From 38a501e17dc237e5971eaab6fac6e32f72799ad9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 6 Jul 2025 09:48:35 +0000 Subject: [PATCH 01/15] Bump numpy from 1.26.4 to 2.2.4 Bumps [numpy](https://github.com/numpy/numpy) from 1.26.4 to 2.2.4. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.2.4) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 557d563bc..cf6f5a7ee 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ classifiers = [ ] dependencies = [ "ase==3.25.0", - "numpy==1.26.4", + "numpy==2.0.2", "scipy==1.15.2", ] dynamic = ["version"] From 614be15d3d03c3a86e1f54ffc05f20202a976a64 Mon Sep 17 00:00:00 2001 From: pyironrunner Date: Sun, 6 Jul 2025 09:48:46 +0000 Subject: [PATCH 02/15] [dependabot skip] Update environment --- .ci_support/environment.yml | 2 +- .ci_support/environment_mini.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 4ac2a652c..4e0dbc6c4 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -9,7 +9,7 @@ dependencies: - matplotlib-base =3.10.1 - nglview =3.1.4 - notebook -- numpy =1.26.4 +- numpy =2.2.4 - phonopy =2.41.1 - plotly =6.2.0 - pymatgen =2025.3.10 diff --git a/.ci_support/environment_mini.yml b/.ci_support/environment_mini.yml index 8041372c6..26aa3472b 100644 --- a/.ci_support/environment_mini.yml +++ b/.ci_support/environment_mini.yml @@ -3,6 +3,6 @@ channels: dependencies: - ase =3.25.0 - coverage -- numpy =1.26.4 +- numpy =2.2.4 - scipy =1.15.2 - setuptools From 8f9e6614f6b8fd90542427706e1f499bc734be11 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 11:52:29 +0200 Subject: [PATCH 03/15] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index cf6f5a7ee..3aa5eab28 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ classifiers = [ ] dependencies = [ "ase==3.25.0", - "numpy==2.0.2", + "numpy==2.3.1", "scipy==1.15.2", ] dynamic = ["version"] From 068a58bc7d05fba2b4d9044254eaacd848432076 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 11:52:44 +0200 Subject: [PATCH 04/15] Update environment_mini.yml --- .ci_support/environment_mini.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment_mini.yml b/.ci_support/environment_mini.yml index 26aa3472b..f197802a4 100644 --- a/.ci_support/environment_mini.yml +++ b/.ci_support/environment_mini.yml @@ -3,6 +3,6 @@ channels: dependencies: - ase =3.25.0 - coverage -- numpy =2.2.4 +- numpy =2.3.1 - scipy =1.15.2 - setuptools From 5813764d4927f1ae1beaed2c56a6b5ce798bbd38 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 11:53:05 +0200 Subject: [PATCH 05/15] Update environment.yml --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 4e0dbc6c4..a83cb5c36 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -9,7 +9,7 @@ dependencies: - matplotlib-base =3.10.1 - nglview =3.1.4 - notebook -- numpy =2.2.4 +- numpy =2.3.1 - phonopy =2.41.1 - plotly =6.2.0 - pymatgen =2025.3.10 From 3833b9c099018b637b5eea5440052374ed7d6ec8 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 11:57:05 +0200 Subject: [PATCH 06/15] Update pipeline.yml --- .github/workflows/pipeline.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index c09fdf25c..350bb181b 100644 --- a/.github/workflows/pipeline.yml +++ b/.github/workflows/pipeline.yml @@ -108,10 +108,6 @@ jobs: python-version: '3.11' label: linux-64-py-3-11 - - operating-system: ubuntu-latest - python-version: '3.10' - label: linux-64-py-3-10 - steps: - uses: actions/checkout@v4 - name: Merge conda environment From cd075737bfb0f1ee5859c961287568e043da161d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 12:00:22 +0200 Subject: [PATCH 07/15] Update test_visualize.py --- tests/test_visualize.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_visualize.py b/tests/test_visualize.py index 5b8f31d7a..3360818b6 100644 --- a/tests/test_visualize.py +++ b/tests/test_visualize.py @@ -31,7 +31,7 @@ def test_get_frame(self): dx, counts = np.unique( np.diff(frame, axis=-2).squeeze().astype(int), axis=0, return_counts=True ) - self.assertEqual(dx.ptp(), 1, msg="Frames not drawn along the nearest edges") + self.assertEqual(np.ptp(dx), 1, msg="Frames not drawn along the nearest edges") msg = ( "There must be four lines along each direction" + " (4 x [1, 0, 0], 4 x [0, 1, 0] and 4 x [0, 0, 1])" From 40cc44d94705f2a5d3d49dcdb6363141579d82d1 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 14:21:21 +0200 Subject: [PATCH 08/15] Update pipeline.yml --- .github/workflows/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index 350bb181b..ff431de6c 100644 --- a/.github/workflows/pipeline.yml +++ b/.github/workflows/pipeline.yml @@ -111,7 +111,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Merge conda environment - if: matrix.operating-system != 'windows-latest' + if: matrix.operating-system == 'ubuntu-latest' run: tail --lines=+4 .ci_support/environment-lammps.yml >> .ci_support/environment.yml - name: Conda config shell: bash -l {0} From cd414f6f2c1f4ab29ed5a8ce16e7d054ff8a3ea3 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 14:24:58 +0200 Subject: [PATCH 09/15] Update test_symmetry.py --- tests/test_symmetry.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_symmetry.py b/tests/test_symmetry.py index 1e29f5b71..cb5ab3ece 100644 --- a/tests/test_symmetry.py +++ b/tests/test_symmetry.py @@ -136,9 +136,9 @@ def test_symmetrize_tensor(self): ).repeat(2) structure.symbols[0] = "Ni" symmetry = stk.analyse.get_symmetry(structure=structure) - self.assertLess(symmetry.symmetrize_tensor(np.random.randn(3)).ptp(), 1.0e-8) + self.assertLess(np.ptp(symmetry.symmetrize_tensor(np.random.randn(3))), 1.0e-8) sym_tensor = symmetry.symmetrize_tensor(np.random.randn(3, 3)) - self.assertLess(sym_tensor.diagonal().ptp(), 1.0e-8) + self.assertLess(np.ptp(sym_tensor.diagonal()), 1.0e-8) self.assertLess(sym_tensor[np.triu_indices(3, k=1)].ptp(), 1.0e-8) i = np.all(structure.positions == [0.5, 0, 0.5], axis=-1) j = np.all(structure.positions == [0, 0.5, 0.5], axis=-1) From 7b727e06c1e53c4273ad7385c66fcaa531c9c6af Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 14:27:23 +0200 Subject: [PATCH 10/15] Update test_symmetry.py --- tests/test_symmetry.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_symmetry.py b/tests/test_symmetry.py index cb5ab3ece..4d390406c 100644 --- a/tests/test_symmetry.py +++ b/tests/test_symmetry.py @@ -139,7 +139,7 @@ def test_symmetrize_tensor(self): self.assertLess(np.ptp(symmetry.symmetrize_tensor(np.random.randn(3))), 1.0e-8) sym_tensor = symmetry.symmetrize_tensor(np.random.randn(3, 3)) self.assertLess(np.ptp(sym_tensor.diagonal()), 1.0e-8) - self.assertLess(sym_tensor[np.triu_indices(3, k=1)].ptp(), 1.0e-8) + self.assertLess(np.ptp(sym_tensor[np.triu_indices(3, k=1)]), 1.0e-8) i = np.all(structure.positions == [0.5, 0, 0.5], axis=-1) j = np.all(structure.positions == [0, 0.5, 0.5], axis=-1) s_tensor = symmetry.symmetrize_tensor(np.random.randn(len(structure))) From 7c967daa8f0ced9b3073d670de8691e043ad648a Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 14:33:21 +0200 Subject: [PATCH 11/15] Update environment.yml --- .ci_support/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index a83cb5c36..6814d099a 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -19,3 +19,4 @@ dependencies: - scipy =1.15.2 - spglib =2.6.0 - sqsgenerator =0.3 +- sparse =0.17.0 From 75412ba66de13bb376d9c5f0e6b0ae51179a784f Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 15:35:20 +0200 Subject: [PATCH 12/15] Update environment.yml --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 6814d099a..3fd52b576 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -9,7 +9,7 @@ dependencies: - matplotlib-base =3.10.1 - nglview =3.1.4 - notebook -- numpy =2.3.1 +- numpy =2.2.6 - phonopy =2.41.1 - plotly =6.2.0 - pymatgen =2025.3.10 From 56ba20d6144dc771d13966dce7e0cc1b34bd24bc Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 15:35:38 +0200 Subject: [PATCH 13/15] Update environment_mini.yml --- .ci_support/environment_mini.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment_mini.yml b/.ci_support/environment_mini.yml index f197802a4..7a391656a 100644 --- a/.ci_support/environment_mini.yml +++ b/.ci_support/environment_mini.yml @@ -3,6 +3,6 @@ channels: dependencies: - ase =3.25.0 - coverage -- numpy =2.3.1 +- numpy =2.2.6 - scipy =1.15.2 - setuptools From 66545c1fc574d8a63d941d712263ef3a029f6a18 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 15:37:44 +0200 Subject: [PATCH 14/15] Update environment.yml --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 3fd52b576..6814d099a 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -9,7 +9,7 @@ dependencies: - matplotlib-base =3.10.1 - nglview =3.1.4 - notebook -- numpy =2.2.6 +- numpy =2.3.1 - phonopy =2.41.1 - plotly =6.2.0 - pymatgen =2025.3.10 From 396ab79a7efd03a0540e526c9db32de3448e8223 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 6 Jul 2025 15:38:01 +0200 Subject: [PATCH 15/15] Update environment_mini.yml --- .ci_support/environment_mini.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment_mini.yml b/.ci_support/environment_mini.yml index 7a391656a..f197802a4 100644 --- a/.ci_support/environment_mini.yml +++ b/.ci_support/environment_mini.yml @@ -3,6 +3,6 @@ channels: dependencies: - ase =3.25.0 - coverage -- numpy =2.2.6 +- numpy =2.3.1 - scipy =1.15.2 - setuptools