build(deps): resolve ipython and starlette vulnerabilities (#346)

Pipfile

@@ -5,7 +5,7 @@ verify_ssl = true
 
 [packages]
 pydantic = ">=1.8.2"
-fastapi = ">=0.72.0"
+fastapi = ">=0.92.0"
 click = "*"
 uvicorn = "*"
 boto3 = "*"
@@ -28,7 +28,7 @@ flake8-docstrings = "*"
 flake8-quotes = "*"
 flake8-import-order = "*"
 flake8-annotations = "*"
-ipython = ">=7.31.1"
+ipython = ">=8.10.0"
 jupyterlab = "*"
 civicpy = "*"
 mypy = "*"

requirements-dev.txt

@@ -1,177 +1,183 @@
 -i https://pypi.org/simple
-anyio==3.6.2 ; python_full_version >= '3.6.2'
-appnope==0.1.3 ; platform_system == 'Darwin'
-argon2-cffi==21.3.0 ; python_version >= '3.6'
-argon2-cffi-bindings==21.2.0 ; python_version >= '3.6'
-arrow==1.2.3 ; python_version >= '3.6'
+aiofiles==22.1.0; python_version >= '3.7' and python_full_version < '4.0.0'
+aiosqlite==0.18.0; python_version >= '3.7'
+anyio==3.6.2; python_full_version >= '3.6.2'
+appnope==0.1.3; platform_system == 'Darwin'
+argon2-cffi==21.3.0; python_version >= '3.6'
+argon2-cffi-bindings==21.2.0; python_version >= '3.6'
+arrow==1.2.3; python_version >= '3.6'
 asttokens==2.2.1
-attrs==22.2.0 ; python_version >= '3.6'
-babel==2.11.0 ; python_version >= '3.6'
+attrs==22.2.0; python_version >= '3.6'
+babel==2.11.0; python_version >= '3.6'
 backcall==0.2.0
-backoff==2.2.1 ; python_version >= '3.7' and python_version < '4.0'
+backoff==2.2.1; python_version >= '3.7' and python_full_version < '4.0.0'
 backports-datetime-fromisoformat==2.0.0
-beautifulsoup4==4.11.1 ; python_full_version >= '3.6.0'
-bioregistry[align]==0.6.51 ; python_version >= '3.7'
+beautifulsoup4==4.11.2; python_version >= '3.6'
+bioregistry[align]==0.6.79; python_version >= '3.7'
 bioversions==0.5.79
-bleach==5.0.1 ; python_version >= '3.7'
-boto3==1.26.47
-botocore==1.29.47 ; python_version >= '3.7'
+bleach==6.0.0; python_version >= '3.7'
+boto3==1.26.75
+botocore==1.29.75; python_version >= '3.7'
 cachier==2.0.0
-certifi==2022.12.7 ; python_version >= '3.6'
+certifi==2022.12.7; python_version >= '3.6'
 cffi==1.15.1
-cfgv==3.3.1 ; python_full_version >= '3.6.1'
-charset-normalizer==2.1.1 ; python_full_version >= '3.6.0'
+cfgv==3.3.1; python_full_version >= '3.6.1'
+charset-normalizer==3.0.1; python_version >= '3.6'
 chembl-downloader==0.4.2
 civicpy==3.0.0
-class-resolver==0.3.10
+class-resolver==0.4.0
 click==8.1.3
 click-default-group==1.2.2
-comm==0.1.2 ; python_version >= '3.6'
-coverage[toml]==7.0.5 ; python_version >= '3.7'
-curies==0.4.1 ; python_version >= '3.7'
-dataclasses-json==0.5.7 ; python_version >= '3.6'
-debugpy==1.6.5 ; python_version >= '3.7'
-decorator==5.1.1 ; python_version >= '3.5'
+comm==0.1.2; python_version >= '3.6'
+coverage[toml]==7.1.0; python_version >= '3.7'
+curies==0.4.2; python_version >= '3.7'
+dataclasses-json==0.5.7; python_version >= '3.6'
+debugpy==1.6.6; python_version >= '3.7'
+decorator==5.1.1; python_version >= '3.5'
 defusedxml==0.7.1
 deprecation==2.1.0
 disease-normalizer==0.2.19
 distlib==0.3.6
-entrypoints==0.4 ; python_version >= '3.6'
-exceptiongroup==1.1.0 ; python_version < '3.11'
+exceptiongroup==1.1.0; python_version < '3.11'
 executing==1.2.0
 fairsharing-client==0.1.0
-fastapi==0.89.1
+fastapi==0.92.0
 fastjsonschema==2.16.2
-filelock==3.9.0 ; python_version >= '3.7'
+filelock==3.9.0; python_version >= '3.7'
 flake8==5.0.4
-flake8-annotations==2.9.1
-flake8-docstrings==1.6.0
+flake8-annotations==3.0.0
+flake8-docstrings==1.7.0
 flake8-import-order==0.18.2
 flake8-quotes==3.3.2
 fqdn==1.5.1
 ga4gh.vrsatile.pydantic==0.0.11
-h11==0.14.0 ; python_version >= '3.7'
-identify==2.5.12 ; python_version >= '3.7'
-idna==3.4 ; python_version >= '3.5'
-iniconfig==2.0.0 ; python_version >= '3.7'
-ipykernel==6.20.1
-ipython==8.8.0
+h11==0.14.0; python_version >= '3.7'
+identify==2.5.18; python_version >= '3.7'
+idna==3.4; python_version >= '3.5'
+iniconfig==2.0.0; python_version >= '3.7'
+ipykernel==6.21.2
+ipython==8.10.0
 ipython-genutils==0.2.0
 isodate==0.6.1
 isoduration==20.11.0
-jedi==0.18.2 ; python_version >= '3.6'
-jinja2==3.1.2 ; python_version >= '3.7'
-jmespath==1.0.1 ; python_version >= '3.7'
+jedi==0.18.2; python_version >= '3.6'
+jinja2==3.1.2; python_version >= '3.7'
+jmespath==1.0.1; python_version >= '3.7'
 json5==0.9.11
 jsonpointer==2.3
-jsonschema==4.17.3 ; python_version >= '3.7'
-jupyter-client==7.4.8 ; python_version >= '3.7'
-jupyter-core==5.1.3 ; python_version >= '3.8'
-jupyter-events==0.6.2 ; python_version >= '3.7'
-jupyter-server==2.0.6 ; python_version >= '3.8'
-jupyter-server-terminals==0.4.4 ; python_version >= '3.8'
-jupyterlab==3.5.2
-jupyterlab-pygments==0.2.2 ; python_version >= '3.7'
-jupyterlab-server==2.18.0 ; python_version >= '3.7'
+jsonschema==4.17.3; python_version >= '3.7'
+jupyter-client==8.0.3; python_version >= '3.8'
+jupyter-core==5.2.0; python_version >= '3.8'
+jupyter-events==0.6.3; python_version >= '3.7'
+jupyter-server==2.3.0; python_version >= '3.8'
+jupyter-server-fileid==0.7.0; python_version >= '3.7'
+jupyter-server-terminals==0.4.4; python_version >= '3.8'
+jupyter-server-ydoc==0.6.1; python_version >= '3.7'
+jupyter-ydoc==0.2.2; python_version >= '3.7'
+jupyterlab==3.6.1
+jupyterlab-pygments==0.2.2; python_version >= '3.7'
+jupyterlab-server==2.19.0; python_version >= '3.7'
 lxml==4.9.2
-markupsafe==2.1.1 ; python_version >= '3.7'
-marshmallow==3.19.0 ; python_version >= '3.7'
+markupsafe==2.1.2; python_version >= '3.7'
+marshmallow==3.19.0; python_version >= '3.7'
 marshmallow-enum==1.5.1
-matplotlib-inline==0.1.6 ; python_version >= '3.5'
-mccabe==0.7.0 ; python_version >= '3.6'
-mistune==2.0.4
-more-click==0.1.2 ; python_version >= '3.7'
-more-itertools==9.0.0 ; python_version >= '3.7'
+matplotlib-inline==0.1.6; python_version >= '3.5'
+mccabe==0.7.0; python_version >= '3.6'
+mistune==2.0.5
+more-click==0.1.2; python_version >= '3.7'
+more-itertools==9.0.0; python_version >= '3.7'
 mwoauth==0.3.8
-mypy==0.991
-mypy-extensions==0.4.3
-nbclassic==0.4.8 ; python_version >= '3.7'
-nbclient==0.7.2 ; python_full_version >= '3.7.0'
-nbconvert==7.2.7 ; python_version >= '3.7'
-nbformat==5.7.2 ; python_version >= '3.7'
-nest-asyncio==1.5.6 ; python_version >= '3.5'
-networkx==3.0 ; python_version >= '3.8'
-nodeenv==1.7.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
-notebook==6.5.2 ; python_version >= '3.7'
-notebook-shim==0.2.2 ; python_version >= '3.7'
-numpy==1.24.1 ; python_version >= '3.10'
-oauthlib==3.2.2 ; python_version >= '3.6'
-obonet==0.3.1 ; python_version >= '3.7'
-owlready2==0.39
-packaging==23.0 ; python_version >= '3.7'
-pandas==1.5.2 ; python_version >= '3.8'
-pandocfilters==1.5.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-parso==0.8.3 ; python_version >= '3.6'
+mypy==1.0.1
+mypy-extensions==1.0.0; python_version >= '3.5'
+nbclassic==0.5.2; python_version >= '3.7'
+nbclient==0.7.2; python_version >= '3.7'
+nbconvert==7.2.9; python_version >= '3.7'
+nbformat==5.7.3; python_version >= '3.7'
+nest-asyncio==1.5.6; python_version >= '3.5'
+networkx==3.0; python_version >= '3.8'
+nodeenv==1.7.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
+notebook==6.5.2; python_version >= '3.7'
+notebook-shim==0.2.2; python_version >= '3.7'
+numpy==1.24.2; python_version >= '3.10'
+oauthlib==3.2.2; python_version >= '3.6'
+obonet==0.3.1; python_version >= '3.7'
+owlready2==0.40
+packaging==23.0; python_version >= '3.7'
+pandas==1.5.3; python_version >= '3.8'
+pandocfilters==1.5.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+parso==0.8.3; python_version >= '3.6'
 pathtools==0.1.2
-pexpect==4.8.0 ; sys_platform != 'win32'
+pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-platformdirs==2.6.2 ; python_version >= '3.7'
-pluggy==1.0.0 ; python_version >= '3.6'
-portalocker==2.6.0 ; python_version >= '3.5'
-pre-commit==2.21.0
-prometheus-client==0.15.0 ; python_version >= '3.6'
-prompt-toolkit==3.0.36 ; python_full_version >= '3.6.2'
-psutil==5.9.4 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+platformdirs==3.0.0; python_version >= '3.7'
+pluggy==1.0.0; python_version >= '3.6'
+portalocker==2.7.0; python_version >= '3.5'
+pre-commit==3.0.4
+prometheus-client==0.16.0; python_version >= '3.6'
+prompt-toolkit==3.0.37; python_version >= '3.7'
+psutil==5.9.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 ptyprocess==0.7.0
 pure-eval==0.2.2
-pycodestyle==2.9.1 ; python_version >= '3.6'
+pycodestyle==2.9.1; python_version >= '3.6'
 pycparser==2.21
-pydantic==1.10.4
-pydocstyle==6.2.3 ; python_version >= '3.6'
-pyflakes==2.5.0 ; python_version >= '3.6'
-pygments==2.14.0 ; python_version >= '3.6'
-pyjwt==2.6.0 ; python_version >= '3.7'
-pyparsing==3.0.9 ; python_full_version >= '3.6.8'
-pyrsistent==0.19.3 ; python_version >= '3.7'
+pydantic==1.10.5
+pydocstyle==6.3.0; python_version >= '3.6'
+pyflakes==2.5.0; python_version >= '3.6'
+pygments==2.14.0; python_version >= '3.6'
+pyjwt==2.6.0; python_version >= '3.7'
+pyparsing==3.0.9; python_full_version >= '3.6.8'
+pyrsistent==0.19.3; python_version >= '3.7'
 pysam==0.20.0
-pystow==0.4.7 ; python_version >= '3.7'
-pytest==7.2.0
+pystow==0.5.0; python_version >= '3.7'
+pytest==7.2.1
 pytest-cov==4.0.0
-python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
-python-json-logger==2.0.4 ; python_version >= '3.5'
+python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+python-json-logger==2.0.7; python_version >= '3.6'
 pytrie==0.4.0
-pytz==2022.7
-pyyaml==6.0 ; python_version >= '3.6'
-pyzmq==24.0.1 ; python_version >= '3.6'
+pytz==2022.7.1
+pyyaml==6.0; python_version >= '3.6'
+pyzmq==25.0.0; python_version >= '3.6'
 rdflib==6.2.0
-requests==2.28.1 ; python_version >= '3.7' and python_version < '4'
+requests==2.28.2; python_version >= '3.7' and python_full_version < '4.0.0'
 requests-ftp==0.3.1
-requests-oauthlib==1.3.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-rfc3339-validator==0.1.4 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-rfc3986-validator==0.1.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-s3transfer==0.6.0 ; python_version >= '3.7'
+requests-oauthlib==1.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+rfc3339-validator==0.1.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+rfc3986-validator==0.1.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+s3transfer==0.6.0; python_version >= '3.7'
 send2trash==1.8.0
-setuptools==65.6.3 ; python_version >= '3.7'
-six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
-sniffio==1.3.0 ; python_version >= '3.7'
+setuptools==67.3.3; python_version >= '3.7'
+six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+sniffio==1.3.0; python_version >= '3.7'
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
-soupsieve==2.3.2.post1 ; python_version >= '3.6'
+soupsieve==2.4; python_version >= '3.7'
 stack-data==0.6.2
-starlette==0.22.0 ; python_version >= '3.7'
-tabulate==0.9.0 ; python_version >= '3.7'
-terminado==0.17.1 ; python_version >= '3.7'
+starlette==0.25.0; python_version >= '3.7'
+tabulate==0.9.0; python_version >= '3.7'
+terminado==0.17.1; python_version >= '3.7'
 -e .
-tinycss2==1.2.1 ; python_version >= '3.7'
-tomli==2.0.1 ; python_version >= '3.7'
-tornado==6.2 ; python_version >= '3.7'
-tqdm==4.64.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.8.1 ; python_version >= '3.7'
-types-pyyaml==6.0.12.2
-types-requests==2.28.11.7
-types-urllib3==1.26.25.4
-typing-extensions==4.4.0 ; python_version >= '3.7'
+tinycss2==1.2.1; python_version >= '3.7'
+tomli==2.0.1; python_version < '3.11'
+tornado==6.2; python_version >= '3.7'
+tqdm==4.64.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+traitlets==5.9.0; python_version >= '3.7'
+types-pyyaml==6.0.12.8
+types-requests==2.28.11.14
+types-urllib3==1.26.25.7
+typing-extensions==4.5.0; python_version >= '3.7'
 typing-inspect==0.8.0
-ujson==5.7.0 ; python_version >= '3.7'
+ujson==5.7.0; python_version >= '3.7'
 uri-template==1.2.0
-urllib3==1.26.14 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+urllib3==1.26.14; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 uvicorn==0.20.0
 vcfpy==0.13.6
-virtualenv==20.17.1 ; python_version >= '3.6'
-watchdog==2.2.1 ; python_version >= '3.6'
-wcwidth==0.2.5
+virtualenv==20.19.0; python_version >= '3.7'
+watchdog==2.2.1; python_version >= '3.6'
+wcwidth==0.2.6
 webcolors==1.12
 webencodings==0.5.1
-websocket-client==1.4.2 ; python_version >= '3.7'
+websocket-client==1.5.1; python_version >= '3.7'
 wikibaseintegrator==0.12.3
 xmlformatter==0.2.4
+y-py==0.5.9
+ypy-websocket==0.8.2; python_version >= '3.7'

requirements.txt

@@ -1,19 +1,19 @@
 -i https://pypi.org/simple
-anyio==3.6.2 ; python_full_version >= '3.6.2'
-boto3==1.26.47
-botocore==1.29.47 ; python_version >= '3.7'
+anyio==3.6.2; python_full_version >= '3.6.2'
+boto3==1.26.75
+botocore==1.29.75; python_version >= '3.7'
 click==8.1.3
-fastapi==0.89.1
+fastapi==0.92.0
 ga4gh.vrsatile.pydantic==0.0.11
-h11==0.14.0 ; python_version >= '3.7'
-idna==3.4 ; python_version >= '3.5'
-jmespath==1.0.1 ; python_version >= '3.7'
-pydantic==1.10.4
-python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
-s3transfer==0.6.0 ; python_version >= '3.7'
-six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
-sniffio==1.3.0 ; python_version >= '3.7'
-starlette==0.22.0 ; python_version >= '3.7'
-typing-extensions==4.4.0 ; python_version >= '3.7'
-urllib3==1.26.14 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+h11==0.14.0; python_version >= '3.7'
+idna==3.4; python_version >= '3.5'
+jmespath==1.0.1; python_version >= '3.7'
+pydantic==1.10.5
+python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+s3transfer==0.6.0; python_version >= '3.7'
+six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+sniffio==1.3.0; python_version >= '3.7'
+starlette==0.25.0; python_version >= '3.7'
+typing-extensions==4.5.0; python_version >= '3.7'
+urllib3==1.26.14; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 uvicorn==0.20.0

setup.cfg

@@ -16,7 +16,7 @@ include_package_data = True
 
 install_requires =
     pydantic >=1.8.2
-    fastapi >= 0.72.0
+    fastapi >= 0.92.0
     click
     uvicorn
     boto3
@@ -40,6 +40,7 @@ dev =
     chembl-downloader
     bioversions >= 0.4.3
     ipykernel
+    ipython >= 8.10
     pre-commit
     flake8 ~= 5.0.4  # pinning until new flake8-quotes release
     flake8-docstrings