Merge branch 'main' into vis

.github/workflows/markdown-check.yml

@@ -10,5 +10,5 @@ jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: gaurav-nelson/github-action-markdown-link-check@v1

.github/workflows/pre-commit-check.yml

@@ -9,6 +9,6 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: pre-commit/[email protected].0
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/[email protected].1

.github/workflows/python-publish.yml

@@ -1,39 +1,56 @@
 # This workflow 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
-
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
+# For more information see: 
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
 
 name: Upload Python Package
 
 on:
   release:
     types: [published]
 
-permissions:
-  contents: read
-
 jobs:
-  deploy:
-
+  build:
+    name: Build distribution
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
       with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pyttb
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
       with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+

.github/workflows/regression-tests.yml

@@ -16,28 +16,27 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install .
+        # Basic check for minimal deployed env requirements
+        python -c "import pyttb"
+    - name: Install dev dependencies
+      run: |
         python -m pip install --upgrade coverage coveralls sphinx_rtd_theme
         pip install ".[dev]"
     - name: Check auto-formatters
       run: |
         black --check .
-#    - 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: Run tests
       run: |
         coverage run --source pyttb -m pytest tests/

CONTRIBUTORS.md

@@ -12,15 +12,19 @@ U.S. Government retains certain rights in this software.
 
 **Main Developers:**
 
-- [Danny Dunlavy](https://github.com/dmdunla) - original author, `sptensor`, `ktensor`, `tensor`, `tenmat`, `cp_als`, `cp_apr`, 
+- [Danny Dunlavy](https://github.com/dmdunla) - original author
 [PRs](https://github.com/sandialabs/pyttb/commits?author=dmdunla) 
-- [Nick Johnson](https://github.com/ntjohnson1) - original author, `sptensor`, `ktensor`, `tensor`, `ttensor`, `cp_als`, `cp_apr`, 
+- [Nick Johnson](https://github.com/ntjohnson1) - original author
 [PRs](https://github.com/sandialabs/pyttb/commits?author=ntjohnson1)
-- [Jordan Medina](https://github.com/DeepBlockDeepak) - documentation, tutorials,
-[PRs](https://github.com/sandialabs/pyttb/commits?author=DeepBlockDeepak)
+- [Jeremy Myers](https://github.com/jeremy-myers) - bug fixes, documentation
+[PRs](https://github.com/sandialabs/pyttb/commits?author=jeremy-myers)
 
 **Other Contributors:**
-- [Brian Kelley](https://github.com/brian-kelley) - `numpy` compatability, 
+- [Brian Kelley](https://github.com/brian-kelley) - dependencies 
 [PRs](https://github.com/sandialabs/pyttb/commits?author=brian-kelley)
-- [Derek Tucker](https://github.com/jdtuck)[#1] - `tensor`, 
+- [Jordan Medina](https://github.com/DeepBlockDeepak) - bug fixes, documentation
+[PRs](https://github.com/sandialabs/pyttb/commits?author=DeepBlockDeepak)
+- [Eric Phipps](https://github.com/etphipp) - bug fixes
+[PRs](https://github.com/sandialabs/pyttb/commits?author=etphipp)
+- [Derek Tucker](https://github.com/jdtuck) - bug fixes
 [PRs](https://github.com/sandialabs/pyttb/commits?author=jdtuck)

pyproject.toml

@@ -10,7 +10,7 @@ readme = "README.md"
 requires-python = ">=3.8"
 
 dependencies = [
-    "numpy",
+    "numpy < 2",
     "numpy_groupies",
     "scipy",
     "matplotlib",
@@ -23,6 +23,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
 [project.urls]

pyttb/__init__.py

@@ -5,7 +5,7 @@
 # U.S. Government retains certain rights in this software.
 from __future__ import annotations
 
-__version__ = "1.6.2"
+__version__ = "1.7.0"
 
 
 import warnings

pyttb/gcp/handles.py

@@ -115,15 +115,17 @@ def huber_grad(data: ttb.tensor, model: ttb.tensor, threshold: float) -> np.ndar
     ) * np.logical_not(below_threshold)
 
 
+# FIXME: Num trials should be enforced as integer here and in MATLAB
+# requires updating our regression test values to calculate MATLAB integer version
 def negative_binomial(
-    data: np.ndarray, model: np.ndarray, num_trials: int
+    data: np.ndarray, model: np.ndarray, num_trials: float
 ) -> np.ndarray:
     """Return objective function for negative binomial distributions"""
     return (num_trials + data) * np.log(model + 1) - data * np.log(model + EPS)
 
 
 def negative_binomial_grad(
-    data: np.ndarray, model: np.ndarray, num_trials: int
+    data: np.ndarray, model: np.ndarray, num_trials: float
 ) -> np.ndarray:
     """Return gradient function for negative binomial distributions"""
     return (num_trials + 1) / (1 + model) - data / (model + EPS)

pyttb/gcp/samplers.py

@@ -349,7 +349,7 @@ def zeros(
 
     # Select out just the zeros
     tmpidx = tt_sub2ind(data.shape, tmpsubs)
-    iszero = np.logical_not(np.in1d(tmpidx, nz_idx))
+    iszero = np.logical_not(np.isin(tmpidx, nz_idx))
     tmpsubs = tmpsubs[iszero, :]
 
     # Trim back to desired numb of samples
@@ -425,7 +425,7 @@ def semistrat(data: ttb.sptensor, num_nonzeros: int, num_zeros: int) -> sample_t
 
 
 def stratified(
-    data: ttb.sptensor,
+    data: Union[ttb.sptensor, ttb.tensor],
     nz_idx: np.ndarray,
     num_nonzeros: int,
     num_zeros: int,
@@ -450,6 +450,9 @@ def stratified(
     -------
     Subscripts, values, and weights of samples (Nonzeros then zeros).
     """
+    assert isinstance(
+        data, ttb.sptensor
+    ), "For stratified sampling Sparse Tensor must be provided"
     [nonzero_subs, nonzero_vals] = nonzeros(data, num_nonzeros, with_replacement=True)
     nonzero_weights = np.ones((num_nonzeros,))
     if num_nonzeros > 0:

pyttb/ktensor.py

@@ -23,13 +23,13 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import scipy.sparse.linalg
-from typing_extensions import Self
 
 import pyttb as ttb
 from pyttb.pyttb_utils import (
     get_mttkrp_factors,
     isrow,
     isvector,
+    np_to_python,
     tt_dimscheck,
     tt_ind2sub,
 )
@@ -696,7 +696,8 @@ def extract(
                         invalid_entries.append(component)
                 if len(invalid_entries) > 0:
                     assert False, (
-                        f"Invalid component indices to be extracted: {invalid_entries} "
+                        f"Invalid component indices to be extracted: "
+                        f"{np_to_python(invalid_entries)} "
                         f"not in range({self.ncomponents})"
                     )
                 new_weights = self.weights[components]
@@ -707,7 +708,7 @@ def extract(
         else:
             assert False, "Input parameter must be an int, tuple, list or numpy.ndarray"
 
-    def fixsigns(self, other: Optional[ktensor] = None) -> Self:  # noqa: PLR0912
+    def fixsigns(self, other: Optional[ktensor] = None) -> ktensor:  # noqa: PLR0912
         """
         Change the elements of a :class:`pyttb.ktensor` in place so that the
         largest magnitude entries for each column vector in each factor
@@ -1185,7 +1186,7 @@ def normalize(
         sort: Optional[bool] = False,
         normtype: float = 2,
         mode: Optional[int] = None,
-    ) -> Self:
+    ) -> ktensor:
         """
         Normalize the columns of the factor matrices of a
         :class:`pyttb.ktensor` in place, then optionally
@@ -1406,7 +1407,7 @@ def permute(self, order: np.ndarray) -> ktensor:
 
         return ttb.ktensor([self.factor_matrices[i] for i in order], self.weights)
 
-    def redistribute(self, mode: int) -> Self:
+    def redistribute(self, mode: int) -> ktensor:
         """
         Distribute weights of a :class:`pyttb.ktensor` to the specified mode.
         The redistribution is performed in place.
@@ -1622,7 +1623,7 @@ def score(
 
             # Rearrange the components of A according to the best matching
             foo = np.arange(RA)
-            tf = np.in1d(foo, best_perm)
+            tf = np.isin(foo, best_perm)
             best_perm[RB : RA + 1] = foo[~tf]
             A.arrange(permutation=best_perm)
             return best_score, A, flag, best_perm
@@ -2000,7 +2001,7 @@ def ttv(
             factor_matrices.append(self.factor_matrices[i])
         return ttb.ktensor(factor_matrices, new_weights, copy=False)
 
-    def update(self, modes: Union[int, Iterable[int]], data: np.ndarray) -> Self:
+    def update(self, modes: Union[int, Iterable[int]], data: np.ndarray) -> ktensor:
         """
         Updates a :class:`pyttb.ktensor` in the specific dimensions with the
         values in `data` (in vector or matrix form). The value of `modes` must

pyttb/pyttb_utils.py

@@ -7,7 +7,16 @@
 
 from enum import Enum
 from inspect import signature
-from typing import List, Literal, Optional, Tuple, Union, get_args, overload
+from typing import (
+    Iterable,
+    List,
+    Literal,
+    Optional,
+    Tuple,
+    Union,
+    get_args,
+    overload,
+)
 
 import numpy as np
 
@@ -921,3 +930,22 @@ def gather_wrap_dims(
 
     assert rdims is not None and cdims is not None
     return rdims.astype(int), cdims.astype(int)
+
+
+def np_to_python(
+    iterable: Iterable,
+) -> Iterable:
+    """Convert a structure containing numpy scalars to pure python types.
+
+    Mostly useful for prettier printing post numpy 2.0.
+
+    Parameters
+    ----------
+    iterable:
+        Structure potentially containing numpy scalars.
+    """
+    output_type = type(iterable)
+    return output_type(  # type: ignore [call-arg]
+        element.item() if isinstance(element, np.generic) else element
+        for element in iterable
+    )

pyttb/sptenmat.py

@@ -129,7 +129,7 @@ def __init__(  # noqa: PLR0913
             # Sum the corresponding values
             # Squeeze to convert from column vector to row vector
             newvals = accumarray(
-                loc, np.squeeze(vals, axis=1), size=newsubs.shape[0], func=sum
+                loc.flatten(), np.squeeze(vals, axis=1), size=newsubs.shape[0], func=sum
             )
 
         # Find the nonzero indices of the new values