From 0b872afc92423a155f74e5137580f36a4bcb8873 Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 23 Oct 2024 12:08:32 +0100
Subject: [PATCH 1/2] Unpin numpy and bump ICF metadata version

Closes #258
---
 CHANGELOG.md             | 7 +++++++
 bio2zarr/vcf2zarr/icf.py | 2 +-
 pyproject.toml           | 4 +++-
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 99b3b38..ecabe9b 100644
--- a/CHANGELOG.md
+++ b/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:
diff --git a/bio2zarr/vcf2zarr/icf.py b/bio2zarr/vcf2zarr/icf.py
index 7646826..1295209 100644
--- a/bio2zarr/vcf2zarr/icf.py
+++ b/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
 )
diff --git a/pyproject.toml b/pyproject.toml
index 42f976d..d911bcd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,9 @@ authors = [
   {name = "sgkit Developers", email = "project@sgkit.dev"},
 ]
 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",

From 4dd205e06ebe53634b7442fdec0aab1e3a70f013 Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 23 Oct 2024 12:40:35 +0100
Subject: [PATCH 2/2] Run tests on numpy 1 and numpy 2

Closes #256
---
 .github/workflows/ci.yml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5060aa3..deeebf5 100644
--- a/.github/workflows/ci.yml
+++ b/.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