Merge remote-tracking branch 'upstream/master'

Author: Francis Motta

.github/workflows/python-app.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 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: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install Cython
+        pip install flake8 ripser
+        pip install -e ".[testing]"
+    - 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 --cov persim
+    - name: Upload coverage results
+      run: |
+        bash <(curl -s https://codecov.io/bash)

.github/workflows/python-publish.yml

@@ -0,0 +1,32 @@
+# 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: [created]
+
+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 Cython
+        pip install ripser
+        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/*

.readthedocs.yml

@@ -0,0 +1,10 @@
+version: 2
+
+python:
+   version: 3.7
+   install:
+      - requirements: docs/requirements.txt
+      - method: pip
+        path: .
+        extra_requirements:
+            - docs

.travis.yml

@@ -1,6 +1,3 @@
-0.1.5
-	- Deprecated PersImage class with implementation of PersistenceImager
-
 0.1.4
     - Migrate to a new CI/CD pipeline
 

DEPLOY.md

@@ -97,7 +97,7 @@
     }
    ],
    "source": [
-    "persim.plot_diagrams([dgm_clean, dgm_noisy] , labels=['Clean $H_1$', 'Noisy $H_1$'])\n"
+    "persim.plot_diagrams([dgm_clean, dgm_noisy] , labels=['Clean $H_1$', 'Noisy $H_1$'])\n",
     "plt.show()"
    ]
   },
@@ -136,7 +136,7 @@
     }
    ],
    "source": [
-    "persim.bottleneck_matching(dgm_clean, dgm_noisy, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])\n"
+    "persim.bottleneck_matching(dgm_clean, dgm_noisy, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])\n",
     "plt.show()"
    ]
   },
@@ -451,7 +451,7 @@
    "source": [
     "plt.scatter(dists_bottleneck[:,0], dists_bottleneck[:,1], label=\"Bottleneck\", alpha=0.3)\n",
     "plt.scatter(dists_sliced[:,0], dists_sliced[:,1], label=\"Sliced Wasserstein\", alpha=0.3)\n",
-    "plt.legend()\n"
+    "plt.legend()\n",
     "plt.show()"
    ]
   },
@@ -499,7 +499,7 @@
     "\n",
     "    plt.title(\"Noise:{} Distance:{:.3f}\".format(n, d))\n",
     "\n",
-    "plt.tight_layout()\n"
+    "plt.tight_layout()\n",
     "plt.show()"
    ]
   }

Makefile

@@ -1 +1 @@
-__version__ = "0.1.5"
+__version__ = "0.1.4"

RELEASE.txt

@@ -36,13 +36,14 @@
       ],
       extras_require={ # use `pip install -e ".[testing]"``
         'testing': [
-          'pytest' 
+          'pytest',
+          'pytest-cov' 
         ],
         'docs': [ # `pip install -e ".[docs]"``
           'sktda_docs_config'
         ]
       },
-      python_requires='>=2.7,!=3.1,!=3.2,!=3.3',
+      python_requires='>=3.6',
       classifiers=[
         'Development Status :: 3 - Alpha',
         'Intended Audience :: Science/Research',
@@ -52,12 +53,9 @@
         'Topic :: Scientific/Engineering :: Information Analysis',
         'Topic :: Scientific/Engineering :: Mathematics',
         'License :: OSI Approved :: MIT License',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
       ],
       keywords='persistent homology, persistence images, persistence diagrams, topological data analysis, algebraic topology, unsupervised learning, supervised learning, machine learning, sliced wasserstein distance, bottleneck distance'
      )