Merge pull request #15 from glotzerlab/numpy2

Add numpy 2 support

.github/workflows/requirements-test.txt

@@ -0,0 +1,11 @@
+hypothesis == 6.103.2
+pytest == 8.2.2
+bottleneck == 1.4
+freud-analysis == 3.1
+kneed == 0.8.5
+numpy == 2.0
+ruptures == 1.1.9
+scikit-learn == 1.5
+pandas == 2.2.2
+numba == 0.60
+xarray == 2024.6

.github/workflows/run-pytest.yml

@@ -16,25 +16,19 @@ concurrency:
   cancel-in-progress: true
 jobs:
   test:
-    name: test (${{ matrix.os }}, ${{ matrix.python }}, ${{ matrix.dependencies }})
+    name: test (${{ matrix.os }}, ${{ matrix.python }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: true
       matrix:
         os: [ubuntu-latest]
         python: ['3.9', '3.10', '3.11', '3.12']
         include:
-          # Defaults to newest dependencies
-          - dependencies: 'newest'
           # Other tests
-          - python: '3.9'
-            dependencies: 'oldest'
           - os: 'macos-latest'
             python: '3.9'
-            dependencies: 'oldest'
           - os: 'macos-latest'
             python: '3.12'
-            dependencies: 'newest'
     steps:
     - uses: actions/checkout@v4
       with:
@@ -46,26 +40,12 @@ jobs:
     - name: Update pip/build packages
       run: |
         pip install setuptools --upgrade
-    - name: Install newest dependencies
+    - name: Install dependencies
       run: |
-        pip install -r requirements/requirements-test.txt
-        pip install -r requirements/requirements-data.txt
-      if: ${{ matrix.dependencies == 'newest' }}
-    - name: Install oldest dependencies
-      run: |
-        pip install -r .github/workflows/ci-oldest-reqs.txt
-        pip install -r requirements/requirements-data.txt
-      if: ${{ matrix.dependencies == 'oldest' }}
-    - name: Install numba (if available)
-      run: |
-        pip install -r requirements/requirements-jit.txt
-      if: ${{ matrix.python != '3.12' }}
+        pip install -r .github/workflows/requirements-test.txt
     - name: Install the package
       run: |
         pip install -e .
     - name: Test with pytest
       run: |
-        pytest --cov=dupin --cov-config=pyproject.toml --cov-report=xml tests -v
-    - uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
+        python -m pytest -v

pyproject.toml

@@ -20,15 +20,12 @@ classifiers = [
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
     ]
-dependencies = [
-    "bottleneck",  # perform moving window array computations
-    "freud-analysis",  # generate features
-    "kneed",  # knee/elbow detection
-    "numpy",  # basic numerical Python
-    "pandas", # Handling DataFrames in functions and signal aggregation.
-    "ruptures",  # event detection
-    "scikit-learn",  # For ML window dimensionality reduction
-]
+
+[tool.setuptools.dynamic]
+dependencies = { file = ["requirements/requirements.txt"] }
+optional-dependencies = { testing = { file = [
+    "requirements/requirements-testing.txt",
+] } }
 
 [project.urls]
 Source = "https://github.com/glotzerlab/dupin"
@@ -71,10 +68,6 @@ select = [
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.coverage.run]
-branch = true
-source = [ "dupin" ]
-
 [tool.pytest.ini_options]
 minversion = "6.0"
 filterwarnings = [

requirements/requirements-testing.txt

@@ -0,0 +1,2 @@
+pytest>6.2.1
+hypothesis>6.30.0

requirements/requirements.txt

@@ -0,0 +1,7 @@
+bottleneck>=1.3.4
+freud-analysis>=2.7.0
+kneed>=0.8.2
+numpy>=1.21
+ruptures>=1.1.5
+scikit-learn>=0.24.0
+pandas>=1.1.3