Transition to Github Actions (soft-matter#640)

.github/workflows/test-conda.yml

@@ -0,0 +1,37 @@
+name: Conda
+
+on: [push, pull_request]
+
+jobs:
+  TestConda:
+    name: ${{ matrix.os }} - ${{ matrix.channel || 'defaults' }} - Python ${{ matrix.python }} (GEOS ${{ matrix.geos || 'latest' }}, numpy ${{ matrix.numpy || 'latest' }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python: [3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup Conda
+        uses: s-weigand/[email protected]
+        with:
+          activate-conda: false
+          conda-channels: conda-forge
+
+      - name: Setup Environment
+        shell: bash
+        run: |
+          conda create --name test python=${{ matrix.python }} pytest numpy scipy matplotlib pillow pandas scikit-image pytables numba scikit-learn pyyaml
+          source activate test
+          python -V
+          conda info
+          conda list
+
+      - name: Run tests
+        shell: bash
+        run: |
+          source activate test
+          pytest trackpy

.github/workflows/test-pip.yml

@@ -0,0 +1,74 @@
+name: Pip
+
+on: [push, pull_request]
+
+jobs:
+  TestLinux:
+    name: Python ${{ matrix.python }} ${{ matrix.display_name }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # "Legacy" environments: oldest supported versions, without and with optional dependencies
+          - python: 3.5
+            display_name: "no optional deps"
+            numpy: "numpy==1.13.*"
+            deps: "scipy==0.19.* matplotlib==2.0.* pandas==0.20.* pyyaml"
+          - python: 3.5
+            display_name: "no numba"
+            numpy: "numpy==1.13.*"
+            deps: "scipy==0.19.* matplotlib==2.0.* pillow==4.2.* pandas==0.20.* scikit-image==0.13.* tables==3.3.* scikit-learn==0.19.* pyyaml==3.12"
+          # 2017
+          - python: 3.6
+            numpy: "numpy==1.14.*"
+            deps: "scipy==1.1.* matplotlib==2.1.* pillow==4.3.* pandas==0.22.* scikit-image==0.13.* tables==3.4.* scikit-learn==0.19.* pyyaml==3.12 numba==0.32.* llvmlite==0.17.*"
+          # 2018
+          - python: 3.7
+            numpy: "numpy==1.16.*"
+            deps: "scipy==1.3.* matplotlib==2.2.* pillow==5.3.* pandas==0.23.* scikit-image==0.14.* tables==3.5.* scikit-learn==0.20.* pyyaml==3.13 numba==0.39.* llvmlite==0.24."
+          # 2019
+          - python: 3.8
+            numpy: "numpy==1.18.*"
+            deps: "scipy==1.4.* matplotlib==3.1.* pillow==6.2.* pandas==0.25.* scikit-image==0.16.* tables==3.6.* scikit-learn==0.22.* pyyaml==5.3.* numba==0.47.* llvmlite==0.31.*"
+          # 2020
+          - python: 3.9
+            numpy: "numpy==1.19.*"
+            deps: "scipy==1.5.* matplotlib==3.3.* pillow==8.0.* pandas==1.1.* scikit-image==0.18.* tables==3.6.* scikit-learn==0.24.* pyyaml==5.4.* numba==0.53rc1.post1 llvmlite==0.36rc1"
+          # most recent
+          - python: '3.x'
+            display_name: "latest, no numba"
+            numpy: "numpy"
+            deps: "scipy matplotlib pillow pandas scikit-image tables scikit-learn pyyaml" 
+          # most recent
+          - python: '3.x'
+            display_name: "pre-releases"
+            numpy: "--pre numpy"
+            deps: "--pre scipy matplotlib pillow pandas scikit-image tables scikit-learn pyyaml numba llvmlite" 
+
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install HDF5 library
+        run: sudo apt-get install libhdf5-dev
+
+      - name: Install python dependencies
+        shell: bash
+        run: |
+          pip install --disable-pip-version-check --upgrade pip
+          pip install --upgrade wheel
+          pip install --no-build-isolation ${{ matrix.numpy }};
+          pip install --no-build-isolation pytest ${{ matrix.deps }};
+          pip list
+
+      - name: Run tests
+        shell: bash
+        continue-on-error: ${{ matrix.display_name == 'pre-releases' }}
+        run: |
+          pytest trackpy

.gitignore

@@ -45,3 +45,6 @@ doc/tutorial/*_files
 .idea
 doc/examples/index.rst
 soft-matter-docs-deploy
+
+# VS Code
+.vscode

.travis.yml

@@ -2,19 +2,9 @@ language: python
 
 jobs:
   include:
-    # "Legacy" environments: oldest supported versions, without and with optional dependencies
-    - python: "3.5"
-      env: DEPS="numpy=1.13.1 scipy=0.19.1 matplotlib=2.0.2 pandas=0.20.3 pyyaml" BUILD_DOCS=true
-    - python: "3.5"
-      env: DEPS="numpy=1.13.1 scipy=0.19.1 matplotlib=2.0.2 pillow=4.2.1 pandas=0.20.3 scikit-image=0.13.0 pytables scikit-learn=0.19.0 pyyaml" BUILD_DOCS=true
-    # "Typical" environments: versions 2-3 years old
-    # Python 3, circa September 2017 (Anaconda 5.0.0)
+    # Python 3, circa September 2017 (Anaconda 5.0.0), used for building docs
     - python: "3.5"
       env: DEPS="numpy=1.13.1 scipy=0.19.1 matplotlib=2.0.2 pillow=4.2.1 pandas=0.20.3 scikit-image=0.13.0 pytables numba=0.35.0 scikit-learn=0.19.0 pyyaml" BUILD_DOCS=true
-    # Environments with most recent versions
-    - python: "3.7"
-      env: DEPS="numpy scipy!=1.5.0 matplotlib pillow pandas scikit-image pytables numba scikit-learn pyyaml pytables"  BUILD_DOCS=false
-
 
 install:
   - conda update --yes conda

README.md

@@ -1,8 +1,8 @@
 trackpy
 =======
 
-[![Build Status](https://travis-ci.org/soft-matter/trackpy.svg?branch=master)](https://travis-ci.org/soft-matter/trackpy)
-[![Build status](https://ci.appveyor.com/api/projects/status/jsd62y3e4rlx3f9u/branch/master?svg=true)](https://ci.appveyor.com/project/caspervdw/trackpy-rixcv/branch/master)
+[![Build status](https://github.com/soft-matter/trackpy/workflows/Linux/badge.svg)](https://github.com/soft-matter/trackpy/actions/)
+[![Build status](https://github.com/soft-matter/trackpy/workflows/Conda/badge.svg)](https://github.com/soft-matter/trackpy/actions/)
 [![DOI](https://zenodo.org/badge/4744355.svg)](https://zenodo.org/badge/latestdoi/4744355)
 
 What is it?

benchmarks/maxima_benchmarks.ipynb

@@ -15,14 +15,14 @@ real_image = scale_to_gamut(tp.bandpass(real_image_raw, 1, 10, threshold=1), np.
 big_image = scale_to_gamut(tp.bandpass(np.tile(real_image_raw, (2, 5)), 1, 10, threshold=1), np.uint8)
 very_small_image = scale_to_gamut(tp.bandpass(real_image_raw[:200, :200], 1, 10, threshold=1), np.uint8)
 
-#print 'Locate using Python Engine with Default Settings (Accurate)'
+#print('Locate using Python Engine with Default Settings (Accurate)')
 #b(u"timeit tp.locate(real_image, 9, engine='python', preprocess=False)")
 
-print '1x: Find local_maxima only'
+print('1x: Find local_maxima only')
 b(u"timeit tp.feature.local_maxima(real_image, 9, 10)")
 
-print '10x: Find local_maxima only'
+print('10x: Find local_maxima only')
 b(u"timeit tp.feature.local_maxima(big_image, 9, 10)")
 
-print '~0.1x: Find local_maxima only'
+print('~0.1x: Find local_maxima only')
 b(u"timeit tp.feature.local_maxima(very_small_image, 9, 10)")

benchmarks/numba_benchmarks.ipy

@@ -13,24 +13,24 @@ real_image_raw = tp.ImageSequence('../trackpy/tests/video/image_sequence')[0]
 real_image = tp.bandpass(real_image_raw, 1, 10, threshold=1)
 big_image = tp.bandpass(np.tile(real_image_raw, (2, 5)), 1, 10, threshold=1)
 
-print 'Compiling Numba...'
+print('Compiling Numba...')
 tp.locate(dummy_noise_image, 9, engine='numba')
 
-#print 'Locate using Python Engine with Default Settings (Accurate)'
+#print('Locate using Python Engine with Default Settings (Accurate)')
 #b(u"timeit tp.locate(real_image, 9, engine='python', preprocess=False)")
 
-print '10x: Locate using Python Engine with Default Settings (Accurate)'
+print('10x: Locate using Python Engine with Default Settings (Accurate)')
 b("timeit tp.locate(big_image, 9, engine='python', preprocess=False)")
 
-print '10x: Locate using Python Engine with Fast Settings (Sloppy)'
+print('10x: Locate using Python Engine with Fast Settings (Sloppy)')
 b("timeit tp.locate(big_image, 9, engine='python', preprocess=False, filter_before=False, filter_after=False, max_iterations=0, characterize=False)")
 
-print '1x: Locate using Numba Engine with Default Settings (Accurate)'
+print('1x: Locate using Numba Engine with Default Settings (Accurate)')
 b("timeit tp.locate(real_image, 9, engine='numba', preprocess=False)")
 
-print '10x: Locate using Numba Engine with Default Settings (Accurate)'
+print('10x: Locate using Numba Engine with Default Settings (Accurate)')
 b("timeit tp.locate(big_image, 9, engine='numba', preprocess=False)")
 
-print '10x: Locate using Numba Engine with Fast Settings (Sloppy)'
+print('10x: Locate using Numba Engine with Fast Settings (Sloppy)')
 b("timeit tp.locate(big_image, 9, engine='numba', preprocess=False, filter_before=False, filter_after=False, max_iterations=0, characterize=False)")
 

benchmarks/simple_benchmarks.ipy

@@ -12,18 +12,18 @@ dummy_noise_image = np.random.randint(0, 100, (100, 100))
 real_image_raw = tp.ImageSequence('../trackpy/tests/video/image_sequence')[0]
 real_image = tp.bandpass(real_image_raw, 1, 10, threshold=1)
 
-print 'Compiling Numba...'
+print('Compiling Numba...')
 tp.locate(dummy_noise_image, 9, engine='numba')
 
-print 'Locate using Python Engine with Default Settings (Accurate)'
+print('Locate using Python Engine with Default Settings (Accurate)')
 b("timeit tp.locate(real_image, 9, engine='python', preprocess=False)")
 
-print 'Locate using Python Engine with Fast Settings (Sloppy)'
+print('Locate using Python Engine with Fast Settings (Sloppy)')
 b("timeit tp.locate(real_image, 9, engine='python', preprocess=False, filter_before=False, filter_after=False, max_iterations=0, characterize=False)")
 
-print 'Locate using Numba Engine with Default Settings (Accurate)'
+print('Locate using Numba Engine with Default Settings (Accurate)')
 b("timeit tp.locate(real_image, 9, engine='numba', preprocess=False)")
 
-print 'Locate using Numba Engine with Fast Settings (Sloppy)'
+print('Locate using Numba Engine with Fast Settings (Sloppy)')
 b("timeit tp.locate(real_image, 9, engine='numba', preprocess=False, filter_before=False, filter_after=False, max_iterations=0, characterize=False)")
 

benchmarks/suite.py

@@ -50,15 +50,15 @@ def generate_rst_files(benchmarks):
     fig_base_path = os.path.join(vb_path, 'figures')
 
     if not os.path.exists(vb_path):
-        print 'creating %s' % vb_path
+        print('creating %s' % vb_path)
         os.makedirs(vb_path)
 
     if not os.path.exists(fig_base_path):
-        print 'creating %s' % fig_base_path
+        print('creating %s' % fig_base_path)
         os.makedirs(fig_base_path)
 
     for bmk in benchmarks:
-        print 'Generating rst file for %s' % bmk.name
+        print('Generating rst file for %s' % bmk.name)
         rst_path = os.path.join(RST_BASE, 'vbench/%s.txt' % bmk.name)
 
         fig_full_path = os.path.join(fig_base_path, '%s.png' % bmk.name)