use staging requirements.txt

requirements.txt

@@ -1,156 +1,90 @@
 agct==0.1.0.dev2
-aiofiles==23.1.0
-annotated-types==0.6.0
-anyio==3.7.1
-appdirs==1.4.4
-appnope==0.1.3
-asttokens==2.2.1
-async-lru==2.0.4
-asyncio-atexit==1.0.1
-asyncpg==0.28.0
-attrs==23.1.0
-backcall==0.2.0
-bcrypt==4.2.0
-beautifulsoup4==4.12.2
-biocommons.seqrepo==0.6.5
+aiofiles==24.1.0
+annotated-types==0.7.0
+anyio==4.4.0
+asttokens==2.4.1
+async-timeout==4.0.3
+asyncpg==0.29.0
+attrs==24.2.0
+biocommons.seqrepo==0.6.9
 bioutils==0.5.8.post1
-black==23.10.1
-boto3==1.28.11
-botocore==1.31.11
-bs4==0.0.1
-bump-pydantic==0.7.0
+black==24.8.0
+boto3==1.35.3
+botocore==1.35.3
 canonicaljson==2.0.0
-certifi==2023.7.22
-cffi==1.17.1
+certifi==2024.7.4
 cfgv==3.4.0
-charset-normalizer==3.2.0
-click==8.1.6
+charset-normalizer==3.3.2
+click==8.1.7
 coloredlogs==15.0.1
-configparser==6.0.0
+configparser==7.1.0
 cool_seq_tool==0.7.1
-coverage==7.3.2
-cryptography==43.0.1
-cssselect==1.2.0
-Cython==3.0.0
+coverage==7.6.1
 decorator==5.1.1
-Deprecated==1.2.14
-distlib==0.3.7
-docutils==0.20.1
-executing==1.2.0
-fake-useragent==1.1.3
-fastapi==0.100.0
-filelock==3.12.4
+distlib==0.3.8
+executing==2.0.1
+fastapi==0.112.1
+filelock==3.15.4
 fusor==0.4.4
 ga4gh.vrs==2.0.0a10
-ga4gh.vrsatile.pydantic==0.2.0
 gene-normalizer==0.4.0
-googleapis-common-protos==1.65.0
 h11==0.14.0
 hgvs==1.5.4
 httpcore==1.0.5
-httpx==0.27.2
+httpx==0.27.0
 humanfriendly==10.0
-identify==2.5.30
-idna==3.4
-importlib-metadata==6.8.0
-inflection==0.5.1
+identify==2.6.0
+idna==3.7
+importlib_metadata==8.4.0
 iniconfig==2.0.0
-ipython==8.14.0
-jedi==0.18.2
-Jinja2==3.1.2
+ipython==8.26.0
+jedi==0.19.1
+Jinja2==3.1.4
 jmespath==1.0.1
-jsonschema==3.2.0
-libcst==1.1.0
-lxml==4.9.3
-Markdown==3.4.4
-markdown-it-py==3.0.0
-MarkupSafe==2.1.3
-matplotlib-inline==0.1.6
-mdurl==0.1.2
+MarkupSafe==2.1.5
+matplotlib-inline==0.1.7
 mypy-extensions==1.0.0
-nest-asyncio==1.6.0
-nodeenv==1.8.0
-numpy==1.25.1
-opentelemetry-api==1.27.0
-opentelemetry-exporter-otlp-proto-common==1.27.0
-opentelemetry-exporter-otlp-proto-http==1.27.0
-opentelemetry-instrumentation==0.48b0
-opentelemetry-instrumentation-httpx==0.48b0
-opentelemetry-instrumentation-requests==0.48b0
-opentelemetry-instrumentation-threading==0.48b0
-opentelemetry-instrumentation-urllib==0.48b0
-opentelemetry-proto==1.27.0
-opentelemetry-sdk==1.27.0
-opentelemetry-semantic-conventions==0.48b0
-opentelemetry-util-http==0.48b0
-packaging==23.2
-pandas==2.0.3
-paramiko==3.5.0
-parse==1.19.1
+nodeenv==1.9.1
+packaging==24.1
 Parsley==1.3
-parso==0.8.3
-pathspec==0.11.2
-pexpect==4.8.0
-pickleshare==0.7.5
-platformdirs==3.11.0
-pluggy==1.3.0
-polars==1.3.0
+parso==0.8.4
+pathspec==0.12.1
+pexpect==4.9.0
+platformdirs==4.2.2
+pluggy==1.5.0
+polars==1.5.0
 pre-commit==3.8.0
-prompt-toolkit==3.0.39
-protobuf==4.25.5
-psutil==5.9.8
-psycopg2==2.9.6
+prompt_toolkit==3.0.47
+psycopg2==2.9.9
 psycopg2-binary==2.9.9
 ptyprocess==0.7.0
-pure-eval==0.2.2
-pycparser==2.22
+pure_eval==0.2.3
 pydantic==2.4.2
-pydantic-to-typescript==1.0.10
 pydantic-to-typescript2==1.0.4
 pydantic_core==2.10.1
-pyee==8.2.2
-Pygments==2.15.1
-pyliftover==0.4
-PyNaCl==1.5.0
-pyppeteer==1.0.2
-pyquery==2.0.0
-pyrsistent==0.19.3
-pysam==0.21.0
-pysftp==0.2.9
-pytest==7.4.2
-pytest-asyncio==0.21.1
-pytest-cov==4.1.0
-python-dateutil==2.8.2
-python-jsonschema-objects==0.4.2
-pytz==2023.3
-PyYAML==6.0.1
-requests==2.31.0
-requests-html==0.10.0
-rich==13.6.0
+Pygments==2.18.0
+pysam==0.22.1
+pytest==8.3.2
+pytest-asyncio==0.24.0
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+PyYAML==6.0.2
+requests==2.32.3
 ruff==0.5.0
-s3transfer==0.6.1
+s3transfer==0.10.2
 six==1.16.0
-sniffio==1.3.0
-soupsieve==2.4.1
-sqlparse==0.4.4
-stack-data==0.6.2
-starlette==0.27.0
-synapseclient==4.5.1
+sniffio==1.3.1
+sqlparse==0.5.1
+stack-data==0.6.3
+starlette==0.38.2
 tabulate==0.9.0
 tqdm==4.66.5
-traitlets==5.9.0
-typer==0.9.0
-typing-inspect==0.9.0
-typing_extensions==4.7.1
-tzdata==2023.3
-urllib3==1.26.20
-uta-tools==0.1.3
-uvicorn==0.23.1
-virtualenv==20.24.5
-w3lib==2.1.1
-wags_tails==0.1.3
-wcwidth==0.2.6
-websockets==10.4
-wrapt==1.16.0
+traitlets==5.14.3
+typing_extensions==4.12.2
+urllib3==1.26.19
+uvicorn==0.30.6
+virtualenv==20.26.3
+wags_tails==0.1.4
+wcwidth==0.2.13
 yoyo-migrations==8.2.0
-zipp==3.16.2
+zipp==3.20.0