Move to ruff instead of alternatives (#31)

.github/workflows/ci.yaml

@@ -21,7 +21,7 @@ jobs:
       - precommit
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -41,7 +41,7 @@ jobs:
       - precommit
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -61,7 +61,7 @@ jobs:
       - precommit
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.11]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -12,26 +12,6 @@ repos:
     - id: requirements-txt-fixer
     - id: trailing-whitespace
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v2.29.1
-  hooks:
-  - id: pyupgrade
-    args: [--py38-plus]
-
-- repo: https://github.com/psf/black
-  rev: 22.3.0
-  hooks:
-  - id: black
-    args: ["--config=pyproject.toml"]
-    files: "(surjectors|examples)"
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    args: ["--settings-path=pyproject.toml"]
-    files: "(surjectors|examples)"
-
 - repo: https://github.com/pycqa/bandit
   rev: 1.7.1
   hooks:
@@ -43,24 +23,16 @@ repos:
     additional_dependencies: ["toml"]
     files: "(surjectors|examples)"
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 5.0.1
-  hooks:
-  - id: flake8
-    additional_dependencies: [
-      flake8-typing-imports==1.14.0,
-      flake8-pyproject==1.1.0.post0
-    ]
-
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: v0.910-1
   hooks:
   - id: mypy
     args: ["--ignore-missing-imports"]
     files: "(surjectors|examples)"
 
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.1.1
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.3.0
   hooks:
-  - id: pydocstyle
-    additional_dependencies: ["toml"]
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format

README.md

@@ -11,14 +11,12 @@
 
 Surjectors is a light-weight library for density estimation using
 inference and generative surjective normalizing flows, i.e., flows can that reduce or increase dimensionality.
-Surjectors builds on Distrax and Haiku and is fully compatible with both of them.
-
 Surjectors makes use of
 
-- Haiku`s module system for neural networks,
-- Distrax for probability distributions and some base bijectors,
-- Optax for gradient-based optimization,
-- JAX for autodiff and XLA computation.
+- [Haiku](https://github.com/deepmind/dm-haiku)`s module system for neural networks,
+- [Distrax](https://github.com/deepmind/distrax) for probability distributions and some base bijectors,
+- [Optax](https://github.com/deepmind/optax) for gradient-based optimization,
+- [JAX](https://github.com/google/jax) for autodiff and XLA computation.
 
 ## Examples
 

docs/conf.py

@@ -42,6 +42,8 @@
     "examples/*py"
 ]
 
+autodoc_typehints = "both"
+
 html_theme = "sphinx_book_theme"
 
 html_theme_options = {
@@ -52,3 +54,13 @@
 }
 
 html_title = "Surjectors 🚀"
+
+
+def skip(app, what, name, obj, would_skip, options):
+    if name == "__init__":
+        return True
+    return would_skip
+
+
+def setup(app):
+    app.connect("autodoc-skip-member", skip)

docs/index.rst

@@ -15,10 +15,10 @@ Surjectors builds on Distrax and Haiku and is fully compatible with both of them
 
 Surjectors makes use of
 
-- Haiku`s module system for neural networks,
-- Distrax for probability distributions and some base bijectors,
-- Optax for gradient-based optimization,
-- JAX for autodiff and XLA computation.
+- `Haiku's <https://github.com/deepmind/dm-haiku>`_ module system for neural networks,
+- `Distrax <https://github.com/deepmind/distrax>`_ for probability distributions and some base bijectors,
+- `Optax <https://github.com/deepmind/optax>`_ for gradient-based optimization,
+- `JAX <https://github.com/google/jax>`_ for autodiff and XLA computation.
 
 Example
 -------
@@ -90,6 +90,23 @@ In order to contribute:
 4) test it by calling :code:`hatch run test` on the (Unix) command line,
 5) submit a PR 🙂
 
+Citing Surjectors
+-----------------
+
+.. code-block:: latex
+
+    @article{dirmeier2024surjectors,
+        author = {Simon Dirmeier},
+        title = {Surjectors: surjection layers for density estimation with normalizing flows},
+        year = {2024},
+        journal = {Journal of Open Source Software},
+        publisher = {The Open Journal},
+        volume = {9},
+        number = {94},
+        pages = {6188},
+        doi = {10.21105/joss.06188}
+    }
+
 License
 -------
 

docs/news.rst

@@ -7,4 +7,5 @@ Latest news on the development of `Surjectors`.
 
 .. note::
 
-    No news so far :).
+    - 29.02.2024. Surjectors has been accepted for publication in the Journal of Open Source Software 🎉🎉🎉.
+      Find the paper here `10.21105/joss.06188 <https://joss.theoj.org/papers/10.21105/joss.06188>`_.

docs/surjectors.rst

@@ -29,6 +29,10 @@ Hence, every normalizing flow can be composed by defining these three components
     >>> flow = Chain([Slice(10, decoder_fn(10)), LULinear(5)])
     >>> pushforward = TransformedDistribution(base_distribution, flow)
 
+Regardless of how the chain of transformations (called :code:`flow` above) is defined,
+each pushforward has access to four methods :code:`sample`, :code:`sample_and_log_prob`:code:`log_prob`, and :code:`inverse_and_log_prob`.
+
+The exact method declarations can be found in the API below.
 
 General
 -------
@@ -41,39 +45,51 @@ TransformedDistribution
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 ..  autoclass:: TransformedDistribution
-    :members:
+    :members: log_prob, sample, inverse_and_log_prob, sample_and_log_prob
 
 Chain
 ~~~~~
 
 ..  autoclass:: Chain
-    :members: __init__
+    :members:
 
 Bijective layers
 ----------------
 
 .. autosummary::
     MaskedAutoregressive
+    AffineMaskedAutoregressive
     MaskedCoupling
+    AffineMaskedCoupling
+    RationalQuadraticSplineMaskedCoupling
     Permutation
 
 Autoregressive bijections
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ..  autoclass:: MaskedAutoregressive
-    :members: __init__
+    :members:
+
+..  autoclass:: AffineMaskedAutoregressive
+    :members:
 
 Coupling bijections
 ~~~~~~~~~~~~~~~~~~~
 
 ..  autoclass:: MaskedCoupling
-    :members: __init__
+    :members:
+
+..  autoclass:: AffineMaskedCoupling
+    :members:
+
+..  autoclass:: RationalQuadraticSplineMaskedCoupling
+    :members:
 
 Other bijections
 ~~~~~~~~~~~~~~~~
 
 ..  autoclass:: Permutation
-    :members: __init__
+    :members:
 
 Inference surjection layers
 ---------------------------
@@ -96,35 +112,34 @@ Coupling inference surjections
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ..  autoclass:: MaskedCouplingInferenceFunnel
-    :members: __init__
-
+    :members:
 
 ..  autoclass:: AffineMaskedCouplingInferenceFunnel
-    :members: __init__
+    :members:
 
 ..  autoclass:: RationalQuadraticSplineMaskedCouplingInferenceFunnel
-    :members: __init__
+    :members:
 
 Autoregressive inference surjections
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ..  autoclass:: MaskedAutoregressiveInferenceFunnel
-    :members: __init__
+    :members:
 
 ..  autoclass:: AffineMaskedAutoregressiveInferenceFunnel
-    :members: __init__
+    :members:
 
 ..  autoclass:: RationalQuadraticSplineMaskedAutoregressiveInferenceFunnel
-    :members: __init__
+    :members:
 
 Other inference surjections
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ..  autoclass:: LULinear
-    :members: __init__
+    :members:
 
 ..  autoclass:: MLPInferenceFunnel
-    :members: __init__
+    :members:
 
 ..  autoclass:: Slice
-    :members: __init__
+    :members:

pyproject.toml

@@ -11,7 +11,7 @@ license = "Apache-2.0"
 homepage = "https://github.com/dirmeier/surjectors"
 keywords = ["normalizing flows", "surjections", "density estimation"]
 classifiers = [
-    "Development Status :: 1 - Planning",
+    "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3",
@@ -49,55 +49,27 @@ dependencies = [
 
 [tool.hatch.envs.test]
 dependencies = [
-    "pylint>=2.15.10",
+    "ruff>=0.3.0",
     "pytest>=7.2.0",
     "pytest-cov>=4.0.0"
 ]
 
 [tool.hatch.envs.test.scripts]
-lint = 'pylint surjectors'
+lint = 'ruff check surjectors'
 test = 'pytest -v --cov=./surjectors --cov-report=xml surjectors'
 
-[tool.black]
-line-length = 80
-extend-ignore = "E203"
-target-version = ['py310']
-exclude = '''
-/(
-    \.eggs
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-)/
-'''
-
+[tool.bandit]
+skips = ["B101"]
 
-[tool.isort]
-profile = "black"
-line_length = 80
-include_trailing_comma = true
+[tool.ruff]
+line-length = 80
+exclude = ["*_test.py", "docs/**", "examples/**"]
 
-[tool.flake8]
-max-line-length = 80
-extend-ignore = ["E203", "W503"]
-per-file-ignores = [
-    '__init__.py:F401',
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F"]
+extend-select = [
+  "UP", "D", "I", "PL", "S"
 ]
 
-[tool.pylint.messages_control]
-disable = """
-invalid-name,missing-module-docstring,R0801
-"""
-
-[tool.bandit]
-skips = ["B101"]
-
-[tool.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention= 'google'
-match = '^surjectors/.*/((?!_test).)*\.py'