adaptivepy-sampling 0.1.1__tar.gz → 0.1.2__tar.gz

adaptivepy_sampling-0.1.2/PKG-INFO

@@ -0,0 +1,108 @@
+Metadata-Version: 2.4
+Name: adaptivepy-sampling
+Version: 0.1.2
+Summary: Adaptive sampling on MD trajectories via clustering and policy-driven seed selection
+Author: AdaptivePy Contributors
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.20
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: click>=8.0
+Requires-Dist: joblib>=1.0
+Requires-Dist: mdtraj>=1.9
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.24; extra == "docs"
+
+# AdaptivePy
+
+**Adaptive sampling for molecular dynamics trajectories**
+
+Clustering-based state space partitioning and policy-driven seed selection for MD workflows.
+
+[![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue?style=for-the-badge)](https://hnadeem2.github.io/AdaptivePy/)
+[![PyPI](https://img.shields.io/badge/PyPI-adaptivepy--sampling-orange?style=for-the-badge)](https://pypi.org/project/adaptivepy-sampling/)
+[![Python](https://img.shields.io/badge/python-3.9+-green?style=for-the-badge)](https://www.python.org/)
+
+---
+
+## Overview
+
+AdaptivePy helps you identify under-sampled regions of conformational space and select seed frames for new simulations. It loads per-trajectory feature arrays, clusters frames, applies adaptive policies, and writes reproducible metadata and optional PDB structures.
+
+**Full documentation:** [https://hnadeem2.github.io/AdaptivePy/](https://hnadeem2.github.io/AdaptivePy/)
+
+| | |
+|---|---|
+| **Input** | Feature arrays (`.npy` / `.pkl`), optional coordinate trajectories |
+| **Clustering** | KMeans, MiniBatch KMeans, regular-space |
+| **Policies** | Least counts, random (extensible) |
+| **Output** | Seeds, cluster assignments, model, logs, optional PDBs |
+
+## Installation
+
+```bash
+pip install adaptivepy-sampling
+```
+
+For development:
+
+```bash
+git clone https://github.com/hnadeem2/AdaptivePy.git
+cd AdaptivePy
+pip install -e ".[dev,docs]"
+```
+
+## Quick start
+
+1. **Prepare features** — one file per trajectory, shape `(n_frames, n_features)`:
+
+   ```text
+   features/
+   ├── traj_0.npy
+   └── traj_1.pkl
+   ```
+
+2. **Configure** — edit `examples/config.yaml` (or create your own).
+
+3. **Run**:
+
+   ```bash
+   adaptivepy run examples/config.yaml
+   ```
+
+See the [Getting Started guide](https://hnadeem2.github.io/AdaptivePy/getting-started/) for a complete walkthrough.
+
+## CLI
+
+```bash
+adaptivepy run config.yaml       # run adaptive sampling
+adaptivepy validate config.yaml  # validate inputs only
+adaptivepy list-policies         # list available policies
+```
+
+## Python API
+
+```python
+from adaptivepy import run_adaptive_sampling
+
+results = run_adaptive_sampling("config.yaml")
+```
+
+## Documentation
+
+| Guide | Description |
+|-------|-------------|
+| [Getting Started](https://hnadeem2.github.io/AdaptivePy/getting-started/) | First run in minutes |
+| [Configuration](https://hnadeem2.github.io/AdaptivePy/configuration/) | YAML options and defaults |
+| [Feature Inputs](https://hnadeem2.github.io/AdaptivePy/features/) | File formats and layout |
+| [Policies](https://hnadeem2.github.io/AdaptivePy/policies/) | Seed selection strategies |
+| [API Reference](https://hnadeem2.github.io/AdaptivePy/reference/api/) | Module documentation |
+
+## License
+
+MIT

adaptivepy_sampling-0.1.2/README.md

@@ -0,0 +1,88 @@
+# AdaptivePy
+
+**Adaptive sampling for molecular dynamics trajectories**
+
+Clustering-based state space partitioning and policy-driven seed selection for MD workflows.
+
+[![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue?style=for-the-badge)](https://hnadeem2.github.io/AdaptivePy/)
+[![PyPI](https://img.shields.io/badge/PyPI-adaptivepy--sampling-orange?style=for-the-badge)](https://pypi.org/project/adaptivepy-sampling/)
+[![Python](https://img.shields.io/badge/python-3.9+-green?style=for-the-badge)](https://www.python.org/)
+
+---
+
+## Overview
+
+AdaptivePy helps you identify under-sampled regions of conformational space and select seed frames for new simulations. It loads per-trajectory feature arrays, clusters frames, applies adaptive policies, and writes reproducible metadata and optional PDB structures.
+
+**Full documentation:** [https://hnadeem2.github.io/AdaptivePy/](https://hnadeem2.github.io/AdaptivePy/)
+
+| | |
+|---|---|
+| **Input** | Feature arrays (`.npy` / `.pkl`), optional coordinate trajectories |
+| **Clustering** | KMeans, MiniBatch KMeans, regular-space |
+| **Policies** | Least counts, random (extensible) |
+| **Output** | Seeds, cluster assignments, model, logs, optional PDBs |
+
+## Installation
+
+```bash
+pip install adaptivepy-sampling
+```
+
+For development:
+
+```bash
+git clone https://github.com/hnadeem2/AdaptivePy.git
+cd AdaptivePy
+pip install -e ".[dev,docs]"
+```
+
+## Quick start
+
+1. **Prepare features** — one file per trajectory, shape `(n_frames, n_features)`:
+
+   ```text
+   features/
+   ├── traj_0.npy
+   └── traj_1.pkl
+   ```
+
+2. **Configure** — edit `examples/config.yaml` (or create your own).
+
+3. **Run**:
+
+   ```bash
+   adaptivepy run examples/config.yaml
+   ```
+
+See the [Getting Started guide](https://hnadeem2.github.io/AdaptivePy/getting-started/) for a complete walkthrough.
+
+## CLI
+
+```bash
+adaptivepy run config.yaml       # run adaptive sampling
+adaptivepy validate config.yaml  # validate inputs only
+adaptivepy list-policies         # list available policies
+```
+
+## Python API
+
+```python
+from adaptivepy import run_adaptive_sampling
+
+results = run_adaptive_sampling("config.yaml")
+```
+
+## Documentation
+
+| Guide | Description |
+|-------|-------------|
+| [Getting Started](https://hnadeem2.github.io/AdaptivePy/getting-started/) | First run in minutes |
+| [Configuration](https://hnadeem2.github.io/AdaptivePy/configuration/) | YAML options and defaults |
+| [Feature Inputs](https://hnadeem2.github.io/AdaptivePy/features/) | File formats and layout |
+| [Policies](https://hnadeem2.github.io/AdaptivePy/policies/) | Seed selection strategies |
+| [API Reference](https://hnadeem2.github.io/AdaptivePy/reference/api/) | Module documentation |
+
+## License
+
+MIT

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/adaptivepy/__init__.py

@@ -1,6 +1,6 @@
 """AdaptivePy: adaptive sampling for molecular dynamics trajectories."""
 
-__version__ = "0.1.1"
+__version__ = "0.1.2"
 
 from adaptivepy.api import run_adaptive_sampling
 

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/adaptivepy/api.py

@@ -11,6 +11,7 @@ import numpy as np
 from adaptivepy.clustering import create_clusterer, fit_clusterer
 from adaptivepy.config.schema import RunConfig, load_config
 from adaptivepy.io.loader import (
+    list_feature_files,
     list_trajectory_files,
     load_features,
     validate_dataset,
@@ -84,7 +85,7 @@ def run_adaptive_sampling(
     np.random.seed(config.random_seed)
 
     # --- Load and validate data ---
-    feature_files = sorted(Path(config.features_dir).glob("*.npy"))
+    feature_files = list_feature_files(config.features_dir)
     trajectory_files: Optional[List[Path]] = None
     trajectory_map: Optional[Dict[int, Path]] = None
 
@@ -199,9 +200,7 @@ def validate_config(config_path: str | Path) -> RunConfig:
     config_path = Path(config_path)
     config = load_config(config_path)
 
-    feature_files = sorted(Path(config.features_dir).glob("*.npy"))
-    if not feature_files:
-        raise ValueError(f"No feature files in {config.features_dir}")
+    feature_files = list_feature_files(config.features_dir)
 
     trajectory_files = None
     if config.trajectories_dir is not None:

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/adaptivepy/config/schema.py

@@ -55,7 +55,7 @@ class RunConfig:
     Attributes
     ----------
     features_dir : Path
-        Directory containing ``*.npy`` feature files.
+        Directory containing ``*.npy`` or ``*.pkl`` feature files.
     output_dir : Path
         Directory where results are written.
     trajectories_dir : Path or None

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/adaptivepy/io/__init__.py

@@ -1,8 +1,10 @@
 """Input/output utilities for AdaptivePy."""
 
 from adaptivepy.io.loader import (
+    FEATURE_EXTENSIONS,
     list_feature_files,
     list_trajectory_files,
+    load_feature_array,
     load_features,
     validate_dataset,
     validate_feature_trajectory_mapping,
@@ -15,10 +17,12 @@ from adaptivepy.io.trajectory import (
 )
 
 __all__ = [
+    "FEATURE_EXTENSIONS",
     "build_trajectory_map",
     "extract_frame",
     "list_feature_files",
     "list_trajectory_files",
+    "load_feature_array",
     "load_features",
     "load_trajectory",
     "validate_dataset",

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/adaptivepy/io/loader.py

@@ -6,15 +6,18 @@ import logging
 from pathlib import Path
 from typing import Dict, List, Optional, Tuple
 
+import joblib
 import numpy as np
 
 from adaptivepy.models import Dataset, FrameRecord
 
 logger = logging.getLogger(__name__)
 
+FEATURE_EXTENSIONS = (".npy", ".pkl")
+
 
 def list_feature_files(features_dir: Path) -> List[Path]:
-    """List ``*.npy`` feature files in a directory, sorted by name.
+    """List ``*.npy`` and ``*.pkl`` feature files in a directory, sorted by stem.
 
     Parameters
     ----------
@@ -24,25 +27,80 @@ def list_feature_files(features_dir: Path) -> List[Path]:
     Returns
     -------
     list of Path
-        Sorted paths to feature files.
+        Sorted paths to feature files (one file per trajectory stem).
 
     Raises
     ------
     FileNotFoundError
         If the directory does not exist.
     ValueError
-        If no ``*.npy`` files are found.
+        If no supported feature files are found or duplicate stems exist.
     """
     features_dir = Path(features_dir)
     if not features_dir.is_dir():
         raise FileNotFoundError(f"Features directory not found: {features_dir}")
 
-    files = sorted(features_dir.glob("*.npy"))
+    files_by_stem: Dict[str, Path] = {}
+    for path in sorted(features_dir.iterdir()):
+        if not path.is_file():
+            continue
+        suffix = path.suffix.lower()
+        if suffix not in FEATURE_EXTENSIONS:
+            continue
+        stem = path.stem
+        if stem in files_by_stem:
+            raise ValueError(
+                f"Duplicate feature files for '{stem}': "
+                f"{files_by_stem[stem].name} and {path.name}"
+            )
+        files_by_stem[stem] = path
+
+    files = [files_by_stem[stem] for stem in sorted(files_by_stem)]
     if not files:
-        raise ValueError(f"No .npy feature files found in {features_dir}")
+        raise ValueError(
+            f"No .npy or .pkl feature files found in {features_dir}"
+        )
     return files
 
 
+def load_feature_array(path: Path) -> np.ndarray:
+    """Load a feature array from a ``.npy`` or ``.pkl`` file.
+
+    Parameters
+    ----------
+    path : Path
+        Path to a feature file.
+
+    Returns
+    -------
+    np.ndarray
+        Loaded feature array.
+
+    Raises
+    ------
+    ValueError
+        If the file extension is unsupported or the loaded object cannot be
+        converted to an array.
+    """
+    suffix = path.suffix.lower()
+    if suffix == ".npy":
+        data = np.load(path)
+    elif suffix == ".pkl":
+        data = joblib.load(path)
+    else:
+        raise ValueError(
+            f"Unsupported feature file extension '{suffix}' in {path}. "
+            f"Use one of: {', '.join(FEATURE_EXTENSIONS)}"
+        )
+
+    try:
+        return np.asarray(data)
+    except (TypeError, ValueError) as exc:
+        raise ValueError(
+            f"Feature file {path} does not contain a numeric array."
+        ) from exc
+
+
 def list_trajectory_files(trajectories_dir: Path) -> List[Path]:
     """List coordinate trajectory files supported by mdtraj.
 
@@ -96,7 +154,7 @@ def validate_feature_trajectory_mapping(
     Parameters
     ----------
     feature_files : list of Path
-        Feature ``.npy`` file paths.
+        Feature ``.npy`` or ``.pkl`` file paths.
     trajectory_files : list of Path or None
         Optional coordinate trajectory file paths.
 
@@ -130,8 +188,9 @@ def validate_feature_trajectory_mapping(
 def load_features(features_dir: Path) -> Dataset:
     """Load feature arrays from disk and build a :class:`Dataset`.
 
-    Each ``*.npy`` file must have shape ``(n_frames, n_features)``. Per-frame
-    ``FrameRecord`` objects are created while preserving trajectory identity.
+    Each ``*.npy`` or ``*.pkl`` file must have shape ``(n_frames, n_features)``.
+    Per-frame ``FrameRecord`` objects are created while preserving trajectory
+    identity.
 
     Parameters
     ----------
@@ -157,7 +216,7 @@ def load_features(features_dir: Path) -> Dataset:
     n_features: Optional[int] = None
 
     for traj_id, feature_path in enumerate(feature_files):
-        features = np.load(feature_path)
+        features = load_feature_array(feature_path)
         if features.ndim != 2:
             raise ValueError(
                 f"Feature file {feature_path} must be 2D (n_frames, n_features), "

adaptivepy_sampling-0.1.2/adaptivepy_sampling.egg-info/PKG-INFO

@@ -0,0 +1,108 @@
+Metadata-Version: 2.4
+Name: adaptivepy-sampling
+Version: 0.1.2
+Summary: Adaptive sampling on MD trajectories via clustering and policy-driven seed selection
+Author: AdaptivePy Contributors
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.20
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: click>=8.0
+Requires-Dist: joblib>=1.0
+Requires-Dist: mdtraj>=1.9
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.24; extra == "docs"
+
+# AdaptivePy
+
+**Adaptive sampling for molecular dynamics trajectories**
+
+Clustering-based state space partitioning and policy-driven seed selection for MD workflows.
+
+[![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue?style=for-the-badge)](https://hnadeem2.github.io/AdaptivePy/)
+[![PyPI](https://img.shields.io/badge/PyPI-adaptivepy--sampling-orange?style=for-the-badge)](https://pypi.org/project/adaptivepy-sampling/)
+[![Python](https://img.shields.io/badge/python-3.9+-green?style=for-the-badge)](https://www.python.org/)
+
+---
+
+## Overview
+
+AdaptivePy helps you identify under-sampled regions of conformational space and select seed frames for new simulations. It loads per-trajectory feature arrays, clusters frames, applies adaptive policies, and writes reproducible metadata and optional PDB structures.
+
+**Full documentation:** [https://hnadeem2.github.io/AdaptivePy/](https://hnadeem2.github.io/AdaptivePy/)
+
+| | |
+|---|---|
+| **Input** | Feature arrays (`.npy` / `.pkl`), optional coordinate trajectories |
+| **Clustering** | KMeans, MiniBatch KMeans, regular-space |
+| **Policies** | Least counts, random (extensible) |
+| **Output** | Seeds, cluster assignments, model, logs, optional PDBs |
+
+## Installation
+
+```bash
+pip install adaptivepy-sampling
+```
+
+For development:
+
+```bash
+git clone https://github.com/hnadeem2/AdaptivePy.git
+cd AdaptivePy
+pip install -e ".[dev,docs]"
+```
+
+## Quick start
+
+1. **Prepare features** — one file per trajectory, shape `(n_frames, n_features)`:
+
+   ```text
+   features/
+   ├── traj_0.npy
+   └── traj_1.pkl
+   ```
+
+2. **Configure** — edit `examples/config.yaml` (or create your own).
+
+3. **Run**:
+
+   ```bash
+   adaptivepy run examples/config.yaml
+   ```
+
+See the [Getting Started guide](https://hnadeem2.github.io/AdaptivePy/getting-started/) for a complete walkthrough.
+
+## CLI
+
+```bash
+adaptivepy run config.yaml       # run adaptive sampling
+adaptivepy validate config.yaml  # validate inputs only
+adaptivepy list-policies         # list available policies
+```
+
+## Python API
+
+```python
+from adaptivepy import run_adaptive_sampling
+
+results = run_adaptive_sampling("config.yaml")
+```
+
+## Documentation
+
+| Guide | Description |
+|-------|-------------|
+| [Getting Started](https://hnadeem2.github.io/AdaptivePy/getting-started/) | First run in minutes |
+| [Configuration](https://hnadeem2.github.io/AdaptivePy/configuration/) | YAML options and defaults |
+| [Feature Inputs](https://hnadeem2.github.io/AdaptivePy/features/) | File formats and layout |
+| [Policies](https://hnadeem2.github.io/AdaptivePy/policies/) | Seed selection strategies |
+| [API Reference](https://hnadeem2.github.io/AdaptivePy/reference/api/) | Module documentation |
+
+## License
+
+MIT

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/adaptivepy_sampling.egg-info/requires.txt

@@ -7,3 +7,7 @@ mdtraj>=1.9
 
 [dev]
 pytest>=7.0
+
+[docs]
+mkdocs-material>=9.0
+mkdocstrings[python]>=0.24

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "adaptivepy-sampling"
-version = "0.1.1"
+version = "0.1.2"
 description = "Adaptive sampling on MD trajectories via clustering and policy-driven seed selection"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -21,6 +21,10 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = ["pytest>=7.0"]
+docs = [
+    "mkdocs-material>=9.0",
+    "mkdocstrings[python]>=0.24",
+]
 
 [project.scripts]
 adaptivepy = "adaptivepy.cli.run:main"

{adaptivepy_sampling-0.1.1 → adaptivepy_sampling-0.1.2}/tests/test_adaptivepy.py

@@ -4,10 +4,12 @@ from __future__ import annotations
 
 from pathlib import Path
 
+import joblib
 import numpy as np
 import pytest
 
 from adaptivepy.api import run_adaptive_sampling, validate_config
+from adaptivepy.io.loader import load_feature_array, load_features
 from adaptivepy.policies import list_policies
 
 
@@ -61,6 +63,22 @@ write_pdbs: false
     assert (output_dir / "combined_metadata.csv").is_file()
 
 
+def test_load_pkl_features(tmp_path: Path) -> None:
+    """Feature loading supports .pkl files with the same shape contract."""
+    features_dir = tmp_path / "features"
+    features_dir.mkdir()
+    rng = np.random.default_rng(1)
+    array = rng.normal(size=(25, 6))
+    joblib.dump(array, features_dir / "traj_0.pkl")
+
+    loaded = load_feature_array(features_dir / "traj_0.pkl")
+    np.testing.assert_array_equal(loaded, array)
+
+    dataset = load_features(features_dir)
+    assert dataset.feature_matrix.shape == (25, 6)
+    assert dataset.traj_names == ["traj_0"]
+
+
 def test_validate_config(tmp_path: Path, synthetic_features: Path) -> None:
     """Validation succeeds for a well-formed configuration."""
     config_path = tmp_path / "config.yaml"

adaptivepy_sampling-0.1.1/PKG-INFO

@@ -1,52 +0,0 @@
-Metadata-Version: 2.4
-Name: adaptivepy-sampling
-Version: 0.1.1
-Summary: Adaptive sampling on MD trajectories via clustering and policy-driven seed selection
-Author: AdaptivePy Contributors
-License: MIT
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-Requires-Dist: numpy>=1.20
-Requires-Dist: scikit-learn>=1.0
-Requires-Dist: pyyaml>=6.0
-Requires-Dist: click>=8.0
-Requires-Dist: joblib>=1.0
-Requires-Dist: mdtraj>=1.9
-Provides-Extra: dev
-Requires-Dist: pytest>=7.0; extra == "dev"
-
-# AdaptivePy
-
-Adaptive sampling on molecular dynamics trajectories using clustering-based state space partitioning and policy-driven seed selection.
-
-## Installation
-
-```bash
-pip install adaptivepy-sampling
-```
-
-## Quick start
-
-1. Prepare feature files (`features/traj_0.npy`, ...) with shape `(n_frames, n_features)`.
-2. Optionally add matching coordinate trajectories (`trajectories/traj_0.xtc`, ...) and a topology file.
-3. Edit `examples/config.yaml` and run:
-
-```bash
-adaptivepy run examples/config.yaml
-```
-
-## CLI
-
-```bash
-adaptivepy run config.yaml
-adaptivepy validate config.yaml
-adaptivepy list-policies
-```
-
-## Python API
-
-```python
-from adaptivepy import run_adaptive_sampling
-
-results = run_adaptive_sampling("config.yaml")
-```

adaptivepy_sampling-0.1.1/README.md

@@ -1,35 +0,0 @@
-# AdaptivePy
-
-Adaptive sampling on molecular dynamics trajectories using clustering-based state space partitioning and policy-driven seed selection.
-
-## Installation
-
-```bash
-pip install adaptivepy-sampling
-```
-
-## Quick start
-
-1. Prepare feature files (`features/traj_0.npy`, ...) with shape `(n_frames, n_features)`.
-2. Optionally add matching coordinate trajectories (`trajectories/traj_0.xtc`, ...) and a topology file.
-3. Edit `examples/config.yaml` and run:
-
-```bash
-adaptivepy run examples/config.yaml
-```
-
-## CLI
-
-```bash
-adaptivepy run config.yaml
-adaptivepy validate config.yaml
-adaptivepy list-policies
-```
-
-## Python API
-
-```python
-from adaptivepy import run_adaptive_sampling
-
-results = run_adaptive_sampling("config.yaml")
-```

adaptivepy_sampling-0.1.1/adaptivepy_sampling.egg-info/PKG-INFO

@@ -1,52 +0,0 @@
-Metadata-Version: 2.4
-Name: adaptivepy-sampling
-Version: 0.1.1
-Summary: Adaptive sampling on MD trajectories via clustering and policy-driven seed selection
-Author: AdaptivePy Contributors
-License: MIT
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-Requires-Dist: numpy>=1.20
-Requires-Dist: scikit-learn>=1.0
-Requires-Dist: pyyaml>=6.0
-Requires-Dist: click>=8.0
-Requires-Dist: joblib>=1.0
-Requires-Dist: mdtraj>=1.9
-Provides-Extra: dev
-Requires-Dist: pytest>=7.0; extra == "dev"
-
-# AdaptivePy
-
-Adaptive sampling on molecular dynamics trajectories using clustering-based state space partitioning and policy-driven seed selection.
-
-## Installation
-
-```bash
-pip install adaptivepy-sampling
-```
-
-## Quick start
-
-1. Prepare feature files (`features/traj_0.npy`, ...) with shape `(n_frames, n_features)`.
-2. Optionally add matching coordinate trajectories (`trajectories/traj_0.xtc`, ...) and a topology file.
-3. Edit `examples/config.yaml` and run:
-
-```bash
-adaptivepy run examples/config.yaml
-```
-
-## CLI
-
-```bash
-adaptivepy run config.yaml
-adaptivepy validate config.yaml
-adaptivepy list-policies
-```
-
-## Python API
-
-```python
-from adaptivepy import run_adaptive_sampling
-
-results = run_adaptive_sampling("config.yaml")
-```