Modernize Python codebase for 2025+

.github/workflows/ci.yml

@@ -0,0 +1,33 @@
+name: CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install cython numpy scipy
+        pip install -e .
+
+    - name: Run tests
+      run: python -m unittest discover bandmat

.gitignore

@@ -1,10 +1,12 @@
-.git/
-_darcs/
+__pycache__/
+*.pyc
+*.so
+*.c
+*.egg
+.eggs/
 bandmat.egg-info/
 build/
 dist/
 env/
+.venv/
 MANIFEST
-*.c
-*.pyc
-*.so

README.rst

@@ -1,14 +1,11 @@
 bandmat
 =======
 
-|Linux build status| |Windows build status|
+|CI status|
 
-.. |Linux build status| image:: https://travis-ci.org/MattShannon/bandmat.svg?branch=master
-   :alt: Linux build status
-   :target: https://travis-ci.org/MattShannon/bandmat
-.. |Windows build status| image:: https://ci.appveyor.com/api/projects/status/cy8ouawd9bnus0ai/branch/master?svg=true
-   :alt: Windows build status
-   :target: https://ci.appveyor.com/project/MattShannon/bandmat/branch/master
+.. |CI status| image:: https://github.com/MattShannon/bandmat/actions/workflows/ci.yml/badge.svg?branch=master
+   :alt: CI status
+   :target: https://github.com/MattShannon/bandmat/actions/workflows/ci.yml
 
 This package provides a simple banded matrix library for python.
 It supports banded matrix-vector and matrix-matrix multiplication, converting
@@ -58,26 +55,16 @@ bandmat.
 Installation
 ------------
 
-For most purposes the simplest way to install bandmat is to use pip.
-For example in Debian and Ubuntu::
+For most purposes the simplest way to install bandmat is to use pip in a
+virtual environment::
 
-    # (for python3, use "python3-numpy python3-scipy" instead)
-    sudo apt-get install python-numpy python-scipy
-    sudo pip install bandmat
+    python3 -m venv env
+    env/bin/pip install bandmat
 
-The first command installs numpy and scipy from the system repository, since
-installing numpy and scipy using pip is generally not recommended.
-The second command installs the latest released version of
+This installs the latest released version of
 `bandmat on PyPI <https://pypi.python.org/pypi/bandmat>`_, together with any
 currently uninstalled python packages required by bandmat.
 
-bandmat can also be installed in a virtualenv::
-
-    # (for python3, use "python3-numpy python3-scipy" instead)
-    sudo apt-get install python-numpy python-scipy
-    virtualenv --system-site-packages env
-    env/bin/pip install bandmat
-
 The latest development version of bandmat is available from a github repository
 (see below).
 
@@ -104,42 +91,17 @@ To obtain the latest source code using git::
 
     git clone git://github.com/MattShannon/bandmat.git
 
-Development is in fact done using `darcs <http://darcs.net/>`_, with the darcs
-repository converted to a git repository using
-`darcs-to-git <https://github.com/purcell/darcs-to-git>`_.
-
-To install any currently uninstalled python packages required by bandmat::
+To install bandmat for development in a virtual environment::
 
-    # (for python3, use "cython3 python3-numpy python3-scipy" instead)
-    sudo apt-get install cython python-numpy python-scipy
-    sudo pip install -r requirements.txt
+    python3 -m venv env
+    env/bin/pip install -e .
 
-To compile the cython part of bandmat in the current directory::
+This will install the build dependencies (cython, numpy) and compile the
+cython extensions automatically.
+To recompile after modifying ``.pyx`` files::
 
     python setup.py build_ext --inplace
 
-This command must be run after every modification to the source ``.pyx`` files.
-
-A note on ``setup.py``
-----------------------
-
-The included ``setup.py`` file operates in one of two modes depending on
-whether or not the file ``dev`` is present in the project root directory.
-In development mode (``dev`` present, as for the github repository), the
-``build_ext`` command uses cython to compile cython modules from their ``.pyx``
-source, and the ``sdist`` command is modified to first use cython to compile
-cython modules from their ``.pyx`` source to ``.c`` files.
-In distribution mode (``dev`` absent, as for source distributions such as the
-code on PyPI), the ``build_ext`` command uses a C compiler to directly compile
-cython modules from the corresponding ``.c`` files.
-This approach ensures that source distributions can be installed on systems
-without cython or with an incompatible version of cython, while ensuring that
-distributed ``.c`` files are always up-to-date and that the source ``.pyx``
-files are used instead of ``.c`` files during development.
-
-The author would welcome any suggestions for more elegant ways to achieve a
-similar effect to the approach described above!
-
 Bugs
 ----
 

bandmat/misc.pyx

@@ -11,7 +11,7 @@ cimport cython
 cnp.import_array()
 cnp.import_ufunc()
 
-def fancy_plus_equals(cnp.ndarray[cnp.int_t, ndim=1] target_index_seq,
+def fancy_plus_equals(cnp.ndarray[cnp.intp_t, ndim=1] target_index_seq,
                       cnp.ndarray[cnp.float64_t, ndim=1] source,
                       cnp.ndarray[cnp.float64_t, ndim=1] target):
     """Implements a += method with fancy indexing.
@@ -26,15 +26,15 @@ def fancy_plus_equals(cnp.ndarray[cnp.int_t, ndim=1] target_index_seq,
     assert target_index_seq.shape[0] == source_size
 
     cdef unsigned long source_index
-    cdef long target_index
+    cdef cnp.intp_t target_index
 
     for source_index in range(source_size):
         target_index = target_index_seq[source_index]
         target[target_index] += source[source_index]
 
     return
 
-def fancy_plus_equals_2d(cnp.ndarray[cnp.int_t, ndim=1] target_index_seq,
+def fancy_plus_equals_2d(cnp.ndarray[cnp.intp_t, ndim=1] target_index_seq,
                          cnp.ndarray[cnp.float64_t, ndim=2] source,
                          cnp.ndarray[cnp.float64_t, ndim=2] target):
     """Implements a += method with fancy indexing.
@@ -52,7 +52,7 @@ def fancy_plus_equals_2d(cnp.ndarray[cnp.int_t, ndim=1] target_index_seq,
     assert target.shape[1] == size1
 
     cdef unsigned long source_index
-    cdef long target_index
+    cdef cnp.intp_t target_index
     cdef unsigned long index1
 
     for source_index in range(source_size):
@@ -62,7 +62,7 @@ def fancy_plus_equals_2d(cnp.ndarray[cnp.int_t, ndim=1] target_index_seq,
 
     return
 
-def fancy_plus_equals_3d(cnp.ndarray[cnp.int_t, ndim=1] target_index_seq,
+def fancy_plus_equals_3d(cnp.ndarray[cnp.intp_t, ndim=1] target_index_seq,
                          cnp.ndarray[cnp.float64_t, ndim=3] source,
                          cnp.ndarray[cnp.float64_t, ndim=3] target):
     """Implements a += method with fancy indexing.
@@ -83,7 +83,7 @@ def fancy_plus_equals_3d(cnp.ndarray[cnp.int_t, ndim=1] target_index_seq,
     assert target.shape[2] == size2
 
     cdef unsigned long source_index
-    cdef long target_index
+    cdef cnp.intp_t target_index
     cdef unsigned long index1
     cdef unsigned long index2
 

bandmat/test_linalg.py

@@ -126,7 +126,7 @@ def test__cholesky_banded(self, its=100):
                 # First part of the message is e.g. "2-th leading minor".
                 msgRe = (r'^' + re.escape(str(e)[:15]) +
                          r'.*not positive definite$')
-                with self.assertRaisesRegexp(la.LinAlgError, msgRe):
+                with self.assertRaisesRegex(la.LinAlgError, msgRe):
                     sla.cholesky(mat_bm.full(), lower=lower)
             else:
                 assert np.shape(chol_data) == (depth + 1, size)
@@ -171,12 +171,12 @@ def test__solve_triangular_banded(self, its=100):
                     badFrame
                 )
                 msgRe = '^' + re.escape(msg) + '$'
-                with self.assertRaisesRegexp(la.LinAlgError, msgRe):
+                with self.assertRaisesRegex(la.LinAlgError, msgRe):
                     bla._solve_triangular_banded(
                         chol_data, b_arg, transposed=transposed, lower=lower,
                         overwrite_b=overwrite_b
                     )
-                with self.assertRaisesRegexp(la.LinAlgError, msgRe):
+                with self.assertRaisesRegex(la.LinAlgError, msgRe):
                     sla.solve_triangular(
                         chol_full, b, trans=transposed, lower=lower
                     )
@@ -299,7 +299,7 @@ def test_solveh(self, its=50):
             if size == 0:
                 x_good = np.zeros((size,))
             else:
-                x_good = sla.solve(a_full, b, sym_pos=True)
+                x_good = sla.solve(a_full, b, assume_a='pos')
             assert_allclose(x, x_good)
             assert not np.may_share_memory(x, a_bm.data)
             assert not np.may_share_memory(x, b)

bandmat/test_misc.py

@@ -7,6 +7,7 @@
 
 import unittest
 import random
+import numpy as np
 from numpy.random import randn, randint
 
 from bandmat.misc import fancy_plus_equals, fancy_plus_equals_2d
@@ -23,7 +24,7 @@ def test_fancy_plus_equals(self, its=100):
             target_size = random.choice([1, randint(1, 10), randint(1, 100)])
             source = randn(source_size)
             target = randn(target_size)
-            target_index_seq = randint(target_size, size=source_size)
+            target_index_seq = randint(target_size, size=source_size, dtype=np.intp)
             array_mem = get_array_mem(target_index_seq, source, target)
 
             target_good = target.copy()
@@ -41,7 +42,7 @@ def test_fancy_plus_equals_fails(self, its=100):
             target_size = random.choice([1, randint(1, 10), randint(1, 100)])
             source = randn(source_size)
             target = randn(target_size)
-            target_index_seq = randint(target_size, size=source_size)
+            target_index_seq = randint(target_size, size=source_size, dtype=np.intp)
             target_index_seq[randint(source_size)] = (
                 (-target_size - 1 - randint(10)) if rand_bool()
                 else target_size + randint(10)
@@ -57,7 +58,7 @@ def test_fancy_plus_equals_2d(self, its=100):
             size1 = random.choice([0, 1, randint(10)])
             source = randn(source_size, size1)
             target = randn(target_size, size1)
-            target_index_seq = randint(target_size, size=source_size)
+            target_index_seq = randint(target_size, size=source_size, dtype=np.intp)
             array_mem = get_array_mem(target_index_seq, source, target)
 
             target_good = target.copy()
@@ -76,7 +77,7 @@ def test_fancy_plus_equals_2d_fails(self, its=100):
             size1 = random.choice([1, randint(1, 10)])
             source = randn(source_size, size1)
             target = randn(target_size, size1)
-            target_index_seq = randint(target_size, size=source_size)
+            target_index_seq = randint(target_size, size=source_size, dtype=np.intp)
             target_index_seq[randint(source_size)] = (
                 (-target_size - 1 - randint(10)) if rand_bool()
                 else target_size + randint(10)
@@ -93,7 +94,7 @@ def test_fancy_plus_equals_3d(self, its=100):
             size2 = random.choice([0, 1, randint(10)])
             source = randn(source_size, size1, size2)
             target = randn(target_size, size1, size2)
-            target_index_seq = randint(target_size, size=source_size)
+            target_index_seq = randint(target_size, size=source_size, dtype=np.intp)
             array_mem = get_array_mem(target_index_seq, source, target)
 
             target_good = target.copy()
@@ -113,7 +114,7 @@ def test_fancy_plus_equals_3d_fails(self, its=100):
             size2 = random.choice([1, randint(1, 10)])
             source = randn(source_size, size1, size2)
             target = randn(target_size, size1, size2)
-            target_index_seq = randint(target_size, size=source_size)
+            target_index_seq = randint(target_size, size=source_size, dtype=np.intp)
             target_index_seq[randint(source_size)] = (
                 (-target_size - 1 - randint(10)) if rand_bool()
                 else target_size + randint(10)

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+requires = [
+    "cython",
+    "numpy",
+    "setuptools",
+    "wheel",
+]

requirements.txt

@@ -1,2 +1,2 @@
-numpy>=1.6.1
-scipy>=0.9.0
+numpy>=1.26.0
+scipy>=1.12.0