Updated dependencies and fixed tests

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ['3.9', '3.11']
+        python-version: ['3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v3

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "calidhayte"
 version = "2.0.0dev"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 description = "Calibrate raw measurements against reference measurements using one or more variables"
 authors = [
 	{name="Idris Hayward", email="[email protected]"}
@@ -72,12 +72,12 @@ no_implicit_reexport = true
 legacy_tox_ini = """
 	[tox]
 	minversion = 4.0
-	envlist = py39, py311, flake8, mypy
+	envlist = py310, py311, flake8, mypy
 	isolated_build = true
 
 	[gh-actions]
 	python =
-		3.9: py39
+		3.9: py310
 		3.11: py311, mypy, flake8
 
 	[testenv]

requirements.txt

@@ -1,64 +1,65 @@
 -i https://pypi.org/simple
-anyio==4.0.0; python_version >= '3.8'
+anyio==4.2.0; python_version >= '3.8'
 argon2-cffi==23.1.0; python_version >= '3.7'
 argon2-cffi-bindings==21.2.0; python_version >= '3.6'
 arrow==1.3.0; python_version >= '3.8'
 asttokens==2.4.1
 async-lru==2.0.4; python_version >= '3.8'
 attrs==23.1.0; python_version >= '3.7'
-babel==2.13.1; python_version >= '3.7'
+babel==2.14.0; python_version >= '3.7'
 beautifulsoup4==4.12.2; python_full_version >= '3.6.0'
+black==23.12.1; python_version >= '3.8'
 bleach==6.1.0; python_version >= '3.8'
 cachetools==5.3.2; python_version >= '3.7'
-certifi==2023.7.22; python_version >= '3.6'
+certifi==2023.11.17; python_version >= '3.6'
 cffi==1.16.0; python_version >= '3.8'
 chardet==5.2.0; python_version >= '3.7'
 charset-normalizer==3.3.2; python_full_version >= '3.7.0'
+click==8.1.7; python_version >= '3.7'
 colorama==0.4.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
-comm==0.1.4; python_version >= '3.6'
-coverage[toml]==7.3.2; python_version >= '3.8'
+comm==0.2.0; python_version >= '3.8'
+coverage[toml]==7.3.4; python_version >= '3.8'
 debugpy==1.8.0; python_version >= '3.8'
 decorator==5.1.1; python_version >= '3.5'
 defusedxml==0.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-distlib==0.3.7
+distlib==0.3.8
 executing==2.0.1; python_version >= '3.5'
-fastjsonschema==2.18.1
+fastjsonschema==2.19.0
 filelock==3.13.1; python_version >= '3.8'
 flake8==6.1.0; python_full_version >= '3.8.1'
 fqdn==1.5.1
-idna==3.4; python_version >= '3.5'
+idna==3.6; python_version >= '3.5'
 iniconfig==2.0.0; python_version >= '3.7'
-ipykernel==6.26.0; python_version >= '3.8'
-ipython==8.17.2; python_version >= '3.9'
-ipython-genutils==0.2.0
+ipykernel==6.27.1; python_version >= '3.8'
+ipython==8.19.0; python_version >= '3.10'
 ipywidgets==8.1.1; python_version >= '3.7'
 isoduration==20.11.0
 jedi==0.19.1; python_version >= '3.6'
 jinja2==3.1.2; python_version >= '3.7'
 json5==0.9.14
 jsonpointer==2.4
-jsonschema[format-nongpl]==4.19.2; python_version >= '3.8'
-jsonschema-specifications==2023.7.1; python_version >= '3.8'
+jsonschema[format-nongpl]==4.20.0; python_version >= '3.8'
+jsonschema-specifications==2023.11.2; python_version >= '3.8'
 jupyter==1.0.0
-jupyter-client==8.5.0; python_version >= '3.8'
+jupyter-client==8.6.0; python_version >= '3.8'
 jupyter-console==6.6.3; python_version >= '3.7'
-jupyter-core==5.5.0; python_version >= '3.8'
-jupyter-events==0.8.0; python_version >= '3.8'
-jupyter-lsp==2.2.0; python_version >= '3.8'
-jupyter-server==2.9.1; python_version >= '3.8'
-jupyter-server-terminals==0.4.4; python_version >= '3.8'
-jupyterlab==4.0.7; python_version >= '3.8'
-jupyterlab-pygments==0.2.2; python_version >= '3.7'
-jupyterlab-server==2.25.0; python_version >= '3.8'
+jupyter-core==5.5.1; python_version >= '3.8'
+jupyter-events==0.9.0; python_version >= '3.8'
+jupyter-lsp==2.2.1; python_version >= '3.8'
+jupyter-server==2.12.1; python_version >= '3.8'
+jupyter-server-terminals==0.5.0; python_version >= '3.8'
+jupyterlab==4.0.9; python_version >= '3.8'
+jupyterlab-pygments==0.3.0; python_version >= '3.8'
+jupyterlab-server==2.25.2; python_version >= '3.8'
 jupyterlab-widgets==3.0.9; python_version >= '3.7'
 markupsafe==2.1.3; python_version >= '3.7'
 matplotlib-inline==0.1.6; python_version >= '3.5'
 mccabe==0.7.0; python_version >= '3.6'
 mistune==3.0.2; python_version >= '3.7'
-mypy==1.6.1; python_version >= '3.8'
+mypy==1.8.0; python_version >= '3.8'
 mypy-extensions==1.0.0; python_version >= '3.5'
-nbclient==0.8.0; python_full_version >= '3.8.0'
-nbconvert==7.10.0; python_version >= '3.8'
+nbclient==0.9.0; python_full_version >= '3.8.0'
+nbconvert==7.13.1; python_version >= '3.8'
 nbformat==5.9.2; python_version >= '3.8'
 nest-asyncio==1.5.8; python_version >= '3.5'
 notebook==7.0.6; python_version >= '3.8'
@@ -67,93 +68,97 @@ overrides==7.4.0; python_version >= '3.6'
 packaging==23.2; python_version >= '3.7'
 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'
-pdoc==14.1.0; python_version >= '3.8'
-pexpect==4.8.0; sys_platform != 'win32'
-platformdirs==3.11.0; python_version >= '3.7'
+pathspec==0.12.1; python_version >= '3.8'
+pdoc==14.3.0; python_version >= '3.8'
+pexpect==4.9.0; sys_platform != 'win32'
+platformdirs==4.1.0; python_version >= '3.8'
 pluggy==1.3.0; python_version >= '3.8'
-prometheus-client==0.18.0; python_version >= '3.8'
-prompt-toolkit==3.0.39; python_full_version >= '3.7.0'
-psutil==5.9.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+prometheus-client==0.19.0; python_version >= '3.8'
+prompt-toolkit==3.0.43; python_full_version >= '3.7.0'
+psutil==5.9.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 ptyprocess==0.7.0
 pure-eval==0.2.2
 pycodestyle==2.11.1; python_version >= '3.8'
 pycparser==2.21
 pyflakes==3.1.0; python_version >= '3.8'
-pygments==2.16.1; python_version >= '3.7'
+pygments==2.17.2; python_version >= '3.7'
 pyproject-api==1.6.1; python_version >= '3.8'
 pytest==7.4.3; python_version >= '3.7'
 pytest-cov==4.1.0; python_version >= '3.7'
-pytest-html==4.0.2; python_version >= '3.8'
+pytest-html==4.1.1; python_version >= '3.8'
 pytest-metadata==3.0.0; 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'
 python-json-logger==2.0.7; python_version >= '3.6'
 pyyaml==6.0.1; python_version >= '3.6'
-pyzmq==25.1.1; python_version >= '3.6'
-qtconsole==5.4.4; python_version >= '3.7'
+pyzmq==25.1.2; python_version >= '3.6'
+qtconsole==5.5.1; python_version >= '3.8'
 qtpy==2.4.1; python_version >= '3.7'
-referencing==0.30.2; python_version >= '3.8'
+referencing==0.32.0; python_version >= '3.8'
 requests==2.31.0; python_version >= '3.7'
 rfc3339-validator==0.1.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 rfc3986-validator==0.1.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-rpds-py==0.10.6; python_version >= '3.8'
+rpds-py==0.15.2; python_version >= '3.8'
 send2trash==1.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 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'
 soupsieve==2.5; python_version >= '3.8'
 stack-data==0.6.3
-terminado==0.17.1; python_version >= '3.7'
+terminado==0.18.0; python_version >= '3.8'
 tinycss2==1.2.1; python_version >= '3.7'
-tornado==6.3.3; python_version >= '3.8'
-tox==4.11.3; python_version >= '3.8'
-traitlets==5.13.0; python_version >= '3.8'
+tornado==6.4; python_version >= '3.8'
+tox==4.11.4; python_version >= '3.8'
+traitlets==5.14.0; python_version >= '3.8'
 types-python-dateutil==2.8.19.14
-typing-extensions==4.8.0; python_version >= '3.8'
+typing-extensions==4.9.0; python_version >= '3.8'
 uri-template==1.3.0
-urllib3==2.0.7; python_version >= '3.7'
-virtualenv==20.24.6; python_version >= '3.7'
-wcwidth==0.2.9
+urllib3==2.1.0; python_version >= '3.8'
+virtualenv==20.25.0; python_version >= '3.7'
+wcwidth==0.2.12
 webcolors==1.13
 webencodings==0.5.1
-websocket-client==1.6.4; python_version >= '3.8'
+websocket-client==1.7.0; python_version >= '3.8'
 widgetsnbextension==4.0.9; python_version >= '3.7'
 arviz==0.16.1; python_version >= '3.9'
 bambi==0.13.0; python_version >= '3.8'
 -e .
 cloudpickle==3.0.0; python_version >= '3.8'
 cons==0.4.6; python_version >= '3.6'
-contourpy==1.1.1; python_version >= '3.8'
+contourpy==1.2.0; python_version >= '3.9'
 cycler==0.12.1; python_version >= '3.8'
 etuples==0.3.9; python_version >= '3.8'
 fastprogress==1.0.3; python_version >= '3.6'
-fonttools==4.43.1; python_version >= '3.8'
+fonttools==4.47.0; python_version >= '3.8'
 formulae==0.5.1; python_version >= '3.7'
 graphviz==0.20.1; python_version >= '3.7'
-h5netcdf==1.2.0; python_version >= '3.9'
+h5netcdf==1.3.0; python_version >= '3.9'
 h5py==3.10.0; python_version >= '3.8'
 joblib==1.3.2; python_version >= '3.7'
 kiwisolver==1.4.5; python_version >= '3.7'
 llvmlite==0.41.1; python_version >= '3.8'
 logical-unification==0.4.6; python_version >= '3.6'
-matplotlib==3.8.1; python_version >= '3.9'
+matplotlib==3.8.2; python_version >= '3.9'
 minikanren==1.0.3; python_version >= '3.6'
 multipledispatch==1.0.0
 numba==0.58.1; python_version >= '3.8'
-numpy==1.25.2; python_version >= '3.9'
-pandas==2.1.2; python_version >= '3.9'
+numpy==1.26.2; python_version >= '3.9'
+pandas==2.1.4; python_version >= '3.9'
 pillow==10.1.0; python_version >= '3.8'
-pymc==5.9.1; python_version >= '3.9'
+progressbar2==4.3.2; python_version >= '3.8'
+pygam==0.9.0; python_version < '3.12' and python_full_version >= '3.8.1'
+pymc==5.10.3; python_version >= '3.9'
 pyparsing==3.1.1; python_full_version >= '3.6.8'
-pytensor==2.17.3; python_version < '3.12' and python_version >= '3.9'
+pytensor==2.18.4; python_version < '3.12' and python_version >= '3.9'
+python-utils==3.8.1; python_version >= '3.9'
 pytz==2023.3.post1
 scikit-learn==1.3.2; python_version >= '3.8'
-scipy==1.11.3; python_version < '3.13' and python_version >= '3.9'
-setuptools==68.2.2; python_version >= '3.8'
-shap==0.43.0; python_version >= '3.8'
+scipy==1.11.4; python_version >= '3.9'
+setuptools==69.0.3; python_version >= '3.8'
+shap==0.44.0; python_version >= '3.8'
 slicer==0.0.7; python_version >= '3.6'
 threadpoolctl==3.2.0; python_version >= '3.8'
 toolz==0.12.0; python_version >= '3.5'
 tqdm==4.66.1; python_version >= '3.7'
 tzdata==2023.3; python_version >= '2'
-xarray==2023.10.1; python_version >= '3.9'
+xarray==2023.12.0; python_version >= '3.9'
 xarray-einstats==0.6.0; python_version >= '3.9'
-xgboost==2.0.1; python_version >= '3.8'
+xgboost==2.0.3; python_version >= '3.8'

src/calidhayte/calibrate.py

@@ -2260,10 +2260,7 @@ def linear_gam(
         random_search: bool = False,
         parameters: dict[
             str, Union[scipy.stats.rv_continuous, List[Union[int, str, float]]]
-        ] = {
-            "max_iter": [100, 500, 1000],
-            "callbacks": ['deviance', 'diffs']
-        },
+        ] = {"max_iter": [100, 500, 1000], "callbacks": ["deviance", "diffs"]},
         **kwargs,
     ):
         """
@@ -2309,8 +2306,8 @@ def expectile_gam(
             str, Union[scipy.stats.rv_continuous, List[Union[int, str, float]]]
         ] = {
             "max_iter": [100, 500, 1000],
-            "callbacks": ['deviance', 'diffs'],
-            "expectile": uniform(loc=0, scale=1)
+            "callbacks": ["deviance", "diffs"],
+            "expectile": uniform(loc=0, scale=1),
         },
         **kwargs,
     ):

src/calidhayte/results.py

@@ -463,7 +463,8 @@ def centered_rmse(self):
         """
         Calculate the centered root mean squared error between pred and true
 
-        $\\sqrt{\\frac{1}{N}\\sum_{n=1}^{N}[(p_n-\\bar{p}) - (t_n-\\bar{t})]^2}$
+        $\\sqrt{\\frac{1}{N}\\sum_{n=1}^{N}[(p_n-\\bar{p}) - \
+(t_n-\\bar{t})]^2}$
         """
         self._sklearn_error_meta(crmse, "Centered Root Mean Squared Error")
 

tests/test_results.py

@@ -67,7 +67,7 @@ def test_prepare_datasets(trained_models):
         Results.ref_mean,
         Results.ref_range,
         Results.ref_sd,
-        Results.unbiased_rmse
+        Results.unbiased_rmse,
     ]
     for err in errs:
         err(results)