Merge pull request #1 from din14970/testing

revised all

.github/workflows/build.yml

@@ -0,0 +1,59 @@
+name: build
+
+on: 
+    push:
+        branches:
+            - master
+    pull_request:
+        branches:
+            - master
+
+jobs:
+  build-and-test:
+    name: ${{ matrix.os }}/py${{ matrix.python-version }}/pip
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    env:
+      MPLBACKEND: agg
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.7, 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: Display versions of Python and Pip
+        run: python -V; pip -V
+      - name: Setup conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          conda-channels: conda-forge
+      - name: Check conda version
+        run: conda --version
+      - name: Install depedencies and package
+        shell: bash
+        run: pip install -U -e .'[tests]'; conda install match-series
+      - name: Run tests
+        run: pytest --cov=pymatchseries --pyargs pymatchseries
+      - name: Generate line coverage
+        if: ${{ matrix.os == 'ubuntu-latest' }}
+        run: coverage report --show-missing
+      - name: Upload coverage to Coveralls
+        if: ${{ matrix.os == 'ubuntu-latest' }}
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel: true
+
+  coveralls-finish:
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls finished
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel-finished: true

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows 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
+
+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.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.gitignore

@@ -1,5 +1,7 @@
 tags
 examples/data/**
+examples/sample_data_HAADF
+examples/tester
 **.hdf5
 
 # Created by https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks

README.md

@@ -1,10 +1,17 @@
+<p align="center">
+<a href="https://github.com/din14970/pyMatchSeries/actions"><img alt="Actions Status" src="https://github.com/din14970/pyMatchSeries/workflows/build/badge.svg"></a>
+<a href="https://coveralls.io/github/din14970/pyMatchSeries?branch=master"><img alt="Coverage Status" src="https://coveralls.io/repos/github/din14970/pyMatchSeries/badge.svg?branch=master"></a>
+<a href="https://pypi.org/project/pyMatchSeries/"><img alt="PyPI" src="https://img.shields.io/pypi/v/pyMatchSeries.svg?style=flat"></a>
+<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
+</p>
+
 # Description
 This is a tool for non-rigid registration, primarily for atomic resolution STEM images, and is a python wrapper of the [match-series](https://github.com/berkels/match-series) code developed by B. Berkels. When using this tool, please cite the papers mentioned in that repository. 
 
 The goal of match-series is to remove slow and fast scan noise in STEM image stacks by comparing the various images against each other. The output of the code are X and Y deformation fields for each image in the stack. These deformations can then be applied to stacks of images or to EDX/EELS spectum maps that were acquired frame by frame. The goal of pymatchseries is to facilitate the set-up of the calculation and to work with the results in python. It is intended to use this tool mainly semi-interactively in a Jupyter notebook, see [the example](https://github.com/din14970/pyMatchSeries/blob/master/examples/example.ipynb).
 
 Try it out here:
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/din14970/pyMatchSeries/master)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/din14970/pyMatchSeries/testing)
 
 To install, simply pip install:
 ```
@@ -16,3 +23,9 @@ Note that, since it directly tries to call the matchSeries binary in a subproces
 ```
 $ conda install -c conda-forge match-series
 ```
+
+# Changelog
+
+## v0.1.0
+* Significantly simplified the API and made code more future proof
+* Trying out CI/CD pipelines

binder/environment.yml

@@ -6,5 +6,5 @@ dependencies:
   - temmeta
   - pywget
   - match-series
-  - pip
+  - pip:
     - pyMatchSeries