Switch to setup.cfg and update package versions (#78)

* Switch to setup.cfg

* Fix package name

* Move to Python 3.8

* Build to 3.7

* Add pyproject.toml

* we are not fastmri

* Add version to gitignore

* Update checkout

* Update other actions to v3

* Update readthedocs

* Rename yaml

* Try changing pip reqs

* Try importlib

* Fix syntax

* Import torchkbnufft

* Early version of torch

* Test index url

* Index URL to diff file

* Update metadata files

* Update all package versions

* Test on Python 3.10

* Num to string

* Update python setup version

.gitattributes

@@ -1 +1 @@
-*.ipynb linguist-documentation
+*.ipynb linguist-documentation

.github/workflows/python-app.yml

@@ -17,21 +17,22 @@ jobs:
       max-parallel: 4
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.7, 3.8]
+        python-version: ["3.8", "3.10"]
 
     runs-on: ${{ matrix.platform }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install
         run: |
           python -m pip install --upgrade pip
-          pip install --upgrade wheel
-          pip install -e .
+          pip install --upgrade wheel build setuptools
+          python -m build .
+          pip install dist/*.whl
       - name: Test Import
         run: |
           python -c 'import torchkbnufft'
@@ -42,21 +43,32 @@ jobs:
       max-parallel: 4
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.7, 3.8]
+        python-version: ["3.8", "3.10"]
 
     runs-on: ${{ matrix.platform }}
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get pip cache dir
+        id: pip-cache
+        run: |
+          echo "::set-output name=dir::$(pip cache dir)"
+      - name: pip cache
+        uses: actions/cache@v3
         with:
-          python-version: 3.8
+          path: ${{ steps.pip-cache.outputs.dir }}
+          key: ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ hashFiles('**/setup.cfg') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-py${{ matrix.python-version }}-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r dev-requirements.txt
-          pip install -e .
+          pip install --upgrade wheel
+          pip install --editable ".[tests]"
       - name: Format and lint
         run: |
           black --check .

.gitignore

@@ -1,10 +1,11 @@
-.pytest_cache/
 __pycache__/
+.pytest_cache/
 .vscode/
-dist/
-build/
-torchkbnufft.egg-info/
 *checkpoint.ipynb
-speedtests/
 _build/
+build/
+dist/
 gram/
+speedtests/
+torchkbnufft/_version.py
+torchkbnufft.egg-info/

.readthedocs.yml

@@ -0,0 +1,8 @@
+python:
+   version: 3.8
+   install:
+      - method: pip
+        path: .
+        extra_requirements:
+            - docs
+   system_packages: true

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 Matthew John Muckley
+Copyright (c) 2022 Matthew John Muckley
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/requirements.txt

@@ -1,4 +1,5 @@
 sphinx>=3.2.0
 sphinx-rtd-theme>=0.5.1
 sphinxcontrib-katex
-sphinx-autodoc-typehints
+sphinx-autodoc-typehints
+torch --extra-index-url https://download.pytorch.org/whl/cpu

docs/source/conf.py

@@ -10,20 +10,21 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+from datetime import date
 import os
 import sys
 
 sys.path.insert(0, os.path.abspath("../.."))
 os.environ["PYTORCH_JIT"] = "0"
+year = date.today().year
 
 import torchkbnufft
-import torch
 
 
 # -- Project information -----------------------------------------------------
 
 project = "torchkbnufft"
-copyright = "2021, Matthew Muckley"
+copyright = f"{year}, Matthew Muckley"
 author = "Matthew Muckley"
 
 # The full version, including alpha/beta/rc tags

pyproject.toml

@@ -0,0 +1,10 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools-scm>=6.3.2",
+    "setuptools>=59.5.0",
+    "wheel>=0.37.0",
+]
+
+[tool.setuptools_scm]
+write_to = "torchkbnufft/_version.py"

setup.cfg

@@ -0,0 +1,70 @@
+[flake8]
+max-line-length=88
+per-file-ignores=__init__.py:F401
+extend-exclude = *brain_challenge*,*2020-08*
+extend-ignore = E203, E266, E501
+
+[metadata]
+author = Matthew Muckley
+author_email = [email protected]
+classifiers =
+    Environment :: Console
+    Natural Language :: English
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.8
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Development Status :: 4 - Beta
+    Intended Audience :: Developers
+    Topic :: Scientific/Engineering :: Artificial Intelligence
+    Topic :: Scientific/Engineering :: Mathematics
+    Topic :: Scientific/Engineering :: Medical Science Apps.
+    Topic :: Scientific/Engineering :: Physics
+description = A high-level, easy-to-deploy non-uniform Fast Fourier Transform in PyTorch.
+license = MIT
+license_files = LICENSE
+long_description = file: README.md
+long_description_content_type = text/markdown
+name = torchkbnufft
+project_urls =
+    Homepage = https://torchkbnufft.readthedocs.io/en/stable/
+    Source = https://github.com/mmuckley/torchkbnufft
+
+[mypy]
+
+# modules that don't play well with mypy
+[mypy-numpy.*,scipy.*]
+ignore_missing_imports=True
+
+# directories we're not tracking
+[mypy-tests.*]
+ignore_missing_imports=True
+
+[options]
+install_requires =
+    numpy>=1.22.4
+    scipy>=1.8.1
+    torch>=1.12
+packages = find:
+python_requires = >=3.8
+
+[options.extras_require]
+dev = 
+    black==22.10.0
+    flake8==5.0.4
+    mypy==0.991
+    pytest==7.2.0
+tests =
+    black==22.10.0
+    flake8==5.0.4
+    mypy==0.991
+    numpy==1.23.5
+    pytest==7.2.0
+    scipy==1.9.3
+    torch==1.13.0
+
+[options.packages.find]
+exclude = 
+    tests
+    notebooks
+    docs

setup.py

@@ -1,58 +1,3 @@
-import builtins
-import pathlib
+from setuptools import setup
 
-from setuptools import find_packages, setup
-
-# https://github.com/williamFalcon/pytorch-lightning/blob/master/setup.py
-
-
-# The directory containing this file
-HERE = pathlib.Path(__file__).parent
-
-# The text of the README file
-README = (HERE / "README.md").read_text()
-
-builtins.__TORCHKBNUFFT_SETUP__ = True
-
-import torchkbnufft  # noqa: E402
-
-install_requires = ["torch>=1.12", "numpy", "scipy"]
-
-# https://packaging.python.org/discussions/install-requires-vs-requirements
-setup(
-    name="torchkbnufft",
-    version=torchkbnufft.__version__,
-    description=torchkbnufft.__docs__,
-    author=torchkbnufft.__author__,
-    author_email=torchkbnufft.__author_email__,
-    url=torchkbnufft.__homepage__,
-    download_url="https://github.com/mmuckley/torchkbnufft",
-    license=torchkbnufft.__license__,
-    packages=find_packages(exclude=["tests", "notebooks", "docs"]),
-    long_description=open("README.md", encoding="utf-8").read(),
-    long_description_content_type="text/markdown",
-    include_package_data=True,
-    zip_safe=False,
-    keywords=["MRI", "pytorch", "nufft", "deep-learning"],
-    python_requires=">=3.7",
-    setup_requires=[],
-    install_requires=install_requires,
-    classifiers=[
-        "Environment :: Console",
-        "Natural Language :: English",
-        # How mature is this project? Common values are
-        #   3 - Alpha, 4 - Beta, 5 - Production/Stable
-        "Development Status :: 4 - Beta",
-        # Indicate who your project is intended for
-        "Topic :: Scientific/Engineering :: Artificial Intelligence",
-        "Topic :: Scientific/Engineering :: Mathematics",
-        "Topic :: Scientific/Engineering :: Medical Science Apps.",
-        "Topic :: Scientific/Engineering :: Physics",
-        # Pick your license as you wish
-        "License :: OSI Approved :: MIT License",
-        # Specify the Python versions you support here. In particular, ensure
-        # that you indicate whether you support Python 2, Python 3 or both.
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.7",
-    ],
-)
+setup()