adaptivepy-sampling 0.1.2__tar.gz → 0.2.0__tar.gz

adaptivepy_sampling-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Hassan
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{adaptivepy_sampling-0.1.2 → adaptivepy_sampling-0.2.0}/PKG-INFO

@@ -1,22 +1,46 @@
 Metadata-Version: 2.4
 Name: adaptivepy-sampling
-Version: 0.1.2
+Version: 0.2.0
 Summary: Adaptive sampling on MD trajectories via clustering and policy-driven seed selection
-Author: AdaptivePy Contributors
-License: MIT
+Author: Hassan
+License: MIT License
+        
+        Copyright (c) 2026 Hassan
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
+License-File: LICENSE
 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
+Requires-Dist: scipy>=1.7
 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"
+Dynamic: license-file
 
 # AdaptivePy
 
@@ -40,7 +64,7 @@ AdaptivePy helps you identify under-sampled regions of conformational space and
 |---|---|
 | **Input** | Feature arrays (`.npy` / `.pkl`), optional coordinate trajectories |
 | **Clustering** | KMeans, MiniBatch KMeans, regular-space |
-| **Policies** | Least counts, random (extensible) |
+| **Policies** | Least counts, random, FAST, MA-REAP (extensible) |
 | **Output** | Seeds, cluster assignments, model, logs, optional PDBs |
 
 ## Installation
@@ -103,6 +127,10 @@ results = run_adaptive_sampling("config.yaml")
 | [Policies](https://hnadeem2.github.io/AdaptivePy/policies/) | Seed selection strategies |
 | [API Reference](https://hnadeem2.github.io/AdaptivePy/reference/api/) | Module documentation |
 
+## Contributors
+
+- Hassan
+
 ## License
 
-MIT
+MIT. See [LICENSE](LICENSE) for details.

{adaptivepy_sampling-0.1.2 → adaptivepy_sampling-0.2.0}/README.md

@@ -20,7 +20,7 @@ AdaptivePy helps you identify under-sampled regions of conformational space and
 |---|---|
 | **Input** | Feature arrays (`.npy` / `.pkl`), optional coordinate trajectories |
 | **Clustering** | KMeans, MiniBatch KMeans, regular-space |
-| **Policies** | Least counts, random (extensible) |
+| **Policies** | Least counts, random, FAST, MA-REAP (extensible) |
 | **Output** | Seeds, cluster assignments, model, logs, optional PDBs |
 
 ## Installation
@@ -83,6 +83,10 @@ results = run_adaptive_sampling("config.yaml")
 | [Policies](https://hnadeem2.github.io/AdaptivePy/policies/) | Seed selection strategies |
 | [API Reference](https://hnadeem2.github.io/AdaptivePy/reference/api/) | Module documentation |
 
+## Contributors
+
+- Hassan
+
 ## License
 
-MIT
+MIT. See [LICENSE](LICENSE) for details.

{adaptivepy_sampling-0.1.2 → adaptivepy_sampling-0.2.0}/adaptivepy/__init__.py

@@ -1,6 +1,6 @@
 """AdaptivePy: adaptive sampling for molecular dynamics trajectories."""
 
-__version__ = "0.1.2"
+__version__ = "0.2.0"
 
 from adaptivepy.api import run_adaptive_sampling
 

{adaptivepy_sampling-0.1.2 → adaptivepy_sampling-0.2.0}/adaptivepy/api.py

@@ -9,7 +9,7 @@ from typing import Dict, List, Optional
 import numpy as np
 
 from adaptivepy.clustering import create_clusterer, fit_clusterer
-from adaptivepy.config.schema import RunConfig, load_config
+from adaptivepy.config.schema import RunConfig, build_policy_kwargs, load_config
 from adaptivepy.io.loader import (
     list_feature_files,
     list_trajectory_files,
@@ -28,6 +28,8 @@ from adaptivepy.output.writer import (
     write_cluster_model,
     write_cluster_statistics,
     write_combined_metadata,
+    write_fast_scores,
+    write_ma_reap_outputs,
     write_policy_outputs,
     write_run_config,
 )
@@ -121,6 +123,7 @@ def run_adaptive_sampling(
 
     cluster_stats = compute_cluster_stats(dataset)
     centers = clusterer.cluster_centers_
+    n_features = dataset.feature_matrix.shape[1]
 
     logger.info(
         "Clustering complete: %d clusters, %d total frames",
@@ -139,9 +142,15 @@ def run_adaptive_sampling(
 
     for policy_name in config.policies:
         logger.info("Applying policy: %s", policy_name)
-        policy_kwargs = {}
-        if policy_name == "random":
-            policy_kwargs["random_state"] = config.random_seed
+        policy_kwargs = build_policy_kwargs(
+            policy_name,
+            config,
+            n_features=n_features,
+            traj_names=dataset.traj_names,
+            n_clusters=len(cluster_stats),
+        )
+        if policy_name == "ma_reap":
+            policy_kwargs["cluster_centers"] = centers
 
         policy = get_policy(policy_name, **policy_kwargs)
         selected_clusters = policy.select_clusters(
@@ -161,6 +170,20 @@ def run_adaptive_sampling(
             policy_name, seeds, cluster_stats, output_dir
         )
 
+        if policy_name == "fast" and hasattr(policy, "last_scores"):
+            write_fast_scores(policy.last_scores, policy_dir)
+
+        if policy_name == "ma_reap" and hasattr(policy, "last_scores"):
+            write_ma_reap_outputs(
+                scores=policy.last_scores,
+                weights=policy.last_weights,
+                stakes=policy.last_stakes,
+                executors=policy.last_executors,
+                agent_names=policy.agent_names,
+                seeds=seeds,
+                output_dir=policy_dir,
+            )
+
         if (
             config.write_pdbs
             and trajectory_map is not None
@@ -209,6 +232,7 @@ def validate_config(config_path: str | Path) -> RunConfig:
 
     dataset = load_features(config.features_dir)
     validate_dataset(dataset, trajectory_files)
+    n_features = dataset.feature_matrix.shape[1]
 
     if config.trajectories_dir is not None and config.topology is not None:
         trajectory_map = build_trajectory_map(
@@ -223,6 +247,14 @@ def validate_config(config_path: str | Path) -> RunConfig:
         )
 
     for policy_name in config.policies:
-        get_policy(policy_name)
+        get_policy(
+            policy_name,
+            **build_policy_kwargs(
+                policy_name,
+                config,
+                n_features=n_features,
+                traj_names=dataset.traj_names,
+            ),
+        )
 
     return config