Merge branch 'gpimm/numpy_2.0' into 'master'

update to numpy 2.0 See merge request minknow/pod5-file-format!347
nanoporetech · Jun 20, 2024 · 66b792a · 66b792a
2 parents dcb2c42 + ddfa729
commit 66b792a
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## Added
 
 - Typechecking on `Writer.add_reads` to inform users incorrectly passing `ReadRecords`
+- Compatibility with numpy 2.0.
 
 ## Fixed
 

diff --git a/c++/pod5_format_pybind/api.h b/c++/pod5_format_pybind/api.h
@@ -65,7 +65,8 @@ class Pod5SignalCacheBatch {
             return py_samples;
         }
         for (auto const & row_samples : m_cached_data.samples()) {
-            py_samples.append(py::array_t<std::int16_t>(row_samples.size(), row_samples.data()));
+            py_samples.append(py::array_t<std::int16_t>(
+                {row_samples.size()}, {sizeof(std::int16_t)}, row_samples.data()));
         }
 
         return py_samples;

diff --git a/python/pod5/pyproject.toml b/python/pod5/pyproject.toml
@@ -28,11 +28,12 @@ dependencies = [
     "more_itertools",
     "numpy >= 1.21.0",
     'typing-extensions; python_version<"3.8"',
-    "pyarrow ~= 14.0.0",
+    "pyarrow ~= 16.1.0",
     "pytz",
     "packaging",
     "polars~=0.19",
-    "h5py~=3.10.0",
+    'h5py~=3.11.0; python_version>"3.8"',
+    'h5py~=3.10.0; python_version<="3.8"',
     "vbz_h5py_plugin",
     "tqdm"
 ]