[MRG] Mac builds

.circleci/config.yml

@@ -92,6 +92,14 @@ jobs:
     - install-gfortran
     - make-unit-test
 
+  cpython38-linux:
+    docker:
+      - image: python:3.8
+    working_directory: ~/skoot
+    steps:
+      - install-gfortran
+      - make-unit-test
+
   # For testing lint
   test-linting:
     docker:
@@ -151,6 +159,17 @@ jobs:
           pythonversion: "3.7"
       - deploy-to-pypi
 
+  deploy-cpython38-whl:
+    machine:
+      image: circleci/classic:latest
+    working_directory: ~/skoot
+    steps:
+      - checkout
+      - sudo-install-gfortran
+      - build-whl-file:
+          pythonversion: "3.8"
+      - deploy-to-pypi
+
   # For documentation deployment. You'll need the following environment vars
   # in your Circle CI settings, otherwise this will not work.
   #
@@ -179,6 +198,8 @@ workflows:
           filters: *test-filters
       - cpython37-linux:
           filters: *test-filters
+      - cpython38-linux:
+          filters: *test-filters
       - test-linting:
           filters: *test-filters
 
@@ -210,3 +231,8 @@ workflows:
           filters: *deploy-filters
           requires:
               - deploy-doc
+
+      - deploy-cpython38-whl:
+          filters: *deploy-filters
+          requires:
+            - deploy-doc

azure-pipelines.yml

@@ -18,9 +18,9 @@ pr:
     include:
     - '*'
 
-variables:
-  # Read deployment variables from our secret group
-  - group: deploy-vars
+#variables:
+#  # Read deployment variables from our secret group
+#  - group: deploy-vars
 
 jobs:
 - template: build_tools/azure/jobs.yml

build_tools/azure/build_and_deploy.yml

@@ -16,10 +16,6 @@ steps:
 - script: pytest --showlocals --durations=20 --pyargs skoot
   displayName: 'Running unit tests'
 
-  # Build source archive here so we don't have to in Circle
-- script: python setup.py sdist
-  displayName: 'Building source archive'
-
 - bash: |
     if python -c "from twine.commands.check import check; check(['dist/*'])" | grep  "warning"; then
         echo "README will not render properly on PyPI"

build_tools/azure/jobs.yml

@@ -1,52 +1,11 @@
 jobs:
-- job: Windows
-
-  pool:
-    vmImage: 'vs2017-win2016'
-
-  strategy:
-    maxParallel: 6
-    matrix:
-      Python35-x86:
-        python.version: '3.5'
-        architecture: 'x86'
-
-      Python35-x64:
-        python.version: '3.5'
-        architecture: 'x64'
-
-      Python36-x86:
-        python.version: '3.6'
-        architecture: 'x86'
-
-      Python36-x64:
-        python.version: '3.6'
-        architecture: 'x64'
-
-      Python37-x86:
-        python.version: '3.7'
-        architecture: 'x86'
-
-      Python37-x64:
-        python.version: '3.7'
-        architecture: 'x64'
-
-  steps:
-  - task: UsePythonVersion@0
-    inputs:
-      versionSpec: '$(python.version)'
-      architecture: '$(architecture)'
-    displayName: 'Setting Python version and system architecture'
-
-  - template: build_and_deploy.yml
-
 - job: macOS
 
   pool:
-    vmImage: 'macOS-10.13'  # Also have the option of 10.14, if we want that
+    vmImage: 'macOS-latest'
 
   strategy:
-    maxParallel: 3
+    maxParallel: 4
     matrix:
       Python35:
         python.version: '3.5'
@@ -57,10 +16,16 @@ jobs:
       Python37:
         python.version: '3.7'
 
+      Python38:
+        python.version: '3.8'
+
   steps:
   - task: UsePythonVersion@0
     inputs:
       versionSpec: '$(python.version)'
     displayName: 'Setting Python version'
 
+  - script: brew cask install gfortran
+    displayName: 'Installing Fortran'
+
   - template: build_and_deploy.yml

build_tools/azure/requirements.txt

@@ -7,6 +7,7 @@ six
 joblib
 patsy
 pytest
+setuptools>=38.6.0
 wheel
 twine>=1.13.0
 readme_renderer[md]

build_tools/doc/doc_requirements.txt

@@ -10,4 +10,5 @@ sphinx_rtd_theme
 matplotlib==2.2.0rc1
 numpydoc==0.7.0
 Django==1.11
-image==1.5.19
+image==1.5.19
+six

doc/conf.py

@@ -16,7 +16,7 @@
 import sys
 import skoot
 from pkg_resources import parse_version
-from sklearn.externals.six import u
+from six import u
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

examples/preprocessing/ex_one_hot.py

@@ -46,7 +46,7 @@
 # #############################################################################
 # Show we can work with levels we've never seen before
 test_row = X_test.iloc[0]
-test_row.set_value("native-country", "Atlantis")
+test_row.at["native-country"] =  "Atlantis"
 trans = encoder.transform(pd.DataFrame([test_row]))
 print("\nApplied on a row with a new native-country:")
 print(trans)

setup.py

@@ -40,6 +40,10 @@
 PYPIDIST = DISTNAME
 DESCRIPTION = DOCLINES[0]
 
+# Get the long desc
+with open("README.md", "r") as fh:
+    LONG_DESCRIPTION = fh.read()
+
 MAINTAINER = 'Taylor G. Smith'
 MAINTAINER_GIT = 'tgsmith61591'
 MAINTAINER_EMAIL = 'taylor.smith@alkaline-ml.com'
@@ -188,6 +192,8 @@ def do_setup():
                     maintainer=MAINTAINER,
                     maintainer_email=MAINTAINER_EMAIL,
                     description=DESCRIPTION,
+                    long_description=LONG_DESCRIPTION,
+                    long_description_content_type='text/markdown',
                     license=LICENSE,
                     version=VERSION,
                     classifiers=[
@@ -196,6 +202,7 @@ def do_setup():
                         'Programming Language :: Python :: 3.5',
                         'Programming Language :: Python :: 3.6',
                         'Programming Language :: Python :: 3.7',
+                        'Programming Language :: Python :: 3.8',
                         'Topic :: Software Development',
                         'Topic :: Scientific/Engineering',
                         'Operating System :: POSIX',

skoot/_build_utils/system_info.py

@@ -3,11 +3,8 @@
 import warnings
 
 import numpy as np
-import numpy.distutils.system_info
 
 from numpy.distutils.system_info import (system_info,
-                                         numpy_info,
-                                         NotFoundError,
                                          BlasNotFoundError,
                                          LapackNotFoundError,
                                          AtlasNotFoundError,
@@ -16,10 +13,9 @@
                                          dict_append,
                                          get_info as old_get_info)
 
-from scipy._lib._version import NumpyVersion
+from scipy._lib._pep440 import parse
 
-
-if NumpyVersion(np.__version__) >= "1.15.0.dev":
+if parse(np.__version__) >= parse("1.15.0.dev"):
     # For new enough numpy.distutils, the ACCELERATE=None environment
     # variable in the top-level setup.py is enough, so no need to
     # customize BLAS detection.
@@ -35,6 +31,7 @@ def get_info(name, notfound_action=0):
             return old_get_info(name, notfound_action)
         return cls().get_info(notfound_action)
 
+
     #
     # The following is copypaste from numpy.distutils.system_info, with
     # OSX Accelerate-related parts removed.
@@ -75,7 +72,7 @@ def calc_info(self):
             if atlas_info:
                 l = atlas_info.get('define_macros', [])
                 if ('ATLAS_WITH_LAPACK_ATLAS', None) in l \
-                       or ('ATLAS_WITHOUT_LAPACK', None) in l:
+                        or ('ATLAS_WITHOUT_LAPACK', None) in l:
                     need_lapack = 1
                 info = atlas_info
 
@@ -87,7 +84,7 @@ def calc_info(self):
 
             if need_lapack:
                 lapack_info = get_info('lapack')
-                #lapack_info = {} ## uncomment for testing
+                # lapack_info = {} ## uncomment for testing
                 if lapack_info:
                     dict_append(info, **lapack_info)
                 else:
@@ -113,6 +110,7 @@ def calc_info(self):
             self.set_info(**info)
             return
 
+
     class blas_opt_info(system_info):
 
         notfounderror = BlasNotFoundError

skoot/decomposition/tests/test_decompose.py

@@ -24,15 +24,15 @@ def test_selective_pca():
 
     # the "other" names, and their corresponding matrix
     comp_column_names = names[1:]
-    compare_cols = original[comp_column_names].as_matrix()
+    compare_cols = original[comp_column_names].to_numpy()
 
     # now fit PCA on the first column only
     transformer = SelectivePCA(cols=cols, n_components=0.85,
                                trans_col_name="PC").fit(original)
     transformed = transformer.transform(original)
 
     # get the untouched columns to compare. These should be equal!!
-    untouched_cols = transformed[comp_column_names].as_matrix()
+    untouched_cols = transformed[comp_column_names].to_numpy()
     assert_array_almost_equal(compare_cols, untouched_cols)
 
     # make sure the component is present in the columns
@@ -60,13 +60,13 @@ def test_selective_tsvd():
     cols = names[:2]
 
     comp_column_names = names[2:]
-    compare_cols = original[comp_column_names].as_matrix()
+    compare_cols = original[comp_column_names].to_numpy()
 
     transformer = SelectiveTruncatedSVD(cols=cols, n_components=1,
                                         trans_col_name="Concept").fit(original)
     transformed = transformer.transform(original)
 
-    untouched_cols = transformed[comp_column_names].as_matrix()
+    untouched_cols = transformed[comp_column_names].to_numpy()
     assert_array_almost_equal(compare_cols, untouched_cols)
 
     assert 'Concept1' in transformed.columns

skoot/feature_extraction/tests/test_interact.py

@@ -78,7 +78,7 @@ def test_interaction_corners():
                 for i, j in zip(X_trans.columns.tolist(),
                                 expected_names)])  # assert col names equal
 
-    assert_array_equal(X_trans.as_matrix(), np.array([
+    assert_array_equal(X_trans.to_numpy(), np.array([
         [0, 1, 0, 1, 0],
         [0, 0, 1, 1, 0],
         [0, 0, 0, 1, 0],

skoot/feature_selection/combos.py

@@ -96,7 +96,7 @@ def fit(self, X, y=None):
         drops = []
 
         # Generate sub matrix for qr decomposition
-        x = X[cols].as_matrix()
+        x = X[cols].to_numpy()
         cols = np.array(cols)  # so we can use boolean masking
 
         # do subroutines

skoot/preprocessing/tests/test_encode.py

@@ -72,7 +72,7 @@ def test_dummy_encoder_ignore():
 
     # get a test sample, make it different
     test_sample = iris.iloc[0].copy()
-    test_sample.set_value("species", 99)
+    test_sample.at["species"] = 99
 
     # show this does not break
     df = pd.DataFrame([test_sample])