Numpy 2 support

.circleci/config.yml

@@ -6,7 +6,7 @@ orbs:
 jobs:
   build:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.9
     steps:
       - checkout
       - run:
@@ -16,7 +16,7 @@ jobs:
             sudo apt-get install -y ninja-build libcunit1-dev valgrind clang doxygen python3-pip
             # Install meson as root so we can install to the system below.
             sudo pip install meson
-            pip install numpy==1.18.5
+            pip install numpy==1.23.5
             pip install --user -r python/requirements/development.txt
             echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
       - run:
@@ -72,17 +72,12 @@ jobs:
           command: |
             cd python
             rm -fR build
-            python setup.py sdist
             python -m venv venv
             source venv/bin/activate
             pip install --upgrade setuptools pip wheel numpy
             pip install build
             python -m build
-            python setup.py build_ext
-            python setup.py egg_info
-            python setup.py bdist_wheel
-            pip wheel dist/*.tar.gz
-            pip install dist/*.tar.gz
+            pip install dist/*.whl
       - run:
           name: Run Python with C coverage
           command: |

.github/workflows/tests.yml

@@ -21,13 +21,12 @@ jobs:
           pip install clang-format==6.0.1
       - uses: pre-commit/action@v3.0.0
 
-
   test:
     name: Python
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.8, 3.11 ]
+        python: [ 3.9, 3.12 ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
@@ -46,12 +45,47 @@ jobs:
           python-version: ${{matrix.python}}
 
       - name: Install pip deps
-        run: pip install -r python/requirements/CI/tests/requirements.txt
+        run: python -m pip install -r python/requirements/CI/tests/requirements.txt
 
       - name: Build module
         working-directory: python
         run: |
-          python setup.py build_ext --inplace
+          python -m pip install .
+
+      - name: Run tests
+        working-directory: python
+        run: |
+          python -m pytest tests
+
+  numpy-versions:
+    name: Numpy compat
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        numpy: [ 1.23.5, "2.0" ]
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.6.0
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install numpy
+        run: python -m pip install numpy==${{matrix.numpy}}
+
+      - name: Install package
+        working-directory: python
+        run: |
+          python -m pip install .
+
+      - name: Install pip deps
+        run: |
+            python -m pip install -r python/requirements/CI/tests/requirements.txt
+            # Make sure we're still using the same version of numpy
+            python -m pip install numpy==${{matrix.numpy}}
 
       - name: Run tests
         working-directory: python

.github/workflows/wheels.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", 3.11]
+        python: [3.9, "3.10", 3.11, 3.12]
         wordsize: [64]
     steps:
       - name: Checkout
@@ -58,7 +58,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", 3.11]
+        python: [3.9, "3.10", 3.11, 3.12]
     steps:
       - name: Checkout
         uses: actions/checkout@v2
@@ -93,10 +93,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Build sdist
         shell: bash
@@ -164,12 +164,12 @@ jobs:
           pip install -r python/requirements/CI/tests/requirements.txt
           python -m pytest -v python
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.12
 
-      - name: Run tests (3.8)
+      - name: Run tests (3.12)
         run: |
           python -VV
           # We install in this odd way to make sure we get both deps and a local kastore

.mergify.yml

@@ -4,12 +4,12 @@ queue_rules:
       - "#approved-reviews-by>=1"
       - "#changes-requested-reviews-by=0"
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.9, macos-latest)
+      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.9, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
+      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
 
 pull_request_rules:
@@ -21,12 +21,12 @@ pull_request_rules:
       - base=main
       - label=AUTOMERGE-REQUESTED
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.9, macos-latest)
+      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.9, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
+      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
     actions:
       queue:
@@ -41,4 +41,4 @@ pull_request_rules:
     actions:
       label:
         remove:
-          - AUTOMERGE-REQUESTED
+          - AUTOMERGE-REQUESTED

python/CHANGELOG.rst

@@ -1,8 +1,11 @@
 --------------------
-[0.3.X] - 202X-XX-XX
+[0.3.3] - 2024-06-20
 --------------------
 
-kastore now requires Python 3.8 or later.
+Maintenance release:
+
+- Support for numpy 1.x and 2.x
+- Require Python >= 3.9
 
 
 --------------------

python/pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 requires = [
+    "numpy>=2",
     "setuptools>=42",
     "wheel",
-    "oldest-supported-numpy"
 ]
-build-backend = "setuptools.build_meta"
+build-backend = "setuptools.build_meta"

python/setup.cfg

@@ -19,10 +19,10 @@ classifiers =
         Topic :: Scientific/Engineering :: Bio-Informatics
         License :: OSI Approved :: MIT License
         Programming Language :: Python :: 3
-        Programming Language :: Python :: 3.8
         Programming Language :: Python :: 3.9
         Programming Language :: Python :: 3.10
         Programming Language :: Python :: 3.11
+        Programming Language :: Python :: 3.12
         Programming Language :: Python :: 3 :: Only
 keywords =
     binary store
@@ -35,10 +35,11 @@ platforms =
 
 [options]
 packages = kastore
-python_requires = >=3.8
-include_package_data = True
+python_requires = >=3.9
+include_package_data = False
+# Follow https://numpy.org/doc/stable/dev/depending_on_numpy.html#numpy-2-abi-handling
 install_requires =
-    numpy>=1.7
+    numpy>=1.23.5
     humanize
 
 [options.entry_points]