Closes #5470: fix attach_all docstring formatting (#5471) #13017

Workflow file for this run

	name: CI

	on:
	push:
	branches: [main]
	pull_request:
	merge_group:
	workflow_dispatch:


	env:
	ARKOUDA_QUICK_COMPILE: true
	ARKOUDA_SKIP_CHECK_DEPS: true

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	lint:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	- name: Check for tabs
	run: \|
	! git --no-pager grep -n $'\t' -- '*.chpl'
	- name: Run doc-example check
	run: make check-doc-examples

	chpl-lint:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	chpl-version: ['2.7.0']
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	- name: Ensure ignore file exists
	# .chplcheckignore should live at your repo root
	run: \|
	if [ ! -f .chplcheckignore ]; then
	echo "# add paths/globs to ignore, e.g. src/generated/*" > .chplcheckignore
	fi
	- name: Run chplcheck (respecting .chplcheckignore)
	run: \|
	make chplcheck

	ruff-format:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Install Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.13"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install ruff==0.11.2
	# Update output format to enable automatic inline annotations.
	- name: ruff version
	run: \|
	ruff --version
	- name: Run Ruff
	run: ruff format --check --diff

	mypy:
	runs-on: ubuntu-latest
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-2.7.0:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	- name: Install dependencies
	run: \|
	python3 -m ensurepip --default-pip
	python3 -m pip install -e .[dev]
	- name: check mypy version
	run: \|
	mypy --version
	- name: Arkouda mypy
	run: \|
	python3 -m mypy arkouda

	docstr-cov:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python
	uses: actions/setup-python@v4
	with: { python-version: '3.x' }
	- name: Install dependencies
	run: pip install docstr-coverage
	- name: Run docstring coverage
	run: \|
	mkdir -p docs
	make docstr-coverage

	flake8:
	runs-on: ubuntu-latest
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-2.7.0:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	- name: Install Dependencies
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	python3 -m ensurepip --default-pip
	python -m pip install --upgrade pip
	pip install flake8 pydoclint[flake8]==0.6.10
	- name: flake8 version
	run: \|
	python3 -m ensurepip --default-pip
	flake8 --version
	- name: Arkouda flake8
	run: \|
	flake8 --config .flake8 .

	arkouda_python_portability:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.10', '3.11', '3.12', '3.13']
	env:
	CHPL_HOME: /opt/chapel-2.7.0
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-2.7.0:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	# Check Python version
	- name: Set python version
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${{ matrix.python-version }} 1
	- name: Check python version
	run: \|
	python3 --version
	- name: Install dependencies
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	python3 -m ensurepip --default-pip
	echo "\$(eval \$(call add-path,/usr/lib/x86_64-linux-gnu/hdf5/serial/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/arrow-install/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/libiconv-install/))" >> Makefile.paths
	- name: Build/Install Arkouda
	run: \|
	make
	python3 -m pip install .[dev]
	- name: pip list
	run: \|
	python3 -m pip list
	- name: Arkouda unit tests
	run: \|
	make test-python size=100

	arkouda_makefile_almalinux:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.13']
	container:
	image: ghcr.io/bears-r-us/almalinux-with-arkouda-deps:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4

	# Install dependencies to build Python from source
	- name: Install dependencies
	run: \|
	dnf update -y
	dnf install -y zlib-devel gcc gcc-c++ make zlib-devel bzip2 bzip2-devel readline-devel sqlite sqlite-devel openssl openssl-devel libffi-devel xz-devel zlib-devel

	# TODO: why does this need to build its own Python when the container has its own?
	# almalinux's python is old, so we build from source. But can we move this into the container build?
	# Download and install Python from source (updated URL for Python 3.13)
	- name: Download Python ${matrix.python-version} source
	run: \|
	curl -O https://www.python.org/ftp/python/${{ matrix.python-version }}.0/Python-${{ matrix.python-version }}.0.tgz
	file Python-${{ matrix.python-version }}.0.tgz # Check the file type

	- name: Extract Python ${matrix.python-version} source
	run: \|
	tar -xvf Python-${{ matrix.python-version }}.0.tgz
	cd Python-${{ matrix.python-version }}.0 && ./configure --enable-optimizations && make -j$(nproc) && make altinstall && cd ..
	update-alternatives --install /usr/bin/python3 python3 /usr/local/bin/python${{ matrix.python-version }} 1

	# Install pip for Python from the get-pip.py script
	- name: Install pip for Python ${{ matrix.python-version }}
	run: \|
	curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python${{ matrix.python-version }} get-pip.py
	- name: Check python version
	run: \|
	python3 --version
	- name: Make install-arrow
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-arrow DEP_BUILD_DIR=/dep/build
	- name: Make install-zmq
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-zmq DEP_BUILD_DIR=/dep/build
	- name: Make install-iconv
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-iconv DEP_BUILD_DIR=/dep/build
	- name: Make install-idn2
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-idn2 DEP_BUILD_DIR=/dep/build
	- name: Make install-blosc
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-blosc DEP_BUILD_DIR=/dep/build
	- name: Make install-hdf5
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-hdf5 DEP_BUILD_DIR=/dep/build
	- name: Make install-pytables
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	HDF5_DIR=$(pwd)/dep/hdf5-install/ make install-pytables

	arkouda_makefile:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	chpl-version: ['2.7.0']
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	python3 -m ensurepip --default-pip
	- name: Check python version
	run: \|
	python3 --version
	- name: Make install-arrow-quick
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-arrow-quick
	- name: Make install-arrow
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	apt-get remove -y apache-arrow-apt-source
	make install-arrow DEP_BUILD_DIR=$DEP_BUILD_DIR
	- name: Make install-zmq
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-zmq DEP_BUILD_DIR=$DEP_BUILD_DIR
	- name: Make install-iconv
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-iconv DEP_BUILD_DIR=$DEP_BUILD_DIR
	- name: Make install-idn2
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-idn2 DEP_BUILD_DIR=$DEP_BUILD_DIR
	- name: Make install-blosc
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-blosc DEP_BUILD_DIR=$DEP_BUILD_DIR
	- name: Make install-hdf5
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	make install-hdf5 DEP_BUILD_DIR=$DEP_BUILD_DIR
	- name: Make install-pytables
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	HDF5_DIR=$(pwd)/dep/hdf5-install/ make install-pytables DEP_BUILD_DIR=$DEP_BUILD_DIR


	arkouda_chpl_portability:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	chpl-version: ['2.5.0','2.6.0','2.7.0']
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	- name: Check Chapel version
	run: \|
	chpl --version
	- name: Install dependencies
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	python3 -m ensurepip --default-pip
	echo "\$(eval \$(call add-path,/usr/lib/x86_64-linux-gnu/hdf5/serial/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/arrow-install/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/libiconv-install/))" >> Makefile.paths
	- name: Build/Install Arkouda
	run: \|
	make
	python3 -m pip install .[dev]
	- name: Arkouda unit tests
	run: \|
	make test-python size=100

	arkouda_multi-dim:
	runs-on: ubuntu-latest
	env:
	ARKOUDA_CONFIG_FILE: .configs/MultiDimTestServerModules.cfg
	strategy:
	matrix:
	chpl-version: ['2.7.0']
	max-parallel: 3
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Show memory available
	run: \|
	echo "Memory info:"
	free -h
	echo "CPU info:"
	nproc
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	- name: Check Chapel version
	run: \|
	chpl --version
	- name: Install dependencies
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	apt-get update && apt-get install -y time
	python3 -m ensurepip --default-pip
	echo "\$(eval \$(call add-path,/usr/lib/x86_64-linux-gnu/hdf5/serial/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/arrow-install/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/libiconv-install/))" >> Makefile.paths
	- name: Build Arkouda
	run: \|
	/usr/bin/time -v make ARRAY_ND_MAX=3
	- name: Install Arkouda
	run: \|
	python3 -m pip install .[dev]
	- name: Arkouda unit tests
	run: \|
	make test-python size=100


	# arkouda_multi-dim_test_coverage:
	# runs-on: ubuntu-latest
	# strategy:
	# matrix:
	# chpl-version: ['2.7.0']
	# max-parallel: 3
	# container:
	# image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
	# credentials:
	# username: ${{ github.actor }}
	# password: ${{ secrets.github_token }}
	# steps:
	# - name: Show memory available
	# run: \|
	# echo "Memory info:"
	# free -h
	# echo "CPU info:"
	# nproc
	# - name: Checkout Repository
	# uses: actions/checkout@v4
	# - name: Set Python version to 3.13
	# run: \|
	# update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	# - name: Check Chapel version
	# run: \|
	# chpl --version
	# - name: Install dependencies
	# uses: nick-fields/retry@v2
	# with:
	# timeout_seconds: 1200 # or use timeout_minutes
	# max_attempts: 2
	# retry_wait_seconds: 60
	# retry_on: error
	# command: \|
	# apt-get update && apt-get install -y time
	# python3 -m ensurepip --default-pip
	# echo "\$(eval \$(call add-path,/usr/lib/x86_64-linux-gnu/hdf5/serial/))" >> Makefile.paths
	# echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/arrow-install/))" >> Makefile.paths
	# echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/libiconv-install/))" >> Makefile.paths
	# - name: Use MultiDim Configs
	# run: \|
	# cp .configs/registration-config-multi-dim.json registration-config.json
	# bash scripts/trim_server_modules.sh
	# - name: Build arkouda_server
	# shell: bash
	# run: \|
	# set -euxo pipefail
	# /usr/bin/time -v make
	# echo "$PWD" >> "$GITHUB_PATH"
	# echo "$PWD"
	# - name: Install Arkouda
	# run: \|
	# python3 -m pip install .[dev]
	# - name: Run tests with coverage (fail if below threshold)
	# run: \|
	# make coverage size=10
	# - name: Sanity check coverage.xml
	# if: always()
	# run: \|
	# pwd
	# ls -l
	# [ -f coverage.xml ] && echo "coverage.xml present" \|\| (echo "coverage.xml MISSING"; exit 1)
	# head -n 20 coverage.xml \|\| true
	# - name: Upload coverage artifacts
	# if: always()
	# uses: actions/upload-artifact@v4
	# with:
	# name: coverage-artifacts
	# path: \|
	# coverage.xml
	# .coverage
	# .pytest/report.html
	# if-no-files-found: warn
	# - name: Upload to Codecov
	# uses: codecov/codecov-action@v4
	# with:
	# token: ${{ secrets.CODECOV_TOKEN }} # not needed for public repos
	# files: coverage.xml
	# flags: python-coverage
	# fail_ci_if_error: true


	arkouda_tests_linux:
	runs-on: ubuntu-latest
	env:
	CHPL_RT_NUM_THREADS_PER_LOCALE: 2
	strategy:
	matrix:
	chpl-version: ['2.7.0']
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	- name: Check Chapel version
	run: \|
	chpl --version
	- name: Install dependencies
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	python3 -m ensurepip --default-pip
	python3 -m pip install pytest-benchmark>=4.0.0 py
	echo "\$(eval \$(call add-path,/usr/lib/x86_64-linux-gnu/hdf5/serial/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/arrow-install/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/libiconv-install/))" >> Makefile.paths
	- name: Build/Install Arkouda
	run: \|
	make
	python3 -m pip install .[dev]
	- name: Arkouda make check
	run: \|
	make check
	- name: Arkouda unit tests
	env:
	ARKOUDA_PYTEST_OPTIONS: "--durations=0 --durations-min=5.0"
	run: \|
	make test-python size=100
	- name: Arkouda benchmark --correctness-only
	run: \|
	ARKOUDA_HOME=$(pwd) ./benchmarks/run_benchmarks.py --correctness-only
	ARKOUDA_HOME=$(pwd) ./benchmarks/run_benchmarks.py --size=100 --gen-graphs

	arkouda_benchmark_linux:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	chpl-version: ['2.7.0']
	container:
	image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
	credentials:
	username: ${{ github.actor }}
	password: ${{ secrets.github_token }}
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v4
	- name: Set Python version to 3.13
	run: \|
	update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
	- name: Check Chapel version
	run: \|
	chpl --version
	- name: Install dependencies
	uses: nick-fields/retry@v2
	with:
	timeout_seconds: 1200 # or use timeout_minutes
	max_attempts: 2
	retry_wait_seconds: 60
	retry_on: error
	command: \|
	python3 -m ensurepip --default-pip
	python3 -m pip install pytest-benchmark>=4.0.0 py
	echo "\$(eval \$(call add-path,/usr/lib/x86_64-linux-gnu/hdf5/serial/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/arrow-install/))" >> Makefile.paths
	echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/libiconv-install/))" >> Makefile.paths
	- name: Build/Install Arkouda
	run: \|
	make
	python3 -m pip install .[dev]
	- name: Arkouda benchmark
	run: \|
	make benchmark size_bm=10
	- name: Arkouda benchmark -- Numpy
	run: \|
	python3 -m pytest -c benchmark.ini --size=10 --numpy

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Closes #5470: fix attach_all docstring formatting (#5471) #13017

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Closes #5470: fix attach_all docstring formatting (#5471) #13017

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