AGeDi 1.0.1__tar.gz

agedi-1.0.1/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Report a problem with AGeDi
+title: "[Bug] "
+labels: bug
+assignees: ''
+---
+
+## Describe the bug
+
+A clear and concise description of what the bug is.
+
+## To reproduce
+
+Minimal reproducible example:
+
+```python
+import agedi
+# ...
+```
+
+## Expected behaviour
+
+What you expected to happen.
+
+## Actual behaviour
+
+What actually happened (include the full traceback).
+
+```
+Traceback (most recent call last):
+  ...
+```
+
+## Environment
+
+- **AGeDi version**: <!-- python -c "import agedi; print(agedi.__version__)" -->
+- **Python version**:
+- **PyTorch version**:
+- **Operating system**:
+- **GPU** (if relevant):

agedi-1.0.1/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest a new feature or improvement
+title: "[Feature] "
+labels: enhancement
+assignees: ''
+---
+
+## Motivation
+
+Describe the use-case or problem that motivates this feature request.
+
+## Proposed solution
+
+A clear description of what you would like to happen, including a sketch of
+the proposed API if applicable.
+
+## Alternatives considered
+
+Have you considered any alternative approaches?  If so, why were they
+rejected?
+
+## Additional context
+
+Any other context, references, or screenshots that may be helpful.

agedi-1.0.1/.github/pull_request_template.md

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+## Summary
+
+<!-- One-paragraph description of the change and why it is needed. -->
+
+## Type of change
+
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Breaking change
+- [ ] Documentation update
+- [ ] Refactor / cleanup
+
+## Checklist
+
+- [ ] Tests added / updated for all new behaviour
+- [ ] `CHANGELOG.md` updated under `[Unreleased]`
+- [ ] All existing tests pass (`pytest`)
+- [ ] Docstrings updated for new/changed public API
+- [ ] No new `print()` calls in library code (use `warnings.warn` or Rich `Console`)
+
+## Related issues
+
+<!-- Closes #<issue number> -->

agedi-1.0.1/.github/workflows/auto-tag.yml

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+name: Auto Tag on Version Bump
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'VERSION'  # The workflow now triggers ONLY when the VERSION file changes
+
+jobs:
+  create_tag:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Extract version from VERSION file
+        id: get_version
+        # Reading a plain text file is as simple as using 'cat'
+        run: |
+          VERSION=$(cat VERSION | tr -d '[:space:]') # tr removes trailing newlines just in case
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "Detected version: $VERSION"
+
+      - name: Check if tag already exists
+        id: check_tag
+        run: |
+          TAG="v${{ steps.get_version.outputs.version }}"
+          if git ls-remote --tags origin | grep -q "refs/tags/$TAG"; then
+            echo "Tag $TAG already exists."
+            echo "exists=true" >> $GITHUB_OUTPUT
+          else
+            echo "Tag $TAG does not exist. Proceeding."
+            echo "exists=false" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Create and push tag
+        if: steps.check_tag.outputs.exists == 'false'
+        run: |
+          TAG="v${{ steps.get_version.outputs.version }}"
+          
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          
+          git tag "$TAG"
+          git push origin "$TAG"

agedi-1.0.1/.github/workflows/publish.yml

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+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on:
+  push:
+    tags:
+      - 'v*' # Triggers on tag pushes
+  workflow_dispatch: # Triggers on manual button clicks
+
+jobs:
+  # ---------------------------------------------------------
+  # JOB 1: Build the package (Runs every time)
+  # ---------------------------------------------------------
+  build:
+    name: Build package
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+          
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip build
+        
+      - name: Build the package
+        run: python -m build
+        
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  # ---------------------------------------------------------
+  # JOB 2: Publish to TestPyPI (ONLY runs on Tag Push)
+  # ---------------------------------------------------------
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    if: github.event_name == 'push' # The magic condition
+    runs-on: ubuntu-latest
+    
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/agedi
+      
+    permissions:
+      id-token: write
+      
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+          
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  # ---------------------------------------------------------
+  # JOB 3: Publish to real PyPI (ONLY runs Manually)
+  # ---------------------------------------------------------
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: build
+    if: github.event_name == 'workflow_dispatch' # The magic condition
+    runs-on: ubuntu-latest
+    
+    environment:
+      name: pypi
+      url: https://pypi.org/p/agedi # Replace with your package name
+      
+    permissions:
+      id-token: write
+      
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+          
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

agedi-1.0.1/.github/workflows/python-package.yml

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+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        pip install -e ".[test,full]"
+    - name: Test with pytest
+      run: |
+        pytest

agedi-1.0.1/.gitignore

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+.pytest_cache
+.coverage
+.coverage.xml
+.report.xml
+docs/_build
+**/__pycache__/
+logs/
+wandb/
+.coverage-html/
+src/AGeDi.egg-info/

agedi-1.0.1/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

agedi-1.0.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to AGeDi will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.0.0] - 2026-05-22
+
+### Added
+- Predictor-corrector (Langevin corrector) sampling via `corrector_steps` /
+  `corrector_step_size` parameters.
+- Force-field guided sampling (`ForcefieldGuidanceConfig`, `--ff_guidance` /
+  `--ff_zeta` CLI flags, `force_field=True` training option).
+- Post-diffusion relaxation loop (auto-triggered when `ff_guidance` is enabled
+  and forces exceed `force_threshold`).
+- `torch.compile` support for the reverse diffusion step (`compile=True` /
+  `--compile`), compiled per-instance to avoid cross-model interference.
+- `agedi predict` CLI command and `functional.predict()` API for energy/force
+  inference with trained regressor heads.
+- `agedi inspect` CLI command for inspecting saved model checkpoints.
+- `agedi train-hydra` CLI command and `train_from_config()` API supporting a
+  full YAML config file (`conf/train.yaml`).
+- Resume training from checkpoint (`--checkpoint` / `checkpoint:` config key).
+- Separate `regressor_data_path` support in config-file training for
+  non-equilibrium regressor data.
+- `Noiser.register()` class method for registering custom noisers.
+- `register_model()` function for registering custom GNN backbone factories.
+- `save_trajectory` parameter on `sample()` / `functional.sample()` (replaces
+  the old `save_path` parameter which has been removed).
+- `print_timings` parameter for per-stage sampling timing breakdown.
+- Skin-based neighbor-list caching in `update_graph()` to skip full rebuilds
+  when atoms have moved less than the skin distance.
+- `canonical_cell` option in `from_atoms()` / CLI / config to store cells in
+  canonical lower-triangular form.
+- `n_classes` option to explicitly set the number of atom-type classes for the
+  `Types` noiser.
+- `repeat` / `repeat_epoch` cell-repeat data augmentation.
+- `batch_naive_neighbor_list` pure-PyTorch fallback neighbor-list (used in the
+  compiled path when `nvalchemiops` is not available).
+
+### Changed
+- **Breaking**: `save_path` parameter removed from `Diffusion.sample()`,
+  `Diffusion._sample()`, and `functional.sample()`.  Use `save_trajectory`
+  instead.
+- `nvalchemiops` is now an **optional** dependency (`pip install agedi[cuda]`).
+  The non-compiled sampling path works without it.
+- `Agedi.__init__` `optim_config` and `scheduler_config` default to `None`
+  (computed internally) rather than shared mutable dicts.
+- `AtomsGraph.from_atoms` cell-canonicalization now emits `warnings.warn`
+  instead of `print`.
+- Compiled reverse step is now a lazy per-instance property instead of a
+  class-level `@torch.compile` decorator.
+- CI matrix extended to macOS runners; `.[test,full]` installed in one step.
+
+### Fixed
+- Python version badge corrected to `3.12+`.
+- `AtomsGraph` class docstring typo corrected.
+- `from_atoms` `canonical_cell` parameter docstring corrected (default is
+  `False`, not `True`).

agedi-1.0.1/CONTRIBUTING.md

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+# Contributing to AGeDi
+
+Thank you for your interest in contributing to AGeDi!  This document describes
+how to set up a development environment and the conventions we follow.
+
+## Setting up the development environment
+
+```bash
+git clone https://github.com/nronne/agedi.git
+cd agedi
+pip install -e ".[test,full]"
+```
+
+The `full` extra installs SchNetPack and the NVIDIA nvalchemi-toolkit-ops package.
+A plain `pip install -e .` omits these for a lightweight install.
+
+## Running the tests
+
+```bash
+pytest
+```
+
+## Code style
+
+We use [Ruff](https://docs.astral.sh/ruff/) for linting and formatting (line
+length 88).  Before opening a pull request please run:
+
+```bash
+ruff check src/
+ruff format src/
+```
+
+## Docstrings
+
+Use [NumPy-style docstrings](https://numpydoc.readthedocs.io/en/latest/format.html)
+for all public classes and functions.
+
+## Opening a pull request
+
+1. Fork the repository and create a feature branch from `main`.
+2. Add tests for any new functionality.
+3. Run the full test suite (`pytest`) and ensure it passes.
+4. Update `CHANGELOG.md` under the `[Unreleased]` section.
+5. Open a pull request against `main` with a clear description of the change.
+
+## Reporting bugs
+
+Please open an issue using the **Bug report** template and include:
+
+- AGeDi version (`python -c "import agedi; print(agedi.__version__)"`)
+- Python version and operating system
+- Minimal reproducible example
+- Full traceback
+
+## Feature requests
+
+Open an issue using the **Feature request** template.  Describe the use-case
+and, if possible, a sketch of the proposed API.