Update for NumPy 2.0 and Python 3.13 (#328)

Author: stefanv

.github/workflows/tests.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/setup-python@v1
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - uses: actions/cache@v2
         with:
@@ -33,9 +33,8 @@ jobs:
       - name: Install dependencies & configure cesium
         run: |
           pip install --upgrade pip
-          pip install wheel numpy requests six python-dateutil pytest pytest-cov mock coverage
+          pip install wheel setuptools_scm numpy cython requests six python-dateutil pytest pytest-cov mock coverage
           make install
-          pip install cython==0.29.23
           python setup.py build_ext -i
           pip install -e .
 

.github/workflows/wheel_tests_and_release.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        cibw_python: ["cp38-*", "cp39-*", "cp310-*", "cp311-*"]
+        cibw_python: ["cp310-*", "cp311-*", "cp312-*"]
         cibw_manylinux: [manylinux2014]
         cibw_arch: ["x86_64"]
     steps:

cesium/featurize.py

@@ -452,8 +452,8 @@ def save_featureset(fset, path, **kwargs):
             kwargs[k] = []
 
     # Bypass savez to allow for `allow_pickle` keyword
-    # See https://github.com/numpy/numpy/pull/5770
-    np.lib.npyio._savez(path, [], kwargs, compress=True, allow_pickle=False)
+    # See also https://github.com/numpy/numpy/pull/27335
+    np.lib._npyio_impl._savez(path, [], kwargs, compress=True, allow_pickle=False)
 
 
 def load_featureset(path):

cesium/time_series.py

@@ -76,7 +76,7 @@ def _make_array_if_possible(x):
     of arrays to (p, n) arrays.
     """
     try:
-        x = np.asfarray(x).squeeze()
+        x = np.asarray(x, dtype=float).squeeze()
     except ValueError:
         pass
     return x

cesium/util.py

@@ -88,7 +88,7 @@ def extract_time_series(
             x for x in archive.getmembers() if not x.name.startswith((".", "/"))
         ]
         extracted_names = [x.name for x in members_to_extract]
-        archive.extractall(path=extract_dir, members=members_to_extract)
+        archive.extractall(path=extract_dir, members=members_to_extract, filter="data")
         all_paths = [os.path.join(extract_dir, f) for f in extracted_names]
     elif zipfile.is_zipfile(data_path):
         archive = zipfile.ZipFile(data_path)

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "setuptools_scm", "numpy", "Cython>=0.25"]
+requires = ["setuptools", "setuptools_scm", "numpy>=2.0,<3.0", "Cython>=3.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -26,7 +26,6 @@ classifiers = [
     "Operating System :: Unix",
     "Operating System :: MacOS",
 ]
-
 dynamic = ["version", "dependencies"]
 
 [project.urls]

requirements.txt

@@ -1,4 +1,4 @@
-numpy>=1.14.3
+numpy>=2.0,<3.0
 scipy>=0.16.0
 scikit-learn>=0.22.1
 pandas>=0.17.0
@@ -7,4 +7,3 @@ toolz
 gatspy>=0.3.0
 cloudpickle
 joblib>=0.14.1
-setuptools-scm>=7.1.0