nb: update reqs.txt

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