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MNT: Revert to code from v1.3.2
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‎.github/workflows/pythonpackage.yml

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@@ -8,68 +8,36 @@ jobs:
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strategy:
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max-parallel: 12
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matrix:
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python-version: [3.7, 3.8, 3.9]
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os: [ubuntu-latest, macOS-latest, windows-latest]
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python-version: [2.7, 3.5, 3.6, 3.7, 3.8]
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os: [ubuntu-latest, macOS-latest]
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exclude:
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- os: macOS-latest
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python-version: 3.8
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/cache@v1
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if: startsWith(runner.os, 'Linux')
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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${{ runner.os }}-py${{ matrix.python-version }}-pip-
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- uses: actions/cache@v1
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if: startsWith(runner.os, 'macOS')
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with:
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path: ~/Library/Caches/pip
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key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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${{ runner.os }}-py${{ matrix.python-version }}-pip-
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- uses: actions/cache@v1
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if: startsWith(runner.os, 'Windows')
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with:
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path: ~\AppData\Local\pip\Cache
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key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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${{ runner.os }}-py${{ matrix.python-version }}-pip-
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- name: Install style dependencies
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if: matrix.python-version == 3.9
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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 flake8 isort>=5 black>=20.8b1
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pip install numpy pytest flake8
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- name: Build
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run: |
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python setup.py build_ext --inplace
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pip install .[test]
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- name: Lint with flake8
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if: matrix.python-version == 3.9
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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 --statistics
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- name: Check import sorting with isort
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if: matrix.python-version == 3.9
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run: |
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isort -c --df .
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- name: Check formatting with black
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if: matrix.python-version == 3.9
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if: matrix.python-version >= 3.6
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run: |
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pip install black
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black . --check --exclude "(build/|dist/|\.git/|\.mypy_cache/|\.tox/|\.venv/\.asv/|env|\.eggs)"
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- name: Check formatting with clang-format
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if: (matrix.python-version == 3.9) && (startsWith(runner.os, 'Linux'))
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run: |
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clang-format -i --style=file bottleneck/**/*.c bottleneck/**/*.h
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git diff --exit-code
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- name: Test with pytest
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run: |
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pytest

‎.gitignore

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@@ -8,10 +8,4 @@ MANIFEST
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*.egg-info
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.*.swp
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*~
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\#*#
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.eggs
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.hypothesis
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.mypy_cache
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**/env
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**/*results
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**/html
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\#*#

‎.travis.yml

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@@ -1,28 +1,102 @@
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os: linux
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language: generic
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cache:
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directories:
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- $HOME/.cache/pip
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- .hypothesis
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sudo: false
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cache: pip
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git:
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depth: false
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jobs:
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matrix:
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fast_finish: true
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include:
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# test installing bottleneck tarball before installing numpy;
14+
# start this test first because it takes the longest
15+
- os: linux
16+
env: TEST_DEPS="numpy pytest"
17+
PYTHON_VERSION="2.7"
18+
PYTHON_ARCH="64"
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TEST_RUN="sdist"
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# flake8 and black
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- os: linux
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env: TEST_DEPS="flake8 black"
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PYTHON_VERSION="3.7"
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PYTHON_ARCH="64"
26+
TEST_RUN="style"
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# doc check
29+
- os: linux
30+
env: TEST_DEPS="sphinx numpydoc gitpython"
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PYTHON_VERSION="3.7"
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PYTHON_ARCH="64"
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TEST_RUN="doc"
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# python 3.5
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- os: linux
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env: TEST_DEPS="pytest"
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PIP_DEPS="numpy>=1.16"
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PYTHON_VERSION="3.5"
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PYTHON_ARCH="64"
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TEST_RUN="sdist"
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# python 3.6
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- os: linux
15-
arch: arm64
16-
env: TEST_DEPS="numpy"
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env: TEST_DEPS="numpy pytest"
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PYTHON_VERSION="3.6"
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PYTHON_ARCH="64"
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# python 3.7
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- os: linux
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env: TEST_DEPS="numpy pytest"
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PYTHON_VERSION="3.7"
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PYTHON_ARCH="64"
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# python 3.8 conda numpy
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- os: linux
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env: TEST_DEPS="numpy pytest"
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PYTHON_VERSION="3.8"
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PYTHON_ARCH="64"
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# python 3.8 conda numpy + sdist
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- os: linux
21-
arch: ppc64le
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env: TEST_DEPS="numpy gfortran_linux-ppc64le=8.2.0"
63+
env: TEST_DEPS="numpy pytest"
64+
PYTHON_VERSION="3.8"
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PYTHON_ARCH="64"
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TEST_RUN="sdist"
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68+
# python 2.7
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- os: osx
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env: TEST_DEPS="numpy pytest"
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PYTHON_VERSION="2.7"
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PYTHON_ARCH="64"
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TEST_RUN="sdist"
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# python 3.5
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- os: osx
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env: TEST_DEPS="pytest"
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PIP_DEPS="numpy>=1.16"
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PYTHON_VERSION="3.5"
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PYTHON_ARCH="64"
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# python 3.6
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- os: osx
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env: TEST_DEPS="numpy pytest"
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PYTHON_VERSION="3.6"
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PYTHON_ARCH="64"
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# python 3.7
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- os: osx
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env: TEST_DEPS="numpy pytest"
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PYTHON_VERSION="3.7"
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PYTHON_ARCH="64"
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94+
# python 3.8
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- os: osx
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env: TEST_DEPS="numpy pytest"
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PYTHON_VERSION="3.8"
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PYTHON_ARCH="64"
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26100
before_install:
27101
- uname -a
28102
- source "tools/travis/conda_setup.sh"
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31105
- source "tools/travis/conda_install.sh"
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33107
script:
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- ./tools/travis/bn_setup.sh
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- source "tools/travis/bn_setup.sh"
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notifications:
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email:

‎MANIFEST.in

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@@ -16,8 +16,6 @@ recursive-include doc *
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recursive-exclude doc/build *
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include versioneer.py
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include bottleneck/_version.py
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include bottleneck/tests/data/template_test/truth.c
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include bottleneck/tests/data/template_test/test_template.c
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global-exclude __pycache__
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global-exclude *.pyc

‎Makefile

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@@ -7,22 +7,19 @@ srcdir := bottleneck
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help:
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@echo "Available tasks:"
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@echo "help --> This help page"
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@echo "all --> clean, flake8, isort, black, build, test"
10+
@echo "all --> clean, build, flake8, test"
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@echo "build --> Build the Python C extensions"
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@echo "clean --> Remove all the build files for a fresh start"
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@echo "test --> Run unit tests"
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@echo "flake8 --> Check for pep8 errors"
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@echo "isort --> Run isort to format imports"
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@echo "black --> Run black formatting tool"
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@echo "clang-format --> Run clang-format tool"
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@echo "readme --> Update benchmark results in README.rst"
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@echo "bench --> Run performance benchmark"
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@echo "detail --> Detailed benchmarks for all functions"
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@echo "sdist --> Make source distribution"
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@echo "doc --> Build Sphinx manual"
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@echo "pypi --> Upload to pypi"
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all: clean flake8 isort black build test
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all: clean build test flake8
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build:
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${PYTHON} setup.py build_ext --inplace
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flake8:
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flake8
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isort:
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isort -rc .
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black:
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black . --exclude "(build/|dist/|\.git/|\.mypy_cache/|\.tox/|\.venv/\.asv/|env|\.eggs)"
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clang-format:
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clang-format --style=file -i bottleneck/**/*.c bottleneck/**/*.h
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readme:
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PYTHONPATH=`pwd`:PYTHONPATH ${PYTHON} tools/update_readme.py
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‎README.rst

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Bottleneck
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==========
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Bottleneck is a collection of fast, NaN-aware NumPy array functions
11-
written in C.
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As one example, to check if a ``np.array`` has any NaNs using numpy,
14-
one must call ``np.any(np.isnan(array))``. The :meth:`bottleneck.anynan`
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function interleaves the :meth:`np.isnan` check with :meth:`np.any`
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pre-exit, enabling up to an ``O(N)`` speedup relative to numpy.
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Bottleneck strives to be a drop-in accelerator for NumPy functions.
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When using the following libraries, Bottleneck support is automatically
20-
enabled and utilized:
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- `pandas <https://pandas.pydata.org/pandas-docs/stable/install.html#recommended-dependencies>`_
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- `xarray <http://xarray.pydata.org/en/stable/installing.html#instructions>`_
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- `astropy <https://docs.astropy.org/en/stable/install.html>`_
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Details on the performance benefits can be found in :ref:`benchmarking`
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Example
29-
=======
10+
Bottleneck is a collection of fast NumPy array functions written in C.
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3112
Let's give it a try. Create a NumPy array::
3213

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4425
>>> bn.move_mean(a, window=2, min_count=1)
4526
array([ 1. , 1.5, 2. , 4. , 4.5])
4627

47-
.. _benchmarking:
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Benchmark
5029
=========
5130

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123102
Requirements:
124103

125104
======================== ====================================================
126-
Bottleneck Python 3.6, 3.7, 3.8; NumPy 1.15.0+ (follows NEP 29)
105+
Bottleneck Python 2.7, 3.5, 3.6, 3.7, 3.8; NumPy 1.16.0+
127106
Compile gcc, clang, MinGW or MSVC
128-
Unit tests pytest, hypothesis
107+
Unit tests pytest
129108
Documentation sphinx, numpydoc
130109
======================== ====================================================
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132-
Detailed installation instructions can be found at :ref:`installing`
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134111
To install Bottleneck on Linux, Mac OS X, et al.::
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136113
$ pip install .
@@ -146,15 +123,6 @@ http://www.lfd.uci.edu/~gohlke/pythonlibs/#bottleneck
146123
Unit tests
147124
==========
148125

149-
To keep the install dependencies light, test dependencies are made available
150-
via a setuptools "extra":
151-
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$ pip install bottleneck[test]
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154-
Or, if working locally:
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$ pip install .[test]
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158126
After you have installed Bottleneck, run the suite of unit tests::
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160128
In [1]: import bottleneck as bn
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166134
rootdir: /home/chris/code/bottleneck, inifile: setup.cfg
167135
plugins: openfiles-0.3.2, remotedata-0.3.2, doctestplus-0.3.0, mock-1.10.4, forked-1.0.2, cov-2.7.1, hypothesis-4.32.2, xdist-1.26.1, arraydiff-0.3
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collected 190 items
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bottleneck/tests/input_modification_test.py ........................... [ 14%]
171139
.. [ 15%]
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bottleneck/tests/list_input_test.py ............................. [ 30%]
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bottleneck/tests/reduce_test.py ....................................... [ 84%]
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............ [ 90%]
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bottleneck/tests/scalar_input_test.py .................. [100%]
179-
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180148
========================= 190 passed in 46.42 seconds =========================
181149
Out[2]: True
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