Support latest scikit-learn (>=0.24) and Python 3.9 (#333)

* Update setup.py * Update .appveyor.yml * Update main.yml * Update main.yml * Update python_tests.sh * Update python_tests.sh * Update python_tests.sh * Update test_rgf_python.py * Update test_rgf_python.py * Update utils.py * Update utils.py * Update rgf_model.py * Update fastrgf_model.py * Update test_rgf_python.py * Update main.yml * Update python_tests.sh * Update .appveyor.yml * Update python_tests.sh * Update main.yml * Update utils.py
RGF-team · Feb 12, 2021 · 2648265 · 2648265
1 parent 493f830
commit 2648265
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Showing 7 changed files with 31 additions and 16 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -13,13 +13,14 @@ environment:
     - PYTHON_VERSION: 3.6
     - PYTHON_VERSION: 3.7
     - PYTHON_VERSION: 3.8
-    - PYTHON_VERSION: 3.8
+    - PYTHON_VERSION: 3.9
+    - PYTHON_VERSION: 3.9
       TASK: R_PACKAGE
 
 matrix:
   exclude:
     - platform: x86
-      PYTHON_VERSION: 3.8
+      PYTHON_VERSION: 3.9
       TASK: R_PACKAGE
 
 install:
@@ -61,7 +62,7 @@ after_test:
       if(
          $env:APPVEYOR_REPO_TAG -eq "false" -or
          $env:APPVEYOR_REPO_BRANCH -ne "master" -or
-         $env:PYTHON_VERSION -ne "3.8" -or
+         $env:PYTHON_VERSION -ne "3.9" -or
          $env:TASK -eq "R_PACKAGE") {
           Exit-AppVeyorBuild
       }
@@ -95,4 +96,4 @@ deploy:
   on:
     appveyor_repo_tag: true
     branch: master
-    PYTHON_VERSION: 3.8
+    PYTHON_VERSION: 3.9
diff --git a/.ci/python_tests.sh b/.ci/python_tests.sh
@@ -27,9 +27,9 @@ conda update -q conda
 if [[ $TASK == "R_PACKAGE" ]]; then
   conda create -q -n $CONDA_ENV python=$PYTHON_VERSION pip openssl libffi --no-deps
   source activate $CONDA_ENV
-  pip install setuptools joblib numpy "scikit-learn<0.24" scipy pandas wheel
+  pip install setuptools joblib numpy scikit-learn scipy pandas wheel
 else
-  conda create -q -n $CONDA_ENV python=$PYTHON_VERSION joblib numpy "scikit-learn<0.24" scipy pandas pytest
+  conda create -q -n $CONDA_ENV python=$PYTHON_VERSION joblib numpy scikit-learn scipy pandas pytest
   source activate $CONDA_ENV
 fi
 cd $GITHUB_WORKSPACE/python-package

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -32,12 +32,17 @@ jobs:
             python_version: 3.8
           - os: macos-latest
             python_version: 3.8
+          - os: ubuntu-latest
+            container: ubuntu:trusty
+            python_version: 3.9
+          - os: macos-latest
+            python_version: 3.9
           - os: ubuntu-latest
             container: rocker/verse:latest
-            python_version: 3.8
+            python_version: 3.9
             task: R_PACKAGE
           - os: macos-latest
-            python_version: 3.8
+            python_version: 3.9
             task: R_PACKAGE
     container: ${{ matrix.container }}
     steps:
@@ -66,7 +71,7 @@ jobs:
             $GITHUB_WORKSPACE/.ci/r_tests.sh || exit -1
           fi
       - name: Create Wheel
-        if: matrix.python_version == 3.8 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
+        if: matrix.python_version == 3.9 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
         shell: bash
         run: |
           export PATH="${{ env.CONDA_PATH }}/bin:$PATH"
@@ -79,7 +84,7 @@ jobs:
             python setup.py bdist_wheel --plat-name=manylinux1_x86_64 --python-tag py3;
           fi
       - name: Create GitHub Release
-        if: matrix.python_version == 3.8 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
+        if: matrix.python_version == 3.9 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
         uses: softprops/action-gh-release@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

diff --git a/python-package/rgf/fastrgf_model.py b/python-package/rgf/fastrgf_model.py
@@ -353,8 +353,7 @@ def _fit_multiclass_task(self, X, y, sample_weight, params):
                                               sample_weight)
 
 
-class FastRGFRegressor(FastRGFEstimatorBase, RegressorMixin,
-                       utils.RGFRegressorMixin):
+class FastRGFRegressor(RegressorMixin, utils.RGFRegressorMixin, FastRGFEstimatorBase):
     def __init__(self,
                  n_estimators=500,
                  max_depth=6,
@@ -409,8 +408,7 @@ def _set_target_and_loss(self):
         __doc__ = __doc__.replace(_template, _value)
 
 
-class FastRGFClassifier(FastRGFEstimatorBase, ClassifierMixin,
-                        utils.RGFClassifierMixin):
+class FastRGFClassifier(ClassifierMixin, utils.RGFClassifierMixin, FastRGFEstimatorBase):
     def __init__(self,
                  n_estimators=500,
                  max_depth=6,

diff --git a/python-package/rgf/rgf_model.py b/python-package/rgf/rgf_model.py
@@ -454,7 +454,7 @@ def feature_importances_(self):
         return np.mean([est.feature_importances_ for est in self._estimators], axis=0)
 
 
-class RGFRegressor(RGFEstimatorBase, RegressorMixin, utils.RGFRegressorMixin):
+class RGFRegressor(RegressorMixin, utils.RGFRegressorMixin, RGFEstimatorBase):
     def __init__(self,
                  max_leaf=500,
                  test_interval=100,
@@ -519,7 +519,7 @@ def save_model(self, filename):
         save_model.__doc__ = save_model.__doc__.replace(_template, _value)
 
 
-class RGFClassifier(RGFEstimatorBase, ClassifierMixin, utils.RGFClassifierMixin):
+class RGFClassifier(ClassifierMixin, utils.RGFClassifierMixin, RGFEstimatorBase):
     def __init__(self,
                  max_leaf=1000,
                  test_interval=100,

diff --git a/python-package/rgf/utils.py b/python-package/rgf/utils.py
@@ -490,6 +490,11 @@ def _fit_regression_task(self, X, y, sample_weight, params):
 
 
 class RGFClassifierMixin(object):
+    def _more_tags(self):
+        return {'X_types': ['2darray', 'sparse', '1dlabels'],
+                'requires_y' : True,
+                '_xfail_checks': {'check_sample_weights_invariance': 'sample_weight must have positive values'}}
+
     @property
     def classes_(self):
         """The classes labels when `fit` is performed."""
@@ -626,6 +631,11 @@ def predict_proba(self, X):
 
 
 class RGFRegressorMixin(object):
+    def _more_tags(self):
+        return {'X_types': ['2darray', 'sparse', '1dlabels'],
+                'requires_y' : True,
+                '_xfail_checks': {'check_sample_weights_invariance': 'sample_weight must have positive values'}}
+
     def fit(self, X, y, sample_weight=None):
         """
         Build a regressor from the training set (X, y).

diff --git a/python-package/setup.py b/python-package/setup.py
@@ -395,4 +395,5 @@ def run(self):
                    'Programming Language :: Python :: 3.6',
                    'Programming Language :: Python :: 3.7',
                    'Programming Language :: Python :: 3.8',
+                   'Programming Language :: Python :: 3.9',
                    'Topic :: Scientific/Engineering :: Artificial Intelligence'])