diff --git a/Pipfile b/Pipfile index 498dbee5..88784494 100644 --- a/Pipfile +++ b/Pipfile @@ -9,8 +9,8 @@ fastapi = "*" uvicorn = "*" click = "*" boto3 = "*" -"ga4gh.vrsatile.pydantic" = "~=0.0.11" -"ga4gh.vrs" = "~=0.7.8" +"ga4gh.vrsatile.pydantic" = "~=0.0.12" +"ga4gh.vrs" = "~=0.8.1" [dev-packages] gene = {editable = true, path = "."} diff --git a/gene/version.py b/gene/version.py index 7766a73f..2a405ac5 100644 --- a/gene/version.py +++ b/gene/version.py @@ -1,2 +1,2 @@ """Gene normalizer version""" -__version__ = "0.1.34" +__version__ = "0.1.35" diff --git a/requirements-dev.txt b/requirements-dev.txt index 4fe1bd0a..15a61118 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,133 +1,130 @@ -i https://pypi.org/simple -alabaster==0.7.13; python_version >= '3.6' -anyio==3.6.2; python_full_version >= '3.6.2' +alabaster==0.7.13 ; python_version >= '3.6' +anyio==3.6.2 ; python_full_version >= '3.6.2' appdirs==1.4.4 -appnope==0.1.3; platform_system == 'Darwin' -argcomplete==3.0.5; python_version >= '3.6' -argh==0.28.1; python_version >= '3.8' +appnope==0.1.3 ; platform_system == 'Darwin' +argcomplete==3.0.5 ; python_version >= '3.6' +argh==0.28.1 ; python_version >= '3.8' asttokens==2.2.1 -attrs==22.2.0; python_version >= '3.6' -babel==2.12.1; python_version >= '3.7' +attrs==23.1.0 ; python_version >= '3.7' +babel==2.12.1 ; python_version >= '3.7' backcall==0.2.0 -beautifulsoup4==4.12.0; python_version >= '3.6' +beautifulsoup4==4.12.2 ; python_full_version >= '3.6.0' biocommons.seqrepo==0.6.5 -bioutils==0.5.7; python_version >= '3.6' -boto3==1.26.104 -botocore==1.29.104; python_version >= '3.7' +bioutils==0.5.7 ; python_version >= '3.6' +boto3==1.26.117 +botocore==1.29.117 ; python_version >= '3.7' bs4==0.0.1 -canonicaljson==2.0.0; python_version >= '3.7' -certifi==2022.12.7; python_version >= '3.6' -cfgv==3.3.1; python_full_version >= '3.6.1' -charset-normalizer==3.1.0; python_version >= '3.7' +canonicaljson==2.0.0 ; python_version >= '3.7' +certifi==2022.12.7 ; python_version >= '3.6' +cfgv==3.3.1 ; python_full_version >= '3.6.1' +charset-normalizer==3.1.0 ; python_full_version >= '3.7.0' click==8.1.3 -coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -comm==0.1.3; python_version >= '3.6' -coverage[toml]==7.2.2; python_version >= '3.7' -cssselect==1.2.0; python_version >= '3.7' -debugpy==1.6.6; python_version >= '3.7' -decorator==5.1.1; python_version >= '3.5' +coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' +comm==0.1.3 ; python_version >= '3.6' +coverage[toml]==7.2.3 ; python_version >= '3.7' +cssselect==1.2.0 ; python_version >= '3.7' +cython==0.29.34 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2' +debugpy==1.6.7 ; python_version >= '3.7' +decorator==5.1.1 ; python_version >= '3.5' distlib==0.3.6 -docutils==0.19; python_version >= '3.7' -exceptiongroup==1.1.1; python_version < '3.11' +docutils==0.19 ; python_version >= '3.7' executing==1.2.0 fake-useragent==1.1.3 -fastapi==0.95.0 -filelock==3.10.7; python_version >= '3.7' +fastapi==0.95.1 +filelock==3.12.0 ; python_version >= '3.7' flake8==6.0.0 flake8-docstrings==1.7.0 -ga4gh.vrs==0.7.8 -ga4gh.vrsatile.pydantic==0.0.11 --e . --e . +ga4gh.vrs==0.8.1 +ga4gh.vrsatile.pydantic==0.0.12 gffutils==0.11.1 -h11==0.14.0; python_version >= '3.7' -humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -identify==2.5.22; python_version >= '3.7' -idna==3.4; python_version >= '3.5' -imagesize==1.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' -importlib-metadata==6.1.0; python_version < '3.10' -importlib-resources==5.12.0; python_version < '3.10' -inflection==0.5.1; python_version >= '3.5' -iniconfig==2.0.0; python_version >= '3.7' +h11==0.14.0 ; python_version >= '3.7' +humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' +identify==2.5.22 ; python_version >= '3.7' +idna==3.4 ; python_version >= '3.5' +imagesize==1.4.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' +importlib-metadata==6.5.0 ; python_version >= '3.7' +inflection==0.5.1 ; python_version >= '3.5' +iniconfig==2.0.0 ; python_version >= '3.7' ipykernel==6.22.0 -ipython==8.12.0; python_version >= '3.8' -jedi==0.18.2; python_version >= '3.6' -jinja2==3.1.2; python_version >= '3.7' -jmespath==1.0.1; python_version >= '3.7' +ipython==8.12.0 ; python_version >= '3.8' +jedi==0.18.2 ; python_version >= '3.6' +jinja2==3.1.2 ; python_version >= '3.7' +jmespath==1.0.1 ; python_version >= '3.7' jsonschema==3.2.0 -jupyter-client==8.1.0; python_version >= '3.8' -jupyter-core==5.3.0; python_version >= '3.8' -lxml==4.9.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -markdown==3.4.3; python_version >= '3.7' -markupsafe==2.1.2; python_version >= '3.7' -matplotlib-inline==0.1.6; python_version >= '3.5' -mccabe==0.7.0; python_version >= '3.6' -mock==5.0.1 -nest-asyncio==1.5.6; python_version >= '3.5' -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' -numpy==1.24.2; python_version >= '3.8' -packaging==23.0; python_version >= '3.7' +jupyter-client==8.2.0 ; python_version >= '3.8' +jupyter-core==5.3.0 ; python_version >= '3.8' +lxml==4.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' +markdown==3.4.3 ; python_version >= '3.7' +markupsafe==2.1.2 ; python_version >= '3.7' +matplotlib-inline==0.1.6 ; python_version >= '3.5' +mccabe==0.7.0 ; python_version >= '3.6' +mock==5.0.2 +nest-asyncio==1.5.6 ; python_version >= '3.5' +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' +numpy==1.24.2 ; python_version >= '3.8' +packaging==23.1 ; python_version >= '3.7' parse==1.19.0 -parso==0.8.3; python_version >= '3.6' -pexpect==4.8.0; sys_platform != 'win32' +parso==0.8.3 ; python_version >= '3.6' +pexpect==4.8.0 ; sys_platform != 'win32' pickleshare==0.7.5 -platformdirs==3.2.0; python_version >= '3.7' -pluggy==1.0.0; python_version >= '3.6' -pre-commit==3.2.1 -prompt-toolkit==3.0.38; python_version >= '3.7' -psutil==5.9.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' +platformdirs==3.2.0 ; python_version >= '3.7' +pluggy==1.0.0 ; python_version >= '3.6' +pre-commit==3.2.2 +prompt-toolkit==3.0.38 ; python_full_version >= '3.7.0' +psutil==5.9.5 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' psycopg[binary]==3.1.8 psycopg-binary==3.1.8 ptyprocess==0.7.0 pure-eval==0.2.2 -pycodestyle==2.10.0; python_version >= '3.6' +pycodestyle==2.10.0 ; python_version >= '3.6' pydantic==1.10.7 -pydocstyle==6.3.0; python_version >= '3.6' +pydocstyle==6.3.0 ; python_version >= '3.6' pyee==8.2.2 -pyfaidx==0.7.2.1; python_version >= '3.7' -pyflakes==3.0.1; python_version >= '3.6' -pygments==2.14.0; python_version >= '3.6' -pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0' +pyfaidx==0.7.2.1 ; python_version >= '3.7' +pyflakes==3.0.1 ; python_version >= '3.6' +pygments==2.15.1 ; python_version >= '3.7' +pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0' pyquery==2.0.0 -pyrsistent==0.19.3; python_version >= '3.7' -pysam==0.20.0 -pytest==7.2.2 +pyrsistent==0.19.3 ; python_version >= '3.7' +pysam==0.21.0 ; python_version >= '3.6' +pytest==7.3.1 pytest-cov==4.0.0 -python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' +python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2' python-jsonschema-objects==0.4.1 -pyyaml==6.0; python_version >= '3.6' -pyzmq==25.0.2; python_version >= '3.6' -requests==2.28.2; python_version >= '3.7' and python_version < '4' -requests-html==0.10.0; python_version >= '3.6' -s3transfer==0.6.0; python_version >= '3.7' -setuptools==67.6.1; python_version >= '3.7' -simplejson==3.18.4; 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==1.3.0; python_version >= '3.7' +pyyaml==6.0 ; python_version >= '3.6' +pyzmq==25.0.2 ; python_version >= '3.6' +requests==2.28.2 ; python_version >= '3.7' and python_version < '4' +requests-html==0.10.0 ; python_full_version >= '3.6.0' +s3transfer==0.6.0 ; python_version >= '3.7' +setuptools==67.7.0 ; python_version >= '3.7' +simplejson==3.19.1 ; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2' +six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2' +sniffio==1.3.0 ; python_version >= '3.7' snowballstemmer==2.2.0 -soupsieve==2.4; python_version >= '3.7' +soupsieve==2.4.1 ; python_version >= '3.7' sphinx==6.1.3 -sphinx-autodoc-typehints==1.22 -sphinxcontrib-applehelp==1.0.4; python_version >= '3.8' -sphinxcontrib-devhelp==1.0.2; python_version >= '3.5' -sphinxcontrib-htmlhelp==2.0.1; python_version >= '3.8' -sphinxcontrib-jsmath==1.0.1; python_version >= '3.5' -sphinxcontrib-qthelp==1.0.3; python_version >= '3.5' -sphinxcontrib-serializinghtml==1.1.5; python_version >= '3.5' -sqlparse==0.4.3; python_version >= '3.5' +sphinx-autodoc-typehints==1.23.0 +sphinxcontrib-applehelp==1.0.4 ; python_version >= '3.8' +sphinxcontrib-devhelp==1.0.2 ; python_version >= '3.5' +sphinxcontrib-htmlhelp==2.0.1 ; python_version >= '3.8' +sphinxcontrib-jsmath==1.0.1 ; python_version >= '3.5' +sphinxcontrib-qthelp==1.0.3 ; python_version >= '3.5' +sphinxcontrib-serializinghtml==1.1.5 ; python_version >= '3.5' +sqlparse==0.4.4 ; python_version >= '3.5' stack-data==0.6.2 -starlette==0.26.1; python_version >= '3.7' -tabulate==0.9.0; python_version >= '3.7' -tomli==2.0.1; python_version < '3.11' -tornado==6.2; python_version >= '3.7' -tqdm==4.65.0; python_version >= '3.7' -traitlets==5.9.0; python_version >= '3.7' -typing-extensions==4.5.0; python_version >= '3.7' -urllib3==1.26.15; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' +starlette==0.26.1 ; python_version >= '3.7' +tabulate==0.9.0 ; python_version >= '3.7' +tornado==6.3 ; python_version >= '3.8' +tqdm==4.65.0 ; python_version >= '3.7' +traitlets==5.9.0 ; python_version >= '3.7' +typing-extensions==4.5.0 ; python_version >= '3.7' +urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' uvicorn==0.21.1 -virtualenv==20.21.0; python_version >= '3.7' -w3lib==2.1.1; python_version >= '3.7' +virtualenv==20.22.0 ; python_version >= '3.7' +w3lib==2.1.1 ; python_version >= '3.7' wcwidth==0.2.6 -websockets==10.4; python_version >= '3.7' +websockets==10.4 ; python_version >= '3.7' +-e . yoyo-migrations==8.2.0 -zipp==3.15.0; python_version >= '3.7' +zipp==3.15.0 ; python_version >= '3.7' diff --git a/requirements.txt b/requirements.txt index 1696b0b9..668fc359 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,38 +1,36 @@ -i https://pypi.org/simple -anyio==3.6.2; python_full_version >= '3.6.2' -attrs==22.2.0; python_version >= '3.6' -bioutils==0.5.7; python_version >= '3.6' -boto3==1.26.104 -botocore==1.29.104; python_version >= '3.7' -canonicaljson==2.0.0; python_version >= '3.7' -certifi==2022.12.7; python_version >= '3.6' -charset-normalizer==3.1.0; python_version >= '3.7' +anyio==3.6.2 ; python_full_version >= '3.6.2' +attrs==23.1.0 ; python_version >= '3.7' +bioutils==0.5.7 ; python_version >= '3.6' +boto3==1.26.117 +botocore==1.29.117 ; python_version >= '3.7' +canonicaljson==2.0.0 ; python_version >= '3.7' +certifi==2022.12.7 ; python_version >= '3.6' +charset-normalizer==3.1.0 ; python_full_version >= '3.7.0' click==8.1.3 -coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -fastapi==0.95.0 -ga4gh.vrs==0.7.8 -ga4gh.vrsatile.pydantic==0.0.11 -h11==0.14.0; python_version >= '3.7' -humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -idna==3.4; python_version >= '3.5' -importlib-metadata==6.1.0; python_version < '3.10' -inflection==0.5.1; python_version >= '3.5' -jmespath==1.0.1; 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' +fastapi==0.95.1 +ga4gh.vrs==0.8.1 +ga4gh.vrsatile.pydantic==0.0.12 +h11==0.14.0 ; python_version >= '3.7' +humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' +idna==3.4 ; python_version >= '3.5' +inflection==0.5.1 ; python_version >= '3.5' +jmespath==1.0.1 ; python_version >= '3.7' jsonschema==3.2.0 -markdown==3.4.3; python_version >= '3.7' -numpy==1.24.2; python_version >= '3.8' +markdown==3.4.3 ; python_version >= '3.7' +numpy==1.24.2 ; python_version >= '3.8' pydantic==1.10.7 -pyrsistent==0.19.3; python_version >= '3.7' -python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' +pyrsistent==0.19.3 ; python_version >= '3.7' +python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2' python-jsonschema-objects==0.4.1 -pyyaml==6.0; python_version >= '3.6' -requests==2.28.2; python_version >= '3.7' and python_version < '4' -s3transfer==0.6.0; python_version >= '3.7' -setuptools==67.6.1; 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==1.3.0; python_version >= '3.7' -starlette==0.26.1; python_version >= '3.7' -typing-extensions==4.5.0; python_version >= '3.7' -urllib3==1.26.15; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' +pyyaml==6.0 ; python_version >= '3.6' +requests==2.28.2 ; python_version >= '3.7' and python_version < '4' +s3transfer==0.6.0 ; python_version >= '3.7' +setuptools==67.7.0 ; python_version >= '3.7' +six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2' +sniffio==1.3.0 ; python_version >= '3.7' +starlette==0.26.1 ; python_version >= '3.7' +typing-extensions==4.5.0 ; python_version >= '3.7' +urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' uvicorn==0.21.1 -zipp==3.15.0; python_version >= '3.7' diff --git a/setup.cfg b/setup.cfg index 552954b1..9bdb4c9d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -29,8 +29,8 @@ install_requires = uvicorn click boto3 - ga4gh.vrsatile.pydantic ~= 0.0.11 - ga4gh.vrs ~= 0.7.8 + ga4gh.vrsatile.pydantic ~= 0.0.12 + ga4gh.vrs ~= 0.8.1 tests_require = pytest