replace setup.py for pyproject.toml

.github/workflows/format.yml

@@ -1,9 +1,12 @@
 name: flake8
 
 on:
+  push:
+    branches:
+      - main
   pull_request:
     paths:
-      - '**.py'
+      - "**.py"
 
 jobs:
   flake8-lint:
@@ -20,4 +23,3 @@ jobs:
 
       - name: flake8-lint
         uses: py-actions/flake8@v2
-

.github/workflows/tests.yml

@@ -22,8 +22,7 @@ jobs:
         run: |
           python -m venv --upgrade-deps .venv
           source .venv/bin/activate
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
+          pip install .[all]
 
       - name: Run Test
         run: |

README.md

@@ -1,25 +1,31 @@
 # Sparse Coding
-Reference sparse coding implementations for efficient learning and inference implemented in PyTorch with GPU support. 
 
-## Dictionary Learning
+Reference sparse coding implementations for efficient learning and inference implemented in PyTorch with GPU support.
+
+## Features
+
+### Dictionary Learning
+
 * Repo currently includes classic patch-wise sparse coding dictionary learning.
 
-## Implemented Inference Methods
+### Implemented Inference Methods
+
 * Locally Competative Algorithm (LCA)
 * Gradient Descent with Euler's method on Laplace Prior (Vanilla)
 * Laplacian Scale Mixture (LSM)
 * Iterative Shrinkage-threshold Algorithm (ISTA)
 * Generic PyTorch minimization of arbitrary loss function (PyTorchOptimizer)
 
-# Setup
+## Setup
+
 1. Clone the repo.
 2. Navigate to the directory containing the repo directory.
-3. Run `pip install -e sparsecoding`
-4. Navigate into the repo and install the requirements using `pip install -r requirements.txt`
-5. Install the natural images dataset from this link: https://rctn.org/bruno/sparsenet/IMAGES.mat
-6. Try running the demo notebook: `examples/sparse_coding.ipynb`
+3. Run `pip install -e ".[all]"`
+4. Install the natural images dataset from this link: https://rctn.org/bruno/sparsenet/IMAGES.mat
+5. Try running the demo notebook: `examples/sparse_coding.ipynb`
 
 Note: If you are using a Jupyter notebook and change a source file, you can either: 1) restart the Jupyter kernel, or 2) follow instructions [here](https://ipython.readthedocs.io/en/stable/config/extensions/autoreload.html#autoreload).
 
-# Contributing
+## Contributing
+
 See the [contributing](docs/contributing.md) document!

pyproject.toml

@@ -0,0 +1,90 @@
+[project]
+name = "sparsecoding"
+version = "0.0.1"
+# Authors are the current, primary stewards of the repo
+# contributors can be found on github
+authors = [
+    { name = "Alex Belsten", email = "belsten@berkeley.edu" },
+    { name = "Christian Shewmake", email = "cshewmake2@gmail.com" },
+]
+description = "Pytorch infrasctructure for sparse coding."
+readme = "README.md"
+requires-python = ">=3.8"
+# Trove classifiers: https://pypi.org/pypi?%3Aaction=list_classifiers
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Development Status :: 3 - Alpha",
+    "Natural Language :: English",
+]
+
+dependencies = [
+    "matplotlib",
+    "numpy",
+    "scipy",
+    "torch",
+    "torchvision",
+]
+
+
+[project.optional-dependencies]
+dev = [
+    "black==24.*",
+    "coverage",
+    "ipykernel",
+    "jupytext",
+    "nbconvert",
+    "pylint>=3.3.0",
+    "pyright",
+    "pytest",
+]
+
+tutorials = [
+  "jupyter",
+  "matplotlib",
+  "tqdm",
+  "scipy",
+]
+
+all = [
+    "sparsecoding[dev,tutorials]",
+]
+
+[project.urls]
+"Homepage" = "sparsecoding.readthedocs.io"
+"Bug Tracker" = "https://github.com/rctn/sparsecoding/issues"
+
+[build-system]
+requires = ["flit_core>=3.2"]
+build-backend = "flit_core.buildapi"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["--tb=short"]
+norecursedirs = ".git examples"
+python_files = "*_test.py test_*.py"
+log_cli = true
+log_cli_level = "INFO"
+log_cli_format = "\n%(asctime)s: %(levelname)s: %(filename)s:%(lineno)s::%(module)s::%(funcName)s:\n%(message)s"
+log_cli_date_format = "%y-%m-%d %H:%M:%S"
+
+[tool.pylint.format]
+max-line-length = "120"
+
+[tool.black]
+line-length = 120
+extend-exclude = "\\.ipynb"
+
+[tool.pylint]
+exclude = [".venv", ".vscode", "docs"]
+
+[tool.pylance]
+exclude = [".venv", ".vscode", "docs"]
+
+[tool.pyright]
+exclude = [".venv", ".vscode", "docs"]
+
+[tool.isort]
+line_length = 120
+profile = "black"

tutorials/vanilla/README.md

@@ -0,0 +1,7 @@
+# Install required dependencies
+
+Install the tutorials dependencies by navigating to the root repo folder and running
+
+```sh
+pip install .[tutorials]
+```