Feature/neb workflow and FIRE logic modified

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,7 +16,9 @@ Before a pull request can be merged, the following items must be checked:
 * [ ] Tests have been added for any new functionality or bug fixes.
 * [ ] All linting and tests pass.
 
+<!--
 Note that the CI system will run all the above checks. But it will be much more
 efficient if you already fix most errors prior to submitting the PR. It is highly
 recommended that you use the pre-commit hook provided in the repository. Simply run
 `pre-commit install` and a check will be run prior to allowing commits.
+-->

.github/workflows/docs.yml

@@ -18,8 +18,6 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-        with:
-          ref: ${{ github.event.workflow_run.head_branch }}
 
       - name: Install pandoc
         run: sudo apt-get install pandoc
@@ -48,6 +46,12 @@ jobs:
           rm docs/tutorials/*.h5*
           rm docs/tutorials/*.traj*
 
+      - name: Generate package treemap
+        run: |
+          uv pip install --system . --config-settings editable-mode=compat
+          uv pip install --system git+https://github.com/janosh/pymatviz
+          python docs/_static/draw_pkg_treemap.py
+
       - name: Build
         run: sphinx-build docs docs_build
 

.gitignore

@@ -31,3 +31,6 @@ docs/reference/torch_sim.*
 # coverage
 coverage.xml
 .coverage
+
+# env
+uv.lock

.pre-commit-config.yaml

@@ -34,10 +34,14 @@ repos:
     hooks:
       - id: codespell
         stages: [pre-commit, commit-msg]
-        args: [--ignore-words-list, "statics,crate,annote,atomate,nd,te,titel,coo,slite,fro"]
+        args: [--ignore-words-list, "statics,atomate,nd,te,titel,coo,slite,fro"]
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.44.0
     hooks:
       - id: markdownlint
-        exclude: \.md$
+        # MD013: line length
+        # 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, "--"]

CHANGELOG.md

@@ -1,12 +1,14 @@
 ## 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)
 
 ### Enhancements 🛠
-* **[breaking]** Rename `HotSwappingAutobatcher` to `InFlightAutobatcher` and `ChunkingAutoBatcher` to `BinningAutoBatcher`, https://github.com/Radical-AI/torch-sim/pull/143 @orionarcher
+
+* **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
@@ -18,10 +20,12 @@
 * New correlation function module, https://github.com/Radical-AI/torch-sim/pull/115 @stefanbringuier
 
 ### Documentation 📖
+
 * Imoved 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
 
 ### 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

CONTRIBUTING.md

@@ -13,6 +13,7 @@ Our CLA-bot will automatically verify your signature on pull requests. For quest
 ## Code Reviews
 
 All submissions require review by project maintainers before merging:
+
 - Submit changes via GitHub pull requests
 - Maintainers' submissions also require review by other maintainers
 - Address any feedback or requested changes promptly

README.md

@@ -123,7 +123,9 @@ To understand how TorchSim works, start with the [comprehensive tutorials](https
 
 ## Core Modules
 
-TorchSim's structure is summarized in the [API reference](https://radical-ai.github.io/torch-sim/reference/index.html) documentation.
+TorchSim's package structure is summarized in the [API reference](https://radical-ai.github.io/torch-sim/reference/index.html) documentation and drawn as a treemap below.
+
+![TorchSim package treemap](https://github.com/user-attachments/assets/1e67879b-cdca-4ebc-bbbd-061fed90dfed)
 
 ## License
 

docs/_static/draw_pkg_treemap.py

@@ -0,0 +1,25 @@
+"""Draw a treemap of the torch_sim package structure.
+
+Run with `uv run docs/_static/draw_pkg_treemap.py`
+"""
+
+# /// script
+# dependencies = [
+#     "pymatviz @ git+https://github.com/janosh/pymatviz",
+# ]
+# ///
+
+import os
+
+import pymatviz as pmv
+
+
+module_dir = os.path.dirname(__file__)
+pmv.set_plotly_template("plotly_white")
+
+pkg_name = "torch-sim"
+fig = pmv.py_pkg_treemap(pkg_name.replace("-", "_"))
+fig.layout.title.update(text=f"{pkg_name} Package Structure", font_size=20, x=0.5, y=0.98)
+fig.show()
+# pmv.io.save_and_compress_svg(fig, f"{module_dir}/{pkg_name}-pkg-treemap.svg")
+fig.write_html(f"{module_dir}/{pkg_name}-pkg-treemap.html", include_plotlyjs="cdn")