diff --git a/.coverage b/.coverage index e24a580..95ad7d6 100644 Binary files a/.coverage and b/.coverage differ diff --git a/.github/workflows/241215_old_github_actions b/.github/workflows/241215_old_github_actions new file mode 100644 index 0000000..b270bc1 --- /dev/null +++ b/.github/workflows/241215_old_github_actions @@ -0,0 +1,29 @@ +name: dcurves + +on: [push, pull_request] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + curl -sSL https://install.python-poetry.org | python - + poetry install + - name: Lint with pylint + run: | + poetry run pylint --fail-under 5 dcurves/*.py + - name: Test with pytest + run: | + poetry run pytest --cov=dcurves --cov-report html + diff --git a/.github/workflows/github-actions.yaml b/.github/workflows/github-actions.yaml index 7d61ff4..c8488e3 100644 --- a/.github/workflows/github-actions.yaml +++ b/.github/workflows/github-actions.yaml @@ -4,26 +4,32 @@ on: [push, pull_request] jobs: build: - runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install dependencies + - name: Install system dependencies + run: | + sudo apt-get update + sudo apt-get install -y libopenblas-dev liblapack-dev gfortran + - name: Install Poetry run: | python -m pip install --upgrade pip curl -sSL https://install.python-poetry.org | python - - poetry install + poetry --version + - name: Install dependencies + run: | + poetry config virtualenvs.create true + poetry install - name: Lint with pylint run: | poetry run pylint --fail-under 5 dcurves/*.py - name: Test with pytest run: | - poetry run pytest --cov=dcurves --cov-report html - + poetry run pytest --cov=dcurves --cov-report html \ No newline at end of file diff --git a/.tox/py310/.tox-info.json b/.tox/py310/.tox-info.json index 3608785..e40e388 100644 --- a/.tox/py310/.tox-info.json +++ b/.tox/py310/.tox-info.json @@ -12,7 +12,7 @@ 0 ], "executable": "/opt/homebrew/Cellar/python@3.10/3.10.14_1/Frameworks/Python.framework/Versions/3.10/bin/python3.10", - "virtualenv version": "20.27.1" + "virtualenv version": "20.19.0" }, "PythonRun": { "deps": { diff --git a/README.md b/README.md index e11e6b6..c4ced62 100755 --- a/README.md +++ b/README.md @@ -22,9 +22,6 @@ This tutorial will guide you through installing and using the `dcurves` package ```bash # Install dcurves for DCA pip install dcurves - -# Install other required packages -pip install pandas numpy statsmodels lifelines ``` ### DCA Example @@ -32,8 +29,6 @@ pip install pandas numpy statsmodels lifelines ```python # Import Libraries from dcurves import dca, plot_graphs, load_test_data -import pandas as pd -import numpy as np # Load Package Simulation Data df_binary = load_test_data.load_binary_df() diff --git a/dcurves/risks.py b/dcurves/risks.py index 1e92d9a..39ff5d9 100644 --- a/dcurves/risks.py +++ b/dcurves/risks.py @@ -7,7 +7,6 @@ import sys from typing import Optional, Union import pandas as pd -import numpy as np import statsmodels.api as sm import lifelines diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index f2f15cb..c5f14ae 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -4,6 +4,21 @@ All notable changes to this project are documented here. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [1.1.2] - 2024-12-15 + +### Added +- Support for Python 3.13. +- Compatibility updates for Black formatting tool. + +### Changed +- Updated project configuration to include Python 3.13 testing environment. +- Removed unnecessary dependencies and imports. +- Fixed broken link in project description. + +### Fixed +- Resolved configuration issues for Python 3.13 compatibility. +- Updated tox configuration and project dependencies. + ## [1.1.1] - 2024-10-25 ### Added diff --git a/docs/NEWS.md b/docs/NEWS.md deleted file mode 100644 index e69de29..0000000 diff --git a/poetry.lock b/poetry.lock index b9b7fc9..9d3d268 100644 --- a/poetry.lock +++ b/poetry.lock @@ -31,24 +31,24 @@ docs = ["sphinx (==7.2.6)", "sphinx-mdinclude (==0.5.3)"] [[package]] name = "anyio" -version = "4.6.2.post1" +version = "4.7.0" description = 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models, molecular markers, and diagnostic tests. For RELEASE NOTES, check RELEASE.md here: https://github.com/MSKCC-Epi-Bio/dcurves/RELEASE.md" +version = "1.1.2" +description = "A Python package for Decision Curve Analysis to evaluate prediction models, molecular markers, and diagnostic tests. For RELEASE NOTES, check: https://github.com/MSKCC-Epi-Bio/dcurves/blob/main/docs/CHANGELOG.md" authors = ["shaunporwal ", "rohansingh "] readme = "README.md" @@ -12,17 +12,14 @@ matplotlib = "^3.7.1" pandas = ">=1.5.3,<3.0.0" statsmodels = "0.14.4" typing = "~3.7.4.3" -mkdocs = "^1.4.2" -mkdocstrings = {extras = ["python"], version = "^0.20.0"} -mkdocs-material = "^9.0.14" -setuptools = "^68.1.2" +setuptools = "^75.6.0" [tool.poetry.group.dev.dependencies] pytest = "~7.2.1" jupyterlab = "~3.6.1" tox = "^4.4.6" pytest-cov = "^4.0.0" -black = "^23.1.0" +black = "^24.10.0" pylint = "^3.3.1" pytest-mock = "^3.11.1" tomli = "^2.0.1" @@ -50,7 +47,7 @@ filterwarnings = [ [tool.black] line-length = 100 -target-version = ['py39', 'py310', 'py311', 'py312'] +target-version = ['py39', 'py310', 'py311', 'py312', 'py313'] include = '\.pyi?$' extend-exclude = ''' /( diff --git a/tests/test_dca_tutorial.py b/tests/test_dca_tutorial.py index 970b616..dd1e196 100644 --- a/tests/test_dca_tutorial.py +++ b/tests/test_dca_tutorial.py @@ -131,10 +131,12 @@ def test_python_joint(): ) df_cancer_dx["conditional"] = df_cancer_dx.apply( - lambda x: 1 - if x["risk_group"] == "high" - or (x["risk_group"] == "intermediate" and x["cancerpredmarker"] > 0.15) - else 0, + lambda x: ( + 1 + if x["risk_group"] == "high" + or (x["risk_group"] == "intermediate" and x["cancerpredmarker"] > 0.15) + else 0 + ), axis=1, ) @@ -153,10 +155,12 @@ def test_python_dca_joint(): ) df_cancer_dx["conditional"] = df_cancer_dx.apply( - lambda x: 1 - if x["risk_group"] == "high" - or (x["risk_group"] == "intermediate" and x["cancerpredmarker"] > 0.15) - else 0, + lambda x: ( + 1 + if x["risk_group"] == "high" + or (x["risk_group"] == "intermediate" and x["cancerpredmarker"] > 0.15) + else 0 + ), axis=1, ) diff --git a/tests/test_optional_gridlines.py b/tests/test_optional_gridlines.py index 6358bf1..c8d6bf1 100644 --- a/tests/test_optional_gridlines.py +++ b/tests/test_optional_gridlines.py @@ -1,6 +1,7 @@ """ This module contains tests for optional gridlines in plot functions. """ + import pytest import pandas as pd from dcurves.plot_graphs import _plot_net_benefit, _plot_net_intervention_avoided diff --git a/tests/test_plotting.py b/tests/test_plotting.py index 189705c..ee528f3 100644 --- a/tests/test_plotting.py +++ b/tests/test_plotting.py @@ -196,8 +196,9 @@ def test_plot_net_benefit_mismatched_color_names(): def test_plot_net_benefit_grid_enabled(): """Test plot net benefit with grid enabled.""" plt.ioff() # Turn off interactive mode - with patch("matplotlib.pyplot.grid") as mock_grid, patch( - "matplotlib.pyplot.show" + with ( + patch("matplotlib.pyplot.grid") as mock_grid, + patch("matplotlib.pyplot.show"), ): # Mock plt.show() to prevent plot display _plot_net_benefit( SAMPLE_DATA_DF, @@ -211,8 +212,9 @@ def test_plot_net_benefit_grid_enabled(): def test_plot_net_benefit_show_legend_enabled(): """Test plot net benefit with legend enabled.""" plt.ioff() # Turn off interactive mode - with patch("matplotlib.pyplot.legend") as mock_legend, patch( - "matplotlib.pyplot.show" + with ( + patch("matplotlib.pyplot.legend") as mock_legend, + patch("matplotlib.pyplot.show"), ): # Mock plt.show() to prevent plot display _plot_net_benefit( SAMPLE_DATA_DF, @@ -226,8 +228,9 @@ def test_plot_net_benefit_show_legend_enabled(): def test_plot_net_benefit_show_legend_disabled(): """Test plot net benefit with legend disabled.""" plt.ioff() # Turn off interactive mode - with patch("matplotlib.pyplot.legend") as mock_legend, patch( - "matplotlib.pyplot.show" + with ( + patch("matplotlib.pyplot.legend") as mock_legend, + patch("matplotlib.pyplot.show"), ): # Mock plt.show() to prevent plot display _plot_net_benefit( SAMPLE_DATA_DF, @@ -241,8 +244,9 @@ def test_plot_net_benefit_show_legend_disabled(): def test_plot_net_intervention_avoided_show_legend_enabled(): """Test plot net intervention avoided with legend enabled.""" plt.ioff() # Turn off interactive mode - with patch("matplotlib.pyplot.legend") as mock_legend, patch( - "matplotlib.pyplot.show" + with ( + patch("matplotlib.pyplot.legend") as mock_legend, + patch("matplotlib.pyplot.show"), ): # Mock plt.show() to prevent plot display _plot_net_intervention_avoided( SAMPLE_DATA_DF, @@ -256,8 +260,9 @@ def test_plot_net_intervention_avoided_show_legend_enabled(): def test_plot_net_intervention_avoided_show_legend_disabled(): """Test plot net intervention avoided with legend disabled.""" plt.ioff() # Turn off interactive mode - with patch("matplotlib.pyplot.legend") as mock_legend, patch( - "matplotlib.pyplot.show" + with ( + patch("matplotlib.pyplot.legend") as mock_legend, + patch("matplotlib.pyplot.show"), ): # Mock plt.show() to prevent plot display _plot_net_intervention_avoided( SAMPLE_DATA_DF, diff --git a/tests/test_surv_consequences.py b/tests/test_surv_consequences.py index c408710..fc182f4 100644 --- a/tests/test_surv_consequences.py +++ b/tests/test_surv_consequences.py @@ -93,9 +93,9 @@ def calculate_risk_rate_for_model(model): r_benchmark_results["risk_rate_among_test_pos"] = ( r_benchmark_results.tp_rate / r_benchmark_results.test_pos_rate ) - r_benchmark_results.loc[ - r_benchmark_results.variable == "none", "risk_rate_among_test_pos" - ] = float(0) + r_benchmark_results.loc[r_benchmark_results.variable == "none", "risk_rate_among_test_pos"] = ( + float(0) + ) # Validate results against benchmarks for model in ["all", "none", "cancerpredmarker"]: diff --git a/tox.ini b/tox.ini index ba76914..ac01512 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,6 @@ [tox] isolated_build = True -envlist = py{39,310,311,312}, lint +envlist = py{39,310,311,312,313}, lint [testenv] allowlist_externals = poetry