Big breaking API redesign

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,4 +11,4 @@ Before a pull request can be merged, the following items must be checked:
 * [ ] Run [ruff](https://beta.ruff.rs/docs/rules/#pydocstyle-d) on your code.
 * [ ] Tests have been added for any new functionality or bug fixes.
 
-We highly recommended installing the pre-commit hooks running in CI locally to speedup the development process. Simply run `pip install pre-commit && pre-commit install` to install the hooks which will check your code before each commit.
+We highly recommended installing the `prek` hooks running in CI locally to speedup the development process. Simply run `pip install prek && prek install` to install the hooks which will check your code before each commit.

.github/release.yml

@@ -1,6 +1,6 @@
 changelog:
   exclude:
-    authors: [github-actions, pre-commit-ci]
+    authors: [github-actions]
   categories:
     - title: 💥 Breaking Changes
       labels: [breaking]
@@ -33,4 +33,4 @@ changelog:
     - title: 🧹 Linting
       labels: [linting]
     - title: 🤷‍♂️ Other Changes
-      labels: ["*"]
+      labels: ['*']

.github/workflows/docs.yml

@@ -24,7 +24,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: '3.12'
 
       - name: Set up uv
         uses: astral-sh/setup-uv@v6

.github/workflows/lint.yml

@@ -6,26 +6,12 @@ on:
   pull_request:
     branches: [main]
 
-permissions:
-  contents: read
-
-concurrency:
-  group: ${{ github.workflow }}-pr-${{ github.event.pull_request.number }}
-  cancel-in-progress: true
-
 jobs:
-  lint:
+  prek:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Install dependencies
-        run: pip install pre-commit
+      - name: Check out repo
+        uses: actions/checkout@v5
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files --show-diff-on-failure
+      - name: Run prek
+        uses: j178/prek-action@v1

.github/workflows/test.yml

@@ -18,8 +18,8 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-14]
         version:
-          - { python: "3.11", resolution: highest }
-          - { python: "3.12", resolution: lowest-direct }
+          - { python: '3.12', resolution: highest }
+          - { python: '3.13', resolution: lowest-direct }
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -55,8 +55,8 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-14]
         version:
-          - { python: "3.11", resolution: highest }
-          - { python: "3.12", resolution: lowest-direct }
+          - { python: '3.12', resolution: highest }
+          - { python: '3.13', resolution: lowest-direct }
         model:
           - { name: fairchem, test_path: "tests/models/test_fairchem.py" }
           - { name: fairchem-legacy, test_path: "tests/models/test_fairchem_legacy.py" }
@@ -66,8 +66,14 @@ jobs:
           - { name: mace, test_path: "tests/test_optimizers_vs_ase.py" }
           - { name: mattersim, test_path: "tests/models/test_mattersim.py" }
           - { name: metatomic, test_path: "tests/models/test_metatomic.py" }
+          - { 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: lowest-direct }
+            model: { name: fairchem-legacy, test_path: "tests/models/test_fairchem_legacy.py" }
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -102,6 +108,7 @@ jobs:
           uv pip install -e fairchem-repo/packages/fairchem-core[dev] --system
           uv pip install -e ".[test]" --resolution=${{ matrix.version.resolution }} --system
 
+
       - name: Install torch_sim with model dependencies
         if: ${{ matrix.model.name != 'fairchem-legacy' }}
         run: |
@@ -152,7 +159,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: '3.12'
 
       - name: Set up uv
         uses: astral-sh/setup-uv@v6

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.11.13
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix]
       - id: ruff-format
 
@@ -39,4 +39,4 @@ repos:
         # MD033: no inline HTML
         # MD041: first line in a file should be a top-level heading
         # MD034: bare URL used
-        args: [--disable, MD013, MD033, MD041, MD034, "--"]
+        args: [--disable, MD013, MD033, MD041, MD034, '--']

CHANGELOG.md

@@ -1,94 +1,158 @@
-## v0.2.1
+<!-- markdownlint-disable -->
+## v0.3.0
+
+Thank you to everyone who contributed to this release! @t-reents, @curtischong, and @CompRhys did great work squashing an issue with `SimState` concatenation. @curtischong continued his crusade to type and improve the TorchSim API. @orionarcher, @kianpu34593, and @janosh all made contributions that continue to improve package quality and usability. 🚀
+
+## What's Changed
+
+### 🛠 Enhancements
+* Define attribute scopes in `SimStates` by @curtischong, @CompRhys, @orionarcher in [#228](https://github.com/Radical-AI/torch-sim/pull/228)
+* Improve typing of `ModelInterface` by @curtischong, @CompRhys in [#215](https://github.com/Radical-AI/torch-sim/pull/215)
+* Make `system_idx` non-optional in `SimState` by @curtischong in [#231](https://github.com/Radical-AI/torch-sim/pull/231)
+* Add new states when the `max_memory_scaler` is updated by @kianpu34593 in [#222](https://github.com/Radical-AI/torch-sim/pull/222)
+* Rename `batch` to `system` by @curtischong in [#217](https://github.com/Radical-AI/torch-sim/pull/217), [#233](https://github.com/Radical-AI/torch-sim/pull/233)
+
+### 🐛 Bug Fixes
+* Initial fix for concatenation of states in `InFlightAutoBatcher` by @t-reents in [#219](https://github.com/Radical-AI/torch-sim/pull/219)
+* Finish fix for `SimState` concatenation by @t-reents and @curtischong in [#232](https://github.com/Radical-AI/torch-sim/pull/232)
+* Fix broken code block in low-level tutorial by @CompRhys in [#226](https://github.com/Radical-AI/torch-sim/pull/226)
+* Update metatomic checkpoint to fix tests by @curtischong in [#223](https://github.com/Radical-AI/torch-sim/pull/223)
+* Fix memory scaling in `determine_max_batch_size` by @t-reents, @janosh in [#212](https://github.com/Radical-AI/torch-sim/pull/212)
+
+### 📖 Documentation
+* Update README plot with more models by @orionarcher in [#236](https://github.com/Radical-AI/torch-sim/pull/236), [#237](https://github.com/Radical-AI/torch-sim/pull/237)
+* Update `citation.cff` by @CompRhys in [#225](https://github.com/Radical-AI/torch-sim/pull/225)
+
+**Full Changelog**: https://github.com/Radical-AI/torch-sim/compare/v0.2.2...v0.3.0
 
-2025-05-01
+## v0.2.2
+
+## What's Changed
+### 💥 Breaking Changes
+* Remove higher level model imports by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/179
+### 🛠 Enhancements
+* Add per atom energies and stresses for batched LJ by @abhijeetgangan in https://github.com/Radical-AI/torch-sim/pull/144
+* throw error if autobatcher type is wrong by @orionarcher in https://github.com/Radical-AI/torch-sim/pull/167
+### 🐛 Bug Fixes
+* Mattersim fix tensors on wrong device (CPU->GPU) by @orionarcher in https://github.com/Radical-AI/torch-sim/pull/154
+* fix `npt_langevin` by @jla-gardner in https://github.com/Radical-AI/torch-sim/pull/153
+* Make sure to move data to CPU before calling vesin by @Luthaf in https://github.com/Radical-AI/torch-sim/pull/156
+* Fix virial calculations in `optimizers` and `integrators` by @janosh in https://github.com/Radical-AI/torch-sim/pull/163
+* Pad memory estimation by @orionarcher in https://github.com/Radical-AI/torch-sim/pull/160
+* Refactor sevennet model by @YutackPark in https://github.com/Radical-AI/torch-sim/pull/172
+* `io` optional dependencies in `pyproject.toml` by @curtischong in https://github.com/Radical-AI/torch-sim/pull/185
+* Fix column->row cell vector mismatch in integrators by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/175
+### 📖 Documentation
+* (tiny) add graph-pes to README by @jla-gardner in https://github.com/Radical-AI/torch-sim/pull/149
+* Better module fig by @janosh in https://github.com/Radical-AI/torch-sim/pull/168
+### 🚀 Performance
+* More efficient Orb `state_to_atoms_graph` calculation by @AdeeshKolluru in https://github.com/Radical-AI/torch-sim/pull/165
+### 🚧 CI
+* Refactor `test_math.py` and `test_transforms.py` by @janosh in https://github.com/Radical-AI/torch-sim/pull/151
+### 🏥 Package Health
+* Try out hatchling for build vs setuptools by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/177
+### 📦 Dependencies
+* Bump `mace-torch` to v0.3.12 by @janosh in https://github.com/Radical-AI/torch-sim/pull/170
+* Update metatrain dependency by @Luthaf in https://github.com/Radical-AI/torch-sim/pull/186
+### 🏷️ Type Hints
+* Add `torch_sim/typing.py` by @janosh in https://github.com/Radical-AI/torch-sim/pull/157
+
+## New Contributors
+* @Luthaf made their first contribution in https://github.com/Radical-AI/torch-sim/pull/156
+* @YutackPark made their first contribution in https://github.com/Radical-AI/torch-sim/pull/172
+* @curtischong made their first contribution in https://github.com/Radical-AI/torch-sim/pull/185
+
+**Full Changelog**: https://github.com/Radical-AI/torch-sim/compare/v0.2.0...v0.2.1
+
+## v0.2.1
 
 ## What's Changed
 
 ### 💥 Breaking Changes
 
-* Remove higher level model imports by @CompRhys in https://github.com/TorchSim/torch-sim/pull/179
+* Remove higher level model imports by @CompRhys in [#179](https://github.com/TorchSim/torch-sim/pull/179)
 
 ### 🛠 Enhancements
 
-* Add per atom energies and stresses for batched LJ by @abhijeetgangan in https://github.com/TorchSim/torch-sim/pull/144
-* throw error if autobatcher type is wrong by @orionarcher in https://github.com/TorchSim/torch-sim/pull/167
+* Add per atom energies and stresses for batched LJ by @abhijeetgangan in [#144](https://github.com/TorchSim/torch-sim/pull/144)
+* throw error if autobatcher type is wrong by @orionarcher in [#167](https://github.com/TorchSim/torch-sim/pull/167)
 
 ### 🐛 Bug Fixes
 
-* Fix column->row cell vector mismatch in integrators by @CompRhys in https://github.com/TorchSim/torch-sim/pull/175
-* Mattersim fix tensors on wrong device (CPU->GPU) by @orionarcher in https://github.com/TorchSim/torch-sim/pull/154
-* fix `npt_langevin` by @jla-gardner in https://github.com/TorchSim/torch-sim/pull/153
-* Make sure to move data to CPU before calling vesin by @Luthaf in https://github.com/TorchSim/torch-sim/pull/156
-* Fix virial calculations in `optimizers` and `integrators` by @janosh in https://github.com/TorchSim/torch-sim/pull/163
-* Pad memory estimation by @orionarcher in https://github.com/TorchSim/torch-sim/pull/160
-* Refactor sevennet model by @YutackPark in https://github.com/TorchSim/torch-sim/pull/172
-* `io` optional dependencies in `pyproject.toml` by @curtischong in https://github.com/TorchSim/torch-sim/pull/185
+* Fix column->row cell vector mismatch in integrators by @CompRhys in [#175](https://github.com/TorchSim/torch-sim/pull/175)
+* Mattersim fix tensors on wrong device (CPU->GPU) by @orionarcher in [#154](https://github.com/TorchSim/torch-sim/pull/154)
+* fix `npt_langevin` by @jla-gardner in [#153](https://github.com/TorchSim/torch-sim/pull/153)
+* Make sure to move data to CPU before calling vesin by @Luthaf in [#156](https://github.com/TorchSim/torch-sim/pull/156)
+* Fix virial calculations in `optimizers` and `integrators` by @janosh in [#163](https://github.com/TorchSim/torch-sim/pull/163)
+* Pad memory estimation by @orionarcher in [#160](https://github.com/TorchSim/torch-sim/pull/160)
+* Refactor sevennet model by @YutackPark in [#172](https://github.com/TorchSim/torch-sim/pull/172)
+* `io` optional dependencies in `pyproject.toml` by @curtischong in [#185](https://github.com/TorchSim/torch-sim/pull/185)
 
 ### 📖 Documentation
 
-* (tiny) add graph-pes to README by @jla-gardner in https://github.com/TorchSim/torch-sim/pull/149
-* Better module fig by @janosh in https://github.com/TorchSim/torch-sim/pull/168
+* (tiny) add graph-pes to README by @jla-gardner in [#149](https://github.com/TorchSim/torch-sim/pull/149)
+* Better module fig by @janosh in [#168](https://github.com/TorchSim/torch-sim/pull/168)
 
 ### 🚀 Performance
 
-* More efficient Orb `state_to_atoms_graph` calculation by @AdeeshKolluru in https://github.com/TorchSim/torch-sim/pull/165
+* More efficient Orb `state_to_atoms_graph` calculation by @AdeeshKolluru in [#165](https://github.com/TorchSim/torch-sim/pull/165)
 
 ### 🚧 CI
 
-* Refactor `test_math.py` and `test_transforms.py` by @janosh in https://github.com/TorchSim/torch-sim/pull/151
+* Refactor `test_math.py` and `test_transforms.py` by @janosh in [#151](https://github.com/TorchSim/torch-sim/pull/151)
 
 ### 🏥 Package Health
 
-* Try out hatchling for build vs setuptools by @CompRhys in https://github.com/TorchSim/torch-sim/pull/177
+* Try out hatchling for build vs setuptools by @CompRhys in [#177](https://github.com/TorchSim/torch-sim/pull/177)
 
 ### 🏷️ Type Hints
 
-* Add `torch_sim/typing.py` by @janosh in https://github.com/TorchSim/torch-sim/pull/157
+* Add `torch-sim/typing.py` by @janosh in [#157](https://github.com/TorchSim/torch-sim/pull/157)
 
 ### 📦 Dependencies
 
-* Bump `mace-torch` to v0.3.12 by @janosh in https://github.com/TorchSim/torch-sim/pull/170
-* Update metatrain dependency by @Luthaf in https://github.com/TorchSim/torch-sim/pull/186
+* Bump `mace-torch` to v0.3.12 by @janosh in [#170](https://github.com/TorchSim/torch-sim/pull/170)
+* Update metatrain dependency by @Luthaf in [#186](https://github.com/TorchSim/torch-sim/pull/186)
 
 ## New Contributors
 
-* @Luthaf made their first contribution in https://github.com/TorchSim/torch-sim/pull/156
-* @YutackPark made their first contribution in https://github.com/TorchSim/torch-sim/pull/172
-* @curtischong made their first contribution in https://github.com/TorchSim/torch-sim/pull/185
+* @Luthaf made their first contribution in [#156](https://github.com/TorchSim/torch-sim/pull/156)
+* @YutackPark made their first contribution in [#172](https://github.com/TorchSim/torch-sim/pull/172)
+* @curtischong made their first contribution in [#185](https://github.com/TorchSim/torch-sim/pull/185)
 
-**Full Changelog**: https://github.com/TorchSim/torch-sim/compare/v0.2.0...v0.2.1
+**Full Changelog**: https://github.com/torchsim/torch-sim/compare/v0.2.0...v0.2.1
 
 ## v0.2.0
 
 ### Bug Fixes 🐛
 
-* Fix integrate reporting kwarg to arg error, https://github.com/TorchSim/torch-sim/issues/113 (raised by @hn-yu)
-* Allow runners to take large initial batches, https://github.com/TorchSim/torch-sim/issues/128 (raised by @YutackPark)
-* Add Fairchem model support for PBC, https://github.com/TorchSim/torch-sim/issues/111 (raised by @ryanliu30)
+* Fix integrate reporting kwarg to arg error, [#113](https://github.com/TorchSim/torch-sim/pull/113) (raised by @hn-yu)
+* Allow runners to take large initial batches, [#128](https://github.com/TorchSim/torch-sim/pull/128) (raised by @YutackPark)
+* Add Fairchem model support for PBC, [#111](https://github.com/TorchSim/torch-sim/pull/111) (raised by @ryanliu30)
 
 ### Enhancements 🛠
 
-* **breaking** Rename `HotSwappingAutobatcher` to `InFlightAutobatcher` and `ChunkingAutoBatcher` to `BinningAutoBatcher`, https://github.com/TorchSim/torch-sim/pull/143 @orionarcher
-* Support for Orbv3, https://github.com/TorchSim/torch-sim/pull/140, @AdeeshKolluru
-* Support metatensor models, https://github.com/TorchSim/torch-sim/pull/141, @frostedoyter @Luthaf
-* Support for graph-pes models, https://github.com/TorchSim/torch-sim/pull/118 @jla-gardner
-* Support MatterSim and fix ASE cell convention issues, https://github.com/TorchSim/torch-sim/pull/112 @CompRhys
-* Implement positions only FIRE optimization, https://github.com/TorchSim/torch-sim/pull/139 @abhijeetgangan
-* Allow different temperatures in batches, https://github.com/TorchSim/torch-sim/pull/123 @orionarcher
-* FairChem model updates: PBC handling, test on OMat24 e-trained model, https://github.com/TorchSim/torch-sim/pull/126 @AdeeshKolluru
-* FairChem model from_data_list support, https://github.com/TorchSim/torch-sim/pull/138 @ryanliu30
-* New correlation function module, https://github.com/TorchSim/torch-sim/pull/115 @stefanbringuier
+* **breaking** Rename `HotSwappingAutobatcher` to `InFlightAutobatcher` and `ChunkingAutoBatcher` to `BinningAutoBatcher`, [#143](https://github.com/TorchSim/torch-sim/pull/143) @orionarcher
+* Support for Orbv3, [#140](https://github.com/TorchSim/torch-sim/pull/140), @AdeeshKolluru
+* Support metatensor models, [#141](https://github.com/TorchSim/torch-sim/pull/141), @frostedoyter @Luthaf
+* Support for graph-pes models, [#118](https://github.com/TorchSim/torch-sim/pull/118) @jla-gardner
+* Support MatterSim and fix ASE cell convention issues, [#112](https://github.com/TorchSim/torch-sim/pull/112) @CompRhys
+* Implement positions only FIRE optimization, [#139](https://github.com/TorchSim/torch-sim/pull/139) @abhijeetgangan
+* Allow different temperatures in batches, [#123](https://github.com/TorchSim/torch-sim/pull/123) @orionarcher
+* FairChem model updates: PBC handling, test on OMat24 e-trained model, [#126](https://github.com/TorchSim/torch-sim/pull/126) @AdeeshKolluru
+* FairChem model from_data_list support, [#138](https://github.com/TorchSim/torch-sim/pull/138) @ryanliu30
+* New correlation function module, [#115](https://github.com/TorchSim/torch-sim/pull/115) @stefanbringuier
 
 ### Documentation 📖
 
-* Improved model documentation, https://github.com/TorchSim/torch-sim/pull/121 @orionarcher
-* Plot of TorchSim module graph in docs, https://github.com/TorchSim/torch-sim/pull/132 @janosh
+* Improved model documentation, [#121](https://github.com/TorchSim/torch-sim/pull/121) @orionarcher
+* Plot of TorchSim module graph in docs, [#132](https://github.com/TorchSim/torch-sim/pull/132) @janosh
 
 ### House-Keeping 🧹
 
-* Only install HF for fairchem tests, https://github.com/TorchSim/torch-sim/pull/134 @CompRhys
-* Don't download MBD in CI, https://github.com/TorchSim/torch-sim/pull/135 @orionarcher
-* Tighten graph-pes test bounds, https://github.com/TorchSim/torch-sim/pull/143 @orionarcher
+* Only install HF for fairchem tests, [#134](https://github.com/TorchSim/torch-sim/pull/134) @CompRhys
+* Don't download MBD in CI, [#135](https://github.com/TorchSim/torch-sim/pull/135) @orionarcher
+* Tighten graph-pes test bounds, [#143](https://github.com/TorchSim/torch-sim/pull/143) @orionarcher
 
 ## v0.1.0