From 713948ed23cb1a0a1e58af7537f17a1e79708c9f Mon Sep 17 00:00:00 2001 From: korikuzma Date: Mon, 13 Jun 2022 20:53:01 -0400 Subject: [PATCH] build: update variation norm + other requirements --- Pipfile | 2 +- metakb/version.py | 4 +-- requirements-dev.txt | 73 ++++++++++++++++++++++---------------------- requirements.txt | 53 ++++++++++++++++---------------- setup.cfg | 2 +- 5 files changed, 68 insertions(+), 66 deletions(-) diff --git a/Pipfile b/Pipfile index 6ba67809..5028a8de 100644 --- a/Pipfile +++ b/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 = "*" diff --git a/metakb/version.py b/metakb/version.py index 47828ae1..a60bab27 100644 --- a/metakb/version.py +++ b/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" diff --git a/requirements-dev.txt b/requirements-dev.txt index 620f478d..04936d7e 100644 --- a/requirements-dev.txt +++ b/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 @@ -45,7 +46,7 @@ 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 @@ -53,26 +54,26 @@ 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 @@ -88,7 +89,7 @@ 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 @@ -96,20 +97,20 @@ 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 diff --git a/requirements.txt b/requirements.txt index 9656b819..576d16cc 100644 --- a/requirements.txt +++ b/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 @@ -45,7 +46,7 @@ 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 @@ -53,26 +54,26 @@ 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 @@ -88,7 +89,7 @@ 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 @@ -96,20 +97,20 @@ 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 diff --git a/setup.cfg b/setup.cfg index 2e1262fc..55689764 100644 --- a/setup.cfg +++ b/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 =