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CHANGELOG.md

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2020-10-19 [ 1.5.1 ]:

  • bugfixes
    • Fixed AB-join so that it now matches the published definition (previously, BA-join)
  • features
    • Added nan/inf support to FLOSS/FLUSS
  • tasks
    • Removed Pandas series in GPU tests to improve unit test speed in CI
    • Identify operating system prior to installing cuda toolkit
    • Changed left/right keywords in all unit tests to ref/comp
    • Split up unit tests and coverage testing
    • Updated displayNames in Azure Pipelines
    • test.sh now accepts unit, custom, and coverage keywords
    • Fixed typos
    • Added pattern searching (MASS) tutorial
    • Added Contribute notebook to RTD table of contents for first time contributors
    • Refactored _compute_diagonal for speed improvements
    • Replaced np.roll with slice indexing in stumpy.floss
    • Refactored and improved aampi and stumpi update performance
    • Added lxml to environment.yml
  • documentation
    • Added plt.show() to code figures in tutorials
    • Updated stumpi tutorial with egress=False

2020-08-31 [ 1.5.0 ]:

  • bugfixes
    • Fixed warning and check when time series has inappropriate dtype
    • Fixed scenarios where identical subsequences produce non-zero distances
  • features
    • For interactive data science work, matrix profile calcs are 10-15x faster
    • Added aamp with non-normalized Euclidean distance (i.e., no z-normalization)
    • Added aamped
    • Added aampi
    • Added gpu_aamp
    • Added egress for stumpi and egress is now the default behavior
    • Added a mass_absolute function for non-normalized distance calculation with FFT convolution
    • Added diagonal pre-processing function to core.py
    • Added centered-sum-of-products and Pearson correlation in place of sliding dot products
    • Added left and right matrix profile indices to scrump and converted to Pearson correlation
  • tasks
    • Removed Pandas series in GPU tests to improve unit test speed in CI
    • Updated to latest version of black for better formatting
    • Refactored redundant test section
    • Added unit test for inappropriate dtype inputs
    • Corrected absolute stumpy import to be relative import
    • Replaced ._illegal attribute with a more obvious ._T_isfinite attribute
    • Moved common diagonal functions to core.py
    • Replaced order variable with the more obvious diag name
    • Added environment.yml for easier installation of dependencies
    • Removed random print statement in code
    • Moved STUMPY thresholds to global parameters in config.py
    • Refactored left/right matrix profile indices
    • Refactored NaN checking
    • Check for Linux OS and add TBB dynamically especially for CI
  • documentation
    • Added aamp reference to README
    • Update docstrings to be less verbose for API documentation
    • Fixed some typos
    • Replaced sep="\s+" with sep="\\s+" in tutorials
    • Added notes and derivations for Pearson correlation and centered-sum-of-products
    • Renamed tutorials with underscores for consistency
    • Added all aamp-like functions to API reference
    • Replaced MS Word docs with LaTeX notebooks

2020-06-15 [ 1.4.0 ]:

  • bugfixes
    • Fixed bad chunking in compute_mean_std
  • features
    • Added parallelized scrump
    • Added NaN/inf support to scrump
    • Added prescrump (and, consequently, scrump++)
    • Added AB-join to scrump
    • Added unit test for scrump
    • Added constrained inclusion motif search for mstump/mstumped
    • Added discord support for mstump/mstumped
    • Changed sorting to pure numpy in mstump/mstumped for better performance
    • Added NaN/inf support to gpu_stump
    • Added new core.preprocess function
    • Added NaN/inf support to core.mass
    • Added core.apply_exclusion_zone for consistent exclusion zone across functions
    • Added stumpi for incrementally updating matrix profiles with streaming data
    • Added stumpi unit tests
    • Added NaN/inf support for stumpi
    • Converted floss.floss generator to class
  • tasks
    • Added Python 3.8 to Azure Pipelines for unit testing
    • Moved stomp to _stomp to prevent public usage
    • Fixed numerous typos
    • Added several np.asarray calls to input arrays
    • Split some unit tests out into separate files
    • Updated distributed teststo use context manager
    • Refactored _calculate_squared_distance
    • Added core.py to JIT-compiled unit test section
    • Remove mypy config file
    • Corrected cuda.jit signature for gpu_stump
    • Shortened time series length for faster GPU tests
    • Removed link to discourse from documentation
    • Added global variables for controlling chunking in compute_mean_std
    • Replaced name of naive_mass with naive_stamp
    • Removed redundant "caption" in RTD ToC
    • Renamed stamp.mass to private stamp._mass_PI
    • Added flake8-docstrings checking
    • Renamed utils.py to naive.py and updated corresponding function calls
    • Added stumpi and scrump to STUMPY API (RTD)
  • documentation
    • Initialized shapelet discovery tutorial (WIP)
    • Updated check_window_size docstring
    • Added gpu_stump to tutorial
    • Added scrump tutorial for Fast Approximate Matrix Profiles
    • Updated string formatting to conform to flake8
    • Added stumpi tutorial
    • Improved mstump tutorial (WIP)
    • Added additional references to original matrix profile papers

2020-03-27 [ 1.3.1 ]:

  • bugfixes
    • Fixed MSTUMP/MSTUMPED input dimensions check
    • Fixed inconsistent MSTUMP/MSTUMPED output
  • features
    • Added support for constant subsequences and added unit tests
    • Improved GPU memory consumption for self-join
    • Added ability to handle NaN and inf values in all matrix profile algorithms (except gpu_stump)
  • tasks
    • Updated performance table with new performance results, better color scheme, intuitive hardware grouping
    • Re-organized ndarray input verification steps
    • Added more unit tests and rearranged test order
    • Removed Python type hints or type annotations
    • Split failing dask unit tests into multiple test files
    • Added PR template
    • Updated Mac OS X image for Azure Pipelines
    • Replaced stddev computation with a memory efficient rolling chunked stddev
    • Modified exclusion zone to be symmetrical
    • Refactored multi-dimensional mass
    • Fixed scenarios where subsequence contains zero mean
    • Added explicit PR trigger to Azure Pipelines
    • Updated installation instructions to use conda-forge channel
    • Fixed time series chains all_c test to handle differences in Python set order
  • documentation
    • Fixed various typos
    • Refactored tutorials for clarity

2019-12-30 [ 1.3.0 ]:

  • bugfixes
    • Fixed MSTUMP/MSTUMPED input dimensions check
    • Fixed inconsistent MSTUMP/MSTUMPED output
  • features
    • Added parallel GPU-STUMP (i.e., multi-GPU support) using Python multiprocessing and file I/O
    • Added Python type hints/type annotations
  • tasks
    • Updated performance table and plots with STUMPY.2, GPU-STUMP.1, GPU-STUMP.2, GPU-STUMP.DGX1, and GPU-STUMP.DGX2 results
    • Fixed test function names
    • Added Python script for easier performance timing conversion
  • documentation
    • Added window size (m = 50) for performance calculations
    • Fixed various typos
    • Added missing and improved docstrings
    • Replaced Bokeh with Matplotlib
    • Updated GPU-STUMP example with multi-GPU support

2019-12-03 [ 1.2.4 ]:

  • features
    • Added ability to select GPU device in gpu_stump
  • tasks
    • Changed all README hyperlinks to double underscores
    • Added API links to README
    • Added STUMPY circle image (logo)
    • Suppressed pytest junit_family deprecation warning
    • Replaced python install with python -m pip install .

2019-11-26 [ 1.2.3 ]:

  • bugfixes
    • Fixed incorrect GPU output for self joins
  • features
    • Added array check for NaNs
    • Improved test script for CI
  • tasks
    • Added discourse group at stumpy.discourse.group
    • Updated formatting and added newline before logo
    • Made logo a hyperlink to Github repo
    • Added custom CSS to sphinx theme

2019-11-03 [ 1.2.2 ]:

  • bugfixes
    • Fixed Python AST utf8 file reading bug on Windows

2019-11-03 [ 1.2.1 ]:

  • bugfixes
    • Fixed driver not found function when no GPU present
    • Fixed gpu_stump docstring in RTD

2019-11-02 [ 1.2.0 ]:

  • bugfixes
    • Fixed transposed Pandas DataFrame issue #66
  • features
    • Added GPU support (NVIDIA Only)
  • tasks
    • Added CHANGELOG
    • Added GPU tests for GPU-STUMP
    • Added CPU tests (via CUDA simulator) for GPU-STUMP
    • Added additional STUMPY logos
    • Disabled bidirectional and left indices for FLOSS
    • Added STUMPY to Python 3 Statement
  • documentation
    • Added reference to semantic segmentation
    • Added gpu_stump API to RTF
    • Added gpu_stump example to README
    • Improved docstring for mstump(ed)
    • Improved time series chains tutorial
    • Added FLUSS to README
    • Added missing docstring for FLOSS
    • Added FLOSS and FLUSS to RTD API
    • Updated docstring DOIs with URLs to primary references
    • Added motif discovery to exisiting tutorial

2019-08-03 [ 1.1.0 ]:

  • bugfixes
    • Removed incorrect compatibility with Py35
    • Split Numba JIT tests tests to ensure proper Dask PyTest teardown
  • features
    • Added FLUSS and FLOSS
    • Added Pandas Series/DataFrame support
  • tasks
    • Added conda-forge support
    • Set up CI with Azure Pipelines
    • Added black and flake8 checks
    • 100% test coverage
    • Added badges
    • Added version attr
    • Added performance graph
    • Published in JOSS
    • Added STUMPY logo suite
    • Added CHANGELOG
  • documentation
    • Added RTD documentation
    • Added Tutorials
    • Added Binder support
    • Added NABDConf presentation

2019-05-12 [ 1.0.0 ]:

  • Initial release