Merge remote-tracking branch 'origin/master' into renerichter-rl

the-lay · Nov 8, 2021 · 6db742e · 6db742e
2 parents fdc38c8 + c494cde
commit 6db742e
Show file tree

Hide file tree

Showing 21 changed files with 1,446 additions and 777 deletions.
diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -0,0 +1,32 @@
+## Bug reports
+Please be as specific as you can, ideally with code to recreate the issue.
+
+
+# Code contribution workflow
+First off, thanks for taking the time!  
+Please feel free to contact me with questions.
+
+1. Fork the repo, then clone it and install in the editable mode:
+```bash
+git clone git@github.com:YOURNAME/tiler.git && cd tiler
+pip install -e .[all]
+```
+
+2. Add your changes! 
+
+3. After you've finished with your changes, please run linter, tests and check that coverage didn't go down too much:
+```bash
+black tiler tests
+coverage run -m pytest
+coverage report
+```
+
+4. If you have made any API and/or documentation changes, please regenerate docs by running the script:
+```bash
+cd misc
+./docs.sh
+```
+
+5. Once you want to share what you've changed, please commit, push make a pull request to the main repo.
+
+6. Github will run lint and tests, but please don't rely on that and test before pull request :)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -3,27 +3,39 @@ name: CI
 on: [push, pull_request]
 
 jobs:
-  build:
+
+  lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: psf/black@stable
         with:
-          python-version: '3.x'
+          options: "--check --diff"
+          src: "tiler tests"
 
-      - name: Install dependencies
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        # 3.6 will reach EoL in December 2021
+        # https://devguide.python.org/#status-of-python-branches
+        python-version: [ "3.7", "3.8", "3.9", "3.10" ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - name: Install test dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install coveralls pytest coverage
-
-      - name: Install tiler
-        run: python setup.py install
-
+          pip install .[test]
+          pip install coveralls
       - name: Run tests
-        run: python -m coverage run --source=tiler -m pytest -vvs tests/
-
-      - name: Run coveralls
+        run: coverage run -m pytest -v
+      - name: Submit coveralls
         if: github.repository == 'the-lay/tiler'
         run: coveralls
         env:

diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
@@ -1,29 +1,34 @@
-name: Upload Python Package
+name: Publish package
 
 on:
   release:
     types: [created]
 
 jobs:
-  deploy:
-
+  pypi-publish:
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
         python-version: '3.x'
-    - name: Install dependencies
+
+    - name: Install build package
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        python -m pip install build --user
+
+    - name: Build distribution
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python -m build --sdist --wheel --outdir dist/ .
+
+    - name: Publish to PyPI
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,9 @@
 # PyCharm stuff
 .idea
 
+# setuptools_scm version
+tiler/version.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md
diff --git a/README.md b/README.md
@@ -2,11 +2,10 @@
 
 ![Tiler teaser image](misc/teaser/tiler_teaser.png)
 
-[![CI](https://github.com/the-lay/tiler/workflows/CI/badge.svg)](https://github.com/the-lay/tiler/actions/workflows/ci.yml)
+[![CI](https://github.com/the-lay/tiler/actions/workflows/ci.yml/badge.svg)](https://github.com/the-lay/tiler/actions/workflows/ci.yml)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Coverage status](https://coveralls.io/repos/github/the-lay/tiler/badge.svg?branch=master)](https://coveralls.io/github/the-lay/tiler?branch=master)
 [![PyPI version](https://badge.fury.io/py/tiler.svg)](https://badge.fury.io/py/tiler)
-[![PyPI Downloads](https://img.shields.io/pypi/dm/tiler)](https://pypistats.org/packages/tiler)
-[![Documentation](https://img.shields.io/badge/documentation-✔-green.svg)](https://the-lay.github.io/tiler)
 
 
 [Github repository](https://github.com/the-lay/tiler) | 
@@ -28,7 +27,7 @@ Features
  - N-dimensional *(note: currently tile shape must have the same number of dimensions as the array)*
  - Optional in-place tiling
  - Optional channel dimension, dimension that is not tiled
- - Optional tile batching
+ - Optional batching
  - Tile overlapping
  - Access individual tiles with iterator or a getter
  - Tile merging, with optional window functions/tapering
@@ -139,40 +138,3 @@ However, other libraries might fit you better:
 Moreover, some related approaches have been described in the literature:
  - [Introducing Hann windows for reducing edge-effects in patch-based image segmentation](https://doi.org/10.1371/journal.pone.0229839
 ), Pielawski and Wählby, March 2020
-
-
-
-
-
-
-
-<!-- for later
-For more examples, please see examples/ folder
-```python
-
- ```
-
-Benchmarks
--------------
- Benchmarks?
- 
-
-Examples
--------------
-https://github.com/BloodAxe/pytorch-toolbelt#inference-on-huge-images
-https://github.com/BloodAxe/pytorch-toolbelt/blob/master/pytorch_toolbelt/inference/tiles.py
-
-https://github.com/vfdev-5/ImageTilingUtils
-
-https://github.com/Vooban/Smoothly-Blend-Image-Patches/blob/master/smooth_tiled_predictions.py
-
-for windows:
-https://stackoverflow.com/questions/1988804/what-is-memoization-and-how-can-i-use-it-in-python
-
-https://en.wikipedia.org/wiki/Window_function#A_list_of_window_functions
-https://github.com/scipy/scipy/blob/v1.4.1/scipy/signal/windows/windows.py
-https://gist.github.com/npielawski/7e77d23209a5c415f55b95d4aba914f6
-
-https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229839#pone.0229839.ref005
-https://arxiv.org/pdf/1803.02786.pdf
--->
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/tiler_teaser.png b/docs/tiler_teaser.png
diff --git a/misc/docs.sh b/misc/docs.sh
@@ -1,8 +1,6 @@
 cd $(dirname "$file_name")/..
-pwd
 
 # build docs
-pip install pdoc==7.1.1
 pdoc -o docs -d google tiler
 
 # add downsized teaser image to the docs directory
@@ -13,4 +11,4 @@ rm docs/index.html
 mv docs/tiler.html docs/index.html
 
 # remove unused search index
-rm docs/search.json
+rm docs/search.js
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,25 @@
+[build-system]
+requires = [
+    "setuptools >= 40.6.0",
+    "setuptools_scm[toml] >= 4, <6",
+    "setuptools_scm_git_archive",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "tiler/version.py"
+
+[tool.coverage.run]
+branch = true
+relative_files = true
+source = ['tiler']
+omit = ['tiler/version.py']
+
+[tool.coverage.report]
+show_missing = true
+fail_under = 95
+
+[tool.black]
+line-length = 88
+target-version = ['py38']
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.cfg b/setup.cfg
@@ -0,0 +1,41 @@
+[metadata]
+name = tiler
+version = attr: tiler.__version__
+description = N-dimensional NumPy array tiling and merging with easy overlapping, padding and tapering support
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/the-lay/tiler
+author = the-lay
+author_email = ilja.gubin@gmail.com
+license = MIT
+license_file = LICENSE.md
+classifiers =
+    Development Status :: 4 - Beta
+    Intended Audience :: Developers
+    Intended Audience :: Science/Research
+    Topic :: Software Development :: Libraries :: Python Modules
+    License :: OSI Approved :: MIT License
+    Programming Language :: Python :: 3 :: Only
+project_urls =
+    Documentation = https://the-lay.github.io/tiler/
+    Source = https://github.com/the-lay/tiler
+    Issues = https://github.com/the-lay/tiler/issues
+
+[options]
+packages = find:
+platforms = any
+python_requires = >= 3.6
+install_requires =
+    numpy
+    tqdm
+
+[options.extras_require]
+test =
+    pytest
+    coverage[toml]
+    black
+docs =
+    pdoc==8.0.1
+all =
+    %(docs)s
+    %(test)s
diff --git a/setup.py b/setup.py
@@ -1,36 +1,6 @@
 #!/usr/bin/env python
+import setuptools
 
-from setuptools import setup, find_packages
-
-# version fetch
-from tiler import __version__
-
-# readme fetch
-with open('README.md', 'r') as f:
-    long_description = f.read()
-
-setup(name='tiler',
-      version=__version__,
-      description='N-dimensional NumPy array tiling and merging with easy overlapping, padding and tapering support',
-      long_description=long_description,
-      long_description_content_type='text/markdown',
-      license='MIT',
-      author='the-lay',
-      author_email='ilja.gubin@gmail.com',
-      url='https://github.com/the-lay/tiler',
-      platforms=['any'],
-      install_requires=[
-          'numpy',
-          'tqdm'
-      ],
-      packages=find_packages(),
-      classifiers=[
-          'Development Status :: 3 - Alpha',
-          'Intended Audience :: Developers',
-          'Intended Audience :: Science/Research',
-          'Topic :: Software Development :: Libraries :: Python Modules',
-          'License :: OSI Approved :: MIT License',
-          'Programming Language :: Python :: 3 :: Only',
-      ]
-)
 
+if __name__ == "__main__":
+    setuptools.setup()