Merge latest updates

.github/workflows/python-publish.yml

@@ -0,0 +1,39 @@
+# 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.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      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
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/regression-tests.yml

@@ -0,0 +1,47 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Regression tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install coverage coveralls sphinx_rtd_theme
+        pip install ".[dev]"
+    - name: Check auto-formatters
+      run: |
+        isort --check .
+        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/
+        coverage report
+    - name: Upload coverage to Coveralls
+      uses: coverallsapp/github-action@v2

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: https://github.com/pycqa/isort
+    rev: 5.11.5
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        language_version: python

CHANGELOG.md

@@ -0,0 +1,109 @@
+# v1.6.1 (2023-04-27)
+- New: 
+  - Tensor generator helpers: 
+    - `tenones`, `tenzeros`, `tendiag`, `sptendiag` (PR https://github.com/sandialabs/pyttb/pull/93)
+    - `tenrand`, `sptenrand` (PR https://github.com/sandialabs/pyttb/pull/100)
+  - Moved to using `logging` instead of `warnings` (PR https://github.com/sandialabs/pyttb/pull/99)
+- Documentation:
+  - Completed: `ktensor` (PR https://github.com/sandialabs/pyttb/pull/101)
+  - Fixed linking for new classes (PR https://github.com/sandialabs/pyttb/pull/98)
+# v1.6.0 (2023-04-16)
+- API Change (PR https://github.com/sandialabs/pyttb/pull/91)
+  - *Not backwards compatible*
+  - `pyttb_utils.tt_dimscheck`
+    - Addresses ambiguity of -0 by using `exclude_dims` (`numpy.ndarray`) parameter
+  - `ktensor.ttv`, `sptensor.ttv`, `tensor.ttv`, `ttensor.ttv`
+    - Use `exlude_dims` parameter instead of `-dims`
+    - Explicit nameing of dimensions to exclude
+  - `tensor.ttsv`
+    - Use `skip_dim` (`int`) parameter instead of `-dims`
+    - Exclude all dimensions up to and including `skip_dim`
+- Fixes/Completed:
+  - Code cleaning: minor changes associated with replacing `-dims` with `exclude_dims`/`skip_dim`
+  - Authorship: PyPI only allows one author, changing to current POC
+
+# v1.5.1 (2023-04-14)
+- New:
+  - Dev Support: 
+    - Linting: support for `pyttb_utils` and `sptensor` (PR https://github.com/sandialabs/pyttb/pull/77)
+    - Pre-commit: support @ntjohnson1 in (PR https://github.com/sandialabs/pyttb/pull/83)
+- Fixed/Completed:
+  - `hosvd`: Negative signs can be permuted for equivalent decomposition (PR https://github.com/sandialabs/pyttb/pull/82)
+  - Versioning: using dynamic version in pyproject.toml (PR https://github.com/sandialabs/pyttb/pull/86)
+  - Package Testing: fixed problem with subprocesses (PR https://github.com/sandialabs/pyttb/pull/87)
+
+# v1.5.0 (2023-03-19)
+- New: 
+  - Added `hosvd` Tuecker decomposition (Issue #56, PR #67)
+  - Added `tucker_als` Tuecker decomposition (PR #66)
+  - Autoformatting using `black` and `isort` (Issue #59, PR #60)
+- Updated/Ongoing:
+  - Included more testing for improved coverage (Issue #78, PR #79)
+
+# v1.4.0 (2023-02-21)
+- New: 
+  - Added `ttensor` class and associated tests (Issue #10, PR #51)
+- Fixed/Completed:
+  -  Tensor slicing now passes through to `numpy` array slicing (Issue #41, PR #50)
+- Updated/Ongoing:
+  - Included more testing for improved coverage (Issue #14, PR #52)
+
+# v1.3.9 (2023-02-20)
+- Remove deprecated `numpy` code associated with aliases to built-in types and ragged arrays (Issue #48, PR #49)
+
+# v1.3.8 (2022-10-12)
+- Fixed `pyttb_utils.tt_ind2sub` (Issue #45, PR #47)
+- Implemented `ktensor.score` (Issue #46, PR #47)
+
+# v1.3.7 (2022-07-17)
+- Fixed `tenmat` to accept empty arrays for `rdims` or `cdims` (Issue #42, PR #43)
+- Implemented `tensor.ttt` (Issue #28, PR #44)
+- Adding GitHub action to publish releases to PyPi
+
+# v1.3.6 (2022-07-15)
+- Implemented `tensor.ttm` (Issue #27, PR #40)
+
+# v1.3.5 (2022-07-12)
+- Fixing `np.reshape` in `tensor.ttv` (Issue #37, PR #38)
+- Fixing `np.reshape` in remainder of `tensor` (Issue #30, PR #39)
+
+# v1.3.4 (2022-07-12)
+- Fixing issues with PyPi uploads
+
+# v1.3.3 (2022-07-11)
+- Fixed indexing bug in `tensor.mttkrp` (Issue #35, PR #36)
+- Updated LICENSE to compliant format (Issue #33 , PR #34)
+- Now using [coveralls.io](https://coveralls.io/github/sandialabs/pyttb) for coverage reporting
+- Now using [readthedocs.io](https://pyttb.readthedocs.io/en/latest/) for documentation
+
+# v1.3.2 (2022-07-06)
+- Update `tensor.nvecs` to use `tenmat` (Issue #25, PR #31)
+- Full implementation of `tensor.collapse` (Issue #2, PR #32)
+- Added `CHANGELOG.md`
+
+# v1.3.1 (2022-07-01)
+- Using `pyttb.__version__` for specifying package version in code and docs
+- Implemented `tenmat.__setitem__` and tests (#23)
+- Fix warnings in `cp_apr` associated with divide by zero (#13)
+- Several documentation fixes.
+
+# v1.3.0 (2022-07-01)
+- Changed package name to `pyttb` (#24)
+
+# v1.2.0 (2022-07-01)
+- Added `tenmat` class and associated tests (#8)
+- Added `tensor.__rmul__` for preadding scalars (#18)
+- Fixed error in `sptensor.__lt__` that led to creation of large boolean tensors when comparing with 0 (#15)
+- Matched output of `cp_als` to Matlab (#17)
+
+# v1.1.1 (2022-06-29)
+- Fixed `tensor/mttkrp` use of `np.reshape` (#16)
+- Now updating version numbers in `setup.py`
+
+# v1.1.0 (2022-06-27)
+- Fixed `import_data` method
+- New `export_data` method
+- More testing
+
+# v1.0.0 (2022-06-27)
+- Initial release of Python Tensor Toolbox

CONTRIBUTING.md

@@ -0,0 +1,54 @@
+# Python Tensor Toolbox Contributor Guide
+
+## Issues
+If you are looking to get started or want to propose a change please start by checking
+current or filing a new [issue](https://github.com/sandialabs/pyttb/issues).
+
+## Working on PYTTB locally
+1. clone your fork and enter the directory
+    ```
+    $ git clone [email protected]:<your username>/pyttb.git
+    $ cd pyttb
+    ```
+    1. setup your desired python environment as appropriate
+
+1. install dependencies
+    ```
+    $ pip install -e ".[dev]"
+    $ make install_dev # shorthand for above
+    ```
+
+1. Checkout a branch and make your changes
+    ```
+    git checkout -b my-new-feature-branch
+    ```
+1. Formatters and linting
+   1. Run autoformatters from root of project (they will change your code)
+       ```commandline
+       $ isort .
+       $ black .
+       ```
+      1. [We](./.pre-commit-config.yaml) optionally support [pre-commit hooks](https://pre-commit.com/) for this
+   1. Pylint and mypy coverage is work in progress (these only raise errors)
+      ```commandline
+      mypy pyttb/
+      pylint pyttb/file_name.py  //Today only tensor is compliant
+      ```
+
+1. Run tests (at desired fidelity)
+    1. Just doctests (enabled by default)
+        ```commandline
+        pytest
+        ```
+   1. Functional tests
+        ```commandline
+        pytest .
+        ```
+   1. All tests (linting and formatting checks)
+        ```commandline
+        pytest . --packaging
+        ```
+   1. With coverage
+        ```commandline
+        pytest . --cov=pyttb --cov-report=term-missing
+        ```

CONTRIBUTORS.md

@@ -8,9 +8,17 @@ U.S. Government retains certain rights in this software.
 
 ## Contributors
 
-**Primary POC:** Danny Dunlavy, [email protected]
+**Primary POC:** [Danny Dunlavy](@dmdunla)
 
-**Contributors:**
-* Danny Dunlavy - original author, `sptensor`, `ktensor`, `tensor`, `tenmat`, `cp_als`, `cp_apr` 
-* Nick Johnson - original author, `sptensor`, `ktensor`, `tensor`, `cp_als`, `cp_apr`
-* Derek Tucker - `tensor`
+**Main Developers:**
+
+- [Danny Dunlavy](@dmdunla) - original author, `sptensor`, `ktensor`, `tensor`, `tenmat`, `cp_als`, `cp_apr`, 
+[PRs](https://github.com/sandialabs/pyttb/commits?author=dmdunla) 
+- [Nick Johnson](@ntjohnson1) - original author, `sptensor`, `ktensor`, `tensor`, `ttensor`, `cp_als`, `cp_apr`, 
+[PRs](https://github.com/sandialabs/pyttb/commits?author=ntjohnson1)
+
+**Other Contributors:**
+- [Brian Kelley](@brian_kelley) - `numpy` compatability, 
+[PRs](https://github.com/sandialabs/pyttb/commits?author=brian-kelley)
+- [Derek Tucker](@jdtuck)[#1] - `tensor`, 
+[PRs](https://github.com/sandialabs/pyttb/commits?author=jdtuck)

LICENSE

@@ -1,8 +1,7 @@
 BSD 2-Clause License
 
-Copyright 2022 National Technology & Engineering Solutions of Sandia,
-LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
-U.S. Government retains certain rights in this software.
+Copyright (c) 2022, National Technology & Engineering Solutions of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.
+All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

Makefile

@@ -14,9 +14,24 @@ BUILDDIR      = ./docs/build
 
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@echo "install: Install release build"
+	@echo "install_dev: Install dev build"
+	@echo "install_docs: Install docs build"
+	@echo "docs_help: Show additional docs commands"
+
+.PHONY: help install install_dev install_docs Makefile
+
+install:
+	python -m pip install -e .
 
-.PHONY: help Makefile
+install_dev:
+	python -m pip install -e ".[dev]"
+
+install_docs:
+	python -m pip install -e ".[doc]"
+
+docs_help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

README.md

@@ -6,30 +6,26 @@ U.S. Government retains certain rights in this software.
 
 # pyttb: Python Tensor Toolbox
 
-## Contributors
-* Danny Dunlavy, Nick Johnson, Derek Tucker
+Welcome to `pyttb`, a set of Python classes and methods functions for 
+manipulating dense, sparse, and structured tensors, along with algorithms 
+for computing low-rank tensor models.
 
-## Quick start
+**Tensor Classes:**
+* `tensor`: dense tensors
+* `sptensor`: sparse tensors
+* `ktensor`: Kruskal tensors
+* `tenmat`: matricized tensors
+* `ttensor`: Tucker tensors
 
-### Install
-* User: ```python setup.py install```
-* Developer: ```python setup.py develop```
+**Tensor Algorithms:**
+* `cp_als`, `cp_apr`: Canonical Polyadic (CP) decompositions
+* `tucker_als`: Tucker decompostions
 
-### Testing
-```
-python -m pytest
-```
+# Getting Started
+Check out the [Documentation](https://pyttb.readthedocs.io) to get started.
 
-### Coverage Testing
-```
-pytest --cov=pyttb  tests/ --cov-report=html
-# output can be accessed via htmlcov/index.html
-```
-
-### Documentation
-```
-# requires `sphinx`
-sphinx-build ./docs/source ./docs/build/html
-# output can be accessed via docs/build/html/index.html
-```
+# Contributing
+Check out our [contributing guide](CONTRIBUTING.md).
 
+---
+[![Regression tests](https://github.com/sandialabs/pyttb/actions/workflows/regression-tests.yml/badge.svg)](https://github.com/sandialabs/pyttb/actions/workflows/regression-tests.yml) [![Coverage Status](https://coveralls.io/repos/github/sandialabs/pyttb/badge.svg?branch=main)](https://coveralls.io/github/sandialabs/pyttb?branch=main)