Add support for Python 3.13

.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
+

.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

.tox/py310/.tox-info.json

@@ -12,7 +12,7 @@
       0
     ],
     "executable": "/opt/homebrew/Cellar/[email protected]/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": {

README.md

@@ -22,18 +22,13 @@ 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
 
 ```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()

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
 

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

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "dcurves"
-version = "1.1.1"
-description = "A Python package for Decision Curve Analysis to evaluate prediction 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 <[email protected]>", "rohansingh <[email protected]>"]
 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 = '''
 /(

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,
     )
 

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

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,

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"]:

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