Modernize Python compatibilities and bump lspopt version

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,11 @@
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.github/workflows/build_and_test.yml

@@ -0,0 +1,45 @@
+name: Build and Test
+
+on:
+    push:
+        branches: [ master, develop ]
+    pull_request:
+        branches: [ master, develop ]
+
+jobs:
+    build_linux:
+        name: "Build and test"
+        runs-on: ${{ matrix.os }}
+        strategy:
+            matrix:
+                os: [ubuntu-latest, windows-latest, macos-latest]
+                python-version: ["3.9", "3.10", "3.11", "3.12"]
+        steps:
+            -   uses: actions/checkout@v4
+            -   name: Set up Python ${{ matrix.python-version }}
+                uses: actions/setup-python@v5
+                with:
+                    python-version: ${{ matrix.python-version }}
+            -   name: Upgrade pip. setuptools and wheel
+                run: python -m pip install --upgrade pip setuptools wheel
+
+            -   name: Install development dependencies
+                run: pip install flake8 pytest pytest-cov
+            -   name: Lint with flake8
+                run: |
+                    # stop the build if there are Python syntax errors or undefined names
+                    flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+                    # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+                    flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+            -   name: Install package as editable
+                run: pip install -e .
+            -   name: Test with pytest
+                run: |
+                    pytest tests --junitxml=junit/test-results-${{ matrix.os }}-${{ matrix.python-version }}.xml --cov=com --cov-report=xml --cov-report=html
+            -   name: Upload pytest test results
+                uses: actions/upload-artifact@v4
+                with:
+                    name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+                    path: junit/test-results-${{ matrix.os }}-${{ matrix.python-version }}.xml
+                # Use always() to always run this step to publish test results when there are test failures
+                if: ${{ always() }}

.github/workflows/pypi-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.gitignore

@@ -117,3 +117,6 @@ docs/_build/
 # PyBuilder
 target/
 
+# Environments
+.conda/
+.vscode/

CHANGELOG.md

@@ -0,0 +1,79 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.4.0] - 2025-01-07
+
+### Added
+
+- Support for Python 3.12
+- Support for `pip>=25`
+- Support for `numpy>=2`
+- Support for Windows and macOS
+
+### Removed
+
+- Support for Python 3.7 and 3.8
+- Unused imports
+
+
+## [1.3.0] - 2023-01-24
+
+### Changed
+
+- Modified test matrix in CI
+
+### Removed
+
+- Support for Python 2.7 and 3.6.
+- Dependency on `six`.
+
+
+## [1.2.0] - 2022-06-08
+
+### Added
+
+- New plot file
+
+### Fixed
+
+- Source distribution was broken on PyPI. Modified `MANIFEST.in` to correct that (#5 and #6)
+- Url to missing plot file
+- Fixed some incorrect int declarations using `1e3` notation
+
+### Removed
+
+- Removed Pipfile
+
+## [1.1.1] - 2020-09-28
+
+### Added
+
+- Added `CHANGELOG.md`
+
+### Changed
+
+- Change CI from Azure Devops to Github Actions
+
+
+## [1.1.0] - 2019-06-19
+
+### Added
+
+- First PyPI-released version
+
+
+## [1.0.0] - 2016-08-22
+
+### Added
+
+- Regarded as a feature-complete, stable library.
+
+
+[Unreleased]: https://github.com/hbldh/lspopt/compare/v1.3.0...HEAD
+[1.3.0]: https://github.com/hbldh/lspopt/compare/v1.2.0...v1.3.0
+[1.2.0]: https://github.com/hbldh/lspopt/compare/v1.1.1...v1.2.0
+[1.1.1]: https://github.com/hbldh/lspopt/compare/v1.1.0...v1.1.1
+[1.1.0]: https://github.com/hbldh/lspopt/compare/v1.0.0...v1.1.0

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015 Henrik Blidh
+Copyright (c) 2022 Henrik Blidh
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -0,0 +1,8 @@
+include LICENSE
+include README.md
+include HISTORY.md
+include requirements.txt
+include Pipfile
+include CHANGELOG.md
+include lspopt/data/c.npy
+include lspopt/data/weights.npy

README.md

@@ -1,7 +1,8 @@
 # LSPOpt
 
-[![Build Status](https://travis-ci.org/hbldh/lspopt.svg)](https://travis-ci.org/hbldh/lspopt)
-[![Coverage Status](https://coveralls.io/repos/github/hbldh/lspopt/badge.svg?branch=master)](https://coveralls.io/github/hbldh/lspopt?branch=master)
+![Build and Test](https://github.com/hbldh/lspopt/workflows/Build%20and%20Test/badge.svg)
+[![PyPI version](https://img.shields.io/pypi/v/lspopt.svg)](https://pypi.org/project/lspopt/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 This module is a Python implementation of the multitaper window method 
 described in [\[1\]](#references) for estimating Wigner spectra for certain locally
@@ -22,24 +23,25 @@ Abstract from [\[1\]](#references):
 
 Install via pip:
 
-    pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt
+    pip install lspopt
+
+If you prefer to use `conda`, see [instructions in this repo](https://github.com/conda-forge/lspopt-feedstock).
 
 ## Testing
 
-Test with `nosetests`:
+Test with `pytest`:
 
-    nosetests tests/ 
+    pytest tests/
 
-Tests are run at every commit to GitHub and the results of this, as well as test 
-coverage, can be studied at [Travis CI](https://travis-ci.org/hbldh/lspopt).
+See test badge at the top of this README for link to test coverage and reports.
 
 ## Usage
 
 To generate the taper windows only, use the `lspopt` method:
 
 ```python
 from lspopt import lspopt
-H, w = lspopt(N=256, c_parameter=20.0)
+H, w = lspopt(n=256, c_parameter=20.0)
 ```
 
 There is also a convenience method for using the [SciPy spectrogram method](https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.spectrogram.html#scipy.signal.spectrogram)
@@ -64,13 +66,13 @@ import matplotlib.pyplot as plt
 
 from lspopt.lsp import spectrogram_lspopt
 
-fs = 10e3
-N = 1e5
+fs = 10000
+N = 100000
 amp = 2 * np.sqrt(2)
 noise_power = 0.001 * fs / 2
 time = np.arange(N) / fs
-freq = np.linspace(1e3, 2e3, N)
-x = amp * chirp(time, 1e3, 2.0, 6e3, method='quadratic') + \
+freq = np.linspace(1000, 2000, N)
+x = amp * chirp(time, 1000, 2.0, 6000, method='quadratic') + \
     np.random.normal(scale=np.sqrt(noise_power), size=time.shape)
 
 f, t, Sxx = spectrogram(x, fs)
@@ -87,14 +89,16 @@ ax.pcolormesh(t, f, Sxx)
 ax.set_ylabel('Frequency [Hz]')
 ax.set_xlabel('Time [sec]')
 
+plt.tight_layout()
 plt.show()
 ```
 
-![Spectrogram plot](https://hbldh.github.com/lspopt/images/plot.png)
+![Spectrogram plot](https://github.com/hbldh/lspopt/blob/master/plot.png "Top: Using SciPy's spectrogram method. Bottom: Using LSPOpt's spectrogram solution.")
+
 *Top: Using SciPy's spectrogram method. Bottom: Using LSPOpt's spectrogram solution.*
 
 ## References
 
 \[1\] [Hansson-Sandsten, M. (2011). Optimal multitaper Wigner spectrum 
 estimation of a class of locally stationary processes using Hermite functions. 
-EURASIP Journal on Advances in Signal Processing, 2011, 10.](http://asp.eurasipjournals.com/content/pdf/1687-6180-2011-980805.pdf)
+EURASIP Journal on Advances in Signal Processing, 2011, 10.](https://dx.doi.org/10.1155/2011/980805)

generate_plot.py

@@ -9,11 +9,6 @@
 
 """
 
-from __future__ import division
-from __future__ import print_function
-from __future__ import unicode_literals
-from __future__ import absolute_import
-
 import six
 import numpy as np
 from scipy.signal import chirp, spectrogram
@@ -26,21 +21,21 @@
 
 
 def generate_chirp_spectrogram_plot():
-    fs = 10e3
-    N = 1e5
+    fs = 10000
+    N = 100000
     amp = 2 * np.sqrt(2)
     noise_power = 0.001 * fs / 2
     time = np.arange(N) / fs
-    freq = np.linspace(1e3, 2e3, N)
-    x = amp * chirp(time, 1e3, 2.0, 6e3, method='quadratic') + \
+    freq = np.linspace(1000, 2000, N)
+    x = amp * chirp(time, 1000, 2.0, 6000, method='quadratic') + \
         np.random.normal(scale=np.sqrt(noise_power), size=time.shape)
 
     f, t, Sxx = spectrogram(x, fs)
 
     ax = plt.subplot(211)
     ax.pcolormesh(t, f, Sxx)
     ax.set_ylabel('Frequency [Hz]')
-    ax.set_xlabel('Time [sec]')
+    ax.set_xlabel('Time [sec]', labelpad=10)
 
     f, t, Sxx = spectrogram_lspopt(x, fs, c_parameter=20.0)
 
@@ -49,6 +44,7 @@ def generate_chirp_spectrogram_plot():
     ax.set_ylabel('Frequency [Hz]')
     ax.set_xlabel('Time [sec]')
 
+    plt.tight_layout()
     plt.show()
 
 
@@ -100,11 +96,12 @@ def generate_lsp_processes_figures():
         ax.set_ylim([-1.5, 1.5])
         ax.set_xlabel('t')
 
+    plt.tight_layout()
     plt.show()
 
 
 def main():
-    #generate_chirp_spectrogram_plot()
+    generate_chirp_spectrogram_plot()
     generate_lsp_processes_figures()
 
 if __name__ == "__main__":