Merge pull request #237 from uwcirg/feature/update-python-3.11

python 3.7 fell off EOL.  upgrade to 3.11

.github/workflows/lint.yaml

@@ -37,7 +37,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install Python linting dependencies
         run: pip install black flake8

.github/workflows/test.yaml

@@ -9,10 +9,10 @@ jobs:
       - name: Checkout git commit
         uses: actions/checkout@v1
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.11
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.11
 
       - name: Install test runner
         run: python3 -m pip install tox

Dockerfile

@@ -11,7 +11,7 @@ COPY . .
 RUN npm run build
 
 # -----------------------------------------------------------------------------
-FROM python:3.7 as backend
+FROM python:3.11 as backend
 
 RUN mkdir /opt/cosri-patientsearch
 WORKDIR /opt/cosri-patientsearch

README.md

@@ -9,7 +9,7 @@ All views require Keycloak authentication.  Keycloak roles determine authorizati
 1) `git clone <this repository>`
 2) `cp client_secrets.json.default client_secrets.json`  # Edit to fit
 3) `cp patientsearch.env.default patientsearch.env`  # Edit to fit
-4) `mkvirtualenv patientsearch`  # Python 3.7
+4) `mkvirtualenv patientsearch`  # Python 3.11
 5) `pip install nodeenv`
 6) `nodeenv --python-virtualenv`
 7) `pip install -e .`

pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "patientsearch"
+dynamic = ["version"]
+dependencies = [
+    "flask",
+    "flask-jwt-extended",
+    "flask-session",
+    "gunicorn",
+    "requests",
+    "redis",
+    "redis-dict",
+    "jmespath",
+    "python-json-logger",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-flask",
+    "pytest-datadir",
+    "pytest-mock",
+]
+
+[tool.setuptools]
+packages = ["patientsearch"]
+
+[tool.pytest.ini_options]
+addopts = "--color yes --verbose"
+console_output_style = "classic"
+filterwarnings = [
+    "module",  # Only print each warning once per module
+    "ignore:^\"localhost\" is not a valid cookie domain, it must contain a.*:Warning",
+    "ignore::DeprecationWarning:dogpile",  # Specific dependency warning
+    "ignore::DeprecationWarning:flask_user",  # Specific dependency warning
+    "error:.*assertion is always true.*",  # Error on bad assertions
+]

requirements.dev.txt

@@ -11,7 +11,7 @@ importlib-metadata==4.8.1  # via pluggy, pytest
 iniconfig==1.1.1          # via pytest
 packaging==21.0           # via pytest
 pluggy==1.0.0             # via pytest
-py==1.10.0                # via pytest
+py==1.11.0                # via pytest
 pyparsing==2.4.7          # via packaging
 pytest-datadir==1.3.1     # via patientsearch (setup.py)
 pytest-flask==1.2.0       # via patientsearch (setup.py)

tox.ini

@@ -21,3 +21,6 @@ commands =
         --cov patientsearch \
         --cov-report xml:"{toxinidir}/coverage.xml" \
     []
+
+[flake8]
+max-line-length = 100