python: update package metadata

.flake8

@@ -2,5 +2,3 @@
 max-line-length = 132
 ignore = E203
 exclude = .git,__pycache__,.eggs/,doc/,docs/,build/,dist/,archive/
-per-file-ignores =
-    __init__.py:F401

.github/workflows/ci.yml

@@ -5,18 +5,15 @@ on:
     paths:
     - "**/*.py"
     - "**/*.f90"
-  pull_request:
-    paths:
-    - "**/*.py"
-    - "**/*.f90"
+
 
 jobs:
 
   fortran:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
@@ -25,36 +22,30 @@ jobs:
     - run: meson setup build
     - run: meson test -C build
 
-  linux:
-    runs-on: ubuntu-latest
+  python:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [windows-latest, macos-latest, ubuntu-latest]
+
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
-    - run: |
-        sudo apt update
-        sudo apt install --no-install-recommends octave
+    - name: Install GNU Octave
+      if: runner.os == 'Linux'
+      run: sudo apt install --no-install-recommends octave
+
+    - name: Install Oct2Py
+      if: runner.os == 'Linux'
+      run: pip install oct2py
 
-    - run: pip install oct2py
     - run: pip install .[tests,lint]
 
     - run: flake8
     - run: mypy
 
     - run: pytest
-
-  integration:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [windows-latest, macos-latest]
-    steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-
-    - run: pip install .[tests]
-    - run: pytest

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2014, Michael Hirsch
+Copyright (c) 2014, SciVision
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -24,4 +24,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,33 +1,25 @@
 # AIRtools
 
-
-[![Actions Status](https://github.com/scivision/airtools/workflows/ci/badge.svg)](https://github.com/scivision/airtools/actions)
-
-[![PyPi versions](https://img.shields.io/pypi/pyversions/airtools.svg)](https://pypi.python.org/pypi/airtools)
-[![PyPi Download stats](http://pepy.tech/badge/airtools)](http://pepy.tech/project/airtools)
+[![Actions Status](https://github.com/geospace-code/airtools/workflows/ci/badge.svg)](https://github.com/geospace-code/airtools/actions)
+[![PyPI Download stats](http://pepy.tech/badge/airtools)](http://pepy.tech/project/airtools)
 
 
 
 Limited subset of P.C. Hansen and J. S. Jørgensen
-[AIRtools 1.0](http://www2.compute.dtu.dk/~pcha/AIRtoolsII/)
+[AIRtools](http://www2.compute.dtu.dk/~pcha/AIRtoolsII/)
 Matlab suite of inversion / regularization tools, along with some ReguTools functions.
 Also includes linear constrained least squares solver using cvxopt in `lsqlin.py`
 
 More function are available in Matlab from
 [AIRtools 2](https://github.com/jakobsj/AIRToolsII).
 
-## Install
-
 ```sh
 python -m pip install -e .
 ```
 
 ## Usage
 
-Just paste the code from each test into your console for the function
-you're interested in. Would you like to submit a pull request for an
-inversion example making a cool plot?
-
+* logmart.py: log-MART
 * picard.py: Picard Plot
 * kaczmarz.py  Kaczmarz ART
 * maxent.py: Maximum Entropy Regularization  (from ReguTools)
@@ -36,16 +28,15 @@ inversion example making a cool plot?
 * matlab/logmart.m:  Implementation of log-MART
 * fortran/logmart.f90: log-MART in Fortran
 
-
-### Examples
-
-[tests/test_all.py](./tests/test_all.py)
+Examples: [tests/test_all.py](./tests/test_all.py)
 
 ### Tests
 
 Run a comparison of the Python code with the Matlab code in the [matlab](./matlab) directory by:
 
-    python airtools/tests/test_octave.py
+```sh
+python airtools/tests/test_octave.py
+```
 
 which runs the Matlab version via
 [Oct2Py](https://blink1073.github.io/oct2py/).

meson.build

@@ -1,5 +1,5 @@
 project('airtools', 'fortran',
-  default_options : ['default_library=static', 'buildtype=release'])
+  default_options : ['buildtype=release'])
 
 
 art = library('art', 'fortran/logmart.f90')
@@ -8,4 +8,4 @@ test_exe = executable('test_logmart',
   sources: ['fortran/test_logmart.f90', 'fortran/random_utils.f90'],
   link_with : art)
 
-test('logmart', test_exe)
+test('logmart', test_exe)

pyproject.toml

@@ -1,5 +1,37 @@
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "airtools"
+description = "Python port of Matlab AIRtools and ReguTools regularization toolbox"
+keywords = [ "regularization", "linear algebra" ]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Environment :: Console",
+  "Intended Audience :: End Users/Desktop",
+  "Intended Audience :: Science/Research",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Utilities"
+]
+dependencies = ["scipy", "numpy"]
+requires-python = ">=3.8"
+dynamic = ["version", "readme"]
+
+[tool.setuptools.dynamic]
+readme = {file = ["README.md"], content-type = "text/markdown"}
+version = {attr = "airtools.__version__"}
+
+[project.optional-dependencies]
+tests = ["pytest"]
+lint = ["flake8", "flake8-bugbear", "flake8-builtins", "flake8-blind-except", "mypy",
+  "types-python-dateutil", "types-requests"]
+
+[tool.mypy]
+files = ["src"]
+ignore_missing_imports = true
 
 [tool.black]
 line-length = 99

airtools/__init__.py → src/airtools/__init__.py

@@ -3,3 +3,7 @@
 from .picard import picard
 from .logmart import logmart
 from .rzr import rzr
+
+__all__ = ["kaczmarz", "maxent", "picard", "logmart", "rzr"]
+
+__version__ = "1.3.0"

airtools/kaczmarz.py → src/airtools/kaczmarz.py

@@ -1,21 +1,22 @@
 from __future__ import annotations
 import logging
+
 import numpy as np
 from numpy.linalg import norm
 import scipy.sparse as sp
 
 
 def kaczmarz(
-    A: np.ndarray | sp.spmatrix,
-    b: np.ndarray,
+    A,
+    b,
     *,
     max_iter: int = 8,
-    x0: np.ndarray = None,
+    x0=None,
     lamb: float = 1.0,
     stop_mdp: bool = False,
     taudelta: float = 0,
-    nonneg: bool = True
-) -> tuple[np.ndarray, np.ndarray]:
+    nonneg: bool = True,
+) -> tuple:
     """
     Michael Hirsch May 2014
 
@@ -104,6 +105,6 @@ def kaczmarz(
                 break
         if i % 200 == 0:
             residualNorm = norm(b - A @ x, 2)
-            print("Iteration {},  ||residual|| = {:.2f}".format(i, residualNorm))
+            print(f"Iteration {i},  ||residual|| = {residualNorm:.2f}")
 
     return x, residual

airtools/logmart.py → src/airtools/logmart.py

@@ -11,14 +11,14 @@
 
 
 def logmart(
-    A: np.ndarray,
-    b: np.ndarray,
+    A,
+    b,
     *,
     relax: float = 1.0,
-    x0: float = None,
+    x0: float | None = None,
     sigma: float = 1.0,
-    max_iter: int = 20
-) -> tuple[np.ndarray, float, int]:
+    max_iter: int = 20,
+) -> tuple:
     """
     estimation halted based on chi**2 value
     A and b must be all NON-NEGATIVE!
@@ -95,5 +95,5 @@ def logmart(
     return x_prev, chi2, i
 
 
-def chi_squared(A: np.ndarray, b: np.ndarray, x: np.ndarray, sigma: float) -> float:
+def chi_squared(A, b, x, sigma: float) -> float:
     return math.sqrt((((A @ x - b) / sigma) ** 2).sum())

airtools/lsqlin.py → src/airtools/lsqlin.py

@@ -5,6 +5,7 @@
 
     See http://maggotroot.blogspot.ch/2013/11/constrained-linear-least-squares-in.html for more info
 """
+
 __author__ = "Valeriy Vishnevskiy", "Michael Hirsch"
 __email__ = "[email protected]"
 __version__ = "1.0"