Update for numpy 2.0

.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml

@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages

.github/workflows/phono3py-pytest-conda-mkl-v2.yml

@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages

.github/workflows/phono3py-pytest-conda-mkl.yml

@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages

.github/workflows/phono3py-pytest-conda-numpy2.yml

@@ -0,0 +1,52 @@
+name: Pytest with openblas and numpy 2.0
+
+on:
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-version: latest
+    - name: Install dependent packages
+      run: |
+        conda activate test
+        conda install --yes python=${{ matrix.python-version }}
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest codecov pytest-cov cmake c-compiler
+    - name: Install spglib develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/spglib/spglib.git
+        cd spglib
+        pip install -e . -vvv
+        cd ..
+    - name: Install phonopy develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        cd phonopy
+        PHONOPY_USE_OPENMP=true pip install -e . -vvv
+        cd ..
+    - name: Install phono3py
+      run: |
+        conda activate test
+        pip install -e . -vvv
+    - name: Run pytest
+      run: |
+        pytest -v test
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        verbose: true

.github/workflows/phono3py-pytest-conda-phphmtblas.yml

@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages

.github/workflows/phono3py-pytest-conda.yml

@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages

.github/workflows/publish-gh-pages.yml

@@ -15,8 +15,8 @@ jobs:
         python-version: ["3.11"]
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         channels: conda-forge

.github/workflows/publish-to-test-pypi.yml

@@ -17,9 +17,9 @@ jobs:
         python-version: ["3.10", ]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         channels: conda-forge

phono3py/file_IO.py

@@ -280,7 +280,7 @@ def write_fc3_to_hdf5(fc3, filename="fc3.hdf5", p2s_map=None, compression="gzip"
 
     """
     with h5py.File(filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("fc3", data=fc3, compression=compression)
         if p2s_map is not None:
             w.create_dataset("p2s_map", data=p2s_map)
@@ -352,9 +352,9 @@ def write_fc2_to_hdf5(
                 dset = w.create_dataset(
                     "physical_unit", (1,), dtype="S%d" % len(physical_unit)
                 )
-                dset[0] = np.string_(physical_unit)
+                dset[0] = np.bytes_(physical_unit)
             if version is not None:
-                w.create_dataset("version", data=np.string_(version))
+                w.create_dataset("version", data=np.bytes_(version))
 
     write_force_constants_to_hdf5(
         force_constants,
@@ -385,7 +385,7 @@ def write_grid_address_to_hdf5(
     suffix = _get_filename_suffix(mesh, filename=filename)
     full_filename = "grid_address" + suffix + ".hdf5"
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
             w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
@@ -577,7 +577,7 @@ def write_real_self_energy_to_hdf5(
     full_filename += ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("grid_point", data=grid_point)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -666,7 +666,7 @@ def write_spectral_function_to_hdf5(
     full_filename += ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("grid_point", data=grid_point)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -713,7 +713,7 @@ def write_collision_to_hdf5(
     )
     full_filename = "collision" + suffix + ".hdf5"
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         if gamma is not None:
             w.create_dataset("gamma", data=gamma)
@@ -751,7 +751,7 @@ def write_collision_to_hdf5(
 def write_full_collision_matrix(collision_matrix, filename="fcm.hdf5"):
     """Write full (non-symmetrized) collision matrix to collision-*.hdf5."""
     with h5py.File(filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("collision_matrix", data=collision_matrix)
 
 
@@ -776,7 +776,7 @@ def write_unitary_matrix_to_hdf5(
     )
     hdf5_filename = "unitary" + suffix + ".hdf5"
     with h5py.File(hdf5_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         if unitary_matrix is not None:
             w.create_dataset("unitary_matrix", data=unitary_matrix)
@@ -816,7 +816,7 @@ def write_collision_eigenvalues_to_hdf5(
         mesh, sigma=sigma, sigma_cutoff=sigma_cutoff, filename=filename
     )
     with h5py.File("coleigs" + suffix + ".hdf5", "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperatures)
         w.create_dataset("collision_eigenvalues", data=collision_eigenvalues)
         w.close()
@@ -885,7 +885,7 @@ def write_kappa_to_hdf5(
     )
     full_filename = "kappa" + suffix + ".hdf5"
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -1159,7 +1159,7 @@ def write_pp_to_hdf5(
     full_filename = "pp" + suffix + ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         if pp is not None:
             if g_zero is None:
                 w.create_dataset("pp", data=pp, compression=compression)
@@ -1323,7 +1323,7 @@ def write_gamma_detail_to_hdf5(
     full_filename = "gamma_detail" + suffix + ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -1397,7 +1397,7 @@ def write_phonon_to_hdf5(
     full_filename = "phonon" + suffix + ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
             w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)

test/phonon/test_grid.py

@@ -2470,7 +2470,6 @@ def test_GridMatrix_with_supercell_symmetry(ph_nacl: Phonopy):
     np.testing.assert_array_equal(gm.D_diag, [4, 4, 4])
 
 
-@pytest.mark.filterwarnings("error")
 def test_GridMatrix_with_supercell_symmetry_grg_false(ph_nacl: Phonopy):
     """Test of GridMatrix with supercell symmetry.