build: fix python3.10 dependency conflict (#279)

Pipfile

@@ -19,7 +19,7 @@ uvloop = "*"
 websockets = ">=9.1"
 httptools = "*"
 typing-extensions = "*"
-wikibaseintegrator = "==0.11.0"
+wikibaseintegrator = ">=0.11.2"
 ipykernel = "*"
 bs4 = "*"
 pyyaml = "*"

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
@@ -30,111 +30,109 @@ 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
 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
 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

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
@@ -30,63 +30,63 @@ 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
 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
 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

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

therapy/version.py

@@ -1,2 +1,2 @@
 """Therapy normalizer version"""
-__version__ = "0.3.5"
+__version__ = "0.3.6"

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