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Merge latest updates (#124)
* Update nvecs to use tenmat. * Full implementation of collapse. Required implementation of tensor.from_tensor_type for tenmat objects. Updated tensor tests. (#32) * Update __init__.py Bump version. * Create CHANGELOG.md Changelog update * Update CHANGELOG.md Consistent formatting * Update CHANGELOG.md Correction * Create ci-tests.yml * Update README.md Adding coverage statistics from coveralls.io * Create requirements.txt * 33 use standard license (#34) * Use standard, correctly formatted LICENSE * Delete LICENSE * Create LICENSE * Update and rename ci-tests.yml to regression-tests.yml * Update README.md * Fix bug in tensor.mttkrp that only showed up when ndims > 3. (#36) * Update __init__.py Bump version * Bump version * Adding files to support pypi dist creation and uploading * Fix PyPi installs. Bump version. * Fixing np.reshape usage. Adding more tests for tensor.ttv. (#38) * Fixing issues with np.reshape; requires order='F' to align with Matlab functionality. (#39) Closes #30 . * Bump version. * Adding tensor.ttm. Adding use case in tenmat to support ttm testing. (#40) Closes #27 * Bump version * Format CHANGELOG * Update CHANGELOG.md * pypi puslishing action on release * Allowing rdims or cdims to be empty array. (#43) Closes #42 * Adding tensor.ttt implementation. (#44) Closes 28 * Bump version * Implement ktensor.score and associated tests. * Changes to supporting pyttb data classes and associated tests to enable ktensor.score. * Bump version. * Compatibility with numpy 1.24.x (#49) Close #48 * Replace "numpy.float" with equivalent "float" numpy.float was deprecated in 1.20 and removed in 1.24 * sptensor.ttv: support 'vector' being a plain list (rather than just numpy.ndarray). Backwards compatible - an ndarray argument still works. This is because in newer numpy, it's not allowed to do np.array(list) where the elements of list are ndarrays of different shapes. * Make ktensor.innerprod call ttv with 'vector' as plain list (instead of numpy.ndarray, because newer versions don't allow ragged arrays) * tensor.ttv: avoid ragged numpy arrays * Fix two unit test failures due to numpy related changes * More numpy updates - numpy.int is removed - use int instead - don't try to construct ragged/inhomogeneous numpy arrays in tests. Use plain lists of vectors instead * Fix typo in assert message * Let ttb.tt_dimscheck catch empty input error In the three ttv methods, ttb.tt_dimscheck checks that 'vector' argument is not an empty list/ndarray. Revert previous changes that checked for this before calling tt_dimscheck. * Bump version * TENSOR: Fix slices ref shen return value isn't scalar or vector. #41 (#50) Closes #41 * Ttensor implementation (#51) * TENSOR: Fix slices ref shen return value isn't scalar or vector. #41 * TTENSOR: Add tensor creation (partial support of core tensor types) and display * SPTENSOR: Add numpy scalar type for multiplication filter. * TTENSOR: Double, full, isequal, mtimes, ndims, size, uminus, uplus, and partial innerprod. * TTENSOR: TTV (finishes innerprod), mttkrp, and norm * TTENSOR: TTM, permute and minor cleanup. * TTENSOR: Reconstruct * TTENSOR: Nvecs * SPTENSOR: * Fix argument mismatch for ttm (modes s.b. dims) * Fix ttm for rectangular matrices * Make error message consitent with tensor TENSOR: * Fix error message * TTENSOR: Improve test coverage and corresponding bug fixes discovered. * Test coverage (#52) * SPTENSOR: * Fix argument mismatch for ttm (modes s.b. dims) * Fix ttm for rectangular matrices * Make error message consitent with tensor TENSOR: * Fix error message * SPTENSOR: Improve test coverage, replace prints, and some doc string fixes. * PYTTUB_UTILS: Improve test coverage * TENMAT: Remove impossible condition. Shape is a property, the property handles the (0,) shape condition. So ndims should never see it. * TENSOR: Improve test coverage. One line left, but logic of setitem is unclear without MATLAB validation of behavior. * CP_APR: Add tests fpr sptensor, and corresponding bug fixes to improve test coverage. --------- Co-authored-by: Danny Dunlavy <[email protected]> * Bump version * TUCKER_ALS: Add tucker_als to validate ttucker implementation. (#53) * Bump version of actions (#55) actions/setup-python@v4 to avoid deprecation warnings * Tensor docs plus Linting and Typing and Black oh my (#54) * TENSOR: Apply black and enforce it * TENSOR: Add isort and pylint. Fix to pass then enforce * TENSOR: Variety of linked fixes: * Add mypy type checking * Update infrastructure for validating package * Fix doc tests and add more examples * DOCTEST: Add doctest automatically to regression * Fix existing failures * DOCTEST: Fix non-uniform array * DOCTEST: Fix precision errors in example * AUTOMATION: Add test directory otherwise only doctests run * TENSOR: Fix bad rebase from numpy fix * Auto formatting (#60) * COVERAGE: Fix some coverage regressions from pylint PR * ISORT: Run isort on source and tests * BLACK: Run black on source and tests * BLACK: Run black on source and tests * FORMATTING: Add tests and verification for autoformatting * FORMATTING: Add black/isort to root to simplify * Add preliminary contributor guide instructions Closes #59 * TUCKER_ALS: TTM with negative values is broken in ttensor (#62) (#66) * Replace usage in tucker_als * Update test for tucker_als to ensure result matches expectation * Add early error handling in ttensor ttm for negative dims * Hosvd (#67) * HOSVD: Preliminary outline of core functionality * HOSVD: Fix numeric bug * Was slicing incorrectly * Update test to check convergence * HOSVD: Finish output and test coverage * TENSOR: Prune numbers real * Real and mypy don't play nice python/mypy#3186 * This allows partial typing support of HOSVD * Add test that matches TTB for MATLAB output of HOSVD (#79) This closes #78 * Bump version (#81) Closes #80 * Lint pyttb_utils and lint/type sptensor (#77) * PYTTB_UTILS: Fix and enforce pylint * PYTTB_UTILS: Pull out utility only used internally in sptensor * SPTENSOR: Fix and enforce pylint * SPTENSOR: Initial pass a typing support * SPTENSOR: Complete initial typing coverage * SPTENSOR: Fix test coverage from typing changes. * PYLINT: Update test to lint files in parallel to improve dev experience. * HOSVD: Negative signs can be permuted for equivalent decomposition (#82) * Pre commit (#83) * Setup and pyproject are redundant. Remove and resolve install issue * Try adding pre-commit hooks * Update Makefile for simplicity and add notes to contributor guide. * Make pre-commit optional opt-in * Make regression tests use simplified dependencies so we track fewer places. * Using dynamic version in pyproject.toml to reduce places where version is set. (#86) * Adding shell=True to subprocess.run() calls (#87) * Adding Nick to authors (#89) * Release prep (#90) * Fix author for PyPI. Bump to dev version. * Exclude dims (#91) * Explicit Exclude_dims: * Updated tt_dimscheck * Update all uses of tt_dimscheck and propagate interface * Add test coverage for exclude dims changes * Tucker_als: Fix workaround that motivated exclude_dims * Bump version * Spelling * Tensor generator helpers (#93) * TENONES: Add initial tenones support * TENZEROS: Add initial tenzeros support * TENDIAG: Add initial tendiag support * SPTENDIAG: Add initial sptendiag support * Link in autodocumentation for recently added code: (#98) * TTENSOR, HOSVD, TUCKER_ALS, Tensor generators * Remove warning for nvecs: (#99) * Make debug level log for now * Remove test enforcement * Rand generators (#100) * Non-functional change: * Fix numpy deprecation warning, logic should be equivalent * Tenrand initial implementation * Sptenrand initial implementation * Complete pass on ktensor docs. (#101) * Bump version * Bump version * Trying to fix coveralls * Trying coveralls github action * Fixing arrange and normalize. (#103) * Fixing arrange and normalize. * Merge main (#104) * Trying to fix coveralls * Trying coveralls github action * Rename contributor guide for github magic (#106) * Rename contributor guide for github magic * Update reference to contributor guide from README * Fixed the mean and stdev typo for cp_als (#117) * Changed cp_als() param 'tensor' to 'input_tensor' to avoid ambiguity (#118) * Changed cp_als() param 'tensor' to 'input_tensor' to avoid ambiguity * Formatted changes with isort and black. * Updated all `tensor`-named paramteres to `input_tensor`, including in docs (#120) * Tensor growth (#109) * Tensor.__setitem__: Break into methods * Non-functional change to make logic flow clearer * Tensor.__setitem__: Fix some types to resolve edge cases * Sptensor.__setitem__: Break into methods * Non-functional change to make flow clearer * Sptensor.__setitem__: Catch additional edge cases in sptensor indexing * Tensor.__setitem__: Catch subtensor additional dim growth * Tensor indexing (#116) * Tensor.__setitem__/__getitem__: Fix linear index * Before required numpy array now works on value/slice/Iterable * Tensor.__getitem__: Fix subscripts usage * Consistent with setitem now * Update usages (primarily in sptensor) * Sptensor.__setitem__/__getitem__: Fix subscripts usage * Consistent with tensor and MATLAB now * Update test usage * sptensor: Add coverage for improved indexing capability * tensor: Add coverage for improved indexing capability --------- Co-authored-by: brian-kelley <[email protected]> Co-authored-by: ntjohnson1 <[email protected]> Co-authored-by: Dunlavy <[email protected]> Co-authored-by: DeepBlockDeepak <[email protected]>
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‎.github/workflows/python-publish.yml

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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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name: Upload Python Package
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on:
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v3
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with:
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python-version: '3.x'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build package
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run: python -m build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/regression-tests.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Regression tests
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on:
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push:
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branches: [ "main" ]
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pull_request:
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branches: [ "main" ]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install coverage coveralls sphinx_rtd_theme
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pip install ".[dev]"
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- name: Check auto-formatters
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run: |
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isort --check .
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black --check .
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# - name: Lint with flake8
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# run: |
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# # stop the build if there are Python syntax errors or undefined names
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# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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# flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Run tests
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run: |
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coverage run --source pyttb -m pytest tests/
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coverage report
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- name: Upload coverage to Coveralls
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uses: coverallsapp/github-action@v2

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pycqa/isort
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rev: 5.11.5
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hooks:
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- id: isort
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name: isort (python)
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- repo: https://github.com/psf/black
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rev: 23.3.0
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hooks:
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- id: black
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language_version: python

‎CHANGELOG.md

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

‎CONTRIBUTING.md

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

‎CONTRIBUTORS.md

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

‎LICENSE

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

‎Makefile

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

‎README.md

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

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