build: update disease + ga4gh.vrsatile.pydantic version

Pipfile

@@ -23,8 +23,8 @@ wikibaseintegrator = ">=0.12.0"
 ipykernel = "*"
 bs4 = "*"
 pyyaml = "*"
-disease-normalizer = ">=0.2.13"
-"ga4gh.vrsatile.pydantic" = ">=0.1.dev2"
+disease-normalizer = ">=0.2.14"
+"ga4gh.vrsatile.pydantic" = ">=0.1.dev3"
 chembl-downloader = "*"
 bioversions = ">=0.4.3"
 pystow = "*"

requirements-dev.txt

@@ -10,14 +10,14 @@ backcall==0.2.0
 backoff==2.1.2; python_version >= '3.7' and python_version < '4'
 backports-datetime-fromisoformat==1.0.0
 beautifulsoup4==4.11.1; python_version >= '3.6'
-bioregistry[align]==0.5.80; python_version >= '3.6'
+bioregistry[align]==0.5.107; python_version >= '3.6'
 bioversions==0.5.79
 bleach==5.0.1; python_version >= '3.7'
-boto3==1.24.61
-botocore==1.27.61; python_version >= '3.7'
+boto3==1.24.79
+botocore==1.27.79; python_version >= '3.7'
 bs4==0.0.1
 cachier==1.5.4
-certifi==2022.6.15; python_version >= '3.6'
+certifi==2022.9.14; python_version >= '3.6'
 cffi==1.15.1
 cfgv==3.3.1; python_full_version >= '3.6.1'
 charset-normalizer==2.1.1; python_version >= '3.6'
@@ -27,49 +27,50 @@ class-resolver==0.3.10
 click==8.1.3
 click-default-group==1.2.2
 coverage[toml]==6.4.4; python_version >= '3.7'
+curies==0.3.0; python_version >= '3.7'
 cython==0.29.32
 dataclasses-json==0.5.7; python_version >= '3.6'
 debugpy==1.6.3; python_version >= '3.7'
 decorator==5.1.1; python_version >= '3.5'
 defusedxml==0.7.1
 deprecation==2.1.0
-disease-normalizer==0.2.13
+disease-normalizer==0.2.14
 distlib==0.3.6
 entrypoints==0.4; python_version >= '3.6'
 executing==1.0.0
-fastapi==0.81.0
-fastjsonschema==2.16.1
+fastapi==0.85.0
+fastjsonschema==2.16.2
 filelock==3.8.0; python_version >= '3.7'
 flake8==5.0.4
 flake8-annotations==2.9.1
 flake8-docstrings==1.6.0
 flake8-import-order==0.18.1
 flake8-quotes==3.3.1
-ga4gh.vrsatile.pydantic==0.1.dev2
+ga4gh.vrsatile.pydantic==0.1.dev3
 h11==0.13.0; python_version >= '3.6'
-httptools==0.4.0
-identify==2.5.3; python_version >= '3.7'
-idna==3.3; python_version >= '3.5'
+httptools==0.5.0
+identify==2.5.5; python_version >= '3.7'
+idna==3.4; python_version >= '3.5'
 importlib-metadata==4.12.0; python_version < '3.10'
 iniconfig==1.1.1
-ipykernel==6.15.1
-ipython==8.4.0; python_version >= '3.8'
+ipykernel==6.15.3
+ipython==8.5.0; python_version >= '3.8'
 ipython-genutils==0.2.0
 isodate==0.6.1
 jedi==0.18.1; python_version >= '3.6'
 jinja2==3.1.2; python_version >= '3.7'
 jmespath==1.0.1; python_version >= '3.7'
 json5==0.9.10
-jsonschema==4.14.0; python_version >= '3.7'
+jsonschema==4.16.0; python_version >= '3.7'
 jupyter-client==7.3.5; python_version >= '3.7'
 jupyter-core==4.11.1; python_version >= '3.7'
 jupyter-server==1.18.1; python_version >= '3.7'
-jupyterlab==3.4.5
+jupyterlab==3.4.7
 jupyterlab-pygments==0.2.2; python_version >= '3.7'
 jupyterlab-server==2.15.1; python_version >= '3.7'
 lxml==4.9.1
 markupsafe==2.1.1; python_version >= '3.7'
-marshmallow==3.17.1; python_version >= '3.7'
+marshmallow==3.18.0; python_version >= '3.7'
 marshmallow-enum==1.5.1
 matplotlib-inline==0.1.6; python_version >= '3.5'
 mccabe==0.7.0; python_version >= '3.6'
@@ -79,20 +80,20 @@ mwoauth==0.3.8
 mypy==0.971
 mypy-extensions==0.4.3
 nbclassic==0.4.3; python_version >= '3.7'
-nbclient==0.6.7; python_version >= '3.7'
+nbclient==0.6.8; python_version >= '3.7'
 nbconvert==7.0.0; python_version >= '3.7'
-nbformat==5.4.0; python_version >= '3.7'
+nbformat==5.6.0; python_version >= '3.7'
 nest-asyncio==1.5.5; python_version >= '3.5'
 networkx==2.8.6; python_version >= '3.8'
 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'
 notebook==6.4.12; python_version >= '3.7'
 notebook-shim==0.1.0; python_version >= '3.7'
-numpy==1.23.2; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
-oauthlib==3.2.0; python_version >= '3.6'
+numpy==1.23.3; python_version < '3.10'
+oauthlib==3.2.1; python_version >= '3.6'
 obonet==0.3.0; python_version >= '3.5'
 owlready2==0.38
 packaging==21.3; python_version >= '3.6'
-pandas==1.4.3; python_version >= '3.8'
+pandas==1.5.0; python_version >= '3.8'
 pandocfilters==1.5.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 parso==0.8.3; python_version >= '3.6'
 pathtools==0.1.2
@@ -103,28 +104,29 @@ pluggy==1.0.0; python_version >= '3.6'
 portalocker==2.5.1; python_version >= '3.5'
 pre-commit==2.20.0
 prometheus-client==0.14.1; python_version >= '3.6'
-prompt-toolkit==3.0.30; python_full_version >= '3.6.2'
-psutil==5.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+prompt-toolkit==3.0.31; python_full_version >= '3.6.2'
+psutil==5.9.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 pycodestyle==2.9.1; python_version >= '3.6'
 pycparser==2.21
-pydantic==1.9.2
+pydantic==1.10.2
 pydocstyle==6.1.1; python_version >= '3.6'
 pyflakes==2.5.0; python_version >= '3.6'
 pygments==2.13.0; python_version >= '3.6'
-pyjwt==2.4.0; python_version >= '3.6'
+pyjwt==2.5.0; python_version >= '3.7'
 pyparsing==2.4.7
 pyrsistent==0.18.1; python_version >= '3.7'
 pysam==0.19.1
 pystow==0.4.6
-pytest==7.1.2
+pytest==7.1.3
 pytest-cov==3.0.0
 python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pytrie==0.4.0
 pytz==2022.2.1
 pyyaml==6.0
-pyzmq==23.2.1; python_version >= '3.6'
+pyzmq==24.0.1; python_version >= '3.6'
 rdflib==6.2.0
 requests==2.28.1; python_version >= '3.7' and python_version < '4'
 requests-ftp==0.3.1
@@ -133,36 +135,37 @@ s3transfer==0.6.0; python_version >= '3.7'
 send2trash==1.8.0
 setuptools==65.3.0; 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==1.2.0; python_version >= '3.5'
+sniffio==1.3.0; python_version >= '3.7'
 snowballstemmer==2.2.0
+sortedcontainers==2.4.0
 soupsieve==2.3.2.post1; python_version >= '3.6'
 stack-data==0.5.0
-starlette==0.19.1; python_version >= '3.6'
+starlette==0.20.4; python_version >= '3.7'
 tabulate==0.8.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 terminado==0.15.0; python_version >= '3.7'
 -e .
 tinycss2==1.1.1; python_version >= '3.6'
 toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 tomli==2.0.1; python_version >= '3.7'
 tornado==6.2; python_version >= '3.7'
-tox==3.25.1
-tqdm==4.64.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.3.0; python_version >= '3.7'
+tox==3.26.0
+tqdm==4.64.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+traitlets==5.4.0; python_version >= '3.7'
 types-pyyaml==6.0.11
-types-requests==2.28.9
-types-urllib3==1.26.23
+types-requests==2.28.11
+types-urllib3==1.26.24
 typing-extensions==4.3.0
 typing-inspect==0.8.0
 ujson==5.4.0; python_version >= '3.7'
 urllib3==1.26.12
 uvicorn==0.18.3
-uvloop==0.16.0
+uvloop==0.17.0
 vcfpy==0.13.4
-virtualenv==20.16.3; python_version >= '3.6'
+virtualenv==20.16.5; python_version >= '3.6'
 watchdog==2.1.9; python_version >= '3.6'
 wcwidth==0.2.5
 webencodings==0.5.1
-websocket-client==1.4.0; python_version >= '3.7'
+websocket-client==1.4.1; python_version >= '3.7'
 websockets==10.3
-wikibaseintegrator==0.12.0
+wikibaseintegrator==0.12.1
 zipp==3.8.1; python_version >= '3.7'

requirements.txt

@@ -5,88 +5,91 @@ asttokens==2.0.8
 backcall==0.2.0
 backoff==2.1.2; python_version >= '3.7' and python_version < '4'
 beautifulsoup4==4.11.1; python_version >= '3.6'
-bioregistry[align]==0.5.80; python_version >= '3.6'
+bioregistry[align]==0.5.107; python_version >= '3.6'
 bioversions==0.5.79
-boto3==1.24.61
-botocore==1.27.61; python_version >= '3.7'
+boto3==1.24.79
+botocore==1.27.79; python_version >= '3.7'
 bs4==0.0.1
 cachier==1.5.4
-certifi==2022.6.15; python_version >= '3.6'
+certifi==2022.9.14; python_version >= '3.6'
 charset-normalizer==2.1.1; python_version >= '3.6'
 chembl-downloader==0.3.0
 class-resolver==0.3.10
 click==8.1.3
 click-default-group==1.2.2
+curies==0.3.0; python_version >= '3.7'
 cython==0.29.32
 dataclasses-json==0.5.7; python_version >= '3.6'
 debugpy==1.6.3; python_version >= '3.7'
 decorator==5.1.1; python_version >= '3.5'
 defusedxml==0.7.1
-disease-normalizer==0.2.13
+disease-normalizer==0.2.14
 entrypoints==0.4; python_version >= '3.6'
 executing==1.0.0
-fastapi==0.81.0
-ga4gh.vrsatile.pydantic==0.1.dev2
+fastapi==0.85.0
+ga4gh.vrsatile.pydantic==0.1.dev3
 h11==0.13.0; python_version >= '3.6'
-httptools==0.4.0
-idna==3.3; python_version >= '3.5'
-ipykernel==6.15.1
-ipython==8.4.0; python_version >= '3.8'
+httptools==0.5.0
+idna==3.4; python_version >= '3.5'
+ipykernel==6.15.3
+ipython==8.5.0; python_version >= '3.8'
 isodate==0.6.1
 jedi==0.18.1; python_version >= '3.6'
 jmespath==1.0.1; python_version >= '3.7'
 jupyter-client==7.3.5; python_version >= '3.7'
 jupyter-core==4.11.1; python_version >= '3.7'
 lxml==4.9.1
-marshmallow==3.17.1; python_version >= '3.7'
+marshmallow==3.18.0; python_version >= '3.7'
 marshmallow-enum==1.5.1
 matplotlib-inline==0.1.6; python_version >= '3.5'
 more-click==0.1.1; python_version >= '3.7'
 mwoauth==0.3.8
 mypy-extensions==0.4.3
 nest-asyncio==1.5.5; python_version >= '3.5'
-oauthlib==3.2.0; python_version >= '3.6'
+oauthlib==3.2.1; python_version >= '3.6'
 owlready2==0.38
 packaging==21.3; python_version >= '3.6'
 parso==0.8.3; python_version >= '3.6'
 pathtools==0.1.2
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
 portalocker==2.5.1; python_version >= '3.5'
-prompt-toolkit==3.0.30; python_full_version >= '3.6.2'
-psutil==5.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+prompt-toolkit==3.0.31; python_full_version >= '3.6.2'
+psutil==5.9.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 ptyprocess==0.7.0
 pure-eval==0.2.2
-pydantic==1.9.2
+pydantic==1.10.2
 pygments==2.13.0; python_version >= '3.6'
-pyjwt==2.4.0; python_version >= '3.6'
+pyjwt==2.5.0; python_version >= '3.7'
 pyparsing==2.4.7
 pystow==0.4.6
 python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+pytrie==0.4.0
 pyyaml==6.0
-pyzmq==23.2.1; python_version >= '3.6'
+pyzmq==24.0.1; python_version >= '3.6'
 rdflib==6.2.0
 requests==2.28.1; python_version >= '3.7' and python_version < '4'
 requests-ftp==0.3.1
 requests-oauthlib==1.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 s3transfer==0.6.0; python_version >= '3.7'
 setuptools==65.3.0; 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==1.2.0; python_version >= '3.5'
+sniffio==1.3.0; python_version >= '3.7'
+sortedcontainers==2.4.0
 soupsieve==2.3.2.post1; python_version >= '3.6'
 stack-data==0.5.0
-starlette==0.19.1; python_version >= '3.6'
+starlette==0.20.4; python_version >= '3.7'
 tabulate==0.8.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 tornado==6.2; python_version >= '3.7'
-tqdm==4.64.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.3.0; python_version >= '3.7'
+tqdm==4.64.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+traitlets==5.4.0; python_version >= '3.7'
 typing-extensions==4.3.0
 typing-inspect==0.8.0
 ujson==5.4.0; python_version >= '3.7'
 urllib3==1.26.12
 uvicorn==0.18.3
-uvloop==0.16.0
+uvloop==0.17.0
 watchdog==2.1.9; python_version >= '3.6'
 wcwidth==0.2.5
 websockets==10.3
-wikibaseintegrator==0.12.0
+wikibaseintegrator==0.12.1

setup.cfg

@@ -34,8 +34,8 @@ install_requires =
     chembl-downloader
     pystow
     bioversions >= 0.4.3
-    disease-normalizer >= 0.2.13
-    ga4gh.vrsatile.pydantic >= 0.1.dev2
+    disease-normalizer >= 0.2.14
+    ga4gh.vrsatile.pydantic >= 0.1.dev3
 
 [options.extras_require]
 test =

therapy/version.py

@@ -1,2 +1,2 @@
 """Therapy normalizer version"""
-__version__ = "0.3.7"
+__version__ = "0.3.8"