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build: update ga4gh packages to use VRS 1.3 models (#189)
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- ga4gh.vrsatile.pydantic ~= 0.0.12
- ga4gh.vrs ~= 0.8.1
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@korikuzma
korikuzma authored Apr 21, 2023
1 parent bc0cf73 commit e845f7e
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Showing 5 changed files with 133 additions and 138 deletions.
4 changes: 2 additions & 2 deletions Pipfile
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Expand Up @@ -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 = "."}
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2 changes: 1 addition & 1 deletion gene/version.py
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@@ -1,2 +1,2 @@
"""Gene normalizer version"""
__version__ = "0.1.34"
__version__ = "0.1.35"
199 changes: 98 additions & 101 deletions requirements-dev.txt
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@@ -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'
62 changes: 30 additions & 32 deletions requirements.txt
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@@ -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'
4 changes: 2 additions & 2 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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