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BorgwardtLab · Jan 7, 2024 · 7f5b035 · 7f5b035
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Showing 44 changed files with 22 additions and 274 deletions.
diff --git a/proteinshake/__init__.py b/proteinshake/__init__.py
@@ -1 +1 @@
-__version__ = '0.3.13'
+__version__ = "1.0.0"
diff --git a/...inshake/backend/adapters/__baseclass__.py → proteinshake/adapter.py b/...inshake/backend/adapters/__baseclass__.py → proteinshake/adapter.py
diff --git a/proteinshake/backend/adapters/alphafold.py → proteinshake/adapters/alphafold.py b/proteinshake/backend/adapters/alphafold.py → proteinshake/adapters/alphafold.py
diff --git a/proteinshake/backend/adapters/pdb.py → proteinshake/adapters/pdb.py b/proteinshake/backend/adapters/pdb.py → proteinshake/adapters/pdb.py
diff --git a/proteinshake/backend/adapters/uniprot.py → proteinshake/adapters/uniprot.py b/proteinshake/backend/adapters/uniprot.py → proteinshake/adapters/uniprot.py
diff --git a/proteinshake/backend/protein.py b/proteinshake/backend/protein.py
diff --git a/proteinshake/backend/structure.py b/proteinshake/backend/structure.py
diff --git a/proteinshake/backend/database.py → proteinshake/database.py b/proteinshake/backend/database.py → proteinshake/database.py
diff --git a/proteinshake/backend/collection.py → proteinshake/dataset.py b/proteinshake/backend/collection.py → proteinshake/dataset.py
diff --git a/proteinshake/frontend/framework.py → proteinshake/framework.py b/proteinshake/frontend/framework.py → proteinshake/framework.py
diff --git a/proteinshake/frontend/README.md b/proteinshake/frontend/README.md
diff --git a/proteinshake/frontend/__init__.py b/proteinshake/frontend/__init__.py
diff --git a/proteinshake/frontend/dataset.py b/proteinshake/frontend/dataset.py
diff --git a/proteinshake/frontend/transforms/__init__.py b/proteinshake/frontend/transforms/__init__.py
diff --git a/proteinshake/frontend/transforms/framework/__init__.py b/proteinshake/frontend/transforms/framework/__init__.py
diff --git a/proteinshake/frontend/transforms/post_framework/note.md b/proteinshake/frontend/transforms/post_framework/note.md
diff --git a/proteinshake/frontend/transforms/post_representation/add_node_degree.py b/proteinshake/frontend/transforms/post_representation/add_node_degree.py
diff --git a/proteinshake/frontend/transforms/pre_framework/random_residue_masking.py b/proteinshake/frontend/transforms/pre_framework/random_residue_masking.py
diff --git a/proteinshake/frontend/transforms/pre_representation/residue_level.py b/proteinshake/frontend/transforms/pre_representation/residue_level.py
diff --git a/proteinshake/frontend/transforms/representation/__init__.py b/proteinshake/frontend/transforms/representation/__init__.py
diff --git a/...einshake/frontend/evaluators/evaluator.py → proteinshake/metric.py b/...einshake/frontend/evaluators/evaluator.py → proteinshake/metric.py
@@ -1,4 +1,4 @@
-class Metrics:
+class Metric:
     """For a collection of predictions and target values, return set of performance metrics.,"""
 
     pass
diff --git a/proteinshake/frontend/evaluators/__init__.py → proteinshake/metrics/__init__.py b/proteinshake/frontend/evaluators/__init__.py → proteinshake/metrics/__init__.py
diff --git a/...ake/frontend/evaluators/classification.py → proteinshake/metrics/classification.py b/...ake/frontend/evaluators/classification.py → proteinshake/metrics/classification.py
diff --git a/...inshake/frontend/evaluators/regression.py → proteinshake/metrics/regression.py b/...inshake/frontend/evaluators/regression.py → proteinshake/metrics/regression.py
diff --git a/...einshake/frontend/evaluators/retrieval.py → proteinshake/metrics/retrieval.py b/...einshake/frontend/evaluators/retrieval.py → proteinshake/metrics/retrieval.py
diff --git a/proteinshake/readme.md b/proteinshake/readme.md
diff --git a/proteinshake/frontend/representation.py → proteinshake/representation.py b/proteinshake/frontend/representation.py → proteinshake/representation.py
diff --git a/proteinshake/frontend/splitters/splitter.py → proteinshake/split.py b/proteinshake/frontend/splitters/splitter.py → proteinshake/split.py
diff --git a/proteinshake/frontend/splitters/__init__.py → proteinshake/splits/__init__.py b/proteinshake/frontend/splitters/__init__.py → proteinshake/splits/__init__.py
diff --git a/proteinshake/frontend/splitters/attribute.py → proteinshake/splits/attribute.py b/proteinshake/frontend/splitters/attribute.py → proteinshake/splits/attribute.py
diff --git a/.../frontend/splitters/pairwise_attribute.py → proteinshake/splits/pairwise_attribute.py b/.../frontend/splitters/pairwise_attribute.py → proteinshake/splits/pairwise_attribute.py
diff --git a/proteinshake/frontend/splitters/random.py → proteinshake/splits/random.py b/proteinshake/frontend/splitters/random.py → proteinshake/splits/random.py
diff --git a/proteinshake/frontend/targets/target.py → proteinshake/target.py b/proteinshake/frontend/targets/target.py → proteinshake/target.py
diff --git a/proteinshake/frontend/targets/__init__.py → proteinshake/targets/__init__.py b/proteinshake/frontend/targets/__init__.py → proteinshake/targets/__init__.py
diff --git a/...ntend/targets/pairwise_property_target.py → ...shake/targets/pairwise_property_target.py b/...ntend/targets/pairwise_property_target.py → ...shake/targets/pairwise_property_target.py
diff --git a/...shake/frontend/targets/property_target.py → proteinshake/targets/property_target.py b/...shake/frontend/targets/property_target.py → proteinshake/targets/property_target.py
diff --git a/proteinshake/frontend/task.py → proteinshake/task.py b/proteinshake/frontend/task.py → proteinshake/task.py
@@ -3,18 +3,18 @@
 import os
 from pathlib import Path
 from functools import partial
-from proteinshake.frontend.splitters import Split
-from proteinshake.frontend.targets import Target
-from proteinshake.frontend.evaluators import Metrics
-from proteinshake.frontend.transforms import Transform, Compose
+from proteinshake.split import Split
+from proteinshake.target import Target
+from proteinshake.metric import Metric
+from proteinshake.transform import Transform, Compose
 from proteinshake.util import amino_acid_alphabet, sharded, save_shards, load, warn
 
 
 class Task:
     dataset: str = ""
     split: Split = None
     target: Target = None
-    metrics: Metrics = None
+    metrics: Metric = None
     augmentation: Transform = None
 
     def __init__(
@@ -31,7 +31,7 @@ def __init__(
             if not os.environ.get("PROTEINSHAKE_ROOT", None) is None:
                 root = os.environ["PROTEINSHAKE_ROOT"]
             else:
-                root = "~/.proteinshake"
+                root = Path.home() / ".proteinshake"
         root = Path(root) / self.__class__.__name__
         os.makedirs(root, exist_ok=True)
         self.root = root

diff --git a/...einshake/frontend/transforms/transform.py → proteinshake/transform.py b/...einshake/frontend/transforms/transform.py → proteinshake/transform.py
diff --git a/proteinshake/transforms/__init__.py b/proteinshake/transforms/__init__.py
@@ -0,0 +1,2 @@
+from .point_cloud import *
+from .torch_framework import *
diff --git a/...frontend/transforms/label/MinMaxScaler.py → proteinshake/transforms/min_max_scaler.py b/...frontend/transforms/label/MinMaxScaler.py → proteinshake/transforms/min_max_scaler.py
diff --git a/...ontend/transforms/representation/point.py → proteinshake/transforms/point_cloud.py b/...ontend/transforms/representation/point.py → proteinshake/transforms/point_cloud.py
@@ -1,5 +1,5 @@
-from ..transform import Transform
-from proteinshake.frontend.representation import Representation
+from proteinshake.transform import Transform
+from proteinshake.representation import Representation
 import numpy as np
 
 

diff --git a/...ke/frontend/transforms/framework/torch.py → proteinshake/transforms/torch_framework.py b/...ke/frontend/transforms/framework/torch.py → proteinshake/transforms/torch_framework.py
@@ -1,8 +1,8 @@
 import torch
 import numpy as np
 from torch.utils.data import DataLoader, IterableDataset
-from ..transform import Transform
-from proteinshake.frontend.framework import Framework
+from proteinshake.transform import Transform
+from proteinshake.framework import Framework
 
 
 class TorchFrameworkTransform(Framework, Transform):

diff --git a/tests/dataset.py b/tests/dataset.py
diff --git a/tests/task.py b/tests/task.py
@@ -1,12 +1,12 @@
 import unittest
 import numpy as np
 import itertools
-from proteinshake.frontend.evaluators import Metrics
-from proteinshake.frontend.targets import Target
-from proteinshake.frontend.splitters import Split
-from proteinshake.frontend.task import Task
-from proteinshake.frontend.transforms import *
-from proteinshake.frontend.transforms import Transform, LabelTransform
+from proteinshake.metric import Metric
+from proteinshake.target import Target
+from proteinshake.split import Split
+from proteinshake.task import Task
+from proteinshake.transform import *
+from proteinshake.transforms import *
 
 
 class TestTask(unittest.TestCase):
@@ -16,7 +16,7 @@ class MyTarget(Target):
             def __call__(self, dataset):
                 return (((p,), p["label"]) for p in dataset)
 
-        class MyMetrics(Metrics):
+        class MyMetric(Metric):
             def __call__(self, y_true, y_pred):
                 return {"Accuracy": np.random.random()}
 
@@ -39,7 +39,7 @@ class MyTask(Task):
             dataset = "test"
             split = MySplit
             target = MyTarget
-            metrics = MyMetrics
+            metrics = MyMetric
             augmentation = MyAugmentation
 
         # END USER
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		from .point_cloud import *
		from .torch_framework import *