diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index 97890ad..3ab318e 100644 --- a/.github/workflows/bar-api.yml +++ b/.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: diff --git a/Dockerfile b/Dockerfile index 5aea506..48efcf7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-bookworm +FROM python:3.13-bookworm WORKDIR /usr/src/app diff --git a/docker-compose.yml b/docker-compose.yml index 2e690b5..5559c36 100644 --- a/docker-compose.yml +++ b/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: diff --git a/docs/requirements.txt b/docs/requirements.txt index 5bcfd2f..f73d28e 100644 --- a/docs/requirements.txt +++ b/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 diff --git a/requirements.txt b/requirements.txt index 56cc25d..41ef7a8 100644 --- a/requirements.txt +++ b/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 @@ -17,7 +17,7 @@ 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 @@ -25,10 +25,10 @@ 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 diff --git a/tests/resources/test_proxy.py b/tests/resources/test_proxy.py index f7467b8..aca80e5 100644 --- a/tests/resources/test_proxy.py +++ b/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)