Bump dependencies for NumPy 2 compatibility

.github/workflows/docs.yml

@@ -0,0 +1,23 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  docs:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r docs/requirements.txt
+      - name: Build documentation
+        run: |
+          cd docs
+          make html

.github/workflows/run-tests.yml → .github/workflows/test.yml

@@ -1,7 +1,5 @@
-# Link repository with GitHub Actions
-# https://docs.github.com/en/actions/learn-github-actions/introduction-to-github-actions
+name: Test
 
-name: run-tests
 on:
   push:
     branches:
@@ -10,30 +8,45 @@ on:
     branches:
       - main
 
-# Set the language, install dependencies, and run the tests
+env:
+  UV_SYSTEM_PYTHON: 1
+  NPY_PROMOTION_STATE: weak_and_warn
+
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
+  test:
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        include:
+          - os: ubuntu-latest
+            python-version: "3.9"
+            numpy: "numpy==1.26.4"
+    runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
-      - name: Setup uv
-        uses: astral-sh/setup-uv@v3
-      - name: Install Python ${{ matrix.python-version }}
-        run: uv python install ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install -y libsndfile1
+      - name: Install dependencies
+        run: |
+          uv pip install ".[dev]" 
+      - if: ${{ matrix.numpy }}
+        run: uv pip install ${{ matrix.numpy }}
       - name: Run tests
-        run: uv run --extra dev pytest
-      - name: Check source code format
-        run: uv run --extra dev black --check --diff .
+        run: pytest
+      - name: Check style
+        run: black --check --diff .
 
   test-deb10-i386:
+    name: Python 3.7 on Debian 10 i386
     runs-on: ubuntu-latest
     container: i386/debian:10
     steps:
@@ -49,26 +62,11 @@ jobs:
                   python3-soundfile \
                   python3-pytest \
                   git
-
+          python3 --version
       # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
       # installed in the container.  To keep things simple, use
       # "actions/checkout@v1" instead.
       # https://github.com/actions/checkout/issues/334
       - uses: actions/checkout@v1
-
       - name: Run tests
-        run: |
-          pytest-3
-
-  build-documentation:
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r docs/requirements.txt
-      - name: Build documentation
-        run: |
-          cd docs
-          make html
+        run: pytest-3

.readthedocs.yml

@@ -5,7 +5,7 @@ version: 2
 build:
   os: "ubuntu-20.04"
   tools:
-    python: "3.9"
+    python: "3.10"
 
 # Build from the docs/ directory with Sphinx
 sphinx:

pyproject.toml

@@ -8,11 +8,11 @@ description = "The WFDB Python package: tools for reading, writing, and processi
 authors = [{name = "The Laboratory for Computational Physiology", email = "[email protected]"}]
 license = {text = "MIT License"}
 readme = "README.md"
-requires-python = ">= 3.8"
+requires-python = ">= 3.9"
 dependencies = [
-    "numpy >= 1.10.1, < 2.0.0",
-    "scipy >= 1.0.0",
-    "pandas >= 1.3.0",
+    "numpy >= 1.26.4",
+    "scipy >= 1.13.0",
+    "pandas >= 2.2.3",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",
     "requests >= 2.8.1",
@@ -35,7 +35,7 @@ documentation = "https://wfdb.readthedocs.io/"
 
 [tool.black]
 line-length = 80
-target-version = ['py37']
+target-version = ["py39"]
 
 [tool.hatch.build.targets.sdist]
 exclude = [

wfdb/io/convert/edf.py

@@ -399,7 +399,7 @@ def read_edf(
         }
 
     sig_data = np.empty((sig_len, n_sig))
-    temp_sig_data = np.fromfile(edf_file, dtype=np.int16)
+    temp_sig_data = np.fromfile(edf_file, dtype=np.int16).astype("int64")
     temp_sig_data = temp_sig_data.reshape((-1, sum(samps_per_block)))
     temp_all_sigs = np.hsplit(temp_sig_data, np.cumsum(samps_per_block)[:-1])
     for i in range(n_sig):

wfdb/processing/peaks.py

@@ -4,7 +4,7 @@
 
 
 def find_peaks(sig):
-    """
+    r"""
     Find hard peaks and soft peaks in a signal, defined as follows:
 
     - Hard peak: a peak that is either /\ or \/.