From 832d72e1b105f904587edc5e94d1c0085fe2fce0 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 16 Jul 2026 09:29:41 +0200 Subject: [PATCH 1/6] Update numpy to 2.5.1 --- .ci_support/environment-docs.yml | 2 +- .ci_support/environment-mini.yml | 2 +- .ci_support/environment.yml | 2 +- binder/environment.yml | 2 +- pyproject.toml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index 2f5f6bf63..7ad92fbf0 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -2,7 +2,7 @@ channels: - conda-forge dependencies: - ase =3.29.0 -- numpy =2.4.6 +- numpy =2.5.1 - scipy =1.17.1 - hatchling =1.31.0 - hatch-vcs =0.5.0 diff --git a/.ci_support/environment-mini.yml b/.ci_support/environment-mini.yml index aa434f055..39e0c444a 100644 --- a/.ci_support/environment-mini.yml +++ b/.ci_support/environment-mini.yml @@ -3,7 +3,7 @@ channels: dependencies: - ase =3.29.0 - coverage -- numpy =2.4.6 +- numpy =2.5.1 - scipy =1.17.1 - hatchling =1.31.0 - hatch-vcs =0.5.0 diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 05128967c..5fc83da4c 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -9,7 +9,7 @@ dependencies: - matplotlib-base =3.10.9 - nglview =4.0.1 - notebook -- numpy =2.4.6 +- numpy =2.5.1 - phonopy =4.3.1 - plotly =6.9.0 - pymatgen =2026.3.23 diff --git a/binder/environment.yml b/binder/environment.yml index 416dd91fe..48e1dec9e 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -7,7 +7,7 @@ dependencies: - dscribe =2.1.2 - matplotlib-base =3.10.9 - notebook -- numpy =2.4.6 +- numpy =2.5.1 - phonopy =4.3.1 - plotly =6.9.0 - pymatgen =2026.3.23 diff --git a/pyproject.toml b/pyproject.toml index b73ab9bd2..9ddc0ed36 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ classifiers = [ ] dependencies = [ "ase==3.29.0", - "numpy==2.4.6", + "numpy==2.5.1", "scipy==1.17.1", ] dynamic = ["version"] From fc6752601ddda25c68b9fcfc04509efad65096f5 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 16 Jul 2026 09:37:32 +0200 Subject: [PATCH 2/6] Update python version --- .github/workflows/pipeline.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index 1901e8952..a053f0c32 100644 --- a/.github/workflows/pipeline.yml +++ b/.github/workflows/pipeline.yml @@ -48,7 +48,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v5 with: - python-version: "3.13" + python-version: "3.14" architecture: x64 - name: Checkout uses: actions/checkout@v4 @@ -123,7 +123,7 @@ jobs: - name: Setup Mambaforge uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.12" + python-version: "3.14" miniforge-version: latest channels: conda-forge conda-remove-defaults: "true" @@ -161,10 +161,6 @@ jobs: python-version: '3.12' label: linux-64-py-3-12 - - operating-system: ubuntu-latest - python-version: '3.11' - label: linux-64-py-3-11 - steps: - uses: actions/checkout@v4 - name: Merge conda environment From 4c737aa263de84b4fec698e5ef663c22f0d1467a Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 16 Jul 2026 09:55:20 +0200 Subject: [PATCH 3/6] Add support for Python 3.14 in pyproject.toml --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 5394b8c1b..bbc4408a6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,7 @@ classifiers = [ "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", ] dependencies = [ "ase==3.29.0", From b4e95d6c5c8bca9cec28807f294361be2cc1841d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 16 Jul 2026 09:57:48 +0200 Subject: [PATCH 4/6] fix test --- tests/test_neighbors.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_neighbors.py b/tests/test_neighbors.py index 72713c965..e17fa7ccb 100644 --- a/tests/test_neighbors.py +++ b/tests/test_neighbors.py @@ -500,9 +500,9 @@ def test_get_distances_arbitrary_array(self): with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") _ = neigh.get_neighborhood(np.random.random(3), num_neighbors=51) - self.assertEqual(len(w), 1) - _ = neigh.get_neighborhood(np.random.random(3), num_neighbors=51).distances self.assertEqual(len(w), 2) + _ = neigh.get_neighborhood(np.random.random(3), num_neighbors=51).distances + self.assertEqual(len(w), 3) def test_repr(self): basis = bulk("Al", a=4.2, cubic=True).repeat(3) From ba5aa44080e216c9213d8251982917b2b4095744 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 16 Jul 2026 10:00:45 +0200 Subject: [PATCH 5/6] more fixes --- tests/test_neighbors.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_neighbors.py b/tests/test_neighbors.py index e17fa7ccb..5716f1878 100644 --- a/tests/test_neighbors.py +++ b/tests/test_neighbors.py @@ -502,7 +502,7 @@ def test_get_distances_arbitrary_array(self): _ = neigh.get_neighborhood(np.random.random(3), num_neighbors=51) self.assertEqual(len(w), 2) _ = neigh.get_neighborhood(np.random.random(3), num_neighbors=51).distances - self.assertEqual(len(w), 3) + self.assertEqual(len(w), 4) def test_repr(self): basis = bulk("Al", a=4.2, cubic=True).repeat(3) From 03b2f986b73787c34fa25d8b400433bb29ab4251 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 16 Jul 2026 10:06:02 +0200 Subject: [PATCH 6/6] Fix sparse version --- .ci_support/environment-docs.yml | 1 + .ci_support/environment-mini.yml | 1 + .ci_support/environment.yml | 1 + binder/environment.yml | 1 + 4 files changed, 4 insertions(+) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index 567c16629..aa83d8908 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -6,6 +6,7 @@ dependencies: - scipy =1.18.0 - hatchling =1.31.0 - hatch-vcs =0.5.0 +- sparse =0.19.0 - myst-parser - nbsphinx - sphinx diff --git a/.ci_support/environment-mini.yml b/.ci_support/environment-mini.yml index 0e22d1dd2..22eef5794 100644 --- a/.ci_support/environment-mini.yml +++ b/.ci_support/environment-mini.yml @@ -5,5 +5,6 @@ dependencies: - coverage - numpy =2.5.1 - scipy =1.18.0 +- sparse =0.19.0 - hatchling =1.31.0 - hatch-vcs =0.5.0 diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 65270f5cb..d0addf845 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -12,6 +12,7 @@ dependencies: - numpy =2.5.1 - phonopy =4.3.1 - plotly =6.9.0 +- sparse =0.19.0 - pymatgen =2026.3.23 - pyscal3 =3.3.2 - scikit-learn =1.8.0 diff --git a/binder/environment.yml b/binder/environment.yml index 1e73e7c64..ab3b90880 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -14,6 +14,7 @@ dependencies: - pyscal3 =3.3.2 - scikit-learn =1.8.0 - scipy =1.18.0 +- sparse =0.19.0 - spglib =2.7.0 - sqsgenerator =0.5.5 - setuptools <80