Merge pull request #283 from jeromekelleher/numpy2

Unpin numpy

Author: tomwhite

.github/workflows/ci.yml

@@ -109,3 +109,26 @@ jobs:
           vcfpartition --help
           python -m bio2zarr vcfpartition --help
 
+  test-numpy-version:
+    name: Test numpy versions
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        numpy: ["==1.26", ">=2"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+      - name: Install numpy${{ matrix.numpy }}
+        run: |
+          python -m pip install 'numpy${{ matrix.numpy }}'
+      - name: Run tests
+        run: |
+          # We just run the CLI tests here because it doesn't require other upstream
+          # packages like sgkit (which are tangled up with the numpy 2 dependency)
+          python -m pytest tests/test_cli.py

CHANGELOG.md

@@ -1,3 +1,10 @@
+# 0.1.2 2024-XX-XX
+
+Breaking changes
+
+- ICF metadata format version bumped to ensure long-term compatility between numpy 1.26.x
+  and numpy >= 2. Existing ICFs will need to be recreated.
+
 # 0.1.1 2024-06-19
 
 Maintenance release:

bio2zarr/vcf2zarr/icf.py

@@ -110,7 +110,7 @@ class VcfPartition:
     num_records: int = -1
 
 
-ICF_METADATA_FORMAT_VERSION = "0.3"
+ICF_METADATA_FORMAT_VERSION = "0.4"
 ICF_DEFAULT_COMPRESSOR = numcodecs.Blosc(
     cname="zstd", clevel=7, shuffle=numcodecs.Blosc.NOSHUFFLE
 )

pyproject.toml

@@ -11,7 +11,9 @@ authors = [
   {name = "sgkit Developers", email = "[email protected]"},
 ]
 dependencies = [
-  "numpy < 2",
+  # Pin numpy to >= 1.26 because this enables ICF files to be supported
+  # across numpy 1 and 2 (due to pickle format)
+  "numpy >= 1.26",
   "zarr >= 2.17,< 3",
   "click",
   "tabulate",