use temporary files first, then os.rename() #5210

Workflow file for this run

.github/workflows/python-package.yml at 80f2330

	# Workflow is based on the Astropy GitHub actions workflow, ci_workflows.yml
	name: CI

	on:
	push:
	branches:
	- '*'
	tags:
	- '*'
	pull_request:

	jobs:
	tests:
	name: Unit tests
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: true
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.9', '3.10'] # fuji+guadalupe, not ready for 3.11 yet?
	astropy-version: ['==5.0', '<6'] # fuji+guadalupe, latest
	fitsio-version: ['==1.1.6', '<2'] # fuji+guadalupe, latest
	numpy-version: ['<1.23'] # to keep asscalar, used by astropy
	env:
	DESIUTIL_VERSION: 3.4.2
	DESIMODEL_DATA: branches/test-0.18

	steps:
	- name: Checkout code
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install pytest
	python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
	python -m pip install -r requirements.txt
	python -m pip install -U 'numpy${{ matrix.numpy-version }}'
	python -m pip install -U 'astropy${{ matrix.astropy-version }}'
	python -m pip cache remove fitsio
	python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}'
	svn export https://desi.lbl.gov/svn/code/desimodel/${DESIMODEL_DATA}/data
	- name: Run the test
	run: DESIMODEL=$(pwd) pytest

	coverage:
	name: Test coverage
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: true
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.10'] # latest
	astropy-version: ['<6'] # latest
	fitsio-version: ['<2'] # latest
	numpy-version: ['<1.23'] # to keep asscalar, used by astropy
	env:
	DESIUTIL_VERSION: 3.4.2
	DESIMODEL_DATA: branches/test-0.18

	steps:
	- name: Checkout code
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install pytest pytest-cov coveralls
	python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
	python -m pip install -r requirements.txt
	python -m pip install specutils
	python -m pip install -U 'numpy${{ matrix.numpy-version }}'
	python -m pip install -U 'astropy${{ matrix.astropy-version }}'
	python -m pip cache remove fitsio
	python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}'
	svn export https://desi.lbl.gov/svn/code/desimodel/${DESIMODEL_DATA}/data
	- name: Run the test with coverage
	run: DESIMODEL=$(pwd) pytest --cov
	- name: Coveralls
	env:
	COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: coveralls

	desilite:
	name: Test minimal env
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: true
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.10']
	steps:
	- name: Checkout code
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install astropy scipy numba "numpy<2.0"
	python -m pip install pytest
	python -m pip cache remove fitsio
	python -m pip install --no-deps --force-reinstall --ignore-installed fitsio
	python -m pip install git+https://github.com/desihub/desiutil.git
	python -m pip install git+https://github.com/desihub/desitarget.git
	- name: Run just the lite env test
	run: pytest py/desispec/test/test_lite.py

	docs:
	name: Doc test
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.9']

	steps:
	- name: Checkout code
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install Python dependencies
	run: python -m pip install --upgrade pip setuptools wheel Sphinx
	# run: python -m pip install --upgrade pip wheel docutils\<0.18 Sphinx==3.1.2
	- name: Test the documentation
	run: sphinx-build -W --keep-going -b html doc doc/_build/html

	api:
	name: API doc completeness test
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.9']
	env:
	DESIUTIL_VERSION: 3.3.0

	steps:
	- name: Checkout code
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
	- name: Generate api.rst
	run: desi_api_file --api ./api.rst desispec
	- name: Compare generated api.rst to checked-in version
	run: diff --ignore-space-change --ignore-blank-lines ./api.rst ./doc/api.rst

	style:
	name: Style check
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.9']

	steps:
	- name: Checkout code
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install Python dependencies
	run: python -m pip install --upgrade pip setuptools wheel pycodestyle
	- name: Test the style; failures are allowed
	# This is equivalent to an allowed falure.
	continue-on-error: true
	run: pycodestyle --count py/desispec


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use temporary files first, then os.rename() #5210

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