Set up deploy/stage branch for ubuntu 22.04 upgrade

.github/workflows/ci.yml

@@ -24,14 +24,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.10"]
         backend: ["sqlite", "mariadb"]
-        mariadb-version: ["10.4"]
+        mariadb-version: ["10.6"]
         include:
-          - python-version: "3.10"  # Future ubuntu 22.04 upgrade.
-            backend: "mariadb"
-            mariadb-version: "10.6"
-            pip-recompile: true
           - python-version: 3.12  # Future ubuntu 24.04.01 upgrade.
             backend: "mariadb"
             mariadb-version: "10.11"

.github/workflows/combine-prs.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
       - name: combine-prs
         id: combine-prs
-        uses: github/combine-prs@v5.0.0
+        uses: github/combine-prs@v5.1.0
         with:
           labels: combined-pr # Optional: add a label to the combined PR
           ci_required: true # require all checks to pass before combining

.github/workflows/pip-compile.yml

@@ -14,10 +14,10 @@ jobs:
         with:
           ref: ${{ github.head_ref }}
 
-      - name: Set up Python 3.8
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: "3.10"
 
       - name: Update requirements files
         uses: UW-GAC/pip-tools-actions/update-requirements-files@v0.1

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.1
+    rev: v0.5.4
     hooks:
       # Run the linter.
       - id: ruff

gregor-apps-activate.sh

@@ -2,6 +2,8 @@ export DJANGO_SITE_DIR=/var/www/django/gregor_apps/
 export DJANGO_SITE_USER=gregorweb
 export DJANGO_SETTINGS_MODULE=config.settings.apps
 export DJANGO_WSGI_FILE=config/gregor_apps_wsgi.py
+export DJANGO_CRONTAB=gregor_apps.cron
 export GAC_ENV=gregor_apps
+
 cd $DJANGO_SITE_DIR
 . venv/bin/activate

gregor-apps-dev-activate.sh

@@ -6,6 +6,8 @@ export DJANGO_SITE_DIR=/var/www/django/gregor_apps_dev/
 export DJANGO_SITE_USER=gregorweb
 export DJANGO_SETTINGS_MODULE=config.settings.apps_dev
 export DJANGO_WSGI_FILE=config/apps_dev_wsgi.py
+export DJANGO_CRONTAB=gregor_apps_dev.cron
 export GAC_ENV=gregor_apps_dev
+
 cd $DJANGO_SITE_DIR
 . venv/bin/activate

requirements/dev-requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.8
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile requirements/dev-requirements.in
@@ -18,11 +18,7 @@ babel==2.14.0
     # via sphinx
 backcall==0.2.0
     # via ipython
-backports-zoneinfo==0.2.1
-    # via
-    #   -c requirements/requirements.txt
-    #   django
-certifi==2023.7.22
+certifi==2024.7.4
     # via
     #   -c requirements/requirements.txt
     #   -c requirements/test-requirements.txt
@@ -50,7 +46,7 @@ django==4.2.14
     #   django-debug-toolbar
     #   django-stubs
     #   django-stubs-ext
-django-debug-toolbar==4.4.5
+django-debug-toolbar==4.4.6
     # via -r requirements/dev-requirements.in
 django-stubs==4.2.7
     # via -r requirements/dev-requirements.in
@@ -71,10 +67,6 @@ idna==3.7
     #   requests
 imagesize==1.4.1
     # via sphinx
-importlib-metadata==6.8.0
-    # via
-    #   -c requirements/requirements.txt
-    #   sphinx
 ipdb==0.13.13
     # via -r requirements/dev-requirements.in
 ipython==8.12.3
@@ -95,7 +87,7 @@ matplotlib-inline==0.1.6
     # via ipython
 mccabe==0.7.0
     # via pylint
-mypy==1.10.1
+mypy==1.11.0
     # via -r requirements/dev-requirements.in
 mypy-extensions==1.0.0
     # via mypy
@@ -136,10 +128,6 @@ pylint-django==2.5.5
     # via -r requirements/dev-requirements.in
 pylint-plugin-utils==0.8.2
     # via pylint-django
-pytz==2023.4
-    # via
-    #   -c requirements/requirements.txt
-    #   babel
 pyyaml==6.0.1
     # via
     #   -c requirements/test-requirements.txt
@@ -149,7 +137,7 @@ requests==2.32.3
     #   -c requirements/requirements.txt
     #   -c requirements/test-requirements.txt
     #   sphinx
-ruff==0.5.1
+ruff==0.5.4
     # via -r requirements/dev-requirements.in
 six==1.16.0
     # via
@@ -177,7 +165,7 @@ sphinxcontrib-qthelp==1.0.3
     # via sphinx
 sphinxcontrib-serializinghtml==1.1.5
     # via sphinx
-sqlparse==0.5.0
+sqlparse==0.5.1
     # via
     #   -c requirements/requirements.txt
     #   django
@@ -212,9 +200,7 @@ typing-extensions==4.8.0
     #   astroid
     #   django-stubs
     #   django-stubs-ext
-    #   ipython
     #   mypy
-    #   pylint
 urllib3==2.2.2
     # via
     #   -c requirements/requirements.txt
@@ -226,10 +212,6 @@ wcwidth==0.2.13
     # via prompt-toolkit
 werkzeug==3.0.3
     # via -r requirements/dev-requirements.in
-zipp==3.17.0
-    # via
-    #   -c requirements/requirements.txt
-    #   importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools

requirements/requirements.in

@@ -45,13 +45,6 @@ mysqlclient # https://github.com/PyMySQL/mysqlclient
 # See issue https://github.com/jazzband/django-simple-history/issues/1255
 asgiref>=3.6
 
-# Temporary fixes to handle security vulnerabilities
-certifi>=2023.7.22
-pyjwt>=2.4.0
-sqlparse>=0.4.4
-idna>=3.7
-urllib3>=2.2.2
-requests>=2.32.0
 
 # Dynamic settings
 django-constance

requirements/requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.8
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile requirements/requirements.in
@@ -12,16 +12,12 @@ asgiref==3.8.1
     # via
     #   -r requirements/requirements.in
     #   django
-backports-zoneinfo==0.2.1
-    # via django
 build==1.0.3
     # via pip-tools
 cachetools==5.3.2
     # via google-auth
-certifi==2023.7.22
-    # via
-    #   -r requirements/requirements.in
-    #   requests
+certifi==2024.7.4
+    # via requests
 cffi==1.16.0
     # via
     #   argon2-cffi-bindings
@@ -61,7 +57,7 @@ django-autocomplete-light==3.11.0
     # via django-anvil-consortium-manager
 django-constance==3.1.0
     # via -r requirements/requirements.in
-django-crispy-forms==2.2
+django-crispy-forms==2.3
     # via
     #   -r requirements/requirements.in
     #   crispy-bootstrap5
@@ -97,11 +93,7 @@ fontawesomefree==6.5.1
 google-auth==2.11.0
     # via django-anvil-consortium-manager
 idna==3.7
-    # via
-    #   -r requirements/requirements.in
-    #   requests
-importlib-metadata==6.8.0
-    # via build
+    # via requests
 mysqlclient==2.2.4
     # via -r requirements/requirements.in
 networkx==3.1
@@ -129,9 +121,7 @@ pyasn1-modules==0.3.0
 pycparser==2.21
     # via cffi
 pyjwt[crypto]==2.8.0
-    # via
-    #   -r requirements/requirements.in
-    #   django-allauth
+    # via django-allauth
 pyproject-hooks==1.0.0
     # via
     #   build
@@ -146,7 +136,6 @@ pytz==2023.4
     #   django-dbbackup
 requests==2.32.3
     # via
-    #   -r requirements/requirements.in
     #   django-allauth
     #   django-anvil-consortium-manager
     #   requests-oauthlib
@@ -156,10 +145,8 @@ rsa==4.9
     # via google-auth
 six==1.16.0
     # via google-auth
-sqlparse==0.5.0
-    # via
-    #   -r requirements/requirements.in
-    #   django
+sqlparse==0.5.1
+    # via django
 tenacity==8.2.3
     # via plotly
 tomli==2.0.1
@@ -170,15 +157,11 @@ tomli==2.0.1
 typing-extensions==4.8.0
     # via asgiref
 urllib3==2.2.2
-    # via
-    #   -r requirements/requirements.in
-    #   requests
+    # via requests
 wheel==0.42.0
     # via pip-tools
 whitenoise==6.7.0
     # via -r requirements/requirements.in
-zipp==3.17.0
-    # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
 # pip

requirements/test-requirements.txt

@@ -1,10 +1,10 @@
 #
-# This file is autogenerated by pip-compile with Python 3.8
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile requirements/test-requirements.in
 #
-certifi==2023.7.22
+certifi==2024.7.4
     # via
     #   -c requirements/requirements.txt
     #   requests
@@ -42,7 +42,7 @@ packaging==23.2
     #   pytest-sugar
 pluggy==1.5.0
     # via pytest
-pytest==8.2.2
+pytest==8.3.1
     # via
     #   -r requirements/test-requirements.in
     #   pytest-cov
@@ -78,13 +78,12 @@ tomli==2.0.1
     #   -c requirements/requirements.txt
     #   coverage
     #   pytest
-types-requests==2.32.0.20240622
+types-requests==2.32.0.20240712
     # via -r requirements/test-requirements.in
 typing-extensions==4.8.0
     # via
     #   -c requirements/requirements.txt
     #   django-test-migrations
-    #   faker
 urllib3==2.2.2
     # via
     #   -c requirements/requirements.txt