update python, tests, and docs (#279)

sarahmish · web-flow · commit a340047f4c52 · 2024-03-14T16:29:47.000-04:00
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
@@ -20,15 +20,17 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install package
-      run: pip install .[dev]
+      run: |
+        pip install --upgrade pip setuptools wheel
+        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]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
@@ -37,15 +39,17 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install package and dependencies
-      run: pip install rundoc .
+      run: |
+        pip install --upgrade pip setuptools wheel
+        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]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
@@ -54,6 +58,8 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install package and dependencies
-      run: pip install .[test]
+      run: |
+        pip install --upgrade pip setuptools wheel
+        pip install .[test]
     - name: make test-unit
       run: make test-unit
diff --git a/mlprimitives/adapters/statsmodels.py b/mlprimitives/adapters/statsmodels.py
@@ -1,5 +1,5 @@
 import numpy as np
-from statsmodels.tsa import arima_model
+from statsmodels.tsa.arima import model
 
 
 class ARIMA(object):
@@ -45,8 +45,8 @@ def predict(self, X):
 
         num_sequences = len(X)
         for sequence in range(num_sequences):
-            arima = arima_model.ARIMA(X[sequence], order=(self.p, self.d, self.q))
-            arima_fit = arima.fit(disp=0)
+            arima = model.ARIMA(X[sequence], order=(self.p, self.d, self.q))
+            arima_fit = arima.fit()
             arima_results.append(arima_fit.forecast(self.steps)[0])
 
         arima_results = np.asarray(arima_results)
diff --git a/mlprimitives/custom/timeseries_preprocessing.py b/mlprimitives/custom/timeseries_preprocessing.py
@@ -269,4 +269,8 @@ def cutoff_window_sequences(X, timeseries, window_size, cutoff_time=None, time_i
 
         output.append(selected.values)
 
-    return np.array(output)
+    output = np.array(output, dtype=object)
+    if output.ndim >= 2:
+        output = output.astype(float)
+
+    return output
diff --git a/mlprimitives/primitives/xgboost.XGBClassifier.json b/mlprimitives/primitives/xgboost.XGBClassifier.json
@@ -29,7 +29,6 @@
         "args": [
             {
                 "name": "X",
-                "keyword": "data",
                 "type": "ndarray"
             }
         ],
diff --git a/mlprimitives/primitives/xgboost.XGBRegressor.json b/mlprimitives/primitives/xgboost.XGBRegressor.json
@@ -29,7 +29,6 @@
         "args": [
             {
                 "name": "X",
-                "keyword": "data",
                 "type": "ndarray"
             }
         ],
diff --git a/setup.py b/setup.py
@@ -12,24 +12,24 @@
     history = history_file.read()
 
 install_requires = [
-    'Keras>=2.4,<2.5',
+    'Keras>=2.4,<2.15',
     'featuretools>=0.6.1,<0.23',
     'iso639>=0.1.4,<0.2',
     'langdetect>=1.0.7,<2',
     'lightfm>=1.15,<2',
-    'mlblocks>=0.4.0.dev0,<0.7',
+    'mlblocks>=0.6,<0.7',
     'networkx>=2.0,<3',
     'nltk>=3.3,<4',
-    'numpy<1.21.0,>=1.16.0',
+    'numpy>=1.16.0,<2',
     'opencv-python>=3.4.0.12,<4.7',
     'pandas>=1,<2',
     'python-louvain>=0.10,<0.14',   # community
     'scikit-image>=0.15',
     'scikit-learn>=0.21',
     'scipy>=1.1.0,<2',
-    'statsmodels>=0.9.0,<0.13',
-    'tensorflow>=2,<2.5',
-    'xgboost>=0.72.1,<1',
+    'statsmodels>=0.9.0,<0.15',
+    'tensorflow>=2,<2.15',
+    'xgboost>=0.72.1,<2',
     'protobuf<4',
 ]
 
@@ -59,6 +59,15 @@
     'mistune>=0.7,<2',
     'Jinja2>=2,<3.1',
 
+    # fails on Sphinx < v3.4
+    'alabaster<=0.7.12',
+    # fails on Sphins < v5.0
+    'sphinxcontrib-applehelp<1.0.8',
+    'sphinxcontrib-devhelp<1.0.6',
+    'sphinxcontrib-htmlhelp<2.0.5',
+    'sphinxcontrib-serializinghtml<1.1.10',
+    'sphinxcontrib-qthelp<1.0.7',
+    
     # style check
     'flake8>=3.7.7,<4',
     'isort>=4.3.4,<5',
@@ -91,9 +100,10 @@
         'License :: OSI Approved :: MIT License',
         'Natural Language :: English',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
     ],
     description='Pipelines and primitives for machine learning and data science.',
     entry_points = {
@@ -117,7 +127,7 @@
     long_description_content_type='text/markdown',
     name='mlprimitives',
     packages=find_packages(include=['mlprimitives', 'mlprimitives.*']),
-    python_requires='>=3.6,<3.9',
+    python_requires='>=3.8,<3.12',
     setup_requires=setup_requires,
     test_suite='tests',
     tests_require=tests_require,
diff --git a/tests/adapters/test_statsmodels.py b/tests/adapters/test_statsmodels.py
@@ -6,7 +6,7 @@
 from mlprimitives.adapters.statsmodels import ARIMA
 
 
-@patch('statsmodels.tsa.arima_model.ARIMA')
+@patch('statsmodels.tsa.arima.model.ARIMA')
 def test_arima_1d(arima_mock):
     arima = ARIMA(1, 0, 0, 3)
     X = np.array([1, 2, 3, 4, 5])
@@ -15,7 +15,7 @@ def test_arima_1d(arima_mock):
     assert arima_mock.call_args[1] == {'order': (1, 0, 0)}
 
 
-@patch('statsmodels.tsa.arima_model.ARMAResults.forecast')
+@patch('statsmodels.tsa.arima.model.ARIMAResultsWrapper.forecast')
 def test_predict_1d(arima_mock):
     arima_mock.return_value = [[1, 2, 3]]
 
@@ -29,7 +29,7 @@ def test_predict_1d(arima_mock):
     arima_mock.assert_called_once_with(3)
 
 
-@patch('statsmodels.tsa.arima_model.ARIMA')
+@patch('statsmodels.tsa.arima.model.ARIMA')
 def test_arima_2d(arima_mock):
     arima = ARIMA(1, 0, 0, 3)
     X = np.array([
@@ -46,7 +46,7 @@ def test_arima_2d(arima_mock):
     assert arima_mock.call_args_list[2][1] == {'order': (1, 0, 0)}
 
 
-@patch('statsmodels.tsa.arima_model.ARMAResults.forecast')
+@patch('statsmodels.tsa.arima.model.ARIMAResultsWrapper.forecast')
 def test_predict_2d(arima_mock):
     arima_mock.side_effect = [
         [[1, 2, 3]],
diff --git a/tests/custom/test_timeseries_preprocessing.py b/tests/custom/test_timeseries_preprocessing.py
@@ -417,7 +417,7 @@ def test_not_enough_data(self):
                 [15, 35],
                 [16, 36]
             ])
-        ])
+        ], dtype=object)
 
         assert_allclose(
             array[0],
diff --git a/tox.ini b/tox.ini
@@ -1,17 +1,19 @@
 [tox]
-envlist = py3{6,7,8}, test-devel
+envlist = py3{8,9,10,11}, test-devel
 
 [travis]
 python =
     3.8: py38, test-devel
-    3.7: py37
-    3.6: py36
+    3.9: py39
+    3.10: py310
+    3.11: py311
 
 [gh-actions]
 python =
     3.8: py38, test-devel
-    3.7: py37
-    3.6: py36
+    3.9: py39
+    3.10: py310
+    3.11: py311
 
 [testenv]
 passenv = CI TRAVIS TRAVIS_*

Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,6 @@`
`29`	`29`	`"args": [`
`30`	`30`	`{`
`31`	`31`	`"name": "X",`
`32`		`- "keyword": "data",`
`33`	`32`	`"type": "ndarray"`
`34`	`33`	`}`
`35`	`34`	`],`