Merge branch 'stumpy-dev:main' into Tutorial_VALMOD

Author: Nima Sarajpoor

.flake8

@@ -16,5 +16,6 @@ exclude =
     setup.py
 per-file-ignores =
     stumpy/__init__.py:D104
-    stumpy/stumpi.py:E743
+    build/lib/stumpy/__init__.py:D104
     tests/*:D101,D102,D103
+    stumpy/cache.py:D414

.fossa.yml

@@ -5,7 +5,7 @@ version: 2
 cli:
   server: https://app.fossa.com
   fetcher: custom
-  project: https://github.com/TDAmeritrade/stumpy
+  project: https://github.com/stumpy-dev/stumpy
 analyze:
   modules:
   - name: .

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @seanlaw

.github/workflows/github-actions.yml

@@ -4,64 +4,51 @@ on:
     branches: main
   pull_request:
     branches: main
+  workflow_dispatch:
+  schedule:
+    - cron: '0 14 * * *'  # 2pm UTC == 9am EST
 jobs:
-  minimum-version-testing:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7']
+  generate_python_matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      python_versions: ${{ steps.set-matrix.outputs.python_versions }}
+      min_python_version: ${{ steps.set-matrix.outputs.min_python_version }}
     steps:
-      - uses: actions/checkout@v3
-      - name: Set Up Python
-        uses: actions/setup-python@v4
+      - name: Checkout STUMPY
+        uses: actions/checkout@v4
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Display Python Version
-        run: python -c "import sys; print(sys.version)"
-        shell: bash
-      - name: Generate Minimum Requirements File
-        run: sed 's/>/=/g' requirements.txt | sed 's/$/\.*/g' > requirements.min.txt
-        shell: bash
-      - name: Install Minimum Requirements
-        run: python -m pip install --upgrade -r requirements.min.txt
-        shell: bash
-      - name: Install STUMPY And Other Dependencies
-        run: python -m pip install --editable .[ci]
-        shell: bash
-      - name: Run Black
-        run: black --check --diff ./
-        shell: bash
-      - name: Run Flake8
-        run: flake8 ./
-        shell: bash
-      - name: Link OpenMP
+          repository: stumpy-dev/stumpy
+      - name: Upgrade Pip, Install Minimum Requirements
         run: |
-             if [ "$RUNNER_OS" == "macOS" ]; then
-                  brew link --force libomp
-             fi
+          python -m pip install --upgrade pip pandas lxml packaging
         shell: bash
-      - name: Show Full Numba Environment
-        run: python -m numba -s
-        shell: bash
-      - name: Run Unit Tests
-        run: ./test.sh unit
+      - name: Generate Python versions
+        id: set-matrix
+        run: |
+          MIN_PYTHON=$(python ./versions.py -mode min | grep python | awk '{print $2}')
+          MAX_PYTHON=$(python ./versions.py -mode max | grep python | awk '{print $2}')
+          echo "python_versions=$(python ./versions.py -mode range $MIN_PYTHON $MAX_PYTHON)" >> $GITHUB_OUTPUT
+          echo "min_python_version=\"$MIN_PYTHON\"" >> $GITHUB_OUTPUT
         shell: bash
   unit-testing:
+    needs: generate_python_matrix
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ${{ fromJSON(needs.generate_python_matrix.outputs.python_versions) }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set Up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python Version
         run: python -c "import sys; print(sys.version)"
         shell: bash
+      - name: Upgrade Pip
+        run: python -m pip install --upgrade pip
+        shell: bash
       - name: Install STUMPY And Other Dependencies
         run: python -m pip install --editable .[ci]
         shell: bash
@@ -71,11 +58,19 @@ jobs:
       - name: Run Flake8
         run: flake8 ./
         shell: bash
-      - name: Link OpenMP
+      - name: Install OpenMP
         run: |
              if [ "$RUNNER_OS" == "macOS" ]; then
+                  echo "Installing OpenMP"
+                  brew install libomp
+                  echo "Linking OpenMP"
                   brew link --force libomp
-             fi
+                  echo "Find OpenMP Linking Location"
+                  libfile=`brew list libomp --verbose | grep libomp.dylib`
+                  echo $libfile
+                  echo "Changing  @rpath for the omppool.cpython-x-darwin.so shared object to look in $libfile"
+                  ls "$(python -c 'import site; print(site.getsitepackages()[0])')"/numba/np/ufunc/omppool.*.so | xargs install_name_tool -change @rpath/libomp.dylib $libfile
+             fi        
         shell: bash
       - name: Show Full Numba Environment
         run: python -m numba -s
@@ -84,20 +79,24 @@ jobs:
         run: ./test.sh unit
         shell: bash
   coverage-testing:
+    needs: generate_python_matrix
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ${{ fromJSON(needs.generate_python_matrix.outputs.python_versions) }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set Up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python Version
         run: python -c "import sys; print(sys.version)"
         shell: bash
+      - name: Upgrade Pip
+        run: python -m pip install --upgrade pip
+        shell: bash
       - name: Install STUMPY And Other Dependencies
         run: python -m pip install --editable .[ci]
         shell: bash
@@ -110,7 +109,15 @@ jobs:
       - name: Link OpenMP
         run: |
              if [ "$RUNNER_OS" == "macOS" ]; then
+                  echo "Installing OpenMP"
+                  brew install libomp
+                  echo "Linking OpenMP"
                   brew link --force libomp
+                  echo "Find OpenMP Linking Location"
+                  libfile=`brew list libomp --verbose | grep libomp.dylib`
+                  echo $libfile
+                  echo "Changing  @rpath for the omppool.cpython-x-darwin.so shared object to look in $libfile"
+                  ls "$(python -c 'import site; print(site.getsitepackages()[0])')"/numba/np/ufunc/omppool.*.so | xargs install_name_tool -change @rpath/libomp.dylib $libfile
              fi
         shell: bash
       - name: Show Full Numba Environment
@@ -119,5 +126,3 @@ jobs:
       - name: Run Coverage Tests
         run: ./test.sh coverage
         shell: bash
-      - name: Upload Coverage Tests Results
-        uses: codecov/codecov-action@v3

.gitignore

@@ -8,7 +8,8 @@
 LOG*
 PID
 .coverage*
-coverage.xml
+coverage.json
+coverage.stumpy.json
 dask-worker-space
 stumpy.egg-info
 build
@@ -20,3 +21,4 @@ docs/_build
 .mypy_cache
 .directory
 test.py
+*.nbconvert.ipynb

.readthedocs.yml

@@ -1,5 +1,11 @@
 version: 2
-formats: all
+sphinx:
+  configuration: docs/conf.py
+formats: []
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
 python:
     install:
         - requirements: docs/requirements.txt

CHANGELOG.md

@@ -1,3 +1,154 @@
+# 2024-07-08    [ 1.13.0 ]:
+---------------------------
+* bugfixes
+  - Fixed Ostinato overwriting original time series
+* features
+  - Added Ray support
+  - Added `numpy` 2.0 support
+  - Added named attributes to matrix profile array
+  - Added Python 3.12 support
+  - Migrated setup.py, setuptools to pyproject.toml
+* tasks
+  - Added version mismatch checker
+  - Added `copy` param to `preprocess`-related functions
+  - Disabled bokeh dashboard in dask
+  - Added `numba` channel to environment.yml
+  - Replace `np.INF` with `-np.infg`
+  - Fixed inability to import packages in tutorials
+  - Added matplotlib to RTD requirements
+  - Removed unnecessary comments in code
+  - Added `tests/__pycache__` to `clean_up` process
+  - Added option to display current dev environment in `test.sh`
+  - Added keyword `test.sh` to only execute `gpu` containing tests
+  - Added "upgrade pip" to Github Actions workflow
+  - Removed Twitter and Zenodo badges, added NumFOCUS badge
+  - Added Github Discussions link
+  - Updated codecove version for Github Actions
+  - Removed `pkg_resources` as a dependency
+  - Added codeowners file
+* documentation
+  - Improved syntax highlighting
+  - Updated class docstrings
+  - Removed napoleon extension
+  - Switched to Myst
+  - Relocated notebooks/tutorials
+  - Fixed named attributes being displayed incorrectly
+  - Fixed typos
+
+
+# 2023-08-20    [ 1.12.0 ]:
+---------------------------
+* bugfixes
+  - Fixed prescrump, scrump, and scraamp miscalculation of AB-joins
+  - Fixed bug in `is False` by converting to `bool` type
+  - Fixed bug in `snippet` that caused loss in precision, add unit tests
+  - Fixed RTD incompatibility with urllib3
+  - Fixed loss of precision in distances computed for self-matches
+  - Fixed libiomp5.dylib Github Actions location
+  - Fixed incorrect post-processing in naive.mass_PI
+  - Fixed incorrect number of contiguous windows in snippets
+* features
+  - Improved matrix profile performance (15-20%) with uint64 indexing
+  - Added top-k nearest neighbor feature
+  - Added rolling_isconstant function
+  - Added `subseq_isconstant` to API for transparent handling of constant time series subsequences
+  - Added parallelized rolling_nanstd
+  - Added abstraction layer for distributed client functions (e.g., Dask, Ray, etc)
+  - Added initial support for `numba` function caching
+  - Added Python 3.11 support
+  - Added `query_idx` to improve distances computed for self-matches in `motifs` function
+  - Added `mmotifs` for multi-dimensional motif discovery
+  - Added function `process_isconstant`
+* tasks
+  - Refactored mpdist
+  - Added MERLIN notebook reproducer
+  - Added negative index checks to mmotifs
+  - Fixed mybinder badge and links
+  - Renamed nave.mass to naive.mass_PI
+  - Added `row_wise` parameter to naive.stump
+  - Added input type (list) check to ostinato
+  - Added ability to return fully filled bfs indices
+  - Updated setup.py to enable Github dependency graph tracking
+  - Improved stability of prescrimp
+  - Split coverage tests for more verbosity
+  - Added more features to custom test function
+  - Removed explicit cancellation of dask futures
+  - Removed max `dask`/`distributed` version requirement
+  - Optimized stumpi and aampi class init
+  - Improve aampi update behavior with constant sequences returning nan
+  - Added pytest notebook link checking
+  - Refactored `match` function
+  - Added warnings to motifs and aamp_motifs
+  - Added `numba -s` step in Github Actions workflow
+  - Added explicit link to OpenMP for MacOS Github Actions workflow
+  - Moved to Actions/Checkout V3 in Github Actions
+  - Improved numba function signatures
+  - Added '--editable' install mode to setup.sh
+  - Updated Github Action codecov/codecov-action@v1 to v3
+  - Maintained 100% code coverage
+  - Used unittest.mock.patch to prevent overwriting of config variables during testing
+  - Added Python 3.11 to test matrix
+  - Added ability to detect missing parameter definitions in docstrings (docstring.py)
+  - Updated pytest flags to report skips and added additional summary
+  - Replaced logging.warning with warnings.warn
+  - Improved multi-line warnings
+  - Ensured `bfs_indices` are sent to correct GPU device
+  - Refactored window size check in mass/mass_absolute functions
+  - Added animated GIF to README
+  - Updated minimum black version
+  - Removed `_parallel_rolling_func` as it conflicted with `numba` caching
+  - Removed mamba timeout
+  - Improved warnings
+  - Added missing p-norm param to idx_to_mp and floss functions
+  - Added test failure when coverage is below 100%
+  - Added boolean array test for rolling_isfinite
+  - Added isort, resolved circular dependencies, updated examples
+  - Only build HTML for RTD
+  - Added `mp` param to stumpi to allow pre-computed matrix profile as input
+  - Added various unit tests
+  - Removed codecov as dependency
+  - Added ability to test the execution of tutorial notebooks
+  - Added check for negative matrix profile indices
+  - Added `test_precision.py` for all issues related to loss-of-precision
+  - Fixed tls deprecation warning
+  - Replaced np.int with np.int64
+  - Specified fastmath flags to include nan/inf values in inputs/outputs
+  - Replaced bool dtype with np.bool_
+  - Replaced np.newaxis with np.expand_dims
+  - Added check for docstring and parameter mismatch
+  - Update URLs for minimum version references
+  - Added explicit shell declaration in Github Actions workflow
+  - Show OpenMP libraries in Github Actions workflow
+  - Added `pip.sh` script for setting up dev environment using `pip`
+  - Removed parallel=True in `core._compute_multi_PI`
+  - Updated coverage testing to include all modules
+  - Improved code consistency for `T_A` and `T_A` definitions
+  - Refactored `test.sh` and include missing test files in unit tests
+  - Added minimum dependency compatibility script (min.py)
+  - Updated minimum dependency bumping instructions
+  - Bumped minimum Python version to 3.8
+  - Update PyPI downloads badge
+* documentation
+  - Improved/updated various docstrings
+  - Added shapelet discovery tutorial
+  - Clarified unanchored chain description
+  - Fixed typos
+  - Improved `core._get_QT docstring`
+  - Fixed imbalanced tree representation in docstring
+  - Improved scrump documentation
+  - Made light mode default and remove theme switcher from header nav bar
+  - Improved dataframe layout display in tutorials
+  - Added multi-dimensional motif and match tutorial
+  = Added T_subseq_isfinite to docstring
+  - Added tutorial for "Discovering motifs under uniform scaling"
+  - Updated docs for using a dask client
+  - Fixed malformed link in floss docstring
+  - Added missing parameter section in various docstrings
+  - Added Minkowski docstring for Euclidean distance
+  - Added missing parameters for GPU functions in docstrings
+  - Improved documentation for `P` in motifs function
+
+
 # 2022-03-31    [ 1.11.1 ]:
 ---------------------------
 * bugfixes

CONTRIBUTING.md

@@ -4,15 +4,15 @@ Contributions of all kinds are welcome. In particular pull requests are apprecia
 
 ## Issues
 
-The easiest contribution to make is to [file an issue](https://github.com/TDAmeritrade/stumpy/issues/new). It is beneficial if you perform a cursory search of [existing issues](https://github.com/TDAmeritrade/stumpy/issues?q=is%3Aissue) and it is also helpful, but not necessary, if you can provide clear instruction for how to reproduce a problem. If you have resolved an issue yourself please consider contributing to this repository so others can benefit from your work.
+The easiest contribution to make is to [file an issue](https://github.com/stumpy-dev/stumpy/issues/new). It is beneficial if you perform a cursory search of [existing issues](https://github.com/stumpy-dev/stumpy/issues?q=is%3Aissue) and it is also helpful, but not necessary, if you can provide clear instruction for how to reproduce a problem. If you have resolved an issue yourself please consider contributing to this repository so others can benefit from your work.
 
 ## Documentation
 
 Contributing to documentation is the easiest way to get started. Providing simple clear or helpful documentation for new users is critical. Anything that *you* as a new user found hard to understand, or difficult to work out, are excellent places to begin. Contributions to more detailed and descriptive error messages is especially appreciated. To contribute to the documentation please 
-[fork the project](https://github.com/TDAmeritrade/stumpy/fork) into your own repository, make changes there, and then submit a pull request.
+[fork the project](https://github.com/stumpy-dev/stumpy/fork) into your own repository, make changes there, and then submit a pull request.
 
 ## Code
 
-Code contributions are always welcome, from simple bug fixes, to new features. To contribute code please [fork the project](https://github.com/TDAmeritrade/stumpy/fork) into your own repository, make changes there, run [black](https://github.com/python/black) and [flake8](http://flake8.pycqa.org/en/latest/) on your code, add tests for bugs/new features, and then submit a pull request. If you are fixing a known issue please add the issue number to the PR message. If you are fixing a new issue feel free to file an issue and then reference it in the PR. You can [browse open issues](https://github.com/TDAmeritrade/stumpy/issues), or consult the [project roadmap](https://github.com/TDAmeritrade/stumpy/issues/1), for potential code contributions. Fixes for issues tagged with 'help wanted' are especially appreciated.
+Code contributions are always welcome, from simple bug fixes, to new features. To contribute code please [fork the project](https://github.com/stumpy-dev/stumpy/fork) into your own repository, make changes there, run [black](https://github.com/python/black) and [flake8](http://flake8.pycqa.org/en/latest/) on your code, add tests for bugs/new features, and then submit a pull request. If you are fixing a known issue please add the issue number to the PR message. If you are fixing a new issue feel free to file an issue and then reference it in the PR. You can [browse open issues](https://github.com/stumpy-dev/stumpy/issues) for potential code contributions. Fixes for issues tagged with 'help wanted' are especially appreciated.
 
 

MANIFEST.in

@@ -1 +1,3 @@
 include LICENSE.txt
+prune docs
+prune notebooks