Fixed #259 Adopt NEP 29

Author: seanlaw

.github/workflows/github-actions.yml

@@ -5,6 +5,39 @@ on:
   pull_request:
     branches: master
 jobs:
+  minimum-version-testing:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.6']
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set Up Python
+        uses: actions/setup-python@v2
+        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: pip install --upgrade -r requirements.min.txt
+        shell: bash
+      - name: Install STUMPY And Other Dependencies
+        run: pip install --editable .[ci]
+        shell: bash
+      - name: Run Black
+        run: black --check --diff ./
+        shell: bash
+      - name: Run Flake8
+        run: flake8 ./
+        shell: bash
+      - name: Run Unit Tests
+        run: ./test.sh unit
+        shell: bash
   unit-testing:
     runs-on: ${{ matrix.os }}
     strategy:

README.rst

@@ -179,6 +179,8 @@ Semantic Segmentation with `Fast Low-cost Unipotent Semantic Segmentation (FLUSS
 Dependencies
 ------------
 
+Supported Python and NumPy versions are determined according to the `NEP 29 deprecation policy <https://numpy.org/neps/nep-0029-deprecation_policy.html>`__.
+
 * `NumPy <http://www.numpy.org/>`__
 * `Numba <http://numba.pydata.org/>`__
 * `SciPy <https://www.scipy.org/>`__
@@ -313,7 +315,7 @@ Tests are written in the ``tests`` directory and processed using `PyTest <https:
 Python Version
 --------------
 
-STUMPY supports `Python 3.6+ <https://python3statement.org/>`__ and, due to the use of unicode variable names/identifiers, is not compatible with Python 2.x. Given the small dependencies, STUMPY may work on older versions of Python but this is beyond the scope of our support and we strongly recommend that you upgrade to the most recent version of Python.
+STUMPY supports `Python 3.7+ <https://python3statement.org/>`__ and, due to the use of unicode variable names/identifiers, is not compatible with Python 2.x. Given the small dependencies, STUMPY may work on older versions of Python but this is beyond the scope of our support and we strongly recommend that you upgrade to the most recent version of Python.
 
 ------------
 Getting Help

conda.sh

@@ -1,13 +1,74 @@
 #!/bin/bash
 
+install_mode="normal"
+
+# Parse first command line argument
+if [ $# -gt 0 ]; then
+    if [ $1 == "min" ]; then
+        install_mode="min"
+        echo "Installing minimum dependencies with install_mode=\"min\""
+    else
+        echo "Using default install_mode=\"normal\""
+    fi
+fi
+
+###############
+#  Functions  #
+###############
+
+generate_min_environment_yaml()
+{
+    echo "Generating \"environment.min.yml\" File"
+    numpy="$(grep -E "numpy" environment.yml)"
+    scipy="$(grep -E "scipy" environment.yml)"
+    numba="$(grep -E "numba" environment.yml)"
+    min_numpy="$(grep -E "numpy" environment.yml | sed 's/>//')"
+    min_scipy="$(grep -E "scipy" environment.yml | sed 's/>//')"
+    min_numba="$(grep -E "numba" environment.yml | sed 's/>//')"
+
+    sed "s/${numpy}/${min_numpy}/" environment.yml | sed "s/${scipy}/${min_scipy}/" | sed "s/${numba}/${min_numba}/" > environment.min.yml
+}
+
+fix_libopenblas()
+{
+    if [ ! -f $CONDA_PREFIX/lib/libopenblas.dylib ]; then
+        if [ -f $CONDA_PREFIX/lib/libopenblas.0.dylib ]; then
+            ln -s $CONDA_PREFIX/lib/libopenblas.0.dylib $CONDA_PREFIX/lib/libopenblas.dylib
+        fi
+    fi
+}
+
+clean_up()
+{
+    echo "Cleaning Up"
+    rm -rf "environment.min.yml"
+}
+
+###########
+#   Main  #
+###########
+
 conda update -y conda
 conda update -y --all
 conda install -y -c conda-forge mamba
-# conda env update --file environment.yml
-mamba env update --file environment.yml
+
+if [ $install_mode == "min" ]; then
+    generate_min_environment_yaml
+    # conda env update --file environment.min.yml
+    mamba env update --file environment.min.yml
+else
+    # conda env update --file environment.yml
+    mamba env update --file environment.yml
+fi
+
+fix_libopenblas
+
 if [[ `uname` == "Linux" && `which nvcc | wc -l` -lt "1" ]]; then
     # conda install -y -c conda-forge cudatoolkit-dev
     mamba install -y -c conda-forge cudatoolkit-dev
 fi
+
 #conda install -y -c conda-forge numpy scipy numba pandas flake8 flake8-docstrings black pytest-cov
 #conda install -y -c conda-forge dask distributed
+
+clean_up

docs/install.rst

@@ -2,6 +2,8 @@
 Installation
 ------------
 
+Supported Python and NumPy versions are determined according to the `NEP 29 deprecation policy <https://numpy.org/neps/nep-0029-deprecation_policy.html>`__.
+
 Using conda/pip
 ===============
 

environment.yml

@@ -3,9 +3,9 @@ channels:
   - defaults
 dependencies:
   - python>=3.6
-  - numpy>=1.13
-  - scipy>=1.2.1
-  - numba>=0.42.0
+  - numpy>=1.15
+  - scipy>=1.5
+  - numba>=0.48
   - pandas>=0.20.0
   - flake8>=3.7.7
   - flake8-docstrings>=1.5.0

pypi.sh

@@ -3,7 +3,16 @@
 # 1. Update version number in setup.py
 # 2. Update CHANGELOG
 # 3. Update README with new features/functions/tutorials
-# 4. Commit all above changes and push
+# 4. Determine minimum dependencies
+#    a) Find the minimum Python and NumPy version you want to support: https://numpy.org/neps/nep-0029-deprecation_policy.html#support-table
+#    b) Then find the SciPy version that has a "Python" version and "Minimum NumPy version" that is supported: https://docs.scipy.org/doc/scipy/reference/toolchain.html#numpy
+#    c) Check Numba release notes for mimumum Python and NumPy versions supported https://numba.pydata.org/numba-doc/dev/release-notes.html
+# 5. Bumpy minimum dependencies
+#    a) setup.py
+#    b) requirements.txt
+#    d) environment.yml
+#    e) recipes/meta.yaml in conda-feedstock
+# 6. Commit all above changes and push
 #
 # For conda-forge
 # 1. Fork the stumpy-feedstock: https://github.com/conda-forge/stumpy-feedstock

requirements.txt

@@ -1,3 +1,3 @@
-numpy>=1.13
-numba>=0.42.0
-scipy>=1.2.1
+numpy>=1.15
+scipy>=1.5
+numba>=0.48

setup.py

@@ -58,7 +58,7 @@ def get_extras_require():
     "maintainer_email": "[email protected]",
     "license": "BSD-3",
     "packages": ["stumpy"],
-    "install_requires": ["numpy >= 1.19", "scipy >= 1.2.1", "numba >= 0.42.0"],
+    "install_requires": ["numpy >= 1.15", "scipy >= 1.5", "numba >= 0.48"],
     "ext_modules": [],
     "cmdclass": {},
     "tests_require": ["pytest"],

stumpy/core.py

@@ -214,7 +214,13 @@ def are_arrays_equal(a, b):  # pragma: no cover
     if id(a) == id(b):
         return True
 
-    return np.array_equal(a, b, equal_nan=True)
+    # For numpy >= 1.19
+    # return np.array_equal(a, b, equal_nan=True)
+
+    if a.shape != b.shape:
+        return False
+
+    return ((a == b) | (np.isnan(a) & np.isnan(b))).all()
 
 
 def are_distances_too_small(a, threshold=10e-6):  # pragma: no cover