Merge pull request #175 from cancervariants/staging

Staging

Pipfile

@@ -22,7 +22,7 @@ httptools = "*"
 typing-extensions = "*"
 boto3 = "*"
 botocore = "*"
-variation-normalizer = ">=0.3.0"
+variation-normalizer = ">= 0.4.0a7"
 "ga4gh.vrsatile.pydantic" = ">=0.0.11"
 asyncclick = "*"
 

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.8"
-LAST_UPDATED = "2022-05-25"
+__version__ = "1.1.0-alpha.9"
+LAST_UPDATED = "2022-06-13"

requirements-dev.txt

@@ -7,27 +7,28 @@ argcomplete==2.0.0
 argh==0.26.2
 asgiref==3.5.2
 asttokens==2.0.5
-asyncclick==8.0.3.2
+asyncclick==8.1.3.2
 asyncpg==0.25.0
 attrs==21.4.0
 backcall==0.2.0
-backoff==2.0.1
+backoff==2.1.2
 backports-datetime-fromisoformat==1.0.0
 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
+bioregistry[align]==0.5.21
+bioutils==0.5.6
+bioversions==0.5.21
+boto3==1.24.8
+botocore==1.27.8
 bs4==0.0.1
 cachier==1.5.4
-canonicaljson==1.6.1
+canonicaljson==1.6.2
 cattrs==1.10.0
 certifi==2022.5.18.1
 charset-normalizer==2.0.12
 chembl-downloader==0.3.0
 civicpy==1.1.3
+class-resolver==0.3.10
 click==8.1.3
 click-default-group==1.2.2
 coloredlogs==15.0.1
@@ -45,34 +46,34 @@ fastapi==0.78.0
 ga4gh.vrs[extras]==0.8a0
 ga4gh.vrsatile.pydantic==0.0.11
 gene-normalizer==0.1.27
-gffutils==0.10.1
+gffutils==0.11.0
 h11==0.13.0
 hgvs==1.5.2
 httptools==0.4.0
 humanfriendly==10.0
 idna==3.3
 importlib-metadata==4.11.4
 inflection==0.5.1
-ipython==8.3.0
+ipython==8.4.0
 isodate==0.6.1
 jedi==0.18.1
 jmespath==1.0.0
 jsondiff==2.0.0
 jsonschema==3.2.0
-lxml==4.8.0
+lxml==4.9.0
 markdown==3.3.7
-marshmallow==3.15.0
+marshmallow==3.16.0
 marshmallow-enum==1.5.1
 matplotlib-inline==0.1.3
 more-click==0.1.1
 mwoauth==0.3.8
 mypy-extensions==0.4.3
-neo4j==4.4.3
-networkx==2.8.2
+neo4j==4.4.4
+networkx==2.8.3
 numpy==1.22.4
 oauthlib==3.2.0
 obonet==0.3.0
-owlready2==0.37
+owlready2==0.38
 packaging==21.3
 pandas==1.4.2
 parse==1.19.0
@@ -88,28 +89,28 @@ ptyprocess==0.7.0
 pure-eval==0.2.2
 pydantic==1.9.1
 pyee==8.2.2
-pyfaidx==0.6.4
+pyfaidx==0.7.0
 pygments==2.12.0
 pyjwt==2.4.0
 pyliftover==0.4
 pyparsing==2.4.7
 pyppeteer==1.0.2
 pyquery==1.4.3
 pyrsistent==0.18.1
-pysam==0.19.0
-pystow==0.4.3
+pysam==0.19.1
+pystow==0.4.4
 python-dateutil==2.8.2
 python-jsonschema-objects==0.4.1
 pytz==2022.1
 pyyaml==6.0
 rdflib==6.1.1
-requests==2.27.1
+requests==2.28.0
 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
+s3transfer==0.6.0
+setuptools==62.4.0
 simplejson==3.17.6
 six==1.16.0
 sniffio==1.2.0
@@ -118,20 +119,20 @@ sqlparse==0.4.2
 stack-data==0.2.0
 starlette==0.19.1
 tabulate==0.8.9
-thera-py==0.3.4
+thera-py==0.3.5
 tqdm==4.64.0
-traitlets==5.2.1.post0
+traitlets==5.2.2.post1
 typing-extensions==4.2.0
 typing-inspect==0.7.1
 url-normalize==1.4.3
 urllib3==1.26.9
-uta-tools==0.0.17
+uta-tools==0.1.1
 uvicorn==0.17.6
 uvloop==0.16.0
-variation-normalizer==0.3.0
+variation-normalizer==0.4.0a7
 vcfpy==0.13.4
 w3lib==1.22.0
-watchdog==2.1.8
+watchdog==2.1.9
 wcwidth==0.2.5
 websockets==10.3
 wikibaseintegrator==0.11.0
@@ -143,29 +144,29 @@ babel==2.10.1
 bleach==5.0.0
 cffi==1.15.0
 cfgv==3.3.1
-coverage==6.4
+coverage==6.4.1
 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
+filelock==3.7.1
 flake8==4.0.1
 flake8-docstrings==1.6.0
 identify==2.5.1
 iniconfig==1.1.1
-ipykernel==6.13.0
+ipykernel==6.14.0
 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-client==7.3.4
 jupyter-console==6.4.3
 jupyter-core==4.10.0
-jupyter-server==1.17.0
-jupyterlab==3.4.2
+jupyter-server==1.17.1
+jupyterlab==3.4.3
 jupyterlab-pygments==0.2.2
 jupyterlab-server==2.14.0
 jupyterlab-widgets==1.1.0
@@ -175,12 +176,12 @@ mccabe==0.6.1
 mistune==0.8.4
 mock==4.0.3
 nbclassic==0.3.7
-nbclient==0.6.3
+nbclient==0.6.4
 nbconvert==6.5.0
 nbformat==5.4.0
 nest-asyncio==1.5.5
 nodeenv==1.6.0
-notebook==6.4.11
+notebook==6.4.12
 notebook-shim==0.1.0
 pandocfilters==1.5.0
 platformdirs==2.5.2
@@ -196,8 +197,8 @@ 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
+pyzmq==23.1.0
+qtconsole==5.3.1
 qtpy==2.1.0
 send2trash==1.8.0
 snowballstemmer==2.2.0

requirements.txt

@@ -7,27 +7,28 @@ argcomplete==2.0.0
 argh==0.26.2
 asgiref==3.5.2
 asttokens==2.0.5
-asyncclick==8.0.3.2
+asyncclick==8.1.3.2
 asyncpg==0.25.0
 attrs==21.4.0
 backcall==0.2.0
-backoff==2.0.1
+backoff==2.1.2
 backports-datetime-fromisoformat==1.0.0
 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
+bioregistry[align]==0.5.21
+bioutils==0.5.6
+bioversions==0.5.21
+boto3==1.24.8
+botocore==1.27.8
 bs4==0.0.1
 cachier==1.5.4
-canonicaljson==1.6.1
+canonicaljson==1.6.2
 cattrs==1.10.0
 certifi==2022.5.18.1
 charset-normalizer==2.0.12
 chembl-downloader==0.3.0
 civicpy==1.1.3
+class-resolver==0.3.10
 click==8.1.3
 click-default-group==1.2.2
 coloredlogs==15.0.1
@@ -45,34 +46,34 @@ fastapi==0.78.0
 ga4gh.vrs[extras]==0.8a0
 ga4gh.vrsatile.pydantic==0.0.11
 gene-normalizer==0.1.27
-gffutils==0.10.1
+gffutils==0.11.0
 h11==0.13.0
 hgvs==1.5.2
 httptools==0.4.0
 humanfriendly==10.0
 idna==3.3
 importlib-metadata==4.11.4
 inflection==0.5.1
-ipython==8.3.0
+ipython==8.4.0
 isodate==0.6.1
 jedi==0.18.1
 jmespath==1.0.0
 jsondiff==2.0.0
 jsonschema==3.2.0
-lxml==4.8.0
+lxml==4.9.0
 markdown==3.3.7
-marshmallow==3.15.0
+marshmallow==3.16.0
 marshmallow-enum==1.5.1
 matplotlib-inline==0.1.3
 more-click==0.1.1
 mwoauth==0.3.8
 mypy-extensions==0.4.3
-neo4j==4.4.3
-networkx==2.8.2
+neo4j==4.4.4
+networkx==2.8.3
 numpy==1.22.4
 oauthlib==3.2.0
 obonet==0.3.0
-owlready2==0.37
+owlready2==0.38
 packaging==21.3
 pandas==1.4.2
 parse==1.19.0
@@ -88,28 +89,28 @@ ptyprocess==0.7.0
 pure-eval==0.2.2
 pydantic==1.9.1
 pyee==8.2.2
-pyfaidx==0.6.4
+pyfaidx==0.7.0
 pygments==2.12.0
 pyjwt==2.4.0
 pyliftover==0.4
 pyparsing==2.4.7
 pyppeteer==1.0.2
 pyquery==1.4.3
 pyrsistent==0.18.1
-pysam==0.19.0
-pystow==0.4.3
+pysam==0.19.1
+pystow==0.4.4
 python-dateutil==2.8.2
 python-jsonschema-objects==0.4.1
 pytz==2022.1
 pyyaml==6.0
 rdflib==6.1.1
-requests==2.27.1
+requests==2.28.0
 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
+s3transfer==0.6.0
+setuptools==62.4.0
 simplejson==3.17.6
 six==1.16.0
 sniffio==1.2.0
@@ -118,20 +119,20 @@ sqlparse==0.4.2
 stack-data==0.2.0
 starlette==0.19.1
 tabulate==0.8.9
-thera-py==0.3.4
+thera-py==0.3.5
 tqdm==4.64.0
-traitlets==5.2.1.post0
+traitlets==5.2.2.post1
 typing-extensions==4.2.0
 typing-inspect==0.7.1
 url-normalize==1.4.3
 urllib3==1.26.9
-uta-tools==0.0.17
+uta-tools==0.1.1
 uvicorn==0.17.6
 uvloop==0.16.0
-variation-normalizer==0.3.0
+variation-normalizer==0.4.0a7
 vcfpy==0.13.4
 w3lib==1.22.0
-watchdog==2.1.8
+watchdog==2.1.9
 wcwidth==0.2.5
 websockets==10.3
 wikibaseintegrator==0.11.0

setup.cfg

@@ -40,7 +40,7 @@ install_requires =
     typing-extensions
     boto3
     botocore
-    variation-normalizer >=0.3.0
+    variation-normalizer >=0.4.0a7
     ga4gh.vrsatile.pydantic >=0.0.11
 
 tests_require =