From 103aadbccadc703eb5e7494108a920a1a2c7b45e Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Thu, 7 Jul 2022 14:14:30 -0400 Subject: [PATCH] build: fix python3.10 dependency conflict (#279) --- Pipfile | 2 +- requirements-dev.txt | 99 +++++++++++++++++++++----------------------- requirements.txt | 52 +++++++++++------------ setup.cfg | 3 +- therapy/version.py | 2 +- tox.ini | 3 +- 6 files changed, 80 insertions(+), 81 deletions(-) diff --git a/Pipfile b/Pipfile index 9b6e7c71..031c7a45 100644 --- a/Pipfile +++ b/Pipfile @@ -19,7 +19,7 @@ uvloop = "*" websockets = ">=9.1" httptools = "*" typing-extensions = "*" -wikibaseintegrator = "==0.11.0" +wikibaseintegrator = ">=0.11.2" ipykernel = "*" bs4 = "*" pyyaml = "*" diff --git a/requirements-dev.txt b/requirements-dev.txt index d0799d71..3e9bac25 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,20 +1,20 @@ -i https://pypi.org/simple anyio==3.6.1 appnope==0.1.3 -asgiref==3.5.2 asttokens==2.0.5 backcall==0.2.0 -backoff==2.0.1 +backoff==1.11.1 beautifulsoup4==4.11.1 -bioregistry[align]==0.5.6 -bioversions==0.5.2 -boto3==1.23.7 -botocore==1.26.7 +bioregistry[align]==0.5.34 +bioversions==0.5.38 +boto3==1.24.22 +botocore==1.27.22 bs4==0.0.1 cachier==1.5.4 -certifi==2022.5.18.1 +certifi==2022.6.15 charset-normalizer==2.0.12 chembl-downloader==0.3.0 +class-resolver==0.3.10 click==8.1.3 click-default-group==1.2.2 cython==0.29.30 @@ -30,15 +30,15 @@ ga4gh.vrsatile.pydantic==0.0.11 h11==0.13.0 httptools==0.4.0 idna==3.3 -ipykernel==6.13.0 -ipython==8.3.0 +ipykernel==6.15.0 +ipython==8.4.0 isodate==0.6.1 jedi==0.18.1 -jmespath==1.0.0 -jupyter-client==7.3.1 +jmespath==1.0.1 +jupyter-client==7.3.4 jupyter-core==4.10.0 -lxml==4.8.0 -marshmallow==3.15.0 +lxml==4.9.1 +marshmallow==3.17.0 marshmallow-enum==1.5.1 matplotlib-inline==0.1.3 more-click==0.1.1 @@ -46,14 +46,14 @@ mwoauth==0.3.8 mypy-extensions==0.4.3 nest-asyncio==1.5.5 oauthlib==3.2.0 -owlready2==0.37 +owlready2==0.38 packaging==21.3 parso==0.8.3 pathtools==0.1.2 pexpect==4.8.0 pickleshare==0.7.5 portalocker==2.4.0 -prompt-toolkit==3.0.29 +prompt-toolkit==3.0.30 psutil==5.9.1 ptyprocess==0.7.0 pure-eval==0.2.2 @@ -61,80 +61,78 @@ pydantic==1.9.1 pygments==2.12.0 pyjwt==2.4.0 pyparsing==2.4.7 -pystow==0.4.3 +pystow==0.4.5 python-dateutil==2.8.2 pyyaml==6.0 -pyzmq==23.0.0 +pyzmq==23.2.0 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 +s3transfer==0.6.0 +setuptools==62.6.0 simplejson==3.17.6 six==1.16.0 sniffio==1.2.0 soupsieve==2.3.2.post1 -stack-data==0.2.0 +stack-data==0.3.0 starlette==0.19.1 -tabulate==0.8.9 +tabulate==0.8.10 tornado==6.1 tqdm==4.64.0 -traitlets==5.2.1.post0 -typing-extensions==4.2.0 +traitlets==5.3.0 +typing-extensions==4.3.0 typing-inspect==0.7.1 urllib3==1.26.9 -uvicorn==0.17.6 +uvicorn==0.18.2 uvloop==0.16.0 -watchdog==2.1.8 +watchdog==2.1.9 wcwidth==0.2.5 websockets==10.3 -wikibaseintegrator==0.11.0 +wikibaseintegrator==0.11.2 argon2-cffi==21.3.0 argon2-cffi-bindings==21.2.0 attrs==21.4.0 -babel==2.10.1 +babel==2.10.3 backports-datetime-fromisoformat==1.0.0 -bleach==5.0.0 -cffi==1.15.0 +bleach==5.0.1 +cffi==1.15.1 cfgv==3.3.1 civicpy==1.1.3 -coverage[toml]==6.4 +coverage[toml]==6.4.1 deprecation==2.1.0 distlib==0.3.4 fastjsonschema==2.15.3 -filelock==3.7.0 +filelock==3.7.1 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 +jsonschema==4.6.1 +jupyter-server==1.18.0 +jupyterlab==3.4.3 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 +mypy==0.961 +nbclassic==0.4.0 +nbclient==0.6.6 nbconvert==6.5.0 nbformat==5.4.0 -networkx==2.8.2 -nodeenv==1.6.0 -notebook==6.4.11 +networkx==2.8.4 +nodeenv==1.7.0 notebook-shim==0.1.0 -numpy==1.22.4 +numpy==1.23.0 obonet==0.3.0 -pandas==1.4.2 +pandas==1.4.3 pandocfilters==1.5.0 platformdirs==2.5.2 pluggy==1.0.0 @@ -146,7 +144,7 @@ pycparser==2.21 pydocstyle==6.1.1 pyflakes==2.4.0 pyrsistent==0.18.1 -pysam==0.19.0 +pysam==0.19.1 pytest==7.1.2 pytest-cov==3.0.0 pytz==2022.1 @@ -157,12 +155,11 @@ terminado==0.15.0 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 +tox==3.25.1 +types-pyyaml==6.0.9 +types-requests==2.28.0 +types-urllib3==1.26.15 vcfpy==0.13.4 -virtualenv==20.14.1 +virtualenv==20.15.1 webencodings==0.5.1 -websocket-client==1.3.2 -zipp==3.8.0 +websocket-client==1.3.3 diff --git a/requirements.txt b/requirements.txt index b4a328a6..b782d78c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,20 +1,20 @@ -i https://pypi.org/simple anyio==3.6.1 appnope==0.1.3 -asgiref==3.5.2 asttokens==2.0.5 backcall==0.2.0 -backoff==2.0.1 +backoff==1.11.1 beautifulsoup4==4.11.1 -bioregistry[align]==0.5.6 -bioversions==0.5.2 -boto3==1.23.7 -botocore==1.26.7 +bioregistry[align]==0.5.34 +bioversions==0.5.38 +boto3==1.24.22 +botocore==1.27.22 bs4==0.0.1 cachier==1.5.4 -certifi==2022.5.18.1 +certifi==2022.6.15 charset-normalizer==2.0.12 chembl-downloader==0.3.0 +class-resolver==0.3.10 click==8.1.3 click-default-group==1.2.2 cython==0.29.30 @@ -30,15 +30,15 @@ ga4gh.vrsatile.pydantic==0.0.11 h11==0.13.0 httptools==0.4.0 idna==3.3 -ipykernel==6.13.0 -ipython==8.3.0 +ipykernel==6.15.0 +ipython==8.4.0 isodate==0.6.1 jedi==0.18.1 -jmespath==1.0.0 -jupyter-client==7.3.1 +jmespath==1.0.1 +jupyter-client==7.3.4 jupyter-core==4.10.0 -lxml==4.8.0 -marshmallow==3.15.0 +lxml==4.9.1 +marshmallow==3.17.0 marshmallow-enum==1.5.1 matplotlib-inline==0.1.3 more-click==0.1.1 @@ -46,14 +46,14 @@ mwoauth==0.3.8 mypy-extensions==0.4.3 nest-asyncio==1.5.5 oauthlib==3.2.0 -owlready2==0.37 +owlready2==0.38 packaging==21.3 parso==0.8.3 pathtools==0.1.2 pexpect==4.8.0 pickleshare==0.7.5 portalocker==2.4.0 -prompt-toolkit==3.0.29 +prompt-toolkit==3.0.30 psutil==5.9.1 ptyprocess==0.7.0 pure-eval==0.2.2 @@ -61,32 +61,32 @@ pydantic==1.9.1 pygments==2.12.0 pyjwt==2.4.0 pyparsing==2.4.7 -pystow==0.4.3 +pystow==0.4.5 python-dateutil==2.8.2 pyyaml==6.0 -pyzmq==23.0.0 +pyzmq==23.2.0 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 +s3transfer==0.6.0 +setuptools==62.6.0 simplejson==3.17.6 six==1.16.0 sniffio==1.2.0 soupsieve==2.3.2.post1 -stack-data==0.2.0 +stack-data==0.3.0 starlette==0.19.1 -tabulate==0.8.9 +tabulate==0.8.10 tornado==6.1 tqdm==4.64.0 -traitlets==5.2.1.post0 -typing-extensions==4.2.0 +traitlets==5.3.0 +typing-extensions==4.3.0 typing-inspect==0.7.1 urllib3==1.26.9 -uvicorn==0.17.6 +uvicorn==0.18.2 uvloop==0.16.0 -watchdog==2.1.8 +watchdog==2.1.9 wcwidth==0.2.5 websockets==10.3 -wikibaseintegrator==0.11.0 +wikibaseintegrator==0.11.2 diff --git a/setup.cfg b/setup.cfg index e2e6023e..af68b30c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -27,7 +27,7 @@ install_requires = owlready2 pyparsing == 2.4.7 rdflib - wikibaseintegrator == 0.11.0 + wikibaseintegrator >= 0.11.2 bs4 pyyaml pydantic >=1.8.2 @@ -44,6 +44,7 @@ test = pytest-cov dev = + pre-commit tox flake8 flake8-docstrings diff --git a/therapy/version.py b/therapy/version.py index c5802fdd..5e46b7da 100644 --- a/therapy/version.py +++ b/therapy/version.py @@ -1,2 +1,2 @@ """Therapy normalizer version""" -__version__ = "0.3.5" +__version__ = "0.3.6" diff --git a/tox.ini b/tox.ini index 0f0ef939..a43aee01 100644 --- a/tox.ini +++ b/tox.ini @@ -1,7 +1,7 @@ [tox] isolated_build = True envlist = - {py38,py39}-{test,lint,mypy} + {py38,py39,py310}-{test,lint,mypy} skipsdist = False [testenv] @@ -28,6 +28,7 @@ description="GitHub Actions-specific testing environment" deps = pytest pytest-cov + -rrequirements.txt setenv = PY_IGNORE_IMPORTMISMATCH=1 TEST=TRUE