Fixup PR: Renaming, vesin in deps, sorti typo, reduce code-rabbit spam

.coderabbit

@@ -0,0 +1,5 @@
+reviews:
+  high_level_summary: false
+  auto_review:
+    enabled: false
+    drafts: false

.github/workflows/docs.yml

@@ -58,7 +58,7 @@ jobs:
           path: ./docs_build
 
   deploy:
-    if: github.repository_owner == 'Radical-AI' && github.ref == 'refs/heads/main'
+    if: github.repository_owner == 'TorchSim' && github.ref == 'refs/heads/main'
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}

CHANGELOG.md

@@ -6,89 +6,89 @@
 
 ### 💥 Breaking Changes
 
-* Remove higher level model imports by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/179
+* Remove higher level model imports by @CompRhys in https://github.com/TorchSim/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
+* 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
 
 ### 🐛 Bug Fixes
 
-* Fix column->row cell vector mismatch in integrators by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/175
-* 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/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
 
 ### 📖 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
+* (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
 
 ### 🚀 Performance
 
-* More efficient Orb `state_to_atoms_graph` calculation by @AdeeshKolluru in https://github.com/Radical-AI/torch-sim/pull/165
+* More efficient Orb `state_to_atoms_graph` calculation by @AdeeshKolluru in https://github.com/TorchSim/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
+* Refactor `test_math.py` and `test_transforms.py` by @janosh in https://github.com/TorchSim/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
+* Try out hatchling for build vs setuptools by @CompRhys in https://github.com/TorchSim/torch-sim/pull/177
 
 ### 🏷️ Type Hints
 
-* Add `torch_sim/typing.py` by @janosh in https://github.com/Radical-AI/torch-sim/pull/157
+* Add `torch_sim/typing.py` by @janosh in https://github.com/TorchSim/torch-sim/pull/157
 
 ### 📦 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
+* 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
 
 ## 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
+* @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
 
-**Full Changelog**: https://github.com/Radical-AI/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/Radical-AI/torch-sim/issues/113 (raised by @hn-yu)
-* Allow runners to take large initial batches, https://github.com/Radical-AI/torch-sim/issues/128 (raised by @YutackPark)
-* Add Fairchem model support for PBC, https://github.com/Radical-AI/torch-sim/issues/111 (raised by @ryanliu30)
+* 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)
 
 ### Enhancements 🛠
 
-* **breaking** Rename `HotSwappingAutobatcher` to `InFlightAutobatcher` and `ChunkingAutoBatcher` to `BinningAutoBatcher`, https://github.com/Radical-AI/torch-sim/pull/143 @orionarcher
-* Support for Orbv3, https://github.com/Radical-AI/torch-sim/pull/140, @AdeeshKolluru
-* Support metatensor models, https://github.com/Radical-AI/torch-sim/pull/141, @frostedoyter @Luthaf
-* Support for graph-pes models, https://github.com/Radical-AI/torch-sim/pull/118 @jla-gardner
-* Support MatterSim and fix ASE cell convention issues, https://github.com/Radical-AI/torch-sim/pull/112 @CompRhys
-* Implement positions only FIRE optimization, https://github.com/Radical-AI/torch-sim/pull/139 @abhijeetgangan
-* Allow different temperatures in batches, https://github.com/Radical-AI/torch-sim/pull/123 @orionarcher
-* FairChem model updates: PBC handling, test on OMat24 e-trained model, https://github.com/Radical-AI/torch-sim/pull/126 @AdeeshKolluru
-* FairChem model from_data_list support, https://github.com/Radical-AI/torch-sim/pull/138 @ryanliu30
-* New correlation function module, https://github.com/Radical-AI/torch-sim/pull/115 @stefanbringuier
+* **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
 
 ### Documentation 📖
 
-* Improved model documentation, https://github.com/Radical-AI/torch-sim/pull/121 @orionarcher
-* Plot of TorchSim module graph in docs, https://github.com/Radical-AI/torch-sim/pull/132 @janosh
+* 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
 
 ### House-Keeping 🧹
 
-* Only install HF for fairchem tests, https://github.com/Radical-AI/torch-sim/pull/134 @CompRhys
-* Don't download MBD in CI, https://github.com/Radical-AI/torch-sim/pull/135 @orionarcher
-* Tighten graph-pes test bounds, https://github.com/Radical-AI/torch-sim/pull/143 @orionarcher
+* 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
 
 ## v0.1.0
 

README.md

@@ -1,6 +1,6 @@
 # TorchSim
 
-[![CI](https://github.com/radical-ai/torch-sim/actions/workflows/test.yml/badge.svg)](https://github.com/radical-ai/torch-sim/actions/workflows/test.yml)
+[![CI](https://github.com/TorchSim/torch-sim/actions/workflows/test.yml/badge.svg)](https://github.com/TorchSim/torch-sim/actions/workflows/test.yml)
 [![codecov](https://codecov.io/gh/radical-ai/torch-sim/branch/main/graph/badge.svg)](https://codecov.io/gh/radical-ai/torch-sim)
 [![This project supports Python 3.11+](https://img.shields.io/badge/Python-3.11+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
 [![PyPI](https://img.shields.io/pypi/v/torch_sim_atomistic?logo=pypi&logoColor=white)](https://pypi.org/project/torch_sim_atomistic)
@@ -113,7 +113,7 @@ pip install torch-sim-atomistic
 ### Installing from source
 
 ```sh
-git clone https://github.com/radical-ai/torch-sim
+git clone https://github.com/TorchSim/torch-sim
 cd torch-sim
 pip install .
 ```

citation.cff

@@ -15,8 +15,8 @@ authors:
   - family-names: Falletta
     given-names: Stefano
 license: MIT
-license-url: https://github.com/Radical-AI/torch-sim/blob/main/LICENSE
-repository-code: https://github.com/Radical-AI/torch-sim
-url: https://github.com/Radical-AI/torch-sim
+license-url: https://github.com/TorchSim/torch-sim/blob/main/LICENSE
+repository-code: https://github.com/TorchSim/torch-sim
+url: https://github.com/TorchSim/torch-sim
 type: software
 date-released: 2025-04-02

docs/conf.py

@@ -156,7 +156,7 @@
     "footer_icons": [
         {
             "name": "GitHub",
-            "url": "https://github.com/Radical-AI/torch-sim",
+            "url": "https://github.com/TorchSim/torch-sim",
             "html": """
 <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
     <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
@@ -165,7 +165,7 @@
             "class": "",
         },
     ],
-    "source_repository": "https://github.com/Radical-AI/torch-sim/",
+    "source_repository": "https://github.com/TorchSim/torch-sim/",
     "source_branch": "main",
     "source_directory": "docs/",
 }

docs/dev/add_model.md

@@ -5,7 +5,7 @@
 We welcome the addition of new models to `torch_sim`. We want
 easy batched simulations to be available to the whole community
 of MLIP developers and users.
-See https://github.com/Radical-AI/torch-sim/discussions/120 for
+See https://github.com/TorchSim/torch-sim/discussions/120 for
 our current posture on adding models to TorchSim.
 
 1. Open a PR or an issue to get feedback. We are happy to take a look,

docs/dev/dev_install.md

@@ -12,10 +12,10 @@ pip install torch-sim-atomistic
 
 ## Install from source
 
-To install torch-sim from source, clone the repository from [github](https://github.com/Radical-AI/torch-sim)
+To install torch-sim from source, clone the repository from [github](https://github.com/TorchSim/torch-sim)
 
 ```bash
-git clone https://github.com/Radical-AI/torch-sim
+git clone https://github.com/TorchSim/torch-sim
 cd torch-sim
 pip install . -e
 ```

docs/index.md

@@ -4,7 +4,6 @@
 :hidden:
 user/introduction
 user/overview
-user/models
 tutorials/index
 ```
 
@@ -19,7 +18,6 @@ reference/index
 :hidden:
 dev/dev_install
 dev/add_model
-dev/batching
 ```
 
 ```{toctree}
@@ -35,8 +33,8 @@ about/license
 **Date**: {sub-ref}`today`
 
 **Useful links**:
-[Source Repository](https://github.com/Radical-AI/torch-sim) |
-[Issues & Ideas](https://github.com/Radical-AI/torch-sim/issues)
+[Source Repository](https://github.com/TorchSim/torch-sim) |
+[Issues & Ideas](https://github.com/TorchSim/torch-sim/issues)
 
 TorchSim is a next-generation open-source atomistic simulation engine for the MLIP era.
 

docs/tutorials/index.rst

@@ -5,7 +5,7 @@ Tutorials
 
 For a high-level overview of the tutorials see :doc:`../user/overview`. Runnable
 versions of the tutorials can also be found in the `torch-sim /examples/tutorials
-<https://github.com/Radical-AI/torch-sim/tree/main/examples/tutorials>`_ directory.
+<https://github.com/TorchSim/torch-sim/tree/main/examples/tutorials>`_ directory.
 
 .. currentmodule:: torch_sim
 

examples/readme.md

@@ -3,7 +3,7 @@
 Examples are provided in two foms:
 
 * Tutorials are intended to provide pedagogical walkthroughs of TorchSim's core functionality
-* Scripts are a holdover from early torch-sim development, they are not currently recommended as a learning resource. See issue [issue 109](https://github.com/Radical-AI/torch-sim/issues/109).
+* Scripts are a holdover from early torch-sim development, they are not currently recommended as a learning resource. See issue [issue 109](https://github.com/TorchSim/torch-sim/issues/109).
 
 ## Tutorial Formatting
 

pyproject.toml

@@ -32,8 +32,7 @@ dependencies = [
     "tables>=3.10.2",
     "torch>=2",
     "tqdm>=4.67",
-    "vesin-torch>=0.3.7",
-    "vesin>=0.3.7",
+    "vesin[torch]>=0.3.7",
 ]
 
 [project.optional-dependencies]
@@ -61,14 +60,14 @@ docs = [
     "jupytext==1.16.7",
     "myst_parser==4.0.0",
     "nbsphinx>=0.9.7",
-    "numpydoc==1.8.0",
+    "numpydoc==1.6.0",
     "sphinx-copybutton==0.5.2",
-    "sphinx==8.1.3",
+    "sphinx==7.2.6",
     "sphinx_design==0.6.1",
 ]
 
 [project.urls]
-Repo = "https://github.com/radical-ai/torch-sim"
+Repo = "https://github.com/TorchSim/torch-sim"
 
 [build-system]
 requires = ["uv_build>=0.7.12"]

tests/test_autobatching.py

@@ -453,7 +453,7 @@ def test_in_flight_auto_batcher_restore_order(
     [
         5,  # At 5 steps, not every state will converge before the next batch.
         #       This tests the merging of partially converged states with new states
-        #       which has been a bug in the past. See https://github.com/Radical-AI/torch-sim/pull/219
+        #       which has been a bug in the past. See https://github.com/TorchSim/torch-sim/pull/219
         10,  # At 10 steps, all states will converge before the next batch
     ],
 )

tests/test_integrators.py

@@ -335,7 +335,7 @@ def test_compare_single_vs_batched_integrators(
 ) -> None:
     """Test NVE single vs batched for a tilted cell to verify PBC wrapping.
 
-    NOTE: added triclinic cell after https://github.com/Radical-AI/torch-sim/issues/171.
+    NOTE: added triclinic cell after https://github.com/TorchSim/torch-sim/issues/171.
     Although the addition doesn't fail if we do not add the changes suggested in issue.
     """
     sim_state = request.getfixturevalue(sim_state_fixture_name)
@@ -383,7 +383,7 @@ def test_compare_single_vs_batched_integrators(
 def test_compute_cell_force_atoms_per_system():
     """Test that compute_cell_force correctly scales by number of atoms per system.
 
-    Covers fix in https://github.com/Radical-AI/torch-sim/pull/153."""
+    Covers fix in https://github.com/TorchSim/torch-sim/pull/153."""
     from torch_sim.integrators.npt import _compute_cell_force
 
     # Setup minimal state with two systems having 8:1 atom ratio

torch_sim/autobatching.py

@@ -591,18 +591,20 @@ def next_batch(
                   where indices are the original positions of the states, or None if no
                   more batches.
 
-        Example::
+        Examples:
+            Get batches one by one:
 
-            # Get batches one by one
-            all_converged_state, convergence = [], None
-            while (result := batcher.next_batch(state, convergence))[0] is not None:
-                state, converged_states = result
-                all_converged_states.extend(converged_states)
+            .. code-block:: python
 
-                evolve_batch(state)
-                convergence = convergence_criterion(state)
-            else:
-                all_converged_states.extend(result[1])
+                all_converged_state, convergence = [], None
+                while (result := batcher.next_batch(state, convergence))[0] is not None:
+                    state, converged_states = result
+                    all_converged_states.extend(converged_states)
+
+                    evolve_batch(state)
+                    convergence = convergence_criterion(state)
+                else:
+                    all_converged_states.extend(result[1])
 
         """
         # TODO: need to think about how this intersects with reporting too
@@ -989,17 +991,20 @@ def next_batch(  # noqa: C901
             AssertionError: If convergence_tensor doesn't match the expected shape or
                 if other validation checks fail.
 
-        Example::
+        Examples:
+            Process states with convergence checking:
 
-            # Initial call
-            batch, completed = batcher.next_batch(None, None)
+            .. code-block:: python
 
-            # Process batch and check for convergence
-            batch = process_batch(batch)
-            convergence = check_convergence(batch)
+                # Initial call
+                batch, completed = batcher.next_batch(None, None)
+
+                # Process batch and check for convergence
+                batch = process_batch(batch)
+                convergence = check_convergence(batch)
 
-            # Get next batch with converged states removed and new states added
-            batch, completed = batcher.next_batch(batch, convergence)
+                # Get next batch with converged states removed and new states added
+                batch, completed = batcher.next_batch(batch, convergence)
 
         Notes:
             When max_iterations is set, states that exceed this limit will be