Update package for PyPI distribution (#143)

* Test the distribution build

* Updates for publishing to PyPI

* Update install instructions

Author: mmuckley

.github/workflows/publish-package.yml

@@ -0,0 +1,35 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -18,3 +18,5 @@ dataset_cache.pkl
 .mypy_cache/
 lightning_logs/
 *.pt
+build/
+dist/

README.md

@@ -52,17 +52,24 @@ We have tested this code using:
 
 First install PyTorch according to the directions at the
 [PyTorch Website](https://pytorch.org/get-started/) for your operating system
-and CUDA setup.
-
-Then, navigate to the `fastmri` root directory and run
+and CUDA setup. Then, run
 
 ```bash
-pip install -e .
+pip install fastmri
 ```
 
 `pip` will handle all package dependencies. After this you should be able to
 run most of the code in the repository.
 
+### Installing Directly from Source
+
+If you want to install directly from the GitHub source, clone the repository,
+navigate to the `fastmri` root directory and run
+
+```bash
+pip install -e .
+```
+
 ## Package Structure & Usage
 
 The repository is centered around the `fastmri` module. The following breaks

fastmri/__init__.py

@@ -4,6 +4,13 @@
 This source code is licensed under the MIT license found in the
 LICENSE file in the root directory of this source tree.
 """
+
+__version__ = "0.1.0.post210716"
+__author__ = "Facebook/NYU fastMRI Team"
+__author_email__ = "fastmri@fb.com"
+__license__ = "MIT"
+__homepage__ = "https://fastmri.org/"
+
 import torch
 from packaging import version
 

setup.py

@@ -5,34 +5,67 @@
 LICENSE file in the root directory of this source tree.
 """
 
+import os
+import re
+
 from setuptools import find_packages, setup
 
+# from https://github.com/facebookresearch/ClassyVision/blob/master/setup.py
+# get version string from module
+with open(os.path.join(os.path.dirname(__file__), "fastmri/__init__.py"), "r") as f:
+    readval = re.search(r"__version__ = ['\"]([^'\"]*)['\"]", f.read(), re.M)
+    if readval is None:
+        raise RuntimeError("Version not found.")
+    version = readval.group(1)
+    print("-- Building version " + version)
+
+with open("README.md", encoding="utf8") as f:
+    readme = f.read()
+
 install_requires = [
     "numpy>=1.18.5",
     "scikit_image>=0.16.2",
-    "torchvision>=0.6.0",
-    "torch>=1.6",
+    "torchvision>=0.8.1",
+    "torch>=1.7.0",
     "runstats>=1.8.0",
-    "pytorch_lightning",
-    "h5py",
-    "PyYAML",
+    "pytorch_lightning>=1.0.6,<1.1",
+    "h5py>=2.10.0",
+    "PyYAML>=5.3.1",
 ]
 
 setup(
     name="fastmri",
     author="Facebook/NYU fastMRI Team",
     author_email="fastmri@fb.com",
-    version="0.1",
+    version=version,
+    license="MIT",
+    description="A large-scale dataset of both raw MRI measurements and clinical MRI images.",
+    long_description_content_type="text/markdown",
+    long_description=readme,
+    project_urls={
+        "Homepage": "https://fastmri.org/",
+        "Source": "https://github.com/facebookresearch/fastMRI",
+    },
+    python_requires=">=3.6",
     packages=find_packages(
         exclude=[
             "tests",
             "fastmri_examples",
-            "data",
-            "common",
             "banding_removal",
-            "models",
         ]
     ),
     setup_requires=["wheel"],
     install_requires=install_requires,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+        "Development Status :: 3 - Alpha",
+        "Intended Audience :: Developers",
+        "Topic :: Scientific/Engineering :: Artificial Intelligence",
+        "Topic :: Scientific/Engineering :: Image Processing",
+        "Topic :: Scientific/Engineering :: Medical Science Apps.",
+        "Topic :: Scientific/Engineering :: Physics",
+    ],
 )