Update dependencies and migrate to GH Actions (#255)

* Update dependencies

* Migrate to GH actions

* Fix github actions

* Test devel instead of just lint

* Test unit only

Author: csala

.github/workflows/docs.yml

@@ -0,0 +1,28 @@
+name: Generate Docs
+
+on:
+  push:
+    branches: [ stable ]
+
+jobs:
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Build
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[dev]
+        make docs
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{secrets.GITHUB_TOKEN}}
+        publish_dir: docs/_build/html

.github/workflows/tests.yml

@@ -0,0 +1,59 @@
+name: Run Tests
+
+on:
+  push:
+    branches: [ '*' ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  devel:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        os: [ubuntu-latest, macos-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package
+      run: pip install .[dev]
+    - name: make test-devel
+      run: make test-devel
+
+  readme:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        os: [ubuntu-latest, macos-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install rundoc .
+    - name: make test-readme
+      run: make test-readme
+
+  unit:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        os: [ubuntu-latest, macos-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install .[test]
+    - name: make test-unit
+      run: make test-unit

.travis.yml

@@ -81,6 +81,12 @@ install-test: clean-build clean-pyc ## install the package and test dependencies
 install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
 	pip install -e .[dev]
 
+MINIMUM := $(shell sed -n '/install_requires = \[/,/]/p' setup.py | grep -v -e '[][]' | sed 's/ *\(.*\),$?$$/\1/g' | tr '>' '=')
+
+.PHONY: install-minimum
+install-minimum: ## install the minimum supported versions of the package dependencies
+	pip install $(MINIMUM)
+
 
 # LINT TARGETS
 
@@ -151,11 +157,11 @@ docs: clean-docs ## generate Sphinx HTML documentation, including API docs
 	$(MAKE) -C docs html
 
 .PHONY: view-docs
-view-docs: docs ## view docs in browser
+view-docs: ## view the docs in a browser
 	$(BROWSER) docs/_build/html/index.html
 
 .PHONY: serve-docs
-serve-docs: view-docs ## compile the docs watching for changes
+serve-docs: ## compile the docs watching for changes
 	watchmedo shell-command -W -R -D -p '*.rst;*.md' -c '$(MAKE) -C docs html' docs
 
 

Makefile

@@ -1,22 +1,24 @@
 <p align="left">
-<img width=25% src="https://dai.lids.mit.edu/wp-content/uploads/2018/06/Logo_DAI_highres.png" alt=“DAI-Lab” />
-<i>An open source project from Data to AI Lab at MIT.</i>
+  <a href="https://dai.lids.mit.edu">
+    <img width=15% src="https://dai.lids.mit.edu/wp-content/uploads/2018/06/Logo_DAI_highres.png" alt="DAI-Lab" />
+  </a>
+  <i>An Open Source Project from the <a href="https://dai.lids.mit.edu">Data to AI Lab, at MIT</a></i>
 </p>
 
-
 [![Development Status](https://img.shields.io/badge/Development%20Status-2%20--%20Pre--Alpha-yellow)](https://pypi.org/search/?c=Development+Status+%3A%3A+2+-+Pre-Alpha)
 [![PyPi Shield](https://img.shields.io/pypi/v/mlprimitives.svg)](https://pypi.python.org/pypi/mlprimitives)
-[![Travis CI Shield](https://travis-ci.com/MLBazaar/MLPrimitives.svg?branch=master)](https://travis-ci.com/MLBazaar/MLPrimitives)
+[![Tests](https://github.com/MLBazaar/MLPrimitives/workflows/Run%20Tests/badge.svg)](https://github.com/MLBazaar/MLPrimitives/actions?query=workflow%3A%22Run+Tests%22+branch%3Amaster)
 [![Downloads](https://pepy.tech/badge/mlprimitives)](https://pepy.tech/project/mlprimitives)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/MLBazaar/MLBlocks/master?filepath=examples/tutorials)
 
 # MLPrimitives
 
 Pipelines and primitives for machine learning and data science.
 
+* Documentation: https://MLBazaar.github.io/MLPrimitives
+* Github: https://github.com/MLBazaar/MLPrimitives
 * License: [MIT](https://github.com/MLBazaar/MLPrimitives/blob/master/LICENSE)
 * Development Status: [Pre-Alpha](https://pypi.org/search/?c=Development+Status+%3A%3A+2+-+Pre-Alpha)
-* Documentation: https://MLBazaar.github.io/MLPrimitives
-* Homepage: https://github.com/MLBazaar/MLPrimitives
 
 # Overview
 

README.md

@@ -6,9 +6,9 @@
 import keras
 import numpy as np
 import pandas as pd
+import tensorflow as tf
 from keras import backend as K
-from keras.layers import Input
-from keras.layers.merge import _Merge
+from keras.layers import Input, Layer
 from keras.models import Model
 from scipy import integrate, stats
 
@@ -18,11 +18,18 @@
 LOGGER = logging.getLogger(__name__)
 
 
-class RandomWeightedAverage(_Merge):
-    def _merge_function(self, inputs):
-        alpha = K.random_uniform((64, 1, 1))
+class RandomWeightedAverage(Layer):
+    def __init__(self, batch_size):
+        super().__init__()
+        self.batch_size = batch_size
+
+    def call(self, inputs, **kwargs):
+        alpha = tf.random_uniform((self.batch_size, 1, 1, 1))
         return (alpha * inputs[0]) + ((1 - alpha) * inputs[1])
 
+    def compute_output_shape(self, input_shape):
+        return input_shape[0]
+
 
 class CycleGAN():
     """CycleGAN class"""
@@ -130,7 +137,7 @@ def _build_cyclegan(self, **kwargs):
         z_ = self.encoder(x)
         fake_x = self.critic_x(x_)
         valid_x = self.critic_x(x)
-        interpolated_x = RandomWeightedAverage()([x, x_])
+        interpolated_x = RandomWeightedAverage(self.batch_size)([x, x_])
 
         validity_interpolated_x = self.critic_x(interpolated_x)
         partial_gp_loss_x = partial(self._gradient_penalty_loss, averaged_samples=interpolated_x)
@@ -143,7 +150,7 @@ def _build_cyclegan(self, **kwargs):
 
         fake_z = self.critic_z(z_)
         valid_z = self.critic_z(z)
-        interpolated_z = RandomWeightedAverage()([z, z_])
+        interpolated_z = RandomWeightedAverage(self.batch_size)([z, z_])
         validity_interpolated_z = self.critic_z(interpolated_z)
         partial_gp_loss_z = partial(self._gradient_penalty_loss, averaged_samples=interpolated_z)
         partial_gp_loss_z.__name__ = 'gradient_penalty'
@@ -210,10 +217,11 @@ def predict(self, X):
                 N-dimensional array containing the input sequences for the model.
 
         Returns:
-            ndarray:
-                N-dimensional array containing the reconstructions for each input sequence.
-            ndarray:
-                N-dimensional array containing the critic scores for each input sequence.
+            typle:
+                ndarray:
+                    N-dimensional array containing the reconstructions for each input sequence.
+                ndarray:
+                    N-dimensional array containing the critic scores for each input sequence.
         """
         X = X.reshape((-1, self.shape[0], 1))
         z_ = self.encoder.predict(X)

mlprimitives/candidates/timeseries/cyclegan.py

@@ -20,21 +20,16 @@
     'mlblocks>=0.4.0.dev0,<0.5',
     'networkx>=2.0,<3',
     'nltk>=3.3,<4',
+    'numpy<1.19.0,>=1.16.0',
     'opencv-python>=3.4.0.12,<5',
     'pandas>=1,<2',
-    'python-louvain>=0.10,<0.14',
+    'python-louvain>=0.10,<0.14',   # community
     'scikit-image>=0.15',
     'scikit-learn>=0.21',
     'scipy>=1.1.0,<2',
-    'statsmodels>=0.9.0,<1',
+    'statsmodels>=0.9.0,<0.13',
     'tensorflow>=2,<2.4',
     'xgboost>=0.72.1,<1',
-
-    # Conflict fixing
-    'docutils<0.16,>=0.10',
-    'urllib3<1.26,>=1.20',
-    'h5py<2.11.0,>=2.10.0',
-    'numpy<1.19.0,>=1.16.0',
 ]
 
 
@@ -45,7 +40,6 @@
 tests_require = [
     'pytest>=3.4.2',
     'pytest-cov>=2.6.0',
-    'jupyter>=1.0.0,<2',
     'rundoc>=0.4.3,<0.5',
 ]
 
@@ -76,10 +70,6 @@
     # Advanced testing
     'coverage>=4.5.1,<6',
     'tox>=2.9.1,<4',
-    'importlib-metadata<2.0.0,>=0.12'
-
-    # Jupyter
-    'jupyter>=1.0.0',
 ]
 
 extras_require = {
@@ -126,7 +116,7 @@
     setup_requires=setup_requires,
     test_suite='tests',
     tests_require=tests_require,
-    url='https://github.com/HDI-Project/MLPrimitives',
+    url='https://github.com/MLBazaar/MLPrimitives',
     version='0.3.0.dev2',
     zip_safe=False,
 )