Switch to tox

Author: kbattocchi

azure-pipelines-steps.yml

@@ -4,8 +4,8 @@
 # https://docs.microsoft.com/azure/devops/pipelines/languages/python
 
 parameters:
-  body: []
-  package: '-e .'
+  post: []
+  env: 'py38'
 
 steps:
 - task: UsePythonVersion@0
@@ -18,13 +18,8 @@ steps:
   displayName: 'Enable long paths on Windows'
   condition: and(succeeded(), eq(variables['Agent.OS'], 'Windows_NT'))
 
-# Install graphviz programmatically on Linux
-- script: 'sudo apt-get -yq install graphviz'
-  displayName: 'Install graphviz on Linux'
-  condition: and(succeeded(), eq(variables['Agent.OS'], 'Linux'))
+# Run tox
+- script: 'python -m pip install --upgrade pip && pip install --upgrade tox && tox -e ${{ parameters.env }}'
+  displayName: 'Install and run tox'
 
-# Install the package
-- script: 'python -m pip install --upgrade pip && pip install --upgrade setuptools wheel Cython && pip install ${{ parameters.package }}'
-  displayName: 'Install dependencies'
-
-- ${{ parameters.body }}
+- ${{ parameters.post }}

azure-pipelines.yml

@@ -55,53 +55,34 @@ jobs:
   pool: 
     vmImage: 'ubuntu-18.04'
   variables:
-    python.version: '3.6'
+    python.version: '3.8'
   steps:
   - template: azure-pipelines-steps.yml
     parameters:
-      body:
-        - script: 'sudo apt-get -yq install graphviz'
-          displayName: 'Install graphviz'
-
-        - script: 'pip install sklearn-contrib-lightning'
-          displayName: 'Install lightning'        
-
-        - script: 'pip install git+https://github.com/slundberg/shap.git@d1d2700acc0259f211934373826d5ff71ad514de'
-          displayName: 'Install specific version of shap'  
-
-        - script: 'python setup.py build_sphinx -W'
-          displayName: 'Build documentation'
-
+      post:
         - publish: 'build/sphinx/html'
           artifact: 'Documentation'
           displayName: 'Publish documentation as artifact'
-
-        - script: 'python setup.py build_sphinx -b doctest'
-          displayName: 'Run doctests'
-      package: '-e .[automl]'
+      env: 'doctest'
 
 - job: 'Notebooks'
   dependsOn: 'EvalChanges'
   condition: eq(dependencies.EvalChanges.outputs['output.buildNbs'], 'True')
-  variables:
-    python.version: '3.8'
   pool:
     vmImage: 'ubuntu-18.04'
+  variables:
+    python.version: '3.8'
   steps:
   - template: azure-pipelines-steps.yml
     parameters:
-      body:
-        - script: 'python setup.py pytest'
-          displayName: 'Unit tests'
-          env:
-            PYTEST_ADDOPTS: '-m "notebook"'
-
+      post:
         - task: PublishTestResults@2
           displayName: 'Publish Test Results **/test-results.xml'
           inputs:
             testResultsFiles: '**/test-results.xml'
             testRunTitle: 'Notebooks'
           condition: succeededOrFailed()
+      env: 'notebooks'
 
 # - job: 'AutoML'
 #   dependsOn: 'EvalChanges'
@@ -141,17 +122,19 @@ jobs:
 - job: 'Linting'
   dependsOn: 'EvalChanges'
   condition: eq(dependencies.EvalChanges.outputs['output.testCode'], 'True')
-  variables:
-    python.version: '3.8'
   pool:
     vmImage: 'macOS-10.15'
   steps:
-  - template: azure-pipelines-steps.yml
-    parameters:
-      body:
-        - script: 'pip install pycodestyle && pycodestyle econml'
-          failOnStderr: true
-          displayName: Linting
+  - task: UsePythonVersion@0
+    displayName: 'Use Python 3.8'
+    inputs:
+      versionSpec: '3.8'  
+  # note: don't need to install the package itself to lint it
+  - script: 'python -m pip install --upgrade pip && pip install pycodestyle'
+    displayName: 'Install pycodestyle'
+  - script: 'pycodestyle econml'
+    failOnStderr: true
+    displayName: Linting
 
 - job: 'Tests'
   dependsOn: 'EvalChanges'
@@ -160,30 +143,39 @@ jobs:
     matrix:
       Linux, Python 3.6:
         imageName: 'ubuntu-18.04'
+        env: 'py36'
         python.version: '3.6'
       macOS, Python 3.6:
         imageName: 'macOS-10.15'
+        env: 'py36'
         python.version: '3.6'
       Windows, Python 3.6:
         imageName: 'windows-2019'
+        env: 'py36'
         python.version: '3.6'
       Linux, Python 3.7:
         imageName: 'ubuntu-18.04'
+        env: 'py37'
         python.version: '3.7'
       macOS, Python 3.7:
         imageName: 'macOS-10.15'
+        env: 'py37'
         python.version: '3.7'
       Windows, Python 3.7:
         imageName: 'windows-2019'
+        env: 'py37'
         python.version: '3.7'
       Linux, Python 3.8:
         imageName: 'ubuntu-18.04'
+        env: 'py38'
         python.version: '3.8'
       macOS, Python 3.8:
         imageName: 'macOS-10.15'
+        env: 'py38'
         python.version: '3.8'
       Windows, Python 3.8:
         imageName: 'windows-2019'
+        env: 'py38'
         python.version: '3.8'
 
   pool:
@@ -194,12 +186,7 @@ jobs:
   steps:
   - template: azure-pipelines-steps.yml
     parameters:
-      body:
-        - script: 'python setup.py pytest'
-          displayName: 'Unit tests'
-          env:
-            PYTEST_ADDOPTS: '-m "not (notebook or automl)"'
-            COVERAGE_PROCESS_START: 'setup.cfg'
+      post:
         - task: PublishTestResults@2
           displayName: 'Publish Test Results **/test-results.xml'
           inputs:
@@ -212,3 +199,4 @@ jobs:
           inputs:
             codeCoverageTool: Cobertura
             summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
+      env: $(env)

pyproject.toml

@@ -14,4 +14,13 @@ markers = [
     "slow",
     "notebook",
     "automl"
+]
+
+[tool.coverage.run]
+omit = "econml/tests/*"
+branch = "True"
+# need to explicitly add support for multiprocessing for OrthoForest
+concurrency = [
+    "thread",
+    "multiprocessing"
 ]

setup.cfg

@@ -32,11 +32,6 @@ classifiers =
 
 [options]
 packages = find_namespace:
-setup_requires =
-    pytest-runner
-    sphinx < 3.2
-    sphinx_rtd_theme
-    Cython
 install_requires =
     numpy
     scipy > 1.4.0
@@ -51,18 +46,6 @@ install_requires =
     matplotlib
     pandas < 1.1
     shap ~= 0.38.1
-test_suite = econml.tests
-tests_require =
-    pytest
-    pytest-xdist < 2.0.0
-    pytest-cov
-    jupyter
-    nbconvert < 6
-    nbformat
-    seaborn
-    lightgbm
-    dowhy
-    xgboost
 
 [options.extras_require]
 automl =
@@ -79,12 +62,3 @@ include =
 [options.package_data]
 ; include all CSV files as data
 * = *.csv
-
-; coverage configuration
-[coverage:run]
-omit = econml/tests/*
-branch = True
-; need to explicitly add support for multiprocessing for OrthoForest
-concurrency =
-    thread
-    multiprocessing

setup.py

@@ -3,9 +3,10 @@
 from Cython.Build import cythonize
 import numpy as np
 
-
 # configuration is all pulled from setup.cfg
-setup(ext_modules=cythonize([Extension("*", ["**/*.pyx"],
+setup(ext_modules=cythonize([Extension("econml.tree.*", ["econml/tree/*.pyx"],
+                                       include_dirs=[np.get_include()]),
+                             Extension("econml.grf.*", ["econml/grf/*.pyx"],
                                        include_dirs=[np.get_include()])],
                             language_level="3"),
       zip_safe=False)

tox.ini

@@ -0,0 +1,43 @@
+[tox]
+envlist = py{36,37,38}, notebooks, doctest
+
+isolated_build = true
+
+[testenv]
+# install additional testing requirements
+deps = 
+    pytest
+    pytest-xdist
+    pytest-cov    
+    coverage[toml]    
+    nbconvert < 6
+
+# run the tests
+commands = 
+    pytest -m "not (notebook or automl)"
+
+[testenv:notebooks]
+deps =
+    {[testenv]deps}
+    jupyter
+    nbconvert < 6
+    shap
+    lightgbm
+    seaborn
+    xgboost
+    dowhy
+
+commands =
+    pytest -m "notebook"
+
+[testenv:doctest]
+deps =
+    sklearn-contrib-lightning
+    sphinx
+extras =
+    automl
+commands =
+    sudo apt-get -yq install graphviz
+    sphinx-build -b html ./doc ./build/sphinx -W
+    sphinx-build -b doctest ./doc ./build/sphinx
+