Merge pull request #23 from WenjieDu/dev

Updating the docs and adding pytorch into dependencies
WenjieDu · Nov 6, 2023 · 9f7929a · 9f7929a
2 parents c748c8e + 8bb1894
commit 9f7929a
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diff --git a/.github/workflows/testing_ci.yml b/.github/workflows/testing_ci.yml
@@ -17,21 +17,25 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ ubuntu-latest, windows-latest, macOS-latest ]
-                python-version: [ 3.7, 3.9 ]
+                python-version: [ '3.7', '3.10' ]
 
         steps:
-            -   uses: actions/checkout@v3
-            -   name: Set up Python ${{ matrix.python-version }}
-                uses: actions/setup-python@v3
-                with:
-                    python-version: ${{ matrix.python-version }}
+            - uses: actions/checkout@v3
 
-            -   name: Install dependencies
-                run: |
-                    python -m pip install --upgrade pip
-                    pip install -r requirements.txt
-                    pip install pytest
-                    pip install coverage
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                python-version: ${{ matrix.python-version }}
+                check-latest: true
+                cache: pip
+                cache-dependency-path: |
+                    requirements.txt
+
+            - name: Install dependencies
+              run: |
+                python -m pip install --upgrade pip
+                pip install -r requirements.txt
+                pip install pytest coverage
 
             -   name: Test with pytest
                 run: |

diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
         <img alt="the latest release version" src="https://img.shields.io/github/v/release/wenjiedu/PyGrinder?color=EE781F&include_prereleases&label=Release&logo=github&logoColor=white">
     </a>
     <a href="https://github.com/WenjieDu/PyGrinder/blob/main/LICENSE">
-        <img alt="GPL-v3 license" src="https://img.shields.io/badge/License-GPL--v3-E9BB41?logo=opensourceinitiative&logoColor=white">
+        <img alt="BSD-3 license" src="https://img.shields.io/badge/License-BSD--3-E9BB41?logo=opensourceinitiative&logoColor=white">
     </a>
     <a  href='https://github.com/WenjieDu/PyGrinder/actions/workflows/testing_ci.yml'>
         <img alt='GitHub Testing' src='https://img.shields.io/github/actions/workflow/status/wenjiedu/PyGrinder/testing_ci.yml?logo=github&color=C8D8E1&label=CI'>

diff --git a/docs/index.rst b/docs/index.rst
@@ -13,7 +13,7 @@ Welcome to PyGrinder's docs!
 .. image:: https://img.shields.io/github/v/release/wenjiedu/pygrinder?color=EE781F&include_prereleases&label=Release&logo=github&logoColor=white
    :alt: the latest release version
    :target: https://img.shields.io/github/v/release/wenjiedu/pygrinder?color=EE781F&include_prereleases&label=Release&logo=github&logoColor=white
-.. image:: https://img.shields.io/badge/License-GPL--v3-E9BB41?logo=opensourceinitiative&logoColor=white
+.. image:: https://img.shields.io/badge/License-BSD--3-E9BB41?logo=opensourceinitiative&logoColor=white
    :alt: License
    :target: https://github.com/WenjieDu/PyGrinder/blob/main/LICENSE
 .. image:: https://img.shields.io/github/actions/workflow/status/wenjiedu/pygrinder/testing_ci.yml?logo=github&color=C8D8E1&label=CI

diff --git a/pygrinder/__init__.py b/pygrinder/__init__.py
@@ -3,7 +3,7 @@
 """
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 # PyGrinder version
 #
@@ -21,7 +21,7 @@
 #
 # Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer.
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
-__version__ = "0.1.1"
+__version__ = "0.2"
 
 try:
     from pygrinder.missing_completely_at_random import mcar, mcar_little_test

diff --git a/pygrinder/missing_at_random/__init__.py b/pygrinder/missing_at_random/__init__.py
@@ -1,5 +1,5 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 from .mar_logistic import mar_logistic
 

diff --git a/pygrinder/missing_at_random/mar_logistic.py b/pygrinder/missing_at_random/mar_logistic.py
@@ -3,18 +3,14 @@
 """
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 from typing import Union, Tuple
 
 import numpy as np
+import torch
 from scipy import optimize
 
-try:
-    import torch
-except ImportError:
-    pass
-
 
 def mar_logistic(
     X: Union[torch.Tensor, np.ndarray],

diff --git a/pygrinder/missing_completely_at_random/__init__.py b/pygrinder/missing_completely_at_random/__init__.py
@@ -3,7 +3,7 @@
 """
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 from .little_test import mcar_little_test
 from .mcar import mcar

diff --git a/pygrinder/missing_completely_at_random/little_test.py b/pygrinder/missing_completely_at_random/little_test.py
@@ -1,5 +1,5 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GPL-v3
+# License: BSD-3-Clause
 
 from typing import Union
 
@@ -14,7 +14,22 @@ def mcar_little_test(X: Union[pd.DataFrame, np.ndarray]) -> float:
     Notes
     -----
     This implementation is inspired by
-    https://github.com/RianneSchouten/pyampute/blob/master/pyampute/exploration/mcar_statistical_tests.py
+    https://github.com/RianneSchouten/pyampute/blob/master/pyampute/exploration/mcar_statistical_tests.py.
+    Note that this function should be used carefully. Rejecting the null hypothesis may not always mean that
+    the data is not MCAR, nor is accepting the null hypothesis a guarantee that the data is MCAR.
+
+    Parameters
+    ----------
+    X:
+        Time series data containing missing values that should be in shape of [n_steps, n_features],
+        i.e. have 2 dimensions.
+
+    Returns
+    -------
+    p_value:
+        The p-value of a chi-square hypothesis test.
+        Null hypothesis: the time series is missing completely at random (MCAR).
+
     """
 
     if isinstance(X, np.ndarray):

diff --git a/pygrinder/missing_completely_at_random/mcar.py b/pygrinder/missing_completely_at_random/mcar.py
@@ -3,16 +3,12 @@
 """
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GPL-v3
+# License: BSD-3-Clause
 
 from typing import Union, Tuple
 
 import numpy as np
-
-try:
-    import torch
-except ImportError:
-    pass
+import torch
 
 
 def mcar(

diff --git a/pygrinder/missing_not_at_random/__init__.py b/pygrinder/missing_not_at_random/__init__.py
@@ -1,5 +1,5 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 from .mnar_t import mnar_t
 from .mnar_x import mnar_x

diff --git a/pygrinder/missing_not_at_random/mnar_t.py b/pygrinder/missing_not_at_random/mnar_t.py
@@ -3,16 +3,12 @@
 """
 
 # Created by Jun Wang <jwangfx@connect.ust.hk> and Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 from typing import Optional, Union, Tuple
 
 import numpy as np
-
-try:
-    import torch
-except ImportError:
-    pass
+import torch
 
 
 def mnar_t(

diff --git a/pygrinder/missing_not_at_random/mnar_x.py b/pygrinder/missing_not_at_random/mnar_x.py
@@ -3,16 +3,12 @@
 """
 
 # Created by Jun Wang <jwangfx@connect.ust.hk> and Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 from typing import Optional, Union, Tuple
 
 import numpy as np
-
-try:
-    import torch
-except ImportError:
-    pass
+import torch
 
 
 def mnar_x(

diff --git a/pygrinder/utils.py b/pygrinder/utils.py
@@ -3,16 +3,12 @@
 """
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GPL-v3
+# License: BSD-3-Clause
 
 from typing import Union
 
 import numpy as np
-
-try:
-    import torch
-except ImportError:
-    pass
+import torch
 
 
 def cal_missing_rate(X: Union[np.ndarray, torch.Tensor]) -> float:

diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,4 @@
 numpy
 scikit-learn
-pandas
+pandas
+torch
diff --git a/setup.cfg b/setup.cfg
@@ -1,7 +1,7 @@
 # This file stores some meta configurations for project PyGrinder.
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 [flake8]
 # People may argue that coding style is personal. This may be true if the project is personal and one works like a

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
     description="A Python toolkit for introducing missing values into datasets",
     long_description=README,
     long_description_content_type="text/markdown",
-    license="GPL-3.0",
+    license="BSD-3-Clause",
     author="Wenjie Du",
     author_email="wenjay.du@gmail.com",
     url="https://github.com/WenjieDu/PyGrinder",
@@ -36,6 +36,16 @@
         "numpy",
         "scipy",
         "pandas",
+        "torch",
     ],
     setup_requires=["setuptools>=38.6.0"],
+    classifiers=[
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Education",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: OS Independent",
+        "Programming Language :: Python :: 3",
+    ],
 )
diff --git a/tests/__init__.py b/tests/__init__.py
@@ -3,4 +3,4 @@
 """
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
diff --git a/tests/test_pygrinder.py b/tests/test_pygrinder.py
@@ -3,7 +3,7 @@
 """
 
 # Created by Wenjie Du <wenjay.du@gmail.com>
-# License: GLP-v3
+# License: BSD-3-Clause
 
 import unittest