Automatic PyPi publishing (#15)

* Changed distribution type from setup.py to pep517

* Update to workflow

* Changed version number. Fixed last problems with the packaging.

* Update README.md

Changed install instructions to represent new way of installation

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

@@ -0,0 +1,39 @@
+name: Publish package
+
+on: [ release ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ 3.8 ]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Install pep517
+        run: |
+          python -m pip install pep517 --user
+
+      - name: Build a binary wheel and a source tarball
+        run: |
+          python -m pep517.build --source --binary --out-dir dist/ .
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

.github/workflows/python-package.yml → .github/workflows/test-package.yml

@@ -1,13 +1,9 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: SLIX
+name: Test package
 
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+on: [push, pull_request]
 
 jobs:
   build:
@@ -19,21 +15,27 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install setuptools wheel
         pip install flake8 pytest
+        pip install pytest-cov
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest
       run: |
-        pytest
+        pytest --doctest-modules --junitxml=junit/test-results.xml --cov=SLIX --cov-report=xml --cov-report=html

.gitignore

@@ -1,7 +1,8 @@
-/dist/
-/build/
-/SLIX.egg-info/
+dist/
+build/
+SLIX.egg-info/
 /venv/
 /.idea/
 /*/__pycache__/
-.vscode/settings.json
+.vscode/settings.json
+SLIX.egg-info/

README.md

@@ -67,7 +67,7 @@ By evaluating the SLI profiles of each image pixel, *SLIX* generates different p
 With [`SLIXLineplotParameterGenerator`](#evaluation-of-sli-profiles), it is possible to evaluate individual SLI profiles and compute characteristics such as the number of peaks, their positions, and in-plane fiber direction angles. For a given SLI image stack, [`SLIXParameterGenerator`](#generation-of-parameter-maps) computes the desired parameter maps for all image pixels.
 
 ## Installation of SLIX
-##### How to clone SLIX
+##### How to clone SLIX (for further work)
 ```
 git clone [email protected]:3d-pli/SLIX.git
 cd SLIX
@@ -81,10 +81,13 @@ pip3 install -r requirements.txt
 
 ##### How to install SLIX as Python package
 ```
+# Install via PyPi
+pip install SLIX
+
+# Install after cloning locally
 git clone [email protected]:3d-pli/SLIX.git
 cd SLIX
-
-python3 setup.py install
+pip install .
 ```
 
 ## Evaluation of SLI Profiles

SLIX/__init__.py

@@ -0,0 +1,5 @@
+"""Module docstring text"""
+__version__ = 'v1.2.1'
+
+from . import toolbox
+from . import visualization

SLIX/toolbox.py

@@ -692,7 +692,7 @@ def create_background_mask(IMAGE, threshold=10):
     return mask
 
 
-def create_roiset(IMAGE, ROISIZE, extend=True):
+def create_roiset(IMAGE, ROISIZE=1, extend=True):
     """
     Create roi set of the given image by creating an image containing the average value of pixels within the
     specified ROISIZE. The returned image will have twice the size in the third axis as the both halfs will be doubled

pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+  "setuptools >= 40.9.0",
+  "wheel",
+]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -0,0 +1,37 @@
+[metadata]
+name = SLIX
+version = v1.2.1-3
+author = Jan Andre Reuter, Miriam Menzel
+author_email = [email protected], [email protected]
+description = SLIX allows an automated evaluation of SLI measurements and generates different parameter maps.
+license_file = LICENSE
+long_description = file: README.md
+long_description_content_type = text/markdown
+license = MIT
+classifiers =
+    Programming Language :: Python :: 3
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+
+[options]
+zip_safe = False
+include_package_data = True
+packages = find:
+scripts =
+    bin/SLIXParameterGenerator
+    bin/SLIXLineplotParameterGenerator
+install_requires =
+    numpy
+    scipy
+    matplotlib
+    pymp-pypi
+    nibabel
+    tifffile
+    tqdm
+    Pillow
+tests_require =
+    pytest
+    flake8
+    pytest-cov
+python_requires =
+    >= 3.6