From 66e4f83cbe02938525f9cc3a242f7fcf522f7dfa Mon Sep 17 00:00:00 2001 From: CaderIdris <61825162+Joppleganger@users.noreply.github.com> Date: Sun, 24 Dec 2023 15:49:48 +0000 Subject: [PATCH] Updated dependencies and fixed tests --- .github/workflows/tests.yml | 2 +- pyproject.toml | 6 +- requirements.txt | 123 +++++++++++++++++++----------------- src/calidhayte/calibrate.py | 9 +-- src/calidhayte/results.py | 3 +- tests/test_results.py | 2 +- 6 files changed, 74 insertions(+), 71 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6cb7a02..930746d 100644 --- a/.github/workflows/tests.yml +++ b/.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 diff --git a/pyproject.toml b/pyproject.toml index 689e787..740cf8c 100644 --- a/pyproject.toml +++ b/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="CaderIdrisGH@outlook.com"} @@ -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] diff --git a/requirements.txt b/requirements.txt index e3d0b0e..8019585 100644 --- a/requirements.txt +++ b/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' diff --git a/src/calidhayte/calibrate.py b/src/calidhayte/calibrate.py index a07d535..29d8063 100644 --- a/src/calidhayte/calibrate.py +++ b/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, ): diff --git a/src/calidhayte/results.py b/src/calidhayte/results.py index f876b8e..d456222 100644 --- a/src/calidhayte/results.py +++ b/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") diff --git a/tests/test_results.py b/tests/test_results.py index 6c2e14e..cb0bcad 100644 --- a/tests/test_results.py +++ b/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)