Merge pull request #290 from cancervariants/staging

Staging

.github/workflows/close_issue.yml

@@ -0,0 +1,18 @@
+name: Close issues related to a merged pull request based on staging branch.
+
+on:
+  pull_request:
+    types: [closed]
+    branches:
+      - staging
+
+jobs:
+  closeIssueOnPrMergeTrigger:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Closes issues related to a merged pull request.
+        uses: ldez/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Pipfile

@@ -25,7 +25,6 @@ psycopg2-binary = "*"
 pytest-asyncio = "*"
 
 [packages]
-hgvs = "*"
 "biocommons.seqrepo" = "*"
 fastapi = "*"
 uvicorn = "*"
@@ -35,4 +34,4 @@ gene-normalizer = ">=0.1.26"
 pyliftover = "*"
 boto3 = "*"
 "ga4gh.vrsatile.pydantic" = ">=0.0.11"
-uta-tools = ">=0.0.15"
+uta-tools = ">=0.0.17"

requirements-dev.txt

@@ -1,196 +1,186 @@
-#
-# 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
-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
-beautifulsoup4==4.11.1; python_version >= '3.6'
+beautifulsoup4==4.11.1
 biocommons.seqrepo==0.6.5
-bioutils==0.5.5; python_version >= '3.6'
-bleach==5.0.0; python_version >= '3.7'
-boto3==1.21.37
-botocore==1.24.37; python_version >= '3.6'
+bioutils==0.5.5
+boto3==1.23.5
+botocore==1.26.5
 bs4==0.0.1
-canonicaljson==1.6.0; python_version ~= '3.7'
-certifi==2021.10.8
+canonicaljson==1.6.1
+certifi==2022.5.18.1
+charset-normalizer==2.0.12
+click==8.1.3
+coloredlogs==15.0.1
+configparser==5.2.0
+cssselect==1.1.0
+decorator==5.1.1
+executing==0.8.3
+fake-useragent==0.1.11
+fastapi==0.78.0
+ga4gh.vrs[extras]==0.8a0
+ga4gh.vrsatile.pydantic==0.0.11
+gene-normalizer==0.1.27
+gffutils==0.10.1
+h11==0.13.0
+hgvs==1.5.2
+humanfriendly==10.0
+idna==3.3
+importlib-metadata==4.11.4
+inflection==0.5.1
+ipython==8.3.0
+jedi==0.18.1
+jmespath==1.0.0
+jsonschema==3.2.0
+lxml==4.8.0
+markdown==3.3.7
+matplotlib-inline==0.1.3
+numpy==1.22.4
+pandas==1.4.2
+parse==1.19.0
+parsley==1.3
+parso==0.8.3
+pexpect==4.8.0
+pickleshare==0.7.5
+prompt-toolkit==3.0.29
+psycopg2==2.9.3
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pydantic==1.9.1
+pyee==8.2.2
+pyfaidx==0.6.4
+pygments==2.12.0
+pyliftover==0.4
+pyppeteer==1.0.2
+pyquery==1.4.3
+pyrsistent==0.18.1
+pysam==0.19.0
+python-dateutil==2.8.2
+python-jsonschema-objects==0.4.1
+pytz==2022.1
+pyyaml==6.0
+requests==2.27.1
+requests-html==0.10.0
+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==0.19.1
+tabulate==0.8.9
+tqdm==4.64.0
+traitlets==5.2.1.post0
+typing-extensions==4.2.0
+urllib3==1.26.9
+uta-tools==0.0.17
+uvicorn==0.17.6
+w3lib==1.22.0
+wcwidth==0.2.5
+websockets==10.3
+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; python_full_version >= '3.6.1'
-charset-normalizer==2.0.12; python_version >= '3'
-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'
+cfgv==3.3.1
 commonmark==0.9.1
-configparser==5.2.0; python_version >= '3.6'
-coverage==6.3.2
+coverage==6.3.3
 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'
-cycler==0.11.0; 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'
+cycler==0.11.0
+debugpy==1.6.0
+defusedxml==0.7.1
 distlib==0.3.4
 docopt==0.6.2
-docutils==0.18.1; 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==0.8.3
-fake-useragent==0.1.11
-fastapi==0.75.1
+docutils==0.18.1
+entrypoints==0.4
 fastjsonschema==2.15.3
-filelock==3.6.0; python_version >= '3.7'
-flake8-annotations==2.8.0
+filelock==3.7.0
+flake8==4.0.1
+flake8-annotations==2.9.0
 flake8-docstrings==1.6.0
 flake8-import-order==0.18.1
 flake8-quotes==3.3.1
-flake8==4.0.1
-fonttools==4.32.0; python_version >= '3.7'
-ga4gh.vrs[extras]==0.8a0
-ga4gh.vrsatile.pydantic==0.0.11
-gene-normalizer==0.1.26
-gffutils==0.10.1
-h11==0.13.0; python_version >= '3.6'
-hgvs==1.5.2
-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 >= '3.5'
-importlib-metadata==4.11.3; python_version < '3.10'
-inflection==0.5.1; python_version >= '3.5'
+fonttools==4.33.3
+identify==2.5.1
 iniconfig==1.1.1
 ipykernel==6.13.0
 ipython-genutils==0.2.0
-ipython==8.2.0; python_version >= '3.8'
 ipywidgets==7.7.0
-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
-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'
+jinja2==3.1.2
+json5==0.9.8
 jupyter==1.0.0
-jupyterlab-pygments==0.2.0; python_version >= '3.7'
-jupyterlab-server==2.12.0; python_version >= '3.7'
-jupyterlab-widgets==1.1.0; python_version >= '3.6'
-jupyterlab==3.3.3
-keyring==23.5.0; python_version >= '3.7'
-kiwisolver==1.4.2; python_version >= '3.7'
-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'
-matplotlib-inline==0.1.3; python_version >= '3.5'
-matplotlib==3.5.1
+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
+keyring==23.5.0
+kiwisolver==1.4.2
+markupsafe==2.1.1
+matplotlib==3.5.2
 mccabe==0.6.1
 mistune==0.8.4
-nbclassic==0.3.7; python_version >= '3.7'
-nbclient==0.5.13; python_version >= '3.7'
-nbconvert==6.5.0; python_version >= '3.7'
-nbformat==5.3.0; python_version >= '3.7'
-nest-asyncio==1.5.5; python_version >= '3.5'
+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-shim==0.1.0; python_version >= '3.7'
-notebook==6.4.10; python_version >= '3.6'
-numpy==1.22.3; python_version >= '3.8'
-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'
-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
-pillow==9.1.0; python_version >= '3.7'
+notebook==6.4.11
+notebook-shim==0.1.0
+packaging==21.3
+pandocfilters==1.5.0
+pillow==9.1.1
 pkginfo==1.8.2
-platformdirs==2.5.1; python_version >= '3.7'
-pluggy==1.0.0; python_version >= '3.6'
-pre-commit==2.18.1
-prometheus-client==0.14.1; 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'
+platformdirs==2.5.2
+pluggy==1.0.0
+pre-commit==2.19.0
+prometheus-client==0.14.1
+psutil==5.9.1
 psycopg2-binary==2.9.3
-psycopg2==2.9.3; python_version >= '3.6'
-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'
-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'
-pyliftover==0.4
-pyparsing==3.0.8; python_full_version >= '3.6.8'
-pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
-pyquery==1.4.3
-pyrsistent==0.18.1; python_version >= '3.7'
-pysam==0.19.0
+py==1.11.0
+pycodestyle==2.8.0
+pycparser==2.21
+pydocstyle==6.1.1
+pyflakes==2.4.0
+pyparsing==3.0.9
+pytest==7.1.2
 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'
-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'
-readme-renderer==34.0; python_version >= '3.6'
-requests-html==0.10.0; python_version >= '3.6'
+pyzmq==23.0.0
+qtconsole==5.3.0
+qtpy==2.1.0
+readme-renderer==35.0
 requests-toolbelt==0.9.1
-requests==2.27.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-rfc3986==2.0.0; python_version >= '3.7'
-rich==12.2.0; python_version < '4' and python_full_version >= '3.6.3'
-s3transfer==0.5.2; python_version >= '3.6'
+rfc3986==2.0.0
+rich==12.4.1
 send2trash==1.8.0
-setuptools==62.1.0; 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'
-stack-data==0.2.0
-starlette==0.17.1; python_version >= '3.6'
-tabulate==0.8.9
-terminado==0.13.3; python_version >= '3.7'
-tinycss2==1.1.1; python_version >= '3.6'
-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'
+terminado==0.15.0
+tinycss2==1.1.1
+toml==0.10.2
+tomli==2.0.1
+tornado==6.1
 twine==4.0.0
-typing-extensions==4.1.1; python_version >= '3.6'
-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
-uvicorn==0.17.6
-virtualenv==20.14.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-w3lib==1.22.0
-wcwidth==0.2.5
+-e .
+virtualenv==20.14.1
 webencodings==0.5.1
-websocket-client==1.3.2; python_version >= '3.7'
-websockets==10.2; python_version >= '3.7'
+websocket-client==1.3.2
 widgetsnbextension==3.6.0
-yoyo-migrations==7.3.2
-zipp==3.8.0; python_version >= '3.7'