From f0508b97dc8a2677634bada55cab3f3b3f9cdc97 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Mon, 2 Mar 2026 13:24:13 -0500 Subject: [PATCH 1/8] maint: bump tables version and py version for highest tests --- .github/workflows/test.yml | 18 ++++-------------- pyproject.toml | 5 +++-- 2 files changed, 7 insertions(+), 16 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index f88a7c86a..0d7f345e8 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -20,8 +20,8 @@ jobs: version: - { python: '3.12', resolution: highest } - { python: '3.12', resolution: lowest-direct } - - { python: '3.13', resolution: highest } - - { python: '3.13', resolution: lowest-direct } + - { python: '3.14', resolution: highest } + - { python: '3.14', resolution: lowest-direct } runs-on: ${{ matrix.os }} steps: @@ -39,12 +39,7 @@ jobs: - name: Install torch_sim run: | uv pip install "torch>2" --index-url https://download.pytorch.org/whl/cpu --system - # always use numpy>=2 with Python 3.13 - if [ "${{ matrix.version.python }}" = "3.13" ]; then - uv pip install -e ".[test]" "numpy>=2" --resolution=${{ matrix.version.resolution }} --system - else - uv pip install -e ".[test]" --resolution=${{ matrix.version.resolution }} --system - fi + uv pip install -e ".[test]" --resolution=${{ matrix.version.resolution }} --system - name: Run core tests run: | @@ -150,12 +145,7 @@ jobs: run: | # setuptools <82 provides pkg_resources needed by mattersim and fairchem (via torchtnt). # setuptools 82+ removed pkg_resources. Remove pin once those packages migrate. - # always use numpy>=2 with Python 3.13 - if [ "${{ matrix.version.python }}" = "3.13" ]; then - uv pip install -e ".[test,${{ matrix.model.name }}]" "numpy>=2" "setuptools>=70,<82" --resolution=${{ matrix.version.resolution }} --system - else - uv pip install -e ".[test,${{ matrix.model.name }}]" "setuptools>=70,<82" --resolution=${{ matrix.version.resolution }} --system - fi + uv pip install -e ".[test,${{ matrix.model.name }}]" "setuptools>=70,<82" --resolution=${{ matrix.version.resolution }} --system - name: Run ${{ matrix.model.test_path }} tests if: ${{ !contains(matrix.model.name, 'fairchem') || github.event.pull_request.head.repo.fork == false }} diff --git a/pyproject.toml b/pyproject.toml index bcbc65ce3..b0e59c838 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,9 +28,10 @@ classifiers = [ requires-python = ">=3.12" dependencies = [ "h5py>=3.12.1", - "numpy>=1.26,<3", + "numpy>=1.26,<3; python_version < '3.13'", + "numpy>=2,<3; python_version >= '3.13'", "nvalchemi-toolkit-ops>=0.2.0", - "tables>=3.10.2,<3.11", + "tables>=3.11.1", "torch>=2", "tqdm>=4.67", ] From 72337ef457c3b64f70d10fc8c58bb1c359346444 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Mon, 2 Mar 2026 21:42:07 -0500 Subject: [PATCH 2/8] bumpy bump --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b0e59c838..50652c01a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,9 +27,9 @@ classifiers = [ ] requires-python = ">=3.12" dependencies = [ - "h5py>=3.12.1", + "h5py>=3.15", "numpy>=1.26,<3; python_version < '3.13'", - "numpy>=2,<3; python_version >= '3.13'", + "numpy>=2.3.2,<3; python_version >= '3.13'", "nvalchemi-toolkit-ops>=0.2.0", "tables>=3.11.1", "torch>=2", From 860990cad4963df0e90f06516a01e7c989482ea4 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Tue, 3 Mar 2026 08:19:12 -0500 Subject: [PATCH 3/8] bump moyo --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index bb38e62e7..0178da6ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ test = [ "spglib>=2.6", ] io = ["ase>=3.26", "phonopy>=2.37.0", "pymatgen>=2025.6.14"] -symmetry = ["moyopy>=0.3"] +symmetry = ["moyopy>=0.7.8"] mace = ["mace-torch>=0.3.15"] mattersim = ["mattersim>=0.1.2"] metatomic = ["metatomic-torch>=0.1.3", "metatrain[pet]>=2025.12"] From acdc2db6d62109193813c1cbfc6a4e61c3410d01 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Tue, 3 Mar 2026 08:37:16 -0500 Subject: [PATCH 4/8] fix merge issue from 339 --- pyproject.toml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 0178da6ef..5f774e8a1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,9 +38,7 @@ dependencies = [ [project.optional-dependencies] test = [ - "ase>=3.26", - "moyopy>=0.3", - "phonopy>=2.37.0", + "torch-sim-atomistic[io,symmetry]", "platformdirs>=4.0.0", "psutil>=7.0.0", "pymatgen>=2025.6.14", From df5950b25afc83616ab6d7b132de3f7d3154aad6 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Tue, 3 Mar 2026 10:54:07 -0500 Subject: [PATCH 5/8] remove brew install of hdf5? --- .github/workflows/test.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 0d7f345e8..9c7c81edb 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -122,10 +122,6 @@ jobs: - name: Set up uv uses: astral-sh/setup-uv@v6 - - name: Install HDF5 on macOS - if: runner.os == 'macOS' - run: brew install hdf5 - - name: Install legacy fairchem repository and dependencies if: ${{ matrix.model.name == 'fairchem-legacy' }} run: | From f81b85fe3c351ebcc9f0114570546dd4fc547e14 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Tue, 3 Mar 2026 11:01:47 -0500 Subject: [PATCH 6/8] try all tests on 3.14 --- .github/workflows/test.yml | 60 +++++++++++++++++++------------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9c7c81edb..0a60b4646 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -58,7 +58,7 @@ jobs: os: [ubuntu-latest, macos-14] version: - { python: '3.12', resolution: lowest-direct } - - { python: '3.13', resolution: highest } + - { python: '3.14', resolution: highest } model: - { name: fairchem, test_path: "tests/models/test_fairchem.py" } - { name: fairchem-legacy, test_path: "tests/models/test_fairchem_legacy.py" } @@ -71,35 +71,35 @@ jobs: - { name: nequip, test_path: "tests/models/test_nequip_framework.py" } - { name: orb, test_path: "tests/models/test_orb.py" } - { name: sevenn, test_path: "tests/models/test_sevennet.py" } - exclude: - - version: { python: '3.13', resolution: lowest-direct } - model: { name: orb, test_path: 'tests/models/test_orb.py' } - - version: { python: '3.13', resolution: highest } - model: { name: orb, test_path: 'tests/models/test_orb.py' } - - version: { python: '3.13', resolution: lowest-direct } - model: - { - name: fairchem-legacy, - test_path: 'tests/models/test_fairchem_legacy.py', - } - - version: { python: '3.13', resolution: highest } - model: - { - name: fairchem-legacy, - test_path: 'tests/models/test_fairchem_legacy.py', - } - - version: { python: '3.13', resolution: lowest-direct } - model: - { - name: nequip, - test_path: 'tests/models/test_nequip_framework.py', - } - - version: { python: '3.13', resolution: highest } - model: - { - name: nequip, - test_path: 'tests/models/test_nequip_framework.py', - } + # exclude: + # - version: { python: '3.14', resolution: lowest-direct } + # model: { name: orb, test_path: 'tests/models/test_orb.py' } + # - version: { python: '3.14', resolution: highest } + # model: { name: orb, test_path: 'tests/models/test_orb.py' } + # - version: { python: '3.14', resolution: lowest-direct } + # model: + # { + # name: fairchem-legacy, + # test_path: 'tests/models/test_fairchem_legacy.py', + # } + # - version: { python: '3.14', resolution: highest } + # model: + # { + # name: fairchem-legacy, + # test_path: 'tests/models/test_fairchem_legacy.py', + # } + # - version: { python: '3.14', resolution: lowest-direct } + # model: + # { + # name: nequip, + # test_path: 'tests/models/test_nequip_framework.py', + # } + # - version: { python: '3.14', resolution: highest } + # model: + # { + # name: nequip, + # test_path: 'tests/models/test_nequip_framework.py', + # } runs-on: ${{ matrix.os }} steps: From dd105ba41461aa8c11fd2d1e532e737af9abf0e6 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Tue, 3 Mar 2026 14:23:13 -0500 Subject: [PATCH 7/8] turn off 3.14 tests for fairchem and other models already turned off for 3.13 --- .github/workflows/test.yml | 38 +++++++++----------------------------- 1 file changed, 9 insertions(+), 29 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 0a60b4646..4ac5403f0 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -71,35 +71,15 @@ jobs: - { name: nequip, test_path: "tests/models/test_nequip_framework.py" } - { name: orb, test_path: "tests/models/test_orb.py" } - { name: sevenn, test_path: "tests/models/test_sevennet.py" } - # exclude: - # - version: { python: '3.14', resolution: lowest-direct } - # model: { name: orb, test_path: 'tests/models/test_orb.py' } - # - version: { python: '3.14', resolution: highest } - # model: { name: orb, test_path: 'tests/models/test_orb.py' } - # - version: { python: '3.14', resolution: lowest-direct } - # model: - # { - # name: fairchem-legacy, - # test_path: 'tests/models/test_fairchem_legacy.py', - # } - # - version: { python: '3.14', resolution: highest } - # model: - # { - # name: fairchem-legacy, - # test_path: 'tests/models/test_fairchem_legacy.py', - # } - # - version: { python: '3.14', resolution: lowest-direct } - # model: - # { - # name: nequip, - # test_path: 'tests/models/test_nequip_framework.py', - # } - # - version: { python: '3.14', resolution: highest } - # model: - # { - # name: nequip, - # test_path: 'tests/models/test_nequip_framework.py', - # } + exclude: + - version: { python: '3.14', resolution: highest } + model: { name: orb, test_path: 'tests/models/test_orb.py' } + - version: { python: '3.14', resolution: highest } + model: { name: fairchem, test_path: 'tests/models/test_fairchem.py'} + - version: { python: '3.14', resolution: highest } + model: { name: fairchem-legacy, test_path: 'tests/models/test_fairchem_legacy.py'} + - version: { python: '3.14', resolution: highest } + model: { name: nequip, test_path: 'tests/models/test_nequip_framework.py'} runs-on: ${{ matrix.os }} steps: From 4129e46f3758fbe045d2a27f13ab5ca9d6a54c27 Mon Sep 17 00:00:00 2001 From: Rhys Goodall Date: Tue, 3 Mar 2026 19:51:54 -0500 Subject: [PATCH 8/8] plz? --- .github/workflows/test.yml | 4 ++++ pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 4ac5403f0..0084d5531 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -99,6 +99,10 @@ jobs: with: python-version: ${{ matrix.version.python }} + - name: Install HDF5 on macOS + if: runner.os == 'macOS' + run: brew install hdf5 + - name: Set up uv uses: astral-sh/setup-uv@v6 diff --git a/pyproject.toml b/pyproject.toml index c5708e6ae..ac4cabe61 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ classifiers = [ ] requires-python = ">=3.12" dependencies = [ - "h5py>=3.15", + "h5py>=3.15.1", "numpy>=1.26,<3; python_version < '3.13'", "numpy>=2.3.2,<3; python_version >= '3.13'", "nvalchemi-toolkit-ops>=0.2.0",