Merge pull request #14 from maxencefaldor/uv

Migrate from `pip` to `uv`

Author: maxencefaldor

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,56 @@
+name: "Deploy Package"
+
+on:
+  push:
+    tags:
+      # Publish on any tag starting with a `v`, e.g. v1.2.3
+      - v*
+
+jobs:
+  run:
+    name: "Deploy Package"
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Build
+        run: uv build
+
+      - name: "Publish to PyPI"
+        run: uv publish -t ${{ secrets.PYPI_API_TOKEN }}
+
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Repo clone is required for --notes-from-tag to work
+        run: |
+          gh repo clone '${{ github.repository }}'
+          cd ${{ github.event.repository.name }}
+          gh release create '${{ github.ref_name }}' --verify-tag --notes-from-tag --title '${{ github.ref_name }}' ${{ contains(github.ref_name, 'dev') && '--prerelease --latest=false' || '--latest=true' }}
+          cd ..
+      - 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 }}'

.github/workflows/ruff.yml

@@ -0,0 +1,25 @@
+name: Ruff
+
+on:
+  push:
+    paths:
+      - "**.py"
+      - "pyproject.toml"
+      - ".github/workflows/ruff.yml"
+  pull_request:
+    paths:
+      - "**.py"
+      - "pyproject.toml"
+      - ".github/workflows/ruff.yml"
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      # Use ruff twice for linting and formatting.
+      # See https://github.com/astral-sh/ruff-action/issues/23#issuecomment-2525574730
+      - uses: astral-sh/ruff-action@v3
+      - uses: astral-sh/ruff-action@v3
+        with:
+          args: "format --check"

.github/workflows/tests.yml

@@ -0,0 +1,29 @@
+name: Tests
+
+on:
+  push:
+    paths:
+      - "**.py"
+      - "pyproject.toml"
+      - ".github/workflows/tests.yml"
+  pull_request:
+    paths:
+      - "**.py"
+      - "pyproject.toml"
+      - ".github/workflows/tests.yml"
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run pytest
+        run: uv run pytest tests/

.gitignore

@@ -1,166 +1,24 @@
-# Datasets
-data/
-1D-ARC/
-
-# Byte-compiled / optimized / DLL files
+# Python-generated files
 __pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
+*.py[oc]
 build/
-develop-eggs/
 dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
 wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
+*.egg-info
 
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
+# Virtual environments
 .venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
 
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
+# ruff
+.ruff_cache
 
 # mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
+.mypy_cache
 
-# Cython debug symbols
-cython_debug/
+# pytest
+.pytest_cache
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+# Custom
+output/
+examples/1D-ARC/
+examples/data/

CONTRIBUTING.md

@@ -12,14 +12,12 @@ Follow these steps to contribute code:
 
 1. Fork the CAX repository by clicking the Fork button on the repository page. This creates a copy of the CAX repository in your own account.
 
-2. Install Python >= 3.10 locally in order to run tests.
+2. Clone your fork and go at the root of the repository.
 
-3. `pip` installing your fork from source. This allows you to modify the code and immediately test it out:
+3. Install your fork from source using [https://docs.astral.sh/uv/](`uv`).
 
 ```bash
-git clone https://github.com/maxencefaldor/cax
-cd cax
-pip install -e ".[dev]"  # Installs CAX from the current directory in editable mode.
+uv run python -c "import cax; print(cax.__doc__)"
 ```
 
 4. Add the CAX repository as an upstream remote, so you can use it to sync your changes.
@@ -39,8 +37,8 @@ And implement your changes using your favorite editor.
 6. Make sure your code passes CAX’s lint and type checks, by running the following from the top of the repository:
 
 ```bash
-ruff format .
-ruff check .
+uv ruff check .   # Linting
+uv ruff format .  # Formatting
 ```
 
 7. Make sure the tests pass by running the following command from the top of the repository:

README.md

@@ -66,10 +66,11 @@ Here, you can see the basic CAX API usage:
 
 ```python
 import jax
+from flax import nnx
+
 from cax.core.ca import CA
 from cax.core.perceive import ConvPerceive
 from cax.core.update import NCAUpdate
-from flax import nnx
 
 seed = 0
 
@@ -105,16 +106,16 @@ For a more detailed overview, get started with this notebook [![Colab](https://c
 
 ## Installation ⚙️
 
-You will need Python 3.10 or later, and a working JAX installation.
+You will need Python 3.10 or later, and a working JAX installation installed in a virtual environment.
 
-Then, install CAX from PyPi:
+Then, install CAX from PyPi with `uv`:
 ```
-pip install cax
+uv pip install cax
 ```
 
-To upgrade to the latest version of CAX, you can use:
+or with `pip`:
 ```
-pip install --upgrade git+https://github.com/maxencefaldor/cax.git
+pip install cax
 ```
 
 ## Citing CAX 📝

cax/core/__init__.py

@@ -738,6 +738,7 @@
    ],
    "source": [
     "import PIL\n",
+    "\n",
     "from cax.utils.emoji import get_emoji\n",
     "\n",
     "size = 40\n",

cax/types.py

@@ -61,8 +61,9 @@
    "source": [
     "import jax.numpy as jnp\n",
     "import mediapy\n",
-    "from cax.models.elementary import ElementaryCA\n",
-    "from flax import nnx"
+    "from flax import nnx\n",
+    "\n",
+    "from cax.models.elementary import ElementaryCA"
    ]
   },
   {