From 59cb2d461b3f0b77c47851e80d13a095f7474464 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Fri, 31 May 2024 21:09:53 -0400 Subject: [PATCH] nb: update reqs.txt --- notebooks/analysis/requirements.txt | 310 +++++++++++++++------------- 1 file changed, 166 insertions(+), 144 deletions(-) diff --git a/notebooks/analysis/requirements.txt b/notebooks/analysis/requirements.txt index 7e4119d..032dda9 100644 --- a/notebooks/analysis/requirements.txt +++ b/notebooks/analysis/requirements.txt @@ -1,147 +1,169 @@ --i https://pypi.org/simple -aiofiles==22.1.0 ; python_version >= '3.7' and python_version < '4.0' -anyio==3.6.2 ; python_full_version >= '3.6.2' -appdirs==1.4.4 -appnope==0.1.3 ; platform_system == 'Darwin' -argcomplete==2.0.0 ; python_version >= '3.6' -argh==0.26.2 -argon2-cffi==21.3.0 ; python_version >= '3.6' -argon2-cffi-bindings==21.2.0 ; python_version >= '3.6' -asttokens==2.1.0 -asyncio==3.4.3 -asyncpg==0.27.0 ; python_full_version >= '3.7.0' -attrs==22.1.0 ; python_version >= '3.5' -babel==2.11.0 ; python_version >= '3.6' -backcall==0.2.0 -beautifulsoup4==4.11.1 ; python_full_version >= '3.6.0' -biocommons.seqrepo==0.6.5 -biopython==1.80 -bioutils==0.5.7 ; python_version >= '3.6' -bleach==5.0.1 ; python_version >= '3.7' -boto3==1.26.16 ; python_version >= '3.7' -botocore==1.29.16 ; python_version >= '3.7' -bs4==0.0.1 -canonicaljson==1.6.4 ; python_version >= '3.7' -certifi==2022.9.24 ; python_version >= '3.6' -cffi==1.15.1 -charset-normalizer==2.1.1 ; python_full_version >= '3.6.0' -click==8.1.3 ; python_version >= '3.7' -coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -configparser==5.3.0 ; python_version >= '3.7' -cool-seq-tool==0.1.4 -cssselect==1.2.0 ; python_version >= '3.7' -debugpy==1.6.3 ; python_version >= '3.7' -decorator==5.1.1 ; python_version >= '3.5' -defusedxml==0.7.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -entrypoints==0.4 ; python_version >= '3.6' -executing==1.2.0 -fake-useragent==1.0.1 -fastapi==0.87.0 ; python_version >= '3.7' -fastjsonschema==2.16.2 -ga4gh.vrs[extras]==0.8.7.dev0 ; python_version >= '3.6' -ga4gh.vrsatile.pydantic==0.0.11 -gene-normalizer==0.1.27 -gffutils==0.11.1 -h11==0.14.0 ; python_version >= '3.7' -hgvs==1.5.4 ; python_version >= '3.6' -humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -idna==3.4 ; python_version >= '3.5' -importlib-metadata==5.0.0 ; python_version >= '3.7' -inflection==0.5.1 ; python_version >= '3.5' -ipykernel==6.17.1 ; python_version >= '3.8' -ipython==8.6.0 ; python_version >= '3.8' -ipython-genutils==0.2.0 -ipywidgets==8.0.2 ; 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==0.9.10 -jsonschema==3.2.0 +## 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 +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 +asyncpg==0.29.0 +attrs==23.2.0 +Babel==2.14.0 +beautifulsoup4==4.12.3 +biocommons.seqrepo==0.6.9 +biopython==1.83 +bioutils==0.5.8.post1 +bleach==6.1.0 +boto3==1.34.88 +botocore==1.34.88 +canonicaljson==2.0.0 +certifi==2024.2.2 +cffi==1.16.0 +cfgv==3.4.0 +charset-normalizer==3.3.2 +click==8.1.7 +coloredlogs==15.0.1 +comm==0.2.2 +configparser==7.0.0 +cool_seq_tool==0.4.0.dev3 +coverage==7.4.4 +-e git+https://github.com/ave-dcd/dcd_mapping/@d00598d6a7535fbe85c567ab56e264e4d3255d4b#egg=dcd_mapping +debugpy==1.8.1 +decorator==5.1.1 +defusedxml==0.7.1 +distlib==0.3.8 +executing==2.0.1 +fastapi==0.110.2 +fastjsonschema==2.19.1 +filelock==3.13.4 +fqdn==1.5.1 +fqfa==1.3.1 +ga4gh.vrs==2.0.0a6 +gene-normalizer==0.3.0.dev1 +gffutils==0.13 +h11==0.14.0 +hgvs==1.5.4 +httpcore==1.0.5 +httpx==0.27.0 +humanfriendly==10.0 +identify==2.5.36 +idna==3.7 +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 +jedi==0.19.1 +Jinja2==3.1.3 +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-client==7.4.7 ; python_version >= '3.7' -jupyter-console==6.4.4 ; python_version >= '3.7' -jupyter-core==5.0.0 ; python_version >= '3.8' -jupyter-server==1.23.3 ; python_version >= '3.7' -jupyterlab==3.5.0 -jupyterlab-pygments==0.2.2 ; python_version >= '3.7' -jupyterlab-server==2.16.3 ; python_version >= '3.7' -jupyterlab-widgets==3.0.3 ; python_version >= '3.7' -lxml==4.9.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -markdown==3.4.1 ; python_version >= '3.7' -markupsafe==2.1.1 ; python_version >= '3.7' -matplotlib-inline==0.1.6 ; python_version >= '3.5' -mistune==2.0.4 -nbclassic==0.4.8 ; python_version >= '3.7' -nbclient==0.7.0 ; python_full_version >= '3.7.0' -nbconvert==7.2.5 ; python_version >= '3.7' -nbformat==5.7.0 ; python_version >= '3.7' -nest-asyncio==1.5.6 -notebook==6.5.2 ; python_version >= '3.7' -notebook-shim==0.2.2 ; python_version >= '3.7' -numpy==1.23.5 ; python_version >= '3.8' -packaging==21.3 ; python_version >= '3.6' -pandas==1.5.2 -pandocfilters==1.5.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' -parse==1.19.0 -parsley==1.3 -parso==0.8.3 ; python_version >= '3.6' -pexpect==4.8.0 ; sys_platform != 'win32' -pickleshare==0.7.5 -platformdirs==2.5.4 ; python_version >= '3.7' -plotly==5.11.0 -prometheus-client==0.15.0 ; python_version >= '3.6' -prompt-toolkit==3.0.33 ; 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' -psycopg2==2.9.5 ; python_version >= '3.6' -psycopg2-binary==2.9.5 -ptyprocess==0.7.0 ; os_name != 'nt' +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 +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 +numpy==1.26.4 +overrides==7.7.0 +packaging==24.0 +pandas==2.2.2 +pandocfilters==1.5.1 +Parsley==1.3 +parso==0.8.4 +pexpect==4.9.0 +platformdirs==4.2.0 +pluggy==1.5.0 +polars==0.20.22 +pre-commit==3.7.0 +prometheus_client==0.20.0 +prompt-toolkit==3.0.43 +psutil==5.9.8 +psycopg==3.1.18 +psycopg-binary==3.1.18 +psycopg2==2.9.9 +ptyprocess==0.7.0 pure-eval==0.2.2 -pycparser==2.21 -pydantic==1.10.2 ; python_version >= '3.7' -pyee==8.2.2 -pyfaidx==0.7.1 -pygments==2.13.0 ; python_version >= '3.6' -pyliftover==0.4 -pyparsing==3.0.9 ; python_full_version >= '3.6.8' -pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0' -pyquery==1.4.3 -pyrsistent==0.19.2 ; python_version >= '3.7' -pysam==0.18.0 -python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' -python-jsonschema-objects==0.4.1 -pytz==2022.6 -pyyaml==6.0 ; python_version >= '3.6' -pyzmq==24.0.1 ; python_version >= '3.6' -qtconsole==5.4.0 ; python_version >= '3.7' -qtpy==2.3.0 ; python_version >= '3.7' -requests==2.28.1 -requests-html==0.10.0 ; python_full_version >= '3.6.0' -s3transfer==0.6.0 ; python_version >= '3.7' -send2trash==1.8.0 -setuptools==65.6.2 ; python_version >= '3.7' -simplejson==3.18.0 ; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3' -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' -soupsieve==2.3.2.post1 ; python_version >= '3.6' -sqlparse==0.4.3 ; python_version >= '3.5' -stack-data==0.6.1 -starlette==0.21.0 ; python_version >= '3.7' -tabulate==0.9.0 ; python_version >= '3.7' -tenacity==8.1.0 ; python_version >= '3.6' -terminado==0.17.0 ; python_version >= '3.7' -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==5.5.0 ; python_version >= '3.7' -typing-extensions==4.4.0 ; python_version >= '3.7' -urllib3==1.26.12 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' and python_version < '4' -uvicorn==0.20.0 ; python_version >= '3.7' -w3lib==2.0.1 ; python_version >= '3.6' -wcwidth==0.2.5 +pycparser==2.22 +pydantic==2.7.0 +pydantic_core==2.18.1 +pyfaidx==0.8.1.1 +Pygments==2.17.2 +pyliftover==0.4.1 +pysam==0.22.0 +pytest==8.1.1 +pytest-asyncio==0.23.6 +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 +pytz==2024.1 +PyYAML==6.0.1 +pyzmq==26.0.2 +qtconsole==5.5.1 +QtPy==2.4.1 +referencing==0.34.0 +requests==2.31.0 +requests-mock==1.12.1 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rpds-py==0.18.0 +ruff==0.2.0 +s3transfer==0.10.1 +Send2Trash==1.8.3 +setuptools==69.5.1 +setuptools-scm==8.1.0 +simplejson==3.19.2 +six==1.16.0 +sniffio==1.3.1 +soupsieve==2.5 +sqlparse==0.5.0 +stack-data==0.6.3 +starlette==0.37.2 +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 +tzdata==2024.1 +uri-template==1.3.0 +urllib3==1.26.18 +uvicorn==0.29.0 +virtualenv==20.25.3 +wags_tails==0.1.3 +wcwidth==0.2.13 +webcolors==1.13 webencodings==0.5.1 -websocket-client==1.4.2 ; python_version >= '3.7' -websockets==10.4 ; python_version >= '3.7' -widgetsnbextension==4.0.3 ; python_version >= '3.7' -yoyo-migrations==8.1.0 -zipp==3.10.0 ; python_version >= '3.7' +websocket-client==1.7.0 +widgetsnbextension==4.0.10 +yoyo-migrations==8.2.0 +zipp==3.18.1