make release-tag: Merge branch 'master' into stable

sarahmish · sarahmish · commit f2582961be00 · 2025-02-17T22:52:01.000-05:00
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -14,7 +14,7 @@ jobs:
     - name: Python
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
 
     - name: Build
       run: |
diff --git a/.github/workflows/latest-dependencies.yml b/.github/workflows/latest-dependencies.yml
@@ -1,30 +1,30 @@
-name: Latest Dependency Checker
-on:
-  schedule:
-    - cron: '0 * * * *'
-  workflow_dispatch:
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
-    - name: Update dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install -e .[test]
-        make checkdeps OUTPUT_PATH=tests/requirement_files/latest_requirements.txt
-    - name: Create pull request
-      uses: peter-evans/create-pull-request@v3
-      with:
-        token: ${{ secrets.REPO_SCOPED_TOKEN }}
-        commit-message: Update latest dependencies
-        title: Automated Latest Dependency Updates
-        body: "This is an auto-generated PR with **latest** dependency updates."
-        branch: latest-dep-update
-        branch-suffix: short-commit-hash
-        base: master
-        team-reviewers: core
+# name: Latest Dependency Checker
+# on:
+#   schedule:
+#     - cron: '0 * * * *'
+#   workflow_dispatch:
+# jobs:
+#   build:
+#     runs-on: ubuntu-latest
+#     steps:
+#     - uses: actions/checkout@v2
+#     - name: Set up Python 3.9
+#       uses: actions/setup-python@v2
+#       with:
+#         python-version: 3.9
+#     - name: Update dependencies
+#       run: |
+#         python -m pip install --upgrade pip
+#         python -m pip install -e .[test]
+#         make checkdeps OUTPUT_PATH=tests/requirement_files/latest_requirements.txt
+#     - name: Create pull request
+#       uses: peter-evans/create-pull-request@v3
+#       with:
+#         token: ${{ secrets.REPO_SCOPED_TOKEN }}
+#         commit-message: Update latest dependencies
+#         title: Automated Latest Dependency Updates
+#         body: "This is an auto-generated PR with **latest** dependency updates."
+#         branch: latest-dep-update
+#         branch-suffix: short-commit-hash
+#         base: master
+#         team-reviewers: core
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: [3.8]
+        python-version: ['3.9']
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
@@ -29,8 +29,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8']
-        os: [ubuntu-20.04]
+        python-version: ['3.9']
+        os: [ubuntu-latest]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
@@ -47,8 +47,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        os: [ubuntu-20.04, macos-latest, windows-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
@@ -68,8 +68,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        os: [ubuntu-20.04, macos-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        os: [ubuntu-latest, macos-latest]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
@@ -79,4 +79,4 @@ jobs:
     - name: Install package and dependencies
       run: pip install invoke .[test]
     - name: invoke minimum
-      run: invoke minimum
+      run: invoke minimum
diff --git a/HISTORY.md b/HISTORY.md
@@ -1,10 +1,18 @@
 # History
 
+## 0.3.0 - 2025-02-17
+
+### Features
+* Add Support for Python 3.12 & Remove 3.8 - [Issue #63](https://github.com/sintel-dev/SigPro/pull/63) by @sarahmish
+* Add fft frequency transformation - [Issue #62](https://github.com/sintel-dev/SigPro/pull/62) by @SaraPido
+* Band rms - [Issue #61](https://github.com/sintel-dev/SigPro/pull/61) by @SaraPido
+
+
 ## 0.2.1 - 2024-04-24
 
 ### Features
 
-* Frequency primitive - [Issue #60](https://github.com/sintel-dev/SigPro/pull/60)
+* Frequency primitive - [Issue #60](https://github.com/sintel-dev/SigPro/pull/60) by @SaraPido 
 
 
 ## 0.2.0 - 2024-02-02
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ in order to solve time series machine learning problems.
 
 ## Requirements
 
-**SigPro** has been developed and tested on [Python 3.8, 3.9, 3.10, and 3.11](https://www.python.org/downloads/)
+**SigPro** has been developed and tested on [Python 3.9, 3.10, 3.11 and 3.12](https://www.python.org/downloads/)
 on GNU/Linux and macOS systems.
 
 Also, although it is not strictly required, the usage of a [virtualenv](
diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.3.0.dev0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<candidate>\d+))?
diff --git a/setup.py b/setup.py
@@ -12,10 +12,10 @@
     history = history_file.read()
 
 install_requires = [
-    'mlblocks>=0.6.1',
+    'mlblocks>=0.6.2',
     'pandas>=1.5.3',
-    'numpy>=1.24.4',
-    'scipy>=1.10.1',
+    'numpy>=1.26.0',
+    'scipy>=1.11.3',
 ]
 
 setup_requires = [
@@ -41,7 +41,16 @@
     'sphinx_rtd_theme>=0.2.4,<0.5',
     'autodocsumm>=0.1.10',
     'markupsafe<2.1.0',
-    'Jinja2>=2,<3',
+    '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',
@@ -62,7 +71,8 @@
     # Advanced testing
     'coverage>=4.5.1,<6',
     'tox>=2.9.1,<4',
-    'importlib-metadata<2,>=0.12',
+    'importlib-metadata<5',
+    'mistune<2',
     'invoke',
 ]
 
@@ -75,12 +85,12 @@
         'License :: OSI Approved :: MIT License',
         'Natural Language :: English',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.8',        
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
-    description='Signal Processing Tools for Machine Mearning',
+    description='Signal Processing Tools for Machine Learning',
     entry_points={
         'mlblocks': [
             'primitives=sigpro:MLBLOCKS_PRIMITIVES',
@@ -98,11 +108,11 @@
     long_description_content_type='text/markdown',
     name='sigpro',
     packages=find_packages(include=['sigpro', 'sigpro.*']),
-    python_requires='>=3.8,<3.12',
+    python_requires='>=3.9,<3.13',
     setup_requires=setup_requires,
     test_suite='tests',
     tests_require=tests_require,
     url='https://github.com/sintel-dev/SigPro',
-    version='0.2.1',
+    version='0.3.0.dev0',
     zip_safe=False,
 )
diff --git a/sigpro/__init__.py b/sigpro/__init__.py
@@ -4,7 +4,7 @@
 
 __author__ = """MIT Data To AI Lab"""
 __email__ = 'dailabmit@gmail.com'
-__version__ = '0.2.1'
+__version__ = '0.3.0.dev0'
 
 import os
 
diff --git a/sigpro/aggregations/frequency/band.py b/sigpro/aggregations/frequency/band.py
@@ -28,3 +28,33 @@ def band_mean(amplitude_values, frequency_values, min_frequency, max_frequency):
     selected_values = amplitude_values[selected_idx]
 
     return np.mean(selected_values)
+
+
+def band_rms(amplitude_values, frequency_values, min_frequency, max_frequency):
+    """
+    Compute the rms values for a specific band.
+
+    Filter between a high and low band (inclusive) and compute the rms value for this
+    specific band.
+
+    Args:
+        amplitude_values (np.ndarray):
+            A numpy array with the signal values.
+        frequency_values (np.ndarray):
+            A numpy array with the frequency values.
+        min_frequency (int or float):
+            Band minimum.
+        max_frequency (int or float):
+            Band maximum.
+
+    Returns:
+        float:
+            rms value for the given band.
+    """
+    lower_frequency_than = frequency_values <= max_frequency
+    higher_frequency_than = frequency_values >= min_frequency
+
+    selected_idx = np.ravel(np.where(higher_frequency_than & lower_frequency_than))
+    selected_values = amplitude_values[selected_idx]
+
+    return np.sqrt(np.mean(np.square(selected_values)))
diff --git a/sigpro/basic_primitives.py b/sigpro/basic_primitives.py
@@ -177,3 +177,24 @@ def __init__(self, min_frequency, max_frequency):
             'min_frequency': min_frequency, 'max_frequency': max_frequency})
         self.set_fixed_hyperparameters({'min_frequency': {'type': 'float'},
                                         'max_frequency': {'type': 'float'}})
+
+
+class BandRMS(primitive.FrequencyAggregation):
+    """
+    BandRMS primitive class.
+
+    Filter between a high and low band (inclusive) and compute the rms value for this
+    specific band.
+
+    Args:
+        min_frequency (int or float):
+            Band minimum.
+        max_frequency (int or float):
+            Band maximum.
+    """
+
+    def __init__(self, min_frequency, max_frequency):
+        super().__init__('sigpro.aggregations.frequency.band.band_rms', init_params={
+            'min_frequency': min_frequency, 'max_frequency': max_frequency})
+        self.set_fixed_hyperparameters({'min_frequency': {'type': 'float'},
+                                        'max_frequency': {'type': 'float'}})
diff --git a/sigpro/primitives/sigpro/aggregations/frequency/band/band_rms.json b/sigpro/primitives/sigpro/aggregations/frequency/band/band_rms.json
@@ -0,0 +1,37 @@
+{
+    "name": "sigpro.aggregations.frequency.band.band_rms",
+    "primitive": "sigpro.aggregations.frequency.band.band_rms",
+    "classifiers": {
+        "type": "aggregation",
+        "subtype": "frequency"
+    },
+    "produce": {
+        "args": [
+            {
+                "name": "amplitude_values",
+                "type": "numpy.ndarray"
+            },
+            {
+                "name": "frequency_values",
+                "type": "numpy.ndarray"
+            }
+        ],
+        "output": [
+            {
+                "name": "value",
+                "type": "float"
+            }
+        ]
+    },
+    "hyperparameters": {
+        "fixed": {
+            "min_frequency": {
+                "type": "float"
+            },
+            "max_frequency": {
+                "type": "float"
+            }
+        },
+        "tunable": {}
+    }
+}
diff --git a/sigpro/transformations/frequency/fftfreq.py b/sigpro/transformations/frequency/fftfreq.py
@@ -16,6 +16,7 @@ def fft_freq(amplitude_values, sampling_frequency):
             * `amplitude_values (numpy.ndarray)`
             * `frequency_values (numpy.ndarray)`
     """
-    frequency_values = np.fft.fftfreq(len(amplitude_values), 1 / sampling_frequency)
+    # frequency_values = np.fft.fftfreq(len(amplitude_values), 1 / sampling_frequency)
+    frequency_values = np.arange(0, len(amplitude_values)) * sampling_frequency
 
     return np.array(amplitude_values), np.array(frequency_values)
diff --git a/tests/integration/test_pipeline.py b/tests/integration/test_pipeline.py
@@ -39,7 +39,11 @@ def _verify_pipeline_outputs(sigpro_pipeline, input_data, output_data, columns_t
         assert column in feature_list
         assert column in processed_signal.columns
     cols_reduced = [i for i in columns_to_check if i in output_data.columns]
-    pd.testing.assert_frame_equal(processed_signal[cols_reduced], output_data[cols_reduced])
+    pd.testing.assert_frame_equal(
+        processed_signal[cols_reduced],
+        output_data[cols_reduced],
+        rtol=1e-2
+    )
 
 
 def test_linear_pipeline():
diff --git a/tests/unit/transformations/frequency/test_fftfreq.py b/tests/unit/transformations/frequency/test_fftfreq.py
@@ -0,0 +1,19 @@
+"""Tests for sigpro.transformations.frequency module."""
+import numpy as np
+
+from sigpro.transformations.frequency.fftfreq import fft_freq
+
+
+def test_fft_freq():
+    # setup
+    amplitude_values = [1.5, -0.5, 2.0, 0.5, -1.0]
+    sampling_frequency = 2
+
+    # run
+    amplitude_result, frequency_result = fft_freq(amplitude_values, sampling_frequency)
+
+    # assert
+    expected_amplitude_values = np.array([1.5, -0.5, 2.0, 0.5, -1.0])
+    expected_frequency_values = np.array([0., 2., 4., 6., 8.])
+    np.testing.assert_array_almost_equal(amplitude_result, expected_amplitude_values)
+    np.testing.assert_array_almost_equal(frequency_result, expected_frequency_values)
