Merge pull request #173 from cancervariants/staging

Staging

metakb/version.py

@@ -1,4 +1,4 @@
 """MetaKB version"""
 # REQ: EACH TIME VERSION IS UPDATED, MUST ALSO UPDATE LAST_UPDATED
-__version__ = "1.1.0-alpha.7"
-LAST_UPDATED = "2022-05-04"
+__version__ = "1.1.0-alpha.8"
+LAST_UPDATED = "2022-05-25"

requirements-dev.txt

@@ -1,222 +1,212 @@
-#
-# These requirements were autogenerated by pipenv
-# To regenerate from the project's Pipfile, run:
-#
-#    pipenv lock --requirements --dev
-#
-
-# Note: in pipenv 2020.x, "--dev" changed to emit both default and development
-# requirements. To emit only development requirements, pass "--dev-only".
-
 -i https://pypi.org/simple
--e .
-aiofiles==0.8.0; python_version >= '3.6' and python_version < '4.0'
-anyio==3.5.0; python_full_version >= '3.6.2'
+aiofiles==0.8.0
+anyio==3.6.1
 appdirs==1.4.4
-appnope==0.1.3; sys_platform == 'darwin'
-argcomplete==2.0.0; python_version >= '3.6'
+appnope==0.1.3
+argcomplete==2.0.0
 argh==0.26.2
-argon2-cffi-bindings==21.2.0; python_version >= '3.6'
-argon2-cffi==21.3.0; python_version >= '3.6'
-asgiref==3.5.0; python_version >= '3.7'
+asgiref==3.5.2
 asttokens==2.0.5
 asyncclick==8.0.3.2
-asyncpg==0.25.0; python_version >= '3.6'
-attrs==21.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-babel==2.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+asyncpg==0.25.0
+attrs==21.4.0
 backcall==0.2.0
-backoff==1.11.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+backoff==2.0.1
 backports-datetime-fromisoformat==1.0.0
-beautifulsoup4==4.10.0; python_version >= '3.1'
-biocommons.seqrepo==0.6.5; python_version >= '3.5'
-bioregistry==0.4.85; python_version >= '3.6'
-bioutils==0.5.5; python_version >= '3.6'
-bioversions==0.4.41; python_version >= '3.6'
-bleach==4.1.0; python_version >= '3.6'
-boto3==1.21.35
-botocore==1.24.35
+beautifulsoup4==4.11.1
+biocommons.seqrepo==0.6.5
+bioregistry[align]==0.5.6
+bioutils==0.5.5
+bioversions==0.5.2
+boto3==1.23.7
+botocore==1.26.7
 bs4==0.0.1
 cachier==1.5.4
-canonicaljson==1.6.0; python_version ~= '3.7'
-cattrs==1.10.0; python_version >= '3.7' and python_version < '4.0'
-certifi==2021.10.8
-cffi==1.15.0
-cfgv==3.3.1; python_full_version >= '3.6.1'
-charset-normalizer==2.0.12; python_version >= '3'
-chembl-downloader==0.3.0; python_version >= '3.7'
+canonicaljson==1.6.1
+cattrs==1.10.0
+certifi==2022.5.18.1
+charset-normalizer==2.0.12
+chembl-downloader==0.3.0
 civicpy==1.1.3
+click==8.1.3
 click-default-group==1.2.2
-click==8.1.2; 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==5.2.0; python_version >= '3.6'
-coverage==6.3.2
-coveralls==3.3.1
-cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-cython==0.29.28; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-dataclasses-json==0.5.7; python_version >= '3.6'
-debugpy==1.6.0; 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'
+coloredlogs==15.0.1
+configparser==5.2.0
+cssselect==1.1.0
+cython==0.29.30
+dataclasses-json==0.5.7
+decorator==5.1.1
+defusedxml==0.7.1
 deprecation==2.1.0
 disease-normalizer==0.2.12
-distlib==0.3.4
-docopt==0.6.2
-entrypoints==0.4; python_version >= '3.6'
 executing==0.8.3
 fake-useragent==0.1.11
-fastapi==0.75.1
-fastjsonschema==2.15.3
-filelock==3.6.0; python_version >= '3.7'
-flake8-docstrings==1.6.0
-flake8==4.0.1
+fastapi==0.78.0
 ga4gh.vrs[extras]==0.8a0
 ga4gh.vrsatile.pydantic==0.0.11
-gene-normalizer==0.1.25
+gene-normalizer==0.1.27
 gffutils==0.10.1
-h11==0.13.0; python_version >= '3.6'
+h11==0.13.0
 hgvs==1.5.2
 httptools==0.4.0
-humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-identify==2.4.12; python_version >= '3.7'
-idna==3.3; python_version >= '3'
-importlib-metadata==4.11.3; python_version < '3.10'
-inflection==0.5.1; python_version >= '3.5'
-iniconfig==1.1.1
-ipykernel==6.12.1
-ipython-genutils==0.2.0
-ipython==8.2.0; python_version >= '3.8'
-ipywidgets==7.7.0
+humanfriendly==10.0
+idna==3.3
+importlib-metadata==4.11.4
+inflection==0.5.1
+ipython==8.3.0
 isodate==0.6.1
-jedi==0.18.1; python_version >= '3.6'
-jinja2==3.1.1; python_version >= '3.7'
-jmespath==1.0.0; python_version >= '3.7'
-json5==0.9.6
-jsondiff==1.3.1
+jedi==0.18.1
+jmespath==1.0.0
+jsondiff==2.0.0
 jsonschema==3.2.0
-jupyter-client==7.2.2; python_version >= '3.7'
-jupyter-console==6.4.3; python_version >= '3.6'
-jupyter-core==4.9.2; python_version >= '3.6'
-jupyter-server==1.16.0; python_version >= '3.7'
-jupyter==1.0.0
-jupyterlab-pygments==0.1.2
-jupyterlab-server==2.12.0; python_version >= '3.7'
-jupyterlab-widgets==1.1.0; python_version >= '3.6'
-jupyterlab==3.3.3
-lxml==4.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-markdown==3.3.6; python_version >= '3.6'
-markupsafe==2.1.1; python_version >= '3.7'
+lxml==4.8.0
+markdown==3.3.7
+marshmallow==3.15.0
 marshmallow-enum==1.5.1
-marshmallow==3.15.0; python_version >= '3.7'
-matplotlib-inline==0.1.3; python_version >= '3.5'
-mccabe==0.6.1
-mistune==0.8.4
-mock==4.0.3
-more-click==0.1.1; python_version >= '3.7'
-mwoauth==0.3.7
+matplotlib-inline==0.1.3
+more-click==0.1.1
+mwoauth==0.3.8
 mypy-extensions==0.4.3
-nbclassic==0.3.7; python_version >= '3.7'
-nbclient==0.5.13; python_version >= '3.7'
-nbconvert==6.4.5; python_version >= '3.7'
-nbformat==5.3.0; python_version >= '3.7'
-neo4j==4.4.2
-nest-asyncio==1.5.5; python_version >= '3.5'
-networkx==2.7.1; python_version >= '3.8'
-nodeenv==1.6.0
-notebook-shim==0.1.0; python_version >= '3.7'
-notebook==6.4.10; python_version >= '3.6'
-numpy==1.22.3; python_version >= '3.8'
-oauthlib==3.2.0; python_version >= '3.6'
-obonet==0.3.0; python_version >= '3.5'
-owlready2==0.37; python_version >= '3.6'
-packaging==21.3; python_version >= '3.6'
-pandas==1.4.2; 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'
+neo4j==4.4.3
+networkx==2.8.2
+numpy==1.22.4
+oauthlib==3.2.0
+obonet==0.3.0
+owlready2==0.37
+packaging==21.3
+pandas==1.4.2
 parse==1.19.0
 parsley==1.3
-parso==0.8.3; python_version >= '3.6'
+parso==0.8.3
 pathtools==0.1.2
-pexpect==4.8.0; sys_platform != 'win32'
+pexpect==4.8.0
 pickleshare==0.7.5
-platformdirs==2.5.1; python_version >= '3.7'
-pluggy==1.0.0; python_version >= '3.6'
-portalocker==2.4.0; python_version >= '3.5'
-pre-commit==2.18.1
-prometheus-client==0.14.0; python_version >= '3.6'
-prompt-toolkit==3.0.29; python_full_version >= '3.6.2'
-psutil==5.9.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-psycopg2==2.9.3; python_version >= '3.6'
+portalocker==2.4.0
+prompt-toolkit==3.0.29
+psycopg2==2.9.3
 ptyprocess==0.7.0
 pure-eval==0.2.2
-py==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-pycodestyle==2.8.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-pycparser==2.21; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pydantic==1.9.0
-pydocstyle==6.1.1; python_version >= '3.6'
+pydantic==1.9.1
 pyee==8.2.2
 pyfaidx==0.6.4
-pyflakes==2.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pygments==2.11.2; python_version >= '3.5'
+pygments==2.12.0
 pyjwt==2.4.0
 pyliftover==0.4
-pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
+pyparsing==2.4.7
+pyppeteer==1.0.2
 pyquery==1.4.3
-pyrsistent==0.18.1; python_version >= '3.7'
+pyrsistent==0.18.1
 pysam==0.19.0
-pystow==0.4.0; python_version >= '3.7'
-pytest-asyncio==0.18.3
-pytest-cov==3.0.0
-pytest==7.1.1
-python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pystow==0.4.3
+python-dateutil==2.8.2
 python-jsonschema-objects==0.4.1
 pytz==2022.1
-pyyaml==6.0; python_version >= '3.6'
-pyzmq==22.3.0; python_version >= '3.6'
-qtconsole==5.3.0; python_version >= '3.7'
-qtpy==2.0.1; python_version >= '3.6'
-rdflib==6.1.1; python_version >= '3.7'
-requests-cache==0.9.3
-requests-ftp==0.3.1
-requests-html==0.10.0; python_version >= '3.6'
-requests-oauthlib==1.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pyyaml==6.0
+rdflib==6.1.1
 requests==2.27.1
-s3transfer==0.5.2; python_version >= '3.6'
-send2trash==1.8.0
-setuptools==62.0.0; python_version >= '3.7'
-simplejson==3.17.6; 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==1.2.0; python_version >= '3.5'
-snowballstemmer==2.2.0
-soupsieve==2.3.2; python_version >= '3.6'
-sqlparse==0.4.2; python_version >= '3.5'
+requests-cache==0.9.4
+requests-ftp==0.3.1
+requests-html==0.10.0
+requests-oauthlib==1.3.1
+s3transfer==0.5.2
+setuptools==62.3.2
+simplejson==3.17.6
+six==1.16.0
+sniffio==1.2.0
+soupsieve==2.3.2.post1
+sqlparse==0.4.2
 stack-data==0.2.0
-starlette==0.17.1; python_version >= '3.6'
+starlette==0.19.1
 tabulate==0.8.9
-terminado==0.13.3; python_version >= '3.7'
-testpath==0.6.0; python_version >= '3.5'
 thera-py==0.3.4
-toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-tomli==2.0.1; python_version >= '3.7'
-tornado==6.1; python_version >= '3.5'
-tqdm==4.64.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.1.1; python_version >= '3.7'
-typing-extensions==4.1.1
+tqdm==4.64.0
+traitlets==5.2.1.post0
+typing-extensions==4.2.0
 typing-inspect==0.7.1
-url-normalize==1.4.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-urllib3==1.26.9; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0'
-uta-tools==0.0.15; python_version >= '3.8'
+url-normalize==1.4.3
+urllib3==1.26.9
+uta-tools==0.0.17
 uvicorn==0.17.6
 uvloop==0.16.0
 variation-normalizer==0.3.0
-vcfpy==0.13.3
-virtualenv==20.14.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+vcfpy==0.13.4
 w3lib==1.22.0
-watchdog==2.1.7; python_version >= '3.6'
+watchdog==2.1.8
 wcwidth==0.2.5
+websockets==10.3
+wikibaseintegrator==0.11.0
+yoyo-migrations==7.3.2
+zipp==3.8.0
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+babel==2.10.1
+bleach==5.0.0
+cffi==1.15.0
+cfgv==3.3.1
+coverage==6.4
+coveralls==3.3.1
+debugpy==1.6.0
+distlib==0.3.4
+docopt==0.6.2
+entrypoints==0.4
+fastjsonschema==2.15.3
+filelock==3.7.0
+flake8==4.0.1
+flake8-docstrings==1.6.0
+identify==2.5.1
+iniconfig==1.1.1
+ipykernel==6.13.0
+ipython-genutils==0.2.0
+ipywidgets==7.7.0
+jinja2==3.1.2
+json5==0.9.8
+jupyter==1.0.0
+jupyter-client==7.3.1
+jupyter-console==6.4.3
+jupyter-core==4.10.0
+jupyter-server==1.17.0
+jupyterlab==3.4.2
+jupyterlab-pygments==0.2.2
+jupyterlab-server==2.14.0
+jupyterlab-widgets==1.1.0
+markupsafe==2.1.1
+mccabe==0.6.1
+-e .
+mistune==0.8.4
+mock==4.0.3
+nbclassic==0.3.7
+nbclient==0.6.3
+nbconvert==6.5.0
+nbformat==5.4.0
+nest-asyncio==1.5.5
+nodeenv==1.6.0
+notebook==6.4.11
+notebook-shim==0.1.0
+pandocfilters==1.5.0
+platformdirs==2.5.2
+pluggy==1.0.0
+pre-commit==2.19.0
+prometheus-client==0.14.1
+psutil==5.9.1
+py==1.11.0
+pycodestyle==2.8.0
+pycparser==2.21
+pydocstyle==6.1.1
+pyflakes==2.4.0
+pytest==7.1.2
+pytest-asyncio==0.18.3
+pytest-cov==3.0.0
+pyzmq==23.0.0
+qtconsole==5.3.0
+qtpy==2.1.0
+send2trash==1.8.0
+snowballstemmer==2.2.0
+terminado==0.15.0
+tinycss2==1.1.1
+toml==0.10.2
+tomli==2.0.1
+tornado==6.1
+virtualenv==20.14.1
 webencodings==0.5.1
-websocket-client==1.3.2; python_version >= '3.7'
-websockets==10.2
+websocket-client==1.3.2
 widgetsnbextension==3.6.0
-wikibaseintegrator==0.11.0; python_version < '3.10' and python_version >= '3.7'
-yoyo-migrations==7.3.2
-zipp==3.8.0; python_version >= '3.7'