Merge branch 'main' into DAMP

Author: NimaSarajpoor

.flake8

@@ -16,6 +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

@@ -10,18 +10,21 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8']
+        python-version: ['3.9']
     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: ${{ matrix.python-version }}
       - name: Display Python Version
         run: python -c "import sys; print(sys.version)"
         shell: bash
+      - name: Upgrade Pip
+        run: python -m pip install --upgrade pip
+        shell: bash
       - name: Generate Minimum Requirements File
-        run: sed 's/>/=/g' requirements.txt | sed 's/$/\.*/g' > requirements.min.txt
+        run: sed 's/>/=/g' requirements.txt | sed 's/$/\.*/g'  > requirements.min.txt
         shell: bash
       - name: Install Minimum Requirements
         run: python -m pip install --upgrade -r requirements.min.txt
@@ -35,10 +38,18 @@ jobs:
       - name: Run Flake8
         run: flake8 ./
         shell: bash
-      - name: Link OpenMP
+      - name: Install and Link OpenMP
         run: |
              if [ "$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
@@ -52,16 +63,19 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     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: ${{ matrix.python-version }}
       - name: Display Python Version
         run: python -c "import sys; print(sys.version)"
         shell: bash
+      - name: Upgrade Pip
+        run: python -m pip install --upgrade pip
+        shell: bash
       - name: Install STUMPY And Other Dependencies
         run: python -m pip install --editable .[ci]
         shell: bash
@@ -71,26 +85,19 @@ jobs:
       - name: Run Flake8
         run: flake8 ./
         shell: bash
-      - name: Link OpenMP
+      - name: Install OpenMP
         run: |
              if [ "$RUNNER_OS" == "macOS" ]; then
-                  # Fix libiomp5.dylib
-                  echo "Install OpenMP via Conda"
-                  conda install -c intel -y openmp
-                  echo "Checking $CONDA/lib for OpenMP"
-                  ls $CONDA/lib/libiomp5.dylib
-                  echo "Changing  @rpath for the omppool.cpython-x-darwin.so shared object to look in $CONDA/lib"
-                  ls "$(python -c 'import site; print(site.getsitepackages()[0])')"/numba/np/ufunc/omppool.*.so | xargs install_name_tool -change @rpath/libiomp5.dylib $CONDA/lib/libiomp5.dylib
-                  # Fix libomp.dylib
-                  echo "Linking OpenMP into /usr/local/lib"
+                  echo "Installing OpenMP"
+                  brew install libomp
+                  echo "Linking OpenMP"
                   brew link --force libomp
-                  echo "Checking /usr/local/lib for OpenMP"
-                  ls /usr/local/lib/libomp.dylib
-                  echo "Changing  @rpath for the omppool.cpython-x-darwin.so shared object to look in /usr/local/lib"
-                  ls "$(python -c 'import site; print(site.getsitepackages()[0])')"/numba/np/ufunc/omppool.*.so | xargs install_name_tool -change @rpath/libomp.dylib /usr/local/lib/libomp.dylib
-                  echo "Checking Numba OpenMP Access"
-                  python -c "from numba.np.ufunc import omppool" 
-             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
@@ -103,16 +110,19 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     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: ${{ matrix.python-version }}
       - name: Display Python Version
         run: python -c "import sys; print(sys.version)"
         shell: bash
+      - name: Upgrade Pip
+        run: python -m pip install --upgrade pip
+        shell: bash
       - name: Install STUMPY And Other Dependencies
         run: python -m pip install --editable .[ci]
         shell: bash
@@ -125,7 +135,15 @@ jobs:
       - name: Link OpenMP
         run: |
              if [ "$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
@@ -134,8 +152,3 @@ jobs:
       - name: Run Coverage Tests
         run: ./test.sh coverage
         shell: bash
-      - name: Check Coverage Report
-        run: coverage report -m --fail-under=100 --skip-covered --omit=setup.py,docstring.py,min.py,stumpy/cache.py
-        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
@@ -20,4 +21,4 @@ docs/_build
 .mypy_cache
 .directory
 test.py
-*.nbconvert.ipynb
+*.nbconvert.ipynb

.readthedocs.yml

@@ -1,4 +1,6 @@
 version: 2
+sphinx:
+  configuration: docs/conf.py
 formats: []
 build:
   os: ubuntu-22.04

CHANGELOG.md

@@ -1,3 +1,41 @@
+# 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

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