Merge branch 'release/0.3.57' into main

.github/workflows/build.yml

@@ -36,9 +36,9 @@ jobs:
           sudo apt-get -y update
           sudo apt-get install libcups2-dev wamerican
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -48,7 +48,7 @@ jobs:
           echo "dir=$(pip cache dir)" >>$GITHUB_OUTPUT
 
       - name: Cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
           key:

.pre-commit-config.yaml

@@ -3,32 +3,32 @@ exclude: tests/etc/user-*
 
 repos:
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.5
+    rev: 1.7.7
     hooks:
       - id: bandit
         args:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.2.0
     hooks:
       - id: black
         language_version: python3.11
 
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         args:
           - "--config=setup.cfg"
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: requirements-txt-fixer
         files: requirements/.*\.txt$
@@ -42,7 +42,7 @@ repos:
       - id: detect-private-key
 
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.32.0
+    rev: v1.34.0
     hooks:
       - id: yamllint
         args:

edc_lab/form_validators/crf_requisition_form_validator_mixin.py

@@ -10,7 +10,6 @@
 
 
 class CrfRequisitionFormValidatorMixin:
-
     """An FormValidator mixin for CRFs (not requisitions).
 
     Used with a CRF that refers to a requisition or requisitions.

edc_lab/identifiers/prefix.py

@@ -10,7 +10,6 @@ class PrefixKeyError(Exception):
 
 
 class Prefix:
-
     """A class to generate an identifier prefix."""
 
     template: str = "{protocol_number}{requisition_identifier}"

edc_lab/lab/aliquot_type.py

@@ -10,7 +10,6 @@ class AliquotTypeNumericCodeError(Exception):
 
 
 class AliquotType:
-
     """A class to represent an aliquot type by an alpha and
     numeric code.
 

edc_lab/lab/lab_profile.py

@@ -11,7 +11,6 @@ class LabProfileRequisitionModelError(Exception):
 
 
 class LabProfile:
-
     """A container class for aliquot types, panels and processing."""
 
     site_model = "sites.site"

edc_lab/lab/primary_aliquot.py

@@ -7,7 +7,6 @@ class PrimaryAliquotPrefixError(Exception):
 
 
 class PrimaryAliquot:
-
     """A class that gets or creates the primary aliquot."""
 
     def __init__(

edc_lab/lab/processing_profile.py

@@ -10,7 +10,6 @@ class ProcessingProfileAlreadyAdded(Exception):
 
 
 class Process:
-
     """A class to represent the resulting aliquot type and number of
     aliquots from the processing of a source aliquot.
     """
@@ -28,7 +27,6 @@ def __str__(self):
 
 
 class ProcessingProfile:
-
     """A container of process instances.
 
     Given a source aliquot, all processes in the profile

edc_lab/lab/requisition_panel.py

@@ -21,7 +21,6 @@ class InvalidProcessingProfile(Exception):
 
 
 class PanelAttrs:
-
     """ "A simple class of panel name attributes."""
 
     def __init__(self, name: str = None, alpha_code: str = None) -> None:
@@ -32,7 +31,6 @@ def __init__(self, name: str = None, alpha_code: str = None) -> None:
 
 
 class RequisitionPanel:
-
     """A panel class that contains processing profile instances."""
 
     panel_attrs_cls = PanelAttrs

edc_lab/lab/specimen.py

@@ -12,7 +12,6 @@ class SpecimenNotDrawnError(Exception):
 
 
 class Specimen:
-
     """A class that represents a collected specimen and it's aliquots
     given the original requisition.
 

edc_lab/model_mixins/requisition/crf_with_requisition_model_mixin.py

@@ -17,7 +17,6 @@
 
 
 class CrfWithRequisitionModelMixin(models.Model):
-
     """You may also wish to override field `requisition`
     to include `limit_choices_to`.
 

edc_lab/pdf_reports/manifest_pdf_report.py

@@ -21,8 +21,7 @@
 
     from ..model_mixins import ManifestModelMixin
 
-    class Model(PdfReportModelMixin, ManifestModelMixin, BaseUuidModel):
-        ...
+    class Model(PdfReportModelMixin, ManifestModelMixin, BaseUuidModel): ...
 
 
 class ManifestPdfReportError(Exception):
@@ -252,9 +251,11 @@ def get_report_story(self, **kwargs):
                 Paragraph(self.contact_name, self.styles["line_data_large"]),
                 "",
                 Paragraph(
-                    self.manifest.export_datetime.strftime("%Y-%m-%d %H:%M")
-                    if self.manifest.shipped
-                    else "PREVIEW",
+                    (
+                        self.manifest.export_datetime.strftime("%Y-%m-%d %H:%M")
+                        if self.manifest.shipped
+                        else "PREVIEW"
+                    ),
                     self.styles["line_data_large"],
                 ),
             ],
@@ -327,9 +328,11 @@ def formatted_address(self, **kwargs):
                 data.get("contact_name"),
                 data.get("name"),
                 data.get("address"),
-                data.get("city")
-                if not data.get("state")
-                else "{} {}".format(data.get("city"), data.get("state")),
+                (
+                    data.get("city")
+                    if not data.get("state")
+                    else "{} {}".format(data.get("city"), data.get("state"))
+                ),
                 data.get("postal_code"),
                 data.get("country"),
             ]

edc_lab/stubs.py

@@ -7,5 +7,4 @@ class AliquotTypeStub(Protocol):
     alpha_code: str
     numeric_code: str
 
-    def add_derivatives(self: "AliquotTypeStub") -> None:
-        ...
+    def add_derivatives(self: "AliquotTypeStub") -> None: ...

edc_lab/tests/tests/test_forms.py

@@ -328,5 +328,6 @@ class Meta:
         form.is_valid()
         self.assertIn("requisition_datetime", form._errors)
         self.assertIn(
-            "Invalid. Expected a date/time between", form.errors.get("requisition_datetime")[0]
+            "Invalid. Date falls outside of the window period",
+            form.errors.get("requisition_datetime")[0],
         )

setup.cfg

@@ -37,7 +37,7 @@ exclude =
     edc_lab.tests*
 
 [flake8]
-ignore = E226,W503,E203,W605
+ignore = E226,W503,E203,E701,E704,W605
 max-line-length = 95
 max-complexity = 10
 exclude = */migrations/*,.tox,.git,__pycache__,build,dist,.eggs