Merge branch 'main' of github.com:FelixBenning/pyrfd

.flake8

@@ -1,2 +1,5 @@
 [flake8]
-max-line-length = 120
+max-line-length = 120
+
+# E266: too many leading '#' for block commment
+extend-ignore = E266

.github/workflows/publish.yml

@@ -0,0 +1,123 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    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 Poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+        installer-parallel: true
+
+    - name: Install library
+      run: poetry install --no-interaction
+
+    - name: Build distribution 📦
+      run: poetry build
+
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pyrfd  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/[email protected]
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/pyrfd
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

.github/workflows/push.yml

@@ -39,3 +39,18 @@ jobs:
         poetry run pylint pyrfd
         poetry run flake8 pyrfd
         poetry run black --check pyrfd
+      
+    - name: Run Tests
+      run: poetry run pytest --cov-report xml --cov-report html --cov=pyrfd tests/
+
+
+    - name: Upload results to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Upload HTML results
+      uses: actions/upload-artifact@v4
+      with:
+        name: Test Coverage Report ${{matrix.python-version}}
+        path: htmlcov

.gitignore

@@ -161,3 +161,17 @@ cython_debug/
 
 # Apple junk
 .DS_Store
+
+
+# Caches
+# cache/*
+logs/*
+!logs/MNIST_CNN7_b=1024
+!logs/MNIST_CNN7_b=128
+!logs/MNIST_AlgoPerf_b=128
+!logs/FashionMNIST_CNN5_b=128
+!logs/MNIST_CNN3_b=128
+data/*
+slurm-*
+wandb
+plot/*.pdf

.vscode/launch.json

@@ -4,6 +4,13 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
+        {
+            "name": "Debugger: Benchmarking Module",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${workspaceFolder}/benchmarking/classification/__main__.py",
+            "args": "${command:pickArgs}"
+        },
         {
             "name": "debug pyrfd",
             "type": "debugpy",

.vscode/settings.json

@@ -1,6 +1,6 @@
 {
   "python.testing.pytestArgs": [
-    "."
+    "tests"
   ],
   "python.testing.unittestEnabled": false,
   "python.testing.pytestEnabled": true,

README.md

@@ -1,6 +1,9 @@
 # pyrfd
 
-Pytorch implementation of RFD
+[![PyPI version](https://badge.fury.io/py/pyrfd.svg)](https://badge.fury.io/py/pyrfd)
+[![codecov](https://codecov.io/gh/FelixBenning/pyrfd/graph/badge.svg?token=DaSPgLnZRc)](https://codecov.io/gh/FelixBenning/pyrfd)
+
+Pytorch implementation of RFD (see [arXiv](https://arxiv.org/abs/2305.01377))
 
 ## Covariance model
 
@@ -22,8 +25,7 @@ pytorch optimizer interface. The end result can be used like `torch.optim.Adam`
 ## Example usage
 
 ```python
-from mnistSimpleCNN.models.modelM3 import ModelM3
-# cf. mnistSimpleCNN directory (example model)
+from benchmaking.classification.mnist.models.cnn3 import CNN3
 
 import torch
 import torchvision as tv
@@ -32,7 +34,7 @@ from pyrfd import RFD, SquaredExponential
 
 cov_model = SquaredExponential()
 cov_model.auto_fit(
-    model_factory=ModelM3,
+    model_factory=CNN3,
     loss=torch.nn.functional.nll_loss,
     data= tv.datasets.MNIST(
         root="mnistSimpleCNN/data",
@@ -43,7 +45,25 @@ cov_model.auto_fit(
     # should be unique for (models, data, loss)
 )
 rfd = RFD(
-    ModelM3().parameters(),
+    CNN3().parameters(),
     covariance_model=cov_model
 )
-```
+```
+
+## How to cite
+
+
+```bibtex
+@inproceedings{benningRandomFunctionDescent2024,
+  title = {Random {{Function Descent}}},
+  booktitle = {Advances in {{Neural Information Processing Systems}}},
+  author = {Benning, Felix and D{\"o}ring, Leif},
+  year = {2024},
+  month = dec,
+  volume = {37},
+  primaryclass = {cs, math, stat},
+  publisher = {Curran Associates, Inc.},
+  address = {Vancouver, Canada},
+}
+```
+

benchmarking/classification/__init__.py

@@ -0,0 +1,6 @@
+""" Classification examples. """
+
+from .classifier import Classifier
+from . import mnist
+
+__all__ = ["Classifier", "mnist"]