Merge pull request #265 from asherpasha/dev

Updated dependancies.

Author: asherpasha

.github/workflows/bar-api.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python-version: [3.10.16, 3.11, 3.12, 3.13]
+        python-version: [3.10.17, 3.11, 3.12, 3.13]
 
     services:
       redis:

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-bookworm
+FROM python:3.13-bookworm
 
 WORKDIR /usr/src/app
 

docker-compose.yml

@@ -1,14 +1,14 @@
 services:
 
   mysqldb:
-    image: mysql:9.0.1
+    image: mysql:9.3.0
     container_name: BAR_mysqldb
     restart: always
     environment:
       - MYSQL_ROOT_PASSWORD=root
 
   redis:
-    image: redis:7.2.5
+    image: redis:7.4.2
     container_name: BAR_redis
     restart: always
     ports:

docs/requirements.txt

@@ -1,27 +1,31 @@
-alabaster==0.7.16
-Babel==2.14.0
-beautifulsoup4==4.12.3
-certifi==2024.2.2
-charset-normalizer==3.3.2
+alabaster==1.0.0
+babel==2.17.0
+beautifulsoup4==4.13.4
+certifi==2025.1.31
+charset-normalizer==3.4.1
 docutils==0.21.2
-furo==2024.4.27
-idna==3.7
+furo==2024.8.6
+idna==3.10
 imagesize==1.4.1
-Jinja2==3.1.3
-MarkupSafe==2.1.5
-packaging==24.0
-Pygments==2.17.2
-pytz==2024.1
-requests==2.31.0
+Jinja2==3.1.6
+MarkupSafe==3.0.2
+packaging==25.0
+Pygments==2.19.1
+pytz==2025.2
+requests==2.32.3
+roman-numerals-py==3.1.0
+setuptools==78.1.1
 snowballstemmer==2.2.0
-soupsieve==2.5
-Sphinx==7.3.7
-sphinx-basic-ng==1.0.0b1
+soupsieve==2.6
+Sphinx==8.2.3
+sphinx-basic-ng==1.0.0b2
 sphinx-copybutton==0.5.2
-sphinxcontrib-applehelp==1.0.8
-sphinxcontrib-devhelp==1.0.6
-sphinxcontrib-htmlhelp==2.0.5
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.7
-sphinxcontrib-serializinghtml==1.1.10
-urllib3==2.2.1
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
+typing_extensions==4.13.2
+urllib3==2.4.0
+wheel==0.45.1

requirements.txt

@@ -1,4 +1,4 @@
-aniso8601==10.0.0
+aniso8601==10.0.1
 async-timeout==5.0.1
 attrs==25.3.0
 black==25.1.0
@@ -7,7 +7,7 @@ cachelib==0.9.0
 certifi==2025.1.31
 charset-normalizer==3.4.1
 click==8.1.8
-coverage==7.7.1
+coverage==7.8.0
 Deprecated==1.2.18
 flake8==7.2.0
 Flask==3.1.0
@@ -17,18 +17,18 @@ Flask-Limiter==3.12
 flask-marshmallow==1.3.0
 flask-restx==1.3.0
 Flask-SQLAlchemy==3.1.1
-greenlet==3.1.1
+greenlet==3.2.0
 idna==3.10
 importlib_resources==6.5.2
 iniconfig==2.1.0
 itsdangerous==2.2.0
 Jinja2==3.1.6
 jsonschema==4.23.0
 jsonschema-specifications==2024.10.1
-limits==4.4.1
+limits==5.0.0
 markdown-it-py==3.0.0
 MarkupSafe==3.0.2
-marshmallow==3.26.1
+marshmallow==4.0.0
 mccabe==0.7.0
 mdurl==0.1.2
 mypy-extensions==1.0.0
@@ -39,7 +39,7 @@ pathspec==0.12.1
 platformdirs==4.3.7
 pluggy==1.5.0
 pycodestyle==2.13.0
-pyflakes==3.3.0
+pyflakes==3.3.2
 Pygments==2.19.1
 pyrsistent==0.20.0
 pytest==8.3.5
@@ -50,11 +50,11 @@ referencing==0.36.2
 requests==2.32.3
 rich==13.9.4
 rpds-py==0.24.0
-setuptools==78.1.0
+setuptools==78.1.1
 six==1.17.0
 SQLAlchemy==2.0.40
-typing_extensions==4.13.0
-urllib3==2.3.0
+typing_extensions==4.13.2
+urllib3==2.4.0
 Werkzeug==3.1.3
 wheel==0.45.1
 wrapt==1.17.2

tests/resources/test_proxy.py

@@ -25,7 +25,6 @@ def test_get_atted_api5(self):
 
         # If no data, the service should return this response
         response = self.app_client.get("/proxy/atted_api5/At1g01011/5")
-
         expected = {"error": "No gene ID specified.", "status_code": 400}
         self.assertEqual(response.json, expected)