Merge pull request #287 from cancervariants/staging

Staging

.ebextensions/01app.config

@@ -0,0 +1,4 @@
+container_commands:
+    01_exports_permissions:
+        test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.8/exports"
+        command: "chmod -R +wrx /var/app/venv/staging-LQM1lest/lib/python3.8/exports"

Pipfile

@@ -19,12 +19,12 @@ uvloop = "*"
 websockets = ">=9.1"
 httptools = "*"
 typing-extensions = "*"
-wikibaseintegrator = "==0.11.0"
+wikibaseintegrator = ">=0.12.0"
 ipykernel = "*"
 bs4 = "*"
 pyyaml = "*"
-disease-normalizer = ">=0.2.12"
-"ga4gh.vrsatile.pydantic" = ">=0.0.5"
+disease-normalizer = ">=0.2.13"
+"ga4gh.vrsatile.pydantic" = ">=0.1.dev1"
 chembl-downloader = "*"
 bioversions = ">=0.4.3"
 pystow = "*"

requirements-dev.txt

@@ -1,168 +1,168 @@
 -i https://pypi.org/simple
-anyio==3.6.1
-appnope==0.1.3
-asgiref==3.5.2
-asttokens==2.0.5
+anyio==3.6.1; python_full_version >= '3.6.2'
+appnope==0.1.3; platform_system == 'Darwin'
+argon2-cffi==21.3.0; python_version >= '3.6'
+argon2-cffi-bindings==21.2.0; python_version >= '3.6'
+asttokens==2.0.8
+attrs==22.1.0; python_version >= '3.5'
+babel==2.10.3; python_version >= '3.6'
 backcall==0.2.0
-backoff==2.0.1
-beautifulsoup4==4.11.1
-bioregistry[align]==0.5.6
-bioversions==0.5.2
-boto3==1.23.7
-botocore==1.26.7
+backoff==2.1.2; python_version >= '3.7' and python_version < '4'
+backports-datetime-fromisoformat==1.0.0
+beautifulsoup4==4.11.1; python_version >= '3.6'
+bioregistry[align]==0.5.75; python_version >= '3.6'
+bioversions==0.5.79
+bleach==5.0.1; python_version >= '3.7'
+boto3==1.24.58
+botocore==1.27.58; python_version >= '3.7'
 bs4==0.0.1
 cachier==1.5.4
-certifi==2022.5.18.1
-charset-normalizer==2.0.12
+certifi==2022.6.15; python_version >= '3.6'
+cffi==1.15.1
+cfgv==3.3.1; python_full_version >= '3.6.1'
+charset-normalizer==2.1.1; python_version >= '3.6'
 chembl-downloader==0.3.0
+civicpy==1.1.3
+class-resolver==0.3.10
 click==8.1.3
 click-default-group==1.2.2
-cython==0.29.30
-dataclasses-json==0.5.7
-debugpy==1.6.0
-decorator==5.1.1
+coverage[toml]==6.4.4; python_version >= '3.7'
+cython==0.29.32
+dataclasses-json==0.5.7; python_version >= '3.6'
+debugpy==1.6.3; python_version >= '3.7'
+decorator==5.1.1; python_version >= '3.5'
 defusedxml==0.7.1
-disease-normalizer==0.2.12
-entrypoints==0.4
-executing==0.8.3
-fastapi==0.78.0
-ga4gh.vrsatile.pydantic==0.0.11
-h11==0.13.0
+deprecation==2.1.0
+disease-normalizer==0.2.13
+distlib==0.3.5
+entrypoints==0.4; python_version >= '3.6'
+executing==0.10.0
+fastapi==0.80.0
+fastjsonschema==2.16.1
+filelock==3.8.0; python_version >= '3.7'
+flake8==5.0.4
+flake8-annotations==2.9.1
+flake8-docstrings==1.6.0
+flake8-import-order==0.18.1
+flake8-quotes==3.3.1
+ga4gh.vrsatile.pydantic==0.1.dev1
+h11==0.13.0; python_version >= '3.6'
 httptools==0.4.0
-idna==3.3
-ipykernel==6.13.0
-ipython==8.3.0
+identify==2.5.3; python_version >= '3.7'
+idna==3.3; python_version >= '3.5'
+importlib-metadata==4.12.0; python_version < '3.10'
+iniconfig==1.1.1
+ipykernel==6.15.1
+ipython==8.4.0; python_version >= '3.8'
+ipython-genutils==0.2.0
 isodate==0.6.1
-jedi==0.18.1
-jmespath==1.0.0
-jupyter-client==7.3.1
-jupyter-core==4.10.0
-lxml==4.8.0
-marshmallow==3.15.0
+jedi==0.18.1; 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==4.14.0; python_version >= '3.7'
+jupyter-client==7.3.4; python_version >= '3.7'
+jupyter-core==4.11.1; python_version >= '3.7'
+jupyter-server==1.18.1; python_version >= '3.7'
+jupyterlab==3.4.5
+jupyterlab-pygments==0.2.2; python_version >= '3.7'
+jupyterlab-server==2.15.1; python_version >= '3.7'
+lxml==4.9.1
+markupsafe==2.1.1; python_version >= '3.7'
+marshmallow==3.17.1; python_version >= '3.7'
 marshmallow-enum==1.5.1
-matplotlib-inline==0.1.3
-more-click==0.1.1
+matplotlib-inline==0.1.6; python_version >= '3.5'
+mccabe==0.7.0; python_version >= '3.6'
+mistune==2.0.4
+more-click==0.1.1; python_version >= '3.7'
 mwoauth==0.3.8
+mypy==0.971
 mypy-extensions==0.4.3
-nest-asyncio==1.5.5
-oauthlib==3.2.0
-owlready2==0.37
-packaging==21.3
-parso==0.8.3
+nbclassic==0.4.3; python_version >= '3.7'
+nbclient==0.6.7; python_version >= '3.7'
+nbconvert==7.0.0; python_version >= '3.7'
+nbformat==5.4.0; python_version >= '3.7'
+nest-asyncio==1.5.5; python_version >= '3.5'
+networkx==2.8.6; python_version >= '3.8'
+nodeenv==1.7.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
+notebook==6.4.12; python_version >= '3.7'
+notebook-shim==0.1.0; python_version >= '3.7'
+numpy==1.23.2; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
+oauthlib==3.2.0; python_version >= '3.6'
+obonet==0.3.0; python_version >= '3.5'
+owlready2==0.38
+packaging==21.3; python_version >= '3.6'
+pandas==1.4.3; 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'
+parso==0.8.3; python_version >= '3.6'
 pathtools==0.1.2
-pexpect==4.8.0
+pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-portalocker==2.4.0
-prompt-toolkit==3.0.29
-psutil==5.9.1
+platformdirs==2.5.2; python_version >= '3.7'
+pluggy==1.0.0; python_version >= '3.6'
+portalocker==2.5.1; python_version >= '3.5'
+pre-commit==2.20.0
+prometheus-client==0.14.1; python_version >= '3.6'
+prompt-toolkit==3.0.30; python_full_version >= '3.6.2'
+psutil==5.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 ptyprocess==0.7.0
 pure-eval==0.2.2
-pydantic==1.9.1
-pygments==2.12.0
-pyjwt==2.4.0
-pyparsing==2.4.7
-pystow==0.4.3
-python-dateutil==2.8.2
-pyyaml==6.0
-pyzmq==23.0.0
-rdflib==6.1.1
-requests==2.27.1
-requests-ftp==0.3.1
-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
-stack-data==0.2.0
-starlette==0.19.1
-tabulate==0.8.9
-tornado==6.1
-tqdm==4.64.0
-traitlets==5.2.1.post0
-typing-extensions==4.2.0
-typing-inspect==0.7.1
-urllib3==1.26.9
-uvicorn==0.17.6
-uvloop==0.16.0
-watchdog==2.1.8
-wcwidth==0.2.5
-websockets==10.3
-wikibaseintegrator==0.11.0
-argon2-cffi==21.3.0
-argon2-cffi-bindings==21.2.0
-attrs==21.4.0
-babel==2.10.1
-backports-datetime-fromisoformat==1.0.0
-bleach==5.0.0
-cffi==1.15.0
-cfgv==3.3.1
-civicpy==1.1.3
-coverage[toml]==6.4
-deprecation==2.1.0
-distlib==0.3.4
-fastjsonschema==2.15.3
-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
-identify==2.5.1
-importlib-metadata==4.11.4
-iniconfig==1.1.1
-ipython-genutils==0.2.0
-jinja2==3.1.2
-json5==0.9.8
-jsonschema==4.5.1
-jupyter-server==1.17.0
-jupyterlab==3.4.2
-jupyterlab-pygments==0.2.2
-jupyterlab-server==2.14.0
-markupsafe==2.1.1
-mccabe==0.6.1
-mistune==0.8.4
-mypy==0.950
-nbclassic==0.3.7
-nbclient==0.6.3
-nbconvert==6.5.0
-nbformat==5.4.0
-networkx==2.8.2
-nodeenv==1.6.0
-notebook==6.4.11
-notebook-shim==0.1.0
-numpy==1.22.4
-obonet==0.3.0
-pandas==1.4.2
-pandocfilters==1.5.0
-platformdirs==2.5.2
-pluggy==1.0.0
-pre-commit==2.19.0
-prometheus-client==0.14.1
-py==1.11.0
-pycodestyle==2.8.0
+py==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+pycodestyle==2.9.1; python_version >= '3.6'
 pycparser==2.21
-pydocstyle==6.1.1
-pyflakes==2.4.0
-pyrsistent==0.18.1
-pysam==0.19.0
+pydantic==1.9.2
+pydocstyle==6.1.1; python_version >= '3.6'
+pyflakes==2.5.0; python_version >= '3.6'
+pygments==2.13.0; python_version >= '3.6'
+pyjwt==2.4.0; python_version >= '3.6'
+pyparsing==2.4.7
+pyrsistent==0.18.1; python_version >= '3.7'
+pysam==0.19.1
+pystow==0.4.6
 pytest==7.1.2
 pytest-cov==3.0.0
-pytz==2022.1
+python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pytz==2022.2.1
+pyyaml==6.0
+pyzmq==23.2.1; python_version >= '3.6'
+rdflib==6.2.0
+requests==2.28.1; python_version >= '3.7' and python_version < '4'
+requests-ftp==0.3.1
+requests-oauthlib==1.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+s3transfer==0.6.0; python_version >= '3.7'
 send2trash==1.8.0
+setuptools==65.3.0; python_version >= '3.7'
+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
-terminado==0.15.0
+soupsieve==2.3.2.post1; python_version >= '3.6'
+stack-data==0.4.0
+starlette==0.19.1; python_version >= '3.6'
+tabulate==0.8.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+terminado==0.15.0; python_version >= '3.7'
 -e .
-tinycss2==1.1.1
-toml==0.10.2
-tomli==2.0.1
-tox==3.25.0
-types-pyyaml==6.0.7
-types-requests==2.27.27
-types-urllib3==1.26.14
+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 < '3.11'
+tornado==6.2; python_version >= '3.7'
+tox==3.25.1
+tqdm==4.64.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+traitlets==5.3.0; python_version >= '3.7'
+types-pyyaml==6.0.11
+types-requests==2.28.9
+types-urllib3==1.26.23
+typing-extensions==4.3.0
+typing-inspect==0.8.0
+ujson==5.4.0; python_version >= '3.7'
+urllib3==1.26.12
+uvicorn==0.18.3
+uvloop==0.16.0
 vcfpy==0.13.4
-virtualenv==20.14.1
+virtualenv==20.16.3; python_version >= '3.6'
+watchdog==2.1.9; python_version >= '3.6'
+wcwidth==0.2.5
 webencodings==0.5.1
-websocket-client==1.3.2
-zipp==3.8.0
+websocket-client==1.4.0; python_version >= '3.7'
+websockets==10.3
+wikibaseintegrator==0.12.0
+zipp==3.8.1; python_version >= '3.7'