FluctuationAnalysisTools 1.10.0__tar.gz → 1.11.0.dev0__tar.gz

fluctuationanalysistools-1.11.0.dev0/.github/workflows/reusable_build-wheels.yml

@@ -0,0 +1,64 @@
+name: Reusable - Build Wheels
+
+on:
+  workflow_call:
+    inputs:
+      os:
+        description: 'The operating system to build on'
+        required: true
+        type: string
+      python-version:
+        description: 'The Python version to use'
+        required: true
+        type: string
+    outputs:
+      artifact-name:
+        description: 'The name of the uploaded artifact'
+        value: ${{ jobs.build-wheels.outputs.artifact-name }}
+
+permissions:
+  contents: read
+
+jobs:
+  build-wheels:
+    runs-on: ${{ inputs.os }}
+
+    outputs:
+      artifact-name: fluctuation-analysis-tools-${{ inputs.os }}-${{ inputs.python-version }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel build
+
+      - name: Build wheels
+        if: ${{ inputs.os != 'ubuntu-latest' }}
+        run: |
+          python -m build --wheel --outdir wheelhouse
+
+      - name: Build sdist (Linux)
+        if: ${{ inputs.os == 'ubuntu-latest' }}
+        run: |
+          python -m build --sdist --outdir sdisthouse
+
+      - name: Upload wheels as artifacts
+        if: ${{ inputs.os != 'ubuntu-latest' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: fluctuation-analysis-tools-${{ inputs.os }}-${{ inputs.python-version }}
+          path: ./wheelhouse/*.whl
+
+      - name: Upload sdist as artifacts
+        if: ${{ inputs.os == 'ubuntu-latest' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: fluctuation-analysis-tools-${{ inputs.os }}-${{ inputs.python-version }}
+          path: ./sdisthouse/*.tar.gz

fluctuationanalysistools-1.11.0.dev0/.github/workflows/reusable_pre-commit-validation.yml

@@ -0,0 +1,47 @@
+name: Reusable - Pre-commit Validation
+
+on:
+  workflow_call:
+    outputs:
+      cache-key:
+        description: 'The cache key used for pip dependencies'
+        value: ${{ jobs.pre-commit-validation.outputs.cache-key }}
+
+permissions:
+  contents: read
+
+jobs:
+  pre-commit-validation:
+    runs-on: ubuntu-latest
+
+    outputs:
+      cache-key: ${{ steps.cache-pip.outputs.key || 'pip-precommit-' }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Cache pip dependencies
+        id: cache-pip
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: pip-precommit-${{ hashFiles('**/pyproject.toml', '**/.pre-commit-config.yaml') }}
+          restore-keys: |
+            pip-precommit-
+
+      - name: Install pre-commit
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          pip install pre-commit
+
+      - name: Run pre-commit validation
+        shell: bash
+        run: |
+          pre-commit run --all-files

fluctuationanalysistools-1.11.0.dev0/.github/workflows/reusable_test.yml

@@ -0,0 +1,78 @@
+name: Reusable - Test
+
+on:
+  workflow_call:
+    inputs:
+      os:
+        description: 'The operating system to test on'
+        required: true
+        type: string
+      python-version:
+        description: 'The Python version to use'
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ${{ inputs.os }}
+
+    env:
+      CI: true
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Install dependencies on MacOS
+        if: ${{ inputs.os == 'macos-latest' }}
+        shell: bash
+        run: |
+          /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+          brew install numpy scipy
+          python -m pip install --upgrade pip wheel setuptools
+          pip install pytest pytest-timeout
+
+      - name: Install dependencies
+        if: inputs.os != 'macos-latest'
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip wheel
+          pip install pytest pytest-timeout
+
+      - name: Download wheels artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: fluctuation-analysis-tools-${{ inputs.os }}-${{ inputs.python-version }}
+          path: wheelhouse
+
+      - name: Install FluctuationAnalysisTools from wheel
+        if: ${{ inputs.os != 'ubuntu-latest' }}
+        shell: bash
+        run: |
+          pip install wheelhouse/*.whl
+
+      - name: Install FluctuationAnalysisTools from sdist
+        if: ${{ inputs.os == 'ubuntu-latest' }}
+        shell: bash
+        run: |
+          pip install wheelhouse/*.tar.gz
+
+      - name: Run tests
+        run: |
+          mkdir -p test-results
+          pytest tests/ --junitxml=test-results/${{ runner.os }}.xml -v
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-results-${{ runner.os }}
+          path: test-results/

fluctuationanalysistools-1.11.0.dev0/.github/workflows/run-tests.yml

@@ -0,0 +1,50 @@
+name: Run Tests
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  pre-commit-validation:
+    uses: ./.github/workflows/reusable_pre-commit-validation.yml
+
+  build-wheels:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.11"]
+      fail-fast: false
+
+    uses: ./.github/workflows/reusable_build-wheels.yml
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+    needs: pre-commit-validation
+
+  test:
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: "3.11"
+            artifact-name: fluctuation-analysis-tools-ubuntu-latest-3.11
+          - os: windows-latest
+            python-version: "3.11"
+            artifact-name: fluctuation-analysis-tools-windows-latest-3.11
+          - os: macos-latest
+            python-version: "3.11"
+            artifact-name: fluctuation-analysis-tools-macos-latest-3.11
+      fail-fast: false
+
+    uses: ./.github/workflows/reusable_test.yml
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+    needs: build-wheels

fluctuationanalysistools-1.11.0.dev0/.github/workflows/test-and-release.yml

@@ -0,0 +1,106 @@
+name: Test and Release
+
+on:
+  push:
+    tags:
+      - 'release/[0-9]+.[0-9]+.[0-9]+*'
+  workflow_dispatch:  # Allow manual triggering
+
+permissions:
+  contents: read
+jobs:
+  pre-commit-validation:
+    uses: ./.github/workflows/reusable_pre-commit-validation.yml
+
+  build-wheels:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.11"]
+      fail-fast: false
+
+    uses: ./.github/workflows/reusable_build-wheels.yml
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+    needs: pre-commit-validation
+
+  test:
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: "3.11"
+            artifact-name: fluctuation-analysis-tools-ubuntu-latest-3.11
+          - os: windows-latest
+            python-version: "3.11"
+            artifact-name: fluctuation-analysis-tools-windows-latest-3.11
+          - os: macos-latest
+            python-version: "3.11"
+            artifact-name: fluctuation-analysis-tools-macos-latest-3.11
+      fail-fast: false
+
+    uses: ./.github/workflows/reusable_test.yml
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+    needs: build-wheels
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: test
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Get release name
+        id: get-release
+        run: |
+          TAG=$(git describe --tags --abbrev=0)
+          RELEASE_NAME=$(echo "$TAG" | sed 's|^release/||')
+          echo "tag=$TAG" >> $GITHUB_OUTPUT
+          echo "release_name=$RELEASE_NAME" >> $GITHUB_OUTPUT
+
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          pattern: fluctuation-analysis-tools-*.tar.gz
+          path: ./artifacts
+
+      - name: Download wheels artifact
+        uses: actions/download-artifact@v4
+        with:
+          pattern: fluctuation-analysis-tools-*
+          path: ./artifacts
+
+      - name: Copy .whl files to dist directory
+        run: |
+          mkdir -p dist
+          find ./artifacts -name "*.whl" -exec cp {} ./dist \;
+
+      - name: Copy .tar.gz files to dist directory
+        run: |
+          mkdir -p dist
+          find ./artifacts -name "*.tar.gz" -exec cp {} ./dist \;
+
+      - name: Create Github Release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ steps.get-release.outputs.tag }}
+          name: fluctuation-analysis-tools ${{ steps.get-release.outputs.release_name }}
+          draft: false
+          prerelease: false
+          body: |
+            This release was created based on the tag **${{ steps.get-release.outputs.tag }}**.
+          files: |
+            ./dist/*.whl
+            ./dist/*.tar.gz
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

{fluctuationanalysistools-1.10.0 → fluctuationanalysistools-1.11.0.dev0}/CHANGELOG.md

@@ -3,19 +3,19 @@
 ## 1.10.0
 
 * [GH-73](https://github.com/Digiratory/FluctuationAnalysisTools/issues/73) refactor: Restructure C++ codebase and add StatTools package with pybind11 bindings.
-* [GH-71](https://github.com/Digiratory/FluctuationAnalysisTools/issues/71) cicd: Add pre-commit validation proir tests.
-* [GH-67](https://github.com/Digiratory/FluctuationAnalysisTools/issues/67) feat: NEW Method multidimantional DFA.
-* [GH-63](https://github.com/Digiratory/FluctuationAnalysisTools/issues/63)[PR-46](https://github.com/Digiratory/FluctuationAnalysisTools/pull/46) feat: fluctiational function analysis and visualization.
+* [GH-71](https://github.com/Digiratory/FluctuationAnalysisTools/issues/71) cicd: Add pre-commit validation prior tests.
+* [GH-67](https://github.com/Digiratory/FluctuationAnalysisTools/issues/67) feat: NEW Method multidimensional DFA.
+* [GH-63](https://github.com/Digiratory/FluctuationAnalysisTools/issues/63)[PR-46](https://github.com/Digiratory/FluctuationAnalysisTools/pull/46) feat: fluctuation function analysis and visualization.
 * [GH-61](https://github.com/Digiratory/FluctuationAnalysisTools/issues/61) feat: Function-style fbn generator (common entry point).
 * [GH-58](https://github.com/Digiratory/FluctuationAnalysisTools/issues/58) feat: NEW Method to generate Power-law colored noise signals of any dimensions.
 * [GH-50](https://github.com/Digiratory/FluctuationAnalysisTools/issues/50) refactor: Extract the core of dpcca in a separate method.
 * [PR-69](https://github.com/Digiratory/FluctuationAnalysisTools/pull/69) refactor: Refactor DFA implementation into modular functions, add function style interface for dfa.
 * [PR-65](https://github.com/Digiratory/FluctuationAnalysisTools/pull/65) feat: NEW Method SVD-DFA.
-* [PR-60](https://github.com/Digiratory/FluctuationAnalysisTools/pull/60)[PR-78](https://github.com/Digiratory/FluctuationAnalysisTools/pull/78)[PR-80](https://github.com/Digiratory/FluctuationAnalysisTools/pull/80)[PR-81](https://github.com/Digiratory/FluctuationAnalysisTools/pull/81)[PR-82](https://github.com/Digiratory/FluctuationAnalysisTools/pull/82)[PR-83](https://github.com/Digiratory/FluctuationAnalysisTools/pull/83)[PR-85](https://github.com/Digiratory/FluctuationAnalysisTools/pull/85): Mutliple minor fixes in CI/CD and code.
+* [PR-60](https://github.com/Digiratory/FluctuationAnalysisTools/pull/60)[PR-78](https://github.com/Digiratory/FluctuationAnalysisTools/pull/78)[PR-80](https://github.com/Digiratory/FluctuationAnalysisTools/pull/80)[PR-81](https://github.com/Digiratory/FluctuationAnalysisTools/pull/81)[PR-82](https://github.com/Digiratory/FluctuationAnalysisTools/pull/82)[PR-83](https://github.com/Digiratory/FluctuationAnalysisTools/pull/83)[PR-85](https://github.com/Digiratory/FluctuationAnalysisTools/pull/85): Multiple minor fixes in CI/CD and code.
 
 ## 1.9.0
 
-* [GH-13](https://github.com/Digiratory/StatTools/issues/13) fix: posible unbalances tuple unpacking from method dpcca.
+* [GH-13](https://github.com/Digiratory/StatTools/issues/13) fix: possible unbalances tuple unpacking from method dpcca.
 * [GH-13](https://github.com/Digiratory/StatTools/issues/13) docs: update documentation for dpcca method.
 * [GH-13](https://github.com/Digiratory/StatTools/issues/13) refactor: update code for dpcca method to improve performance and readability.
 * [GH-18](https://github.com/Digiratory/StatTools/issues/18) feat: Enhanced Kalman filter with auto calculation of transition matrix and measurement covariance matrix based on Kasdin model.
@@ -44,7 +44,7 @@
 
 ## 1.6.0
 
-* [GH-1](https://github.com/Digiratory/StatTools/issues/1) Add argument `n_integral=1` in `StatTools.analysis.dpcca.dpcca` to provide possibility to control integretion in the beggining of the dpcca(dfa) analysis pipeline.
+* [GH-1](https://github.com/Digiratory/StatTools/issues/1) Add argument `n_integral=1` in `StatTools.analysis.dpcca.dpcca` to provide possibility to control integration in the beginning of the dpcca(dfa) analysis pipeline.
 * fix: failure is processes == 1 and 1d array
 * fix: remove normalization from dpcca processing
 

{fluctuationanalysistools-1.10.0 → fluctuationanalysistools-1.11.0.dev0/FluctuationAnalysisTools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: FluctuationAnalysisTools
-Version: 1.10.0
+Version: 1.11.0.dev0
 Summary: Python library for DFA, Hurst exponent, and fluctuation analysis of time series.
 Author: Maya Gavrichenkova, Timofey Baburin, Olga Ivleva
 Author-email: Aleksandr Sinitca <amsinitca@etu.ru>, Alexandr Kuzmenko <alexander.k.spb@gmail.com>, Asya Lyanova <ailianova@etu.ru>

{fluctuationanalysistools-1.10.0 → fluctuationanalysistools-1.11.0.dev0}/FluctuationAnalysisTools.egg-info/SOURCES.txt

@@ -2,7 +2,7 @@
 .gitignore
 .pre-commit-config.yaml
 CHANGELOG.md
-CONTRIBUTION.md
+CONTRIBUTING.md
 LICENSE.txt
 MANIFEST.in
 README.md
@@ -10,6 +10,9 @@ pyproject.toml
 setup.py
 .github/ISSUE_TEMPLATE/bug_report.md
 .github/ISSUE_TEMPLATE/feature_request.md
+.github/workflows/reusable_build-wheels.yml
+.github/workflows/reusable_pre-commit-validation.yml
+.github/workflows/reusable_test.yml
 .github/workflows/run-tests.yml
 .github/workflows/test-and-release.yml
 FluctuationAnalysisTools.egg-info/PKG-INFO
@@ -22,6 +25,7 @@ StatTools/__init__.py
 StatTools/_version.py
 StatTools/auxiliary.py
 StatTools/analysis/__init__.py
+StatTools/analysis/bma.py
 StatTools/analysis/dfa.py
 StatTools/analysis/dpcca.py
 StatTools/analysis/dpcca_as_class.py
@@ -57,6 +61,7 @@ StatTools/visualization/__init__.py
 StatTools/visualization/plot_ff.py
 research/Video-based_marker-free_tracking_and_multi-scale_analysis.ipynb
 research/__init__.py
+research/bma.ipynb
 research/ff_analysis.ipynb
 research/lbfbm_generator.ipynb
 research/ndfnoise_generator.ipynb
@@ -73,6 +78,7 @@ src/cpp/StatTools_C_API.cpp
 src/cpp/StatTools_bindings.cpp
 src/cpp/StatTools_core.cpp
 src/cpp/StatTools_core.h
+tests/test_bma.py
 tests/test_dfa.py
 tests/test_dfa_func.py
 tests/test_dpcca.py

{fluctuationanalysistools-1.10.0/FluctuationAnalysisTools.egg-info → fluctuationanalysistools-1.11.0.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: FluctuationAnalysisTools
-Version: 1.10.0
+Version: 1.11.0.dev0
 Summary: Python library for DFA, Hurst exponent, and fluctuation analysis of time series.
 Author: Maya Gavrichenkova, Timofey Baburin, Olga Ivleva
 Author-email: Aleksandr Sinitca <amsinitca@etu.ru>, Alexandr Kuzmenko <alexander.k.spb@gmail.com>, Asya Lyanova <ailianova@etu.ru>

{fluctuationanalysistools-1.10.0 → fluctuationanalysistools-1.11.0.dev0}/StatTools/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.10.0'
-__version_tuple__ = version_tuple = (1, 10, 0)
+__version__ = version = '1.11.0.dev0'
+__version_tuple__ = version_tuple = (1, 11, 0, 'dev0')
 
-__commit_id__ = commit_id = 'g8d5d8f2bc'
+__commit_id__ = commit_id = 'g90f7796de'

{fluctuationanalysistools-1.10.0 → fluctuationanalysistools-1.11.0.dev0}/StatTools/analysis/__init__.py

@@ -1,3 +1,4 @@
+from .bma import bma
 from .dpcca import dpcca
 from .fa import fa
 from .nd_dfa import nd_dfa