_identifier=None, report_datetime=None) -> list[str]:
+def get_offschedule_models(subject_identifier: str, report_datetime: datetime) -> list[str]:
     """Returns a list of offschedule models, in label_lower format,
     for this subject and date.
 
@@ -141,7 +139,7 @@ def off_schedule_or_raise(
         )
 
 
-def off_all_schedules_or_raise(subject_identifier: str = None):
+def off_all_schedules_or_raise(subject_identifier: str):
     """Raises an exception if subject is still on any schedule."""
     for visit_schedule in site_visit_schedules.get_visit_schedules().values():
         for schedule in visit_schedule.schedules.values():
@@ -171,8 +169,8 @@ def off_all_schedules_or_raise(subject_identifier: str = None):
 
 
 def offstudy_datetime_after_all_offschedule_datetimes(
-    subject_identifier: str = None,
-    offstudy_datetime: datetime = None,
+    subject_identifier: str,
+    offstudy_datetime: datetime,
     exception_cls=None,
 ) -> None:
     exception_cls = exception_cls or forms.ValidationError
@@ -206,10 +204,10 @@ def offstudy_datetime_after_all_offschedule_datetimes(
 
 
 def report_datetime_within_onschedule_offschedule_datetimes(
-    subject_identifier: str = None,
-    report_datetime: datetime = None,
-    visit_schedule_name: str = None,
-    schedule_name: str = None,
+    subject_identifier: str,
+    report_datetime: datetime,
+    visit_schedule_name: str,
+    schedule_name: str,
     exception_cls=None,
 ):
     exception_cls = exception_cls or forms.ValidationError
@@ -219,11 +217,11 @@ def report_datetime_within_onschedule_offschedule_datetimes(
         onschedule_obj = schedule.onschedule_model_cls.objects.get(
             subject_identifier=subject_identifier
         )
-    except ObjectDoesNotExist:
+    except ObjectDoesNotExist as e:
         raise OnScheduleError(
             f"Subject is not on schedule. {visit_schedule_name}.{schedule_name}. "
             f"Got {subject_identifier}"
-        )
+        ) from e
     try:
         offschedule_obj = schedule.offschedule_model_cls.objects.get(
             subject_identifier=subject_identifier,
@@ -280,7 +278,7 @@ def get_onschedule_model_instance(
         raise OffScheduleError(
             "Subject is not on a schedule. Using subject_identifier="
             f"`{subject_identifier}` and appt_datetime=`{dte_as_str}`. Got {e}"
-        )
+        ) from e
     return onschedule_obj
 
 
@@ -302,6 +300,7 @@ def get_proxy_root_model(proxy_model: models.Model) -> models.Model | None:
     """
     if proxy_model._meta.proxy:
         return proxy_model._meta.concrete_model
+    return None
 
 
 def check_models_in_visit_schedule() -> dict[str, list]:

edc_visit_schedule/view_mixins.py

@@ -37,7 +37,7 @@ class VisitScheduleViewMixin:
                         pass
                     else:
                         self.onschedule_models.append(onschedule_model_obj)
-                        self.visit_schedules.update({visit_schedule.name: visit_schedule})
+                        self.visit_schedules.update(**{visit_schedule.name: visit_schedule})
                         if schedule.is_onschedule(self.subject_identifier, timezone.now()):
                             self.current_schedule = schedule
                             self.current_visit_schedule = visit_schedule

edc_visit_schedule/visit/crf.py

@@ -15,12 +15,13 @@ class CrfModelNotProxyModelError(Exception):
 class Crf:
     def __init__(
         self,
-        show_order: int = None,
-        model: str = None,
-        required: bool = None,
-        additional: bool = None,
-        site_ids: list[int] = None,
-        shares_proxy_root: bool = None,
+        *,
+        show_order: int,
+        model: str,
+        required: bool | None = None,
+        additional: bool | None = None,
+        site_ids: list[int] | None = None,
+        shares_proxy_root: bool | None = None,
     ) -> None:
         self.additional = additional
         self.model = model.lower()

edc_visit_schedule/visit/forms_collection.py

@@ -19,7 +19,7 @@ class FormsCollection:
         *forms: Crf | Requisition,
         name: str | None = None,
         check_sequence: bool | None = None,
-        **kwargs,
+        **kwargs,  # noqa: ARG002
     ):
         check_sequence = True if check_sequence is None else check_sequence
         self.collection_is_unique_or_raise(forms)
@@ -85,7 +85,7 @@ class FormsCollection:
     def insert(self, index, value):
         if value:
             forms = list(self._forms)
-            for index, item in forms:
+            for _, item in forms:
                 if item.name == value.name:
                     raise FormsCollectionError(
                         f"Insert failed. Item is not unique. Got {value.name}"

edc_visit_schedule/visit/requisition.py

@@ -14,7 +14,7 @@ class ScheduledRequisitionError(Exception):
 
 
 class Requisition(Crf):
-    def __init__(self, panel=None, required: bool = None, **kwargs):
+    def __init__(self, panel=None, required: bool | None = None, **kwargs):
         required = False if required is None else required
         self.panel = panel
         if not self.panel.requisition_model:
@@ -52,10 +52,10 @@ class Requisition(Crf):
 
         See also: edc_lab.
         """
-        from edc_lab.site_labs import site_labs
+        from edc_lab.site_labs import site_labs  # noqa: PLC0415
 
         try:
-            self.panel.requisition_model_cls
+            self.panel.requisition_model_cls  # noqa: B018
         except LookupError as e:
             raise RequisitionLookupError(e) from e
 

edc_visit_schedule/visit/visit.py

@@ -20,7 +20,7 @@ if TYPE_CHECKING:
 
     from dateutil.relativedelta import relativedelta
 
-    from edc_facility import Facility
+    from edc_facility.facility import Facility
 
     from .crf import Crf
     from .requisition import Requisition
@@ -38,7 +38,7 @@ class VisitError(Exception):
     pass
 
 
-class BaseDatetimeNotSet(Exception):
+class BaseDatetimeNotSet(Exception):  # noqa: N818
     pass
 
 
@@ -53,10 +53,11 @@ class VisitDate:
 
     def __init__(
         self,
-        rlower: relativedelta = None,
-        rupper: relativedelta = None,
-        timepoint: Decimal = None,
-        base_timepoint: Decimal = None,
+        *,
+        rlower: relativedelta,
+        rupper: relativedelta,
+        timepoint: Decimal | None = None,
+        base_timepoint: Decimal | None = None,
     ):
         self._base: datetime | None = None
         self._lower: datetime | None = None
@@ -73,7 +74,7 @@ class VisitDate:
         return self._base
 
     @base.setter
-    def base(self, dt: datetime = None):
+    def base(self, dt: datetime):
         self._base = to_local(dt)
         self._lower, self._upper = self._window_period.get_window(dt=self._base)
 
@@ -100,25 +101,25 @@ class Visit:
 
     def __init__(
         self,
-        code: str = None,
-        timepoint: int | float | Decimal = None,
-        rbase: relativedelta = None,
-        rlower: relativedelta = None,
-        rupper: relativedelta = None,
-        rlower_late: relativedelta = None,
-        rupper_late: relativedelta = None,
-        add_window_gap_to_lower: bool | None = None,
-        max_window_gap_to_lower: int | None = None,
+        code: str,
+        timepoint: int | float | Decimal,
+        rbase: relativedelta,
+        rlower: relativedelta,
+        rupper: relativedelta,
+        title: str | None = None,
+        facility_name: str | None = None,
         crfs: CrfCollection | None = None,
-        requisitions: RequisitionCollection | None = None,
+        crfs_prn: CrfCollection | None = None,
         crfs_unscheduled: CrfCollection | None = None,
         crfs_missed: CrfCollection | None = None,
-        requisitions_unscheduled: RequisitionCollection | None = None,
-        crfs_prn: CrfCollection | None = None,
+        requisitions: RequisitionCollection | None = None,
         requisitions_prn: RequisitionCollection | None = None,
-        title: str = None,
+        requisitions_unscheduled: RequisitionCollection | None = None,
+        rlower_late: relativedelta = None,
+        rupper_late: relativedelta = None,
+        add_window_gap_to_lower: bool | None = None,
+        max_window_gap_to_lower: int | None = None,
         allow_unscheduled: bool | None = None,
-        facility_name: str | None = None,
         instructions: str | None = None,
         base_timepoint: int | float | Decimal | None = None,
         grouping=None,
@@ -162,14 +163,14 @@ class Visit:
             raise VisitCodeError(f"Invalid visit code. Got '{code}'")
         self.code = code  # unique
         self.dates = self.visit_date_cls(
-            rlower=rlower,
-            rupper=rupper,
+            rlower=self.rlower,
+            rupper=self.rupper,
             timepoint=self.timepoint,
             base_timepoint=self.base_timepoint,
         )
         self.late_dates = self.visit_date_cls(
-            rlower=rlower_late or rlower,
-            rupper=rupper_late or rupper,
+            rlower=self.rlower_late,
+            rupper=self.rupper_late,
             timepoint=self.timepoint,
             base_timepoint=self.base_timepoint,
         )
@@ -252,11 +253,10 @@ class Visit:
         return get_requisition
 
     def get_models(self) -> list:
-        models = []
-        for crf in self.crfs:
-            models.append(django_apps.get_model(crf.model))
-        for crf in self.requisitions:
-            models.append(django_apps.get_model(crf.model))
+        models = [django_apps.get_model(crf.model) for crf in self.crfs]
+        models.extend(
+            [django_apps.get_model(requisition.model) for requisition in self.requisitions]
+        )
         return models
 
     @property

edc_visit_schedule/visit/window_period.py

@@ -14,8 +14,9 @@ from edc_utils import to_local
 class WindowPeriod:
     def __init__(
         self,
-        rlower: relativedelta = None,
-        rupper: relativedelta = None,
+        *,
+        rlower: relativedelta,
+        rupper: relativedelta,
         timepoint: Decimal | None = None,
         base_timepoint: Decimal | None = None,
         no_floor: bool | None = None,

edc_visit_schedule/visit_schedule/schedules_collection.py

@@ -10,11 +10,13 @@ class SchedulesCollection(OrderedCollection):
     key = "name"
     ordering_attr = "sequence"
 
-    def __init__(self, visit_schedule_name: str = None, *args, **kwargs) -> None:
+    def __init__(self, visit_schedule_name: str, *args, **kwargs) -> None:
         self.visit_schedule_name = visit_schedule_name
         super().__init__(*args, **kwargs)
 
-    def get_schedule(self, model: str = None, schedule_name: str = None) -> Schedule:
+    def get_schedule(
+        self, model: str | None = None, schedule_name: str | None = None
+    ) -> Schedule:
         """Returns a schedule or raises; by name, by onschedule/offschedule model
         or by model label_lower.
         """
@@ -22,7 +24,7 @@ class SchedulesCollection(OrderedCollection):
         if model:
             model = model.lower()
             for item in self.values():
-                if item.onschedule_model == model or item.offschedule_model == model:
+                if model in (item.onschedule_model, item.offschedule_model):
                     schedule = item
                 if schedule:
                     break

edc_visit_schedule/visit_schedule/visit_schedule.py

@@ -27,7 +27,7 @@ class VisitScheduleAppointmentModelError(Exception):
     pass
 
 
-class AlreadyRegisteredSchedule(Exception):
+class AlreadyRegisteredSchedule(Exception):  # noqa: N818
     pass
 
 
@@ -35,8 +35,8 @@ class VisitSchedule:
     name_regex = r"[a-z0-9\_\-]+$"
     name_regex_msg = "numbers, lower case letters and '_'"
     schedules_collection = SchedulesCollection
-    create_metadata_on_reasons = [SCHEDULED, UNSCHEDULED, MISSED_VISIT]
-    delete_metadata_on_reasons = []
+    create_metadata_on_reasons: tuple[str, ...] = (SCHEDULED, UNSCHEDULED, MISSED_VISIT)
+    delete_metadata_on_reasons: tuple[str, ...] = ()
 
     def __init__(
         self,
@@ -77,7 +77,7 @@ class VisitSchedule:
 
         if not re.match(self.name_regex, name):
             raise VisitScheduleNameError(
-                f"Visit schedule name may only contain {self.name_regex_msg}. " f"Got {name}"
+                f"Visit schedule name may only contain {self.name_regex_msg}. Got {name}"
             )
         self.title = self.verbose_name = verbose_name or " ".join(
             [s.capitalize() for s in name.split("_")]
@@ -107,7 +107,7 @@ class VisitSchedule:
             raise AlreadyRegisteredSchedule(
                 f"Schedule '{schedule.name}' is already registered. See '{self}'"
             )
-        self.schedules.update({schedule.name: schedule})
+        self.schedules.update(**{schedule.name: schedule})
         self._all_post_consent_models = None
         return schedule