some re-arrangement & additions for python packaging

.github/workflows/build.yaml

@@ -0,0 +1,65 @@
+name: Python package
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.12"]
+        # We aim to support the versions on pytorch.org
+        # as well as selected previous versions on
+        # https://pytorch.org/get-started/previous-versions/
+        torch-version: ["2.4.0"]
+        include:
+          - os: windows-latest
+            torch-version: 2.4.0
+            python-version: "3.12"
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Cache dependencies
+        id: pip-cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: pip-os_${{ runner.os }}-python_${{ matrix.python-version }}-torch_${{ matrix.torch-version }}
+
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install package
+        run: |
+          python -m pip install git+https://github.com/RobustBench/robustbench.git
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install torch==${{ matrix.torch-version }} --extra-index-url https://download.pytorch.org/whl/cpu
+          pip install '.[dev]'
+
+      - name: Run pytest tests
+        timeout-minutes: 10
+        run: |
+          pip install pytest
+          python -m pytest
+
+      - name: Build package
+        run: |
+          make build
+
+      - name: Check reinstall script
+        timeout-minutes: 3
+        run: |
+          ./reinstall.sh

.github/workflows/codespell.yml

@@ -0,0 +1,21 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1
+        with:
+           ignore_words_list: aros, fpr, tpr, idx, fpr95

.github/workflows/release-pypi.yml

@@ -0,0 +1,52 @@
+name: release
+
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+  pull_request:
+    branches:
+      - main
+    types:
+      - labeled
+      - opened
+      - edited
+      - synchronize
+      - reopened
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Cache dependencies
+        id: pip-cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Build and publish to Test PyPI
+        if: ${{ (github.ref != 'refs/heads/main') && (github.event.label.name == 'release') }}
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+        run: |
+          make dist
+          ls dist/
+          tar tvf dist/aros-node-*.tar.gz
+          python3 -m twine upload --repository testpypi dist/*
+
+      - name: Build and publish to PyPI
+        if: ${{ github.event_name == 'push' }}
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          make dist
+          ls dist/
+          tar tvf dist/aros-node-*.tar.gz
+          python3 -m twine upload dist/*

.gitignore

@@ -1,4 +1,5 @@
 .DS_Store
+.tar.gz
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

aros_node/__init__.py

@@ -0,0 +1,9 @@
+# © M.W. Mathis Lab | Hossein Mirzaei & M.W. Mathis
+# https://github.com/AdaptiveMotorControlLab/AROS
+# Licensed under Apache 2.0
+
+from aros_node.version import __version__
+from aros_node.data_loader import LabelChangedDataset, get_subsampled_subset, get_loaders
+from aros_node.evaluate import compute_fpr95, compute_auroc, compute_aupr, get_clean_AUC, wrapper_method
+from aros_node.stability_loss_function import *
+from aros_node.utils import *

AROS/evaluate.py → aros_node/evaluate.py

@@ -1,7 +1,7 @@
 import numpy as np
 from tqdm.notebook import tqdm
 from sklearn.metrics import roc_curve, roc_auc_score, precision_recall_curve, auc
-from utils import *
+from aros_node.utils import *
 import argparse
 import torch
 import torch.nn as nn

AROS/stability_loss_function.py → aros_node/stability_loss_function.py

@@ -2,8 +2,8 @@
 from robustbench.utils import load_model
 import torch.nn as nn
 from torch.nn.parameter import Parameter
-import utils
-from utils import *
+import aros_node.utils
+from aros_node.utils import *
 from torch.utils.data import DataLoader, Dataset, TensorDataset, Subset, SubsetRandomSampler, ConcatDataset
 import numpy as np
 from tqdm.notebook import tqdm

aros_node/version.py

@@ -0,0 +1 @@
+__version__ = "0.0.1"

AROS/main.py → main.py

@@ -1,13 +1,13 @@
 
-!pip install -r requirements.txt
+import aros_node
 import argparse
 import torch
 import torch.nn as nn
-from evaluate import *
-from utils import *
+from aros_node.evaluate import *
+from aros_node.utils import *
 from tqdm.notebook import tqdm
-from data_loader import *
-from stability_loss_function import *
+from aros_node.data_loader import *
+from aros_node.stability_loss_function import *
 
 def main():
     parser = argparse.ArgumentParser(description="Hyperparameters for the script")

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"

reinstall.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# Re-install the package. By running './reinstall.sh'
+#
+# Note that AROS uses the build
+# system specified in
+# PEP517 https://peps.python.org/pep-0517/ and
+# PEP518 https://peps.python.org/pep-0518/
+# and hence there is no setup.py file.
+
+set -e # abort on error
+
+pip uninstall -y aros-node
+
+# Get version
+VERSION=0.0.1
+echo "Upgrading to AROS v${VERSION}"
+
+# Upgrade the build system (PEP517/518 compatible)
+python3 -m pip install virtualenv
+python3 -m pip install --upgrade build
+python3 -m build --sdist --wheel .
+
+# Reinstall the package with most recent version
+pip install --upgrade --no-cache-dir "dist/aros_node-${VERSION}-py3-none-any.whl"

requirements.txt

@@ -1,4 +1,9 @@
 geotorch
+torch
 torchdiffeq
-git+https://github.com/RobustBench/robustbench.git
-timm==1.0.9
+timm==1.0.9
+robustbench
+numpy
+scikit-learn
+scipy
+tqdm

setup.cfg

@@ -1,41 +1,23 @@
 [metadata]
-name = aros
-version = 0.0.1
+name = aros-node
+version = attr: aros_node.version.__version__
 author = Hossein Mirzaei, Mackenzie Mathis
 author_email = mackenzie@post.harvard.edu
 description = AROS: Adversarially Robust Out-of-Distribution Detection through Stability
 long_description = file: README.md
 long_description_content_type = text/markdown
-license_files = LICENSE.md
-license_file_type = text/markdown
 url = https://github.com/AdaptiveMotorControlLab/AROS
-project_urls =
-    Bug Tracker = https://github.com/AdaptiveMotorControlLab/AROS/issues
-classifiers =
-    Development Status :: 4 - Beta
-    Environment :: GPU :: NVIDIA CUDA
-    Intended Audience :: Science/Research
-    Operating System :: OS Independent
-    Programming Language :: Python :: 3
-    Topic :: Scientific/Engineering :: Artificial Intelligence
-    License :: OSI Approved :: Apache Software License
 
 [options]
 packages = find:
 include_package_data = True
 python_requires = >=3.10
-install_requires =
-    geotorch
-    torchdiffeq
-    git+https://github.com/RobustBench/robustbench.git
+install_requires = file: requirements.txt
 
 [options.extras_require]
 dev =
     pylint
     toml
     yapf
     black
-    pytest
-
-[bdist_wheel]
-universal=0
+    pytest

tests/test_dataloaders.py

@@ -0,0 +1,69 @@
+import pytest
+import torch
+from torch.utils.data import DataLoader, Subset
+from torchvision.datasets import CIFAR10, CIFAR100
+from torchvision.transforms import ToTensor
+from aros_node import (
+    LabelChangedDataset,
+    get_subsampled_subset,
+    get_loaders,
+)
+
+# Set up transformations and datasets for tests
+transform_tensor = ToTensor()
+
+@pytest.fixture
+def cifar10_datasets():
+    trainset = CIFAR10(root='./data', train=True, download=True, transform=transform_tensor)
+    testset = CIFAR10(root='./data', train=False, download=True, transform=transform_tensor)
+    return trainset, testset
+
+@pytest.fixture
+def cifar100_datasets():
+    trainset = CIFAR100(root='./data', train=True, download=True, transform=transform_tensor)
+    testset = CIFAR100(root='./data', train=False, download=True, transform=transform_tensor)
+    return trainset, testset
+
+def test_label_changed_dataset(cifar10_datasets):
+    _, testset = cifar10_datasets
+    new_label = 99
+    relabeled_dataset = LabelChangedDataset(testset, new_label)
+
+    assert len(relabeled_dataset) == len(testset), "Relabeled dataset should match the original dataset length"
+
+    for img, label in relabeled_dataset:
+        assert label == new_label, "All labels should be changed to the new label"
+
+def test_get_subsampled_subset(cifar10_datasets):
+    trainset, _ = cifar10_datasets
+    subset_ratio = 0.1
+    subset = get_subsampled_subset(trainset, subset_ratio=subset_ratio)
+
+    expected_size = int(len(trainset) * subset_ratio)
+    assert len(subset) == expected_size, f"Subset size should be {expected_size}"
+
+def test_get_loaders_cifar10(cifar10_datasets):
+    train_loader, test_loader, test_set, test_loader_vs_other = get_loaders('cifar10')
+
+    assert isinstance(train_loader, DataLoader)
+    assert isinstance(test_loader, DataLoader)
+    assert isinstance(test_loader_vs_other, DataLoader)
+
+    for images, labels in test_loader:
+        assert images.shape[0] == 16, "Test loader batch size should be 16"
+        break
+
+def test_get_loaders_cifar100(cifar100_datasets):
+    train_loader, test_loader, test_set, test_loader_vs_other = get_loaders('cifar100')
+
+    assert isinstance(train_loader, DataLoader)
+    assert isinstance(test_loader, DataLoader)
+    assert isinstance(test_loader_vs_other, DataLoader)
+
+    for images, labels in test_loader:
+        assert images.shape[0] == 16, "Test loader batch size should be 16"
+        break
+
+def test_get_loaders_invalid_dataset():
+    with pytest.raises(ValueError, match="Dataset 'invalid_dataset' is not supported."):
+        get_loaders('invalid_dataset')