Add Python 3.14 support, bump deps, upgrade GitHub Actions (#171)

* Add Python 3.14 support, make it the default CI version

Bump requires-python upper bound from <3.14 to <3.15 and update CI
matrix to test on 3.12 (smoke) + 3.14 (full).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Add Python 3.14 support, bump deps, upgrade GitHub Actions

- Bump requires-python from <3.14 to <3.15
- Update CI matrix: 3.12 (smoke) + 3.14 (full) across all workflows
- Widen dependency upper bounds:
  - pandas: <3.0.0 → <4.0.0
  - plotly: <6.0.0 → <7.0.0
  - scipy: <1.17.0 → <2.0.0
  - pytest: <9.0.0 → <10.0.0
  - pytest-cov: <7.0.0 → <8.0.0
- Upgrade GitHub Actions:
  - checkout v3 → v4
  - setup-python v4 → v5
  - codecov-action v3 → v5

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: MaxGhenis

.github/workflows/pr_code_changes.yaml

@@ -7,11 +7,11 @@ jobs:
   Lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.13"
+          python-version: "3.14"
       - name: Install uv
         uses: astral-sh/setup-uv@v5
       - name: Install relevant dependencies
@@ -25,7 +25,7 @@ jobs:
     outputs:
       mdn_changed: ${{ steps.check.outputs.mdn_changed }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Check for MDN-related file changes
@@ -50,63 +50,63 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: ["3.12", "3.13"]
+        python-version: ["3.12", "3.14"]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Install uv
         uses: astral-sh/setup-uv@v5
       - 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 slim version
         run: |
           uv pip install -e "." --system
-      - name: Install R and dependencies (Python 3.13 only)
-        if: matrix.python-version == '3.13'
+      - name: Install R and dependencies (Python 3.14 only)
+        if: matrix.python-version == '3.14'
         run: |
           sudo apt-get update
           sudo apt-get install -y r-base r-base-dev libtirpc-dev
-      - name: Install R packages (Python 3.13 only)
-        if: matrix.python-version == '3.13'
+      - name: Install R packages (Python 3.14 only)
+        if: matrix.python-version == '3.14'
         run: |
           sudo Rscript -e 'install.packages("StatMatch", repos="https://cloud.r-project.org")'
           sudo Rscript -e 'install.packages("clue", repos="https://cloud.r-project.org")'
-      - name: Install full test dependencies without MDN (Python 3.13)
-        if: matrix.python-version == '3.13' && needs.Check-MDN-Changes.outputs.mdn_changed != 'true'
+      - name: Install full test dependencies without MDN (Python 3.14)
+        if: matrix.python-version == '3.14' && needs.Check-MDN-Changes.outputs.mdn_changed != 'true'
         run: |
           uv pip install -e ".[dev,matching]" --system
-      - name: Install full test dependencies with MDN (Python 3.13)
-        if: matrix.python-version == '3.13' && needs.Check-MDN-Changes.outputs.mdn_changed == 'true'
+      - name: Install full test dependencies with MDN (Python 3.14)
+        if: matrix.python-version == '3.14' && needs.Check-MDN-Changes.outputs.mdn_changed == 'true'
         run: |
           uv pip install -e ".[dev,matching,mdn]" --system
       - name: Install minimal test dependencies (Python 3.12)
         if: matrix.python-version == '3.12'
         run: |
           uv pip install -e ".[dev]" --system
-      - name: Run full tests with coverage (Python 3.13)
-        if: matrix.python-version == '3.13'
+      - name: Run full tests with coverage (Python 3.14)
+        if: matrix.python-version == '3.14'
         run: make test
       - name: Run smoke test only (Python 3.12)
         if: matrix.python-version == '3.12'
         run: |
           python -m pytest tests/test_smoke_qrf.py -v
           python -m pytest tests/test_basic.py -v
       - name: Run pipeline example
-        if: matrix.python-version == '3.13'
+        if: matrix.python-version == '3.14'
         run: |
           python examples/pipeline.py
       - name: Upload microimputation results
-        if: always() && matrix.python-version == '3.13'
+        if: always() && matrix.python-version == '3.14'
         uses: actions/upload-artifact@v4
         with:
           name: microimputation-results-${{ github.sha }}
           path: microimputation-dashboard/public/microimputation_results.csv
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
           file: ./coverage.xml
           fail_ci_if_error: false

.github/workflows/pr_docs_changes.yaml

@@ -24,7 +24,7 @@ jobs:
           - name: Set up Python
             uses: actions/setup-python@v5
             with:
-                python-version: '3.13'
+                python-version: '3.14'
 
           - name: Install R and dependencies
             run: |

.github/workflows/versioning.yaml

@@ -24,7 +24,7 @@ jobs:
             - name: Setup Python
               uses: actions/setup-python@v5
               with:
-                python-version: 3.13
+                python-version: 3.14
             - name: Bump version and build changelog
               run: |
                 pip install towncrier
@@ -41,7 +41,7 @@ jobs:
       runs-on: ubuntu-latest
       strategy:
         matrix:
-          python-version: ["3.13"]
+          python-version: ["3.14"]
       steps:
         - name: Checkout code
           uses: actions/checkout@v4

changelog.d/python-3.14.changed.md

@@ -0,0 +1 @@
+Added Python 3.14 support, bumped dependency upper bounds (pandas, plotly, scipy, pytest, pytest-cov), and upgraded GitHub Actions versions.

pyproject.toml

@@ -14,13 +14,13 @@ authors = [
     { name = "María Juaristi", email = "juaristi@uni.minerva.edu" },
     { name = "Nikhil Woodruff", email = "nikhil.woodruff@outlook.com" }
 ]
-requires-python = ">=3.12,<3.14"
+requires-python = ">=3.12,<3.15"
 dependencies = [
     "numpy>=2.0.0,<3.0.0",
-    "pandas>=2.2.0,<3.0.0",
-    "plotly>=5.24.0,<6.0.0",
+    "pandas>=2.2.0,<4.0.0",
+    "plotly>=5.24.0,<7.0.0",
     "scikit-learn>=1.7.0,<2.0.0",
-    "scipy>=1.16.0,<1.17.0",
+    "scipy>=1.16.0,<2.0.0",
     "requests>=2.32.0,<3.0.0",
     "tqdm>=4.65.0,<5.0.0",
     "statsmodels>=0.14.5,<0.16.0",
@@ -33,8 +33,8 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    "pytest>=8.0.0,<9.0.0",
-    "pytest-cov>=6.0.0,<7.0.0",
+    "pytest>=8.0.0,<10.0.0",
+    "pytest-cov>=6.0.0,<8.0.0",
     "ruff>=0.9.0",
     "mypy>=1.2.3,<2.0.0",
     "build>=1.2.0,<2.0.0",
@@ -54,7 +54,7 @@ docs = [
     "jupyter-book",
     "furo>=2024.0.0",  # Sphinx theme for documentation
     "ipywidgets>=8.0.0,<9.0.0",
-    "plotly>=5.24.0,<6.0.0",
+    "plotly>=5.24.0,<7.0.0",
     "h5py>=3.1.0,<4.0.0",
 ]