diff --git a/notebooks/analysis/requirements.txt b/notebooks/analysis/requirements.txt index 97ebc8a..93f4ca0 100644 --- a/notebooks/analysis/requirements.txt +++ b/notebooks/analysis/requirements.txt @@ -1,107 +1,96 @@ -## The following requirements were added by pip freeze: agct==0.1.0.dev1 aiofiles==23.2.1 annotated-types==0.6.0 anyio==4.3.0 +appdirs==1.4.4 appnope==0.1.4 -argcomplete==3.3.0 -argh==0.31.2 -argon2-cffi==23.1.0 -argon2-cffi-bindings==21.2.0 -arrow==1.3.0 asttokens==2.4.1 -async-lru==2.0.4 +async-timeout==4.0.3 asyncpg==0.29.0 attrs==23.2.0 -Babel==2.14.0 beautifulsoup4==4.12.3 +biocommons==0.0.0 biocommons.seqrepo==0.6.9 biopython==1.83 +bioservices==1.11.2 bioutils==0.5.8.post1 -bleach==6.1.0 -boto3==1.34.88 -botocore==1.34.88 +boto3==1.34.69 +botocore==1.34.69 +bs4==0.0.2 canonicaljson==2.0.0 +cattrs==24.1.2 +cdot==0.2.26 certifi==2024.2.2 -cffi==1.16.0 cfgv==3.4.0 charset-normalizer==3.3.2 click==8.1.7 +colorama==0.4.6 coloredlogs==15.0.1 +colorlog==6.8.2 comm==0.2.2 -configparser==7.0.0 -cool_seq_tool==0.4.0.dev3 -coverage==7.4.4 -dcd_mapping==0.1.3 +configparser==6.0.1 +contourpy==1.3.0 +cool_seq_tool==0.6.0 +coverage==7.6.1 +cycler==0.12.1 +dcd_mapping==0.3.0 debugpy==1.8.1 decorator==5.1.1 -defusedxml==0.7.1 distlib==0.3.8 +easydev==0.13.2 +eutils==0.6.0 executing==2.0.1 -fastapi==0.110.2 -fastjsonschema==2.19.1 -filelock==3.13.4 -fqdn==1.5.1 +fastapi==0.110.0 +filelock==3.16.1 +fonttools==4.54.1 fqfa==1.3.1 -ga4gh.vrs==2.0.0a6 -gene-normalizer==0.3.0.dev1 -gffutils==0.13 +ga4gh.vrs==2.0.0a10 +gene-normalizer==0.4.1 +gevent==24.2.1 +greenlet==3.1.1 +grequests==0.7.0 h11==0.14.0 hgvs==1.5.4 -httpcore==1.0.5 -httpx==0.27.0 +httpcore==1.0.6 +httpx==0.26.0 humanfriendly==10.0 -identify==2.5.36 -idna==3.7 +identify==2.6.1 +idna==3.6 +idutils==1.2.1 importlib_metadata==7.1.0 iniconfig==2.0.0 -ipykernel==6.29.4 -ipython==8.23.0 -ipywidgets==8.1.2 -isoduration==20.11.0 +intervaltree==3.1.0 +ipykernel==6.29.3 +ipython==8.22.2 +isbnlib==3.10.14 jedi==0.19.1 -Jinja2==3.1.3 +Jinja2==3.1.5 jmespath==1.0.1 -json5==0.9.25 -jsonpointer==2.4 -jsonschema==4.21.1 -jsonschema-specifications==2023.12.1 -jupyter==1.0.0 -jupyter-console==6.6.3 -jupyter-events==0.10.0 -jupyter-lsp==2.2.5 jupyter_client==8.6.1 jupyter_core==5.7.2 -jupyter_server==2.14.0 -jupyter_server_terminals==0.5.3 -jupyterlab==4.1.6 -jupyterlab_pygments==0.3.0 -jupyterlab_server==2.27.0 -jupyterlab_widgets==3.0.10 -MarkupSafe==2.1.5 -matplotlib-inline==0.1.7 +kiwisolver==1.4.7 +lazy==1.6 +line_profiler==4.1.3 +lxml==5.3.0 +MarkupSafe==3.0.2 +matplotlib==3.9.2 +matplotlib-inline==0.1.6 +mavedb==2024.1.0 mavehgvs==0.6.1 -mistune==3.0.2 -nbclient==0.10.0 -nbconvert==7.16.3 -nbformat==5.10.4 nest-asyncio==1.6.0 -nodeenv==1.8.0 -notebook==7.1.3 -notebook_shim==0.2.4 +nodeenv==1.9.1 numpy==1.26.4 -overrides==7.7.0 packaging==24.0 -pandas==2.2.2 -pandocfilters==1.5.1 +pandas==1.4.4 Parsley==1.3 -parso==0.8.4 +parso==0.8.3 pexpect==4.9.0 +pillow==10.4.0 platformdirs==4.2.0 +plottable==0.1.5 pluggy==1.5.0 -polars==0.20.22 -pre-commit==3.7.0 -prometheus_client==0.20.0 +polars==1.8.2 +pre-commit==3.8.0 prompt-toolkit==3.0.43 psutil==5.9.8 psycopg==3.1.18 @@ -109,61 +98,51 @@ psycopg-binary==3.1.18 psycopg2==2.9.9 ptyprocess==0.7.0 pure-eval==0.2.2 -pycparser==2.22 -pydantic==2.7.0 -pydantic_core==2.18.1 -pyfaidx==0.8.1.1 +pydantic==2.9.2 +pydantic_core==2.23.4 Pygments==2.17.2 -pyliftover==0.4.1 +pyhumps==3.8.0 +pyparsing==3.1.4 pysam==0.22.0 -pytest==8.1.1 -pytest-asyncio==0.23.6 +pytest==8.3.3 +pytest-asyncio==0.24.0 pytest-cov==5.0.0 pytest-mock==3.14.0 python-dateutil==2.9.0.post0 -python-dotenv==1.0.1 -python-json-logger==2.0.7 +python-dotenv==0.20.0 pytz==2024.1 PyYAML==6.0.1 -pyzmq==26.0.2 -qtconsole==5.5.1 -QtPy==2.4.1 -referencing==0.34.0 +pyzmq==25.1.2 requests==2.31.0 +requests-cache==1.2.1 requests-mock==1.12.1 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rpds-py==0.18.0 -ruff==0.2.0 +ruff==0.5.0 s3transfer==0.10.1 -Send2Trash==1.8.3 -setuptools==69.5.1 -setuptools-scm==8.1.0 -simplejson==3.19.2 +seaborn==0.13.2 six==1.16.0 sniffio==1.3.1 +sortedcontainers==2.4.0 soupsieve==2.5 -sqlparse==0.5.0 +SQLAlchemy==2.0.35 +sqlparse==0.4.4 stack-data==0.6.3 -starlette==0.37.2 +starlette==0.36.3 +suds-community==1.2.0 tabulate==0.9.0 -terminado==0.18.1 -tinycss2==1.2.1 tornado==6.4 tqdm==4.66.2 -traitlets==5.14.3 -types-python-dateutil==2.9.0.20240316 -typing_extensions==4.11.0 +traitlets==5.14.2 +typing_extensions==4.10.0 tzdata==2024.1 -uri-template==1.3.0 +url-normalize==1.4.3 urllib3==1.26.18 uvicorn==0.29.0 -virtualenv==20.25.3 +virtualenv==20.26.6 wags_tails==0.1.3 wcwidth==0.2.13 -webcolors==1.13 -webencodings==0.5.1 -websocket-client==1.7.0 -widgetsnbextension==4.0.10 +wrapt==1.16.0 +xmltodict==0.14.0 yoyo-migrations==8.2.0 zipp==3.18.1 +zope.event==5.0 +zope.interface==7.0.3