Merge branch 'release/0.3.46'

.github/workflows/build.yml

@@ -5,14 +5,13 @@ on: [push, pull_request]
 
 jobs:
   build:
-    name: build (Python ${{ matrix.python-version }}, Django ${{ matrix.django-version }})
+    name: build (Python ${{ matrix.python-version }})
     runs-on: ubuntu-latest
 
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10']
-        django-version: ['3.2', '4.0', '4.1', 'dev']
+        python-version: ['3.10', '3.11']
 
     services:
       mysql:
@@ -31,20 +30,19 @@ jobs:
           sudo apt-get -y update
           sudo apt-get install libcups2-dev wamerican
 
-      - uses: actions/checkout@v2
-
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Get pip cache dir
         id: pip-cache
         run: |
-          echo "::set-output name=dir::$(pip cache dir)"
+          echo "dir=$(pip cache dir)" >>$GITHUB_OUTPUT
 
       - name: Cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
           key:
@@ -64,7 +62,7 @@ jobs:
         env:
           DJANGO: ${{ matrix.django-version }}
 
-      - name: Upload coverage
-        uses: codecov/codecov-action@v1
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
         with:
           name: Python ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -1,5 +1,6 @@
 ---
 exclude: tests/etc/user-*
+
 repos:
   - repo: https://github.com/PyCQA/bandit
     rev: 1.7.5
@@ -9,10 +10,10 @@ repos:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
       - id: black
-        language_version: python3.9
+        language_version: python3.10
 
   - repo: https://github.com/pycqa/flake8
     rev: 6.0.0
@@ -40,8 +41,13 @@ repos:
       - id: debug-statements
       - id: detect-private-key
 
+  - repo: https://github.com/rstcheck/rstcheck
+    rev: v6.1.2
+    hooks:
+      - id: rstcheck
+
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.30.0
+    rev: v1.31.0
     hooks:
       - id: yamllint
         args:

edc_constants/disease_constants.py

@@ -1,3 +1,4 @@
+ANAEMIA = "anaemia"
 BACTERAEMIA = "bacteraemia"
 BACTERAEMIA_SEPSIS = "bacteraemia_sepsis"
 BACTERIAL_PNEUMONIA = "bacterial_pneumonia"
@@ -10,7 +11,11 @@
 CRYPTOCOCCAL_MENINGITIS = "cm"
 DIARRHOEAL_WASTING = "diarrhoeal_wasting"
 FOCAL_NEUROLOGIC_DEFICIT_OTHER = "focal_neurologic_deficit_other"
+NEUTROPAENIA = "neutropaenia"
+PNEUMONIA = "pneumonia"
+RENAL_IMPAIRMENT = "renal_impairment"
 SEPSIS = "sepsis"
 TB_EXTRAPULMONARY = "tb_extrapulmonary"
 TB_PULMONARY = "tb_pulmonary"
 THERAPEUTIC_LP = "therapeutic_lp"
+THROMBOCYTOPENIA = "thrombocytopenia"

pyproject.toml

@@ -7,12 +7,12 @@ write_to = "_version.py"
 
 [tool.black]
 line-length = 95
-target-version = ["py39"]
+target-version = ["py310"]
 extend-exclude = '''^(.*\/)*\b(migrations)\b($|\/.*$)'''
 
 [tool.isort]
 profile = "black"
-py_version = "39"
+py_version = "310"
 skip = [".tox", ".eggs", "migrations"]
 
 [tool.coverage.run]
@@ -27,21 +27,23 @@ source = ["edc_constants"]
 show_missing = true
 skip_covered = true
 omit = ["requirements.txt"]
+exclude_lines = [
+  "pragma: no cover",
+  "if TYPE_CHECKING:",
+]
 
 [tool.tox]
 legacy_tox_ini = """
-
-
 [tox]
 envlist =
     lint
+
 isolated_build = true
 
 [gh-actions]
 python =
-    3.8: py38
-    3.9: py39, lint
-    3.10: py310
+    3.10: py310, lint
+    3.11: py311, lint
 
 [testenv]
 deps =
@@ -50,6 +52,7 @@ deps =
 commands =
     pip install -U pip
     pip --version
+    pip freeze
 
 [testenv:lint]
 deps = -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/lint.txt

setup.cfg

@@ -12,20 +12,17 @@ keywords = django edc choices constants, clinicedc, clinical trials
 classifiers=
     Environment :: Web Environment
     Framework :: Django
-    Framework :: Django :: 3.2
-    Framework :: Django :: 4.0
     Framework :: Django :: 4.1
     Intended Audience :: Developers
     Intended Audience :: Science/Research
     Operating System :: OS Independent
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 
 
 [options]
-python_requires = >=3.9
+python_requires = >=3.10
 zip_safe = False
 include_package_data = True
 packages = find: