Update configparser SafeConfigParser and readfp, new in python 3.12 #1

Workflow file for this run

	name: Docs
	on: [push, release]

	jobs:
	fast_notebooks:
	name: "Build the fast notebooks"
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.9
	- name: install latex
	uses: xu-cheng/texlive-action/small@v1

	- name: Init Environment
	shell: bash -l {0}
	run: \|
	set -e
	# brew update
	# brew install --cask basictex

	pip install -U cython
	pip install -U numpy scipy matplotlib
	pip install -U jupytext jupyterthemes jupyter_latex_envs
	pip install -U astropy
	pip install emcee ultranest


	pip install zeus-mcmc
	#pip install git+https://github.com/desihub/speclite.git
	pip install --upgrade speclite
	pip install "black<24"
	pip install astromodels


	- name: Install the package
	shell: bash -l {0}
	run: \|
	if [[ "${ISDEV}" == "true" ]]; then
	pip install --upgrade --pre astromodels
	#pip install git+https://github.com/threeML/astromodels.git@dev
	else
	pip install --upgrade astromodels
	fi
	pip install -e .
	env:
	ISDEV: ${{contains(github.ref, 'dev') \|\| contains(github.base_ref, 'dev')}}

	- name: Execute the notebooks
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# copy the doc configuration over
	mkdir -p ~/.config/threeML
	cp threeML/data/doc_config.yml ~/.config/threeML/

	jupytext --to ipynb --pipe black --execute docs/md_docs/fast_execute/*.md

	mv docs/md_docs/fast_execute/*.ipynb docs/notebooks/

	ls docs/notebooks

	env:
	OMP_NUM_THREADS: 1
	MKL_NUM_THREADS: 1
	NUMEXPR_NUM_THREADS: 1
	MPLBACKEND: "Agg"

	- uses: actions/upload-artifact@v4
	with:
	name: notebooks-for-fast-${{ github.sha }}
	path: docs/notebooks


	hal_notebooks:
	name: "Build the HAL notebooks"
	runs-on: macos-12
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if etc/example-environment.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: conda-hal_notebooks-python-3.9-${{ hashFiles('ci/environment_hal.yml') }}

	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	auto-activate-base: false
	#mamba-version: "*"
	activate-environment: test_env
	python-version: 3.9
	channels: conda-forge, threeml, defaults
	environment-file: ci/environment_hal.yml
	use-only-tar-bz2: true

	- name: Init Environment
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e

	# miniconda_os=Linux
	# compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"

	miniconda_os=MacOSX
	compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"

	brew update
	brew install --cask basictex

	eval "$(/usr/libexec/path_helper)"
	#sudo apt-get install texlive

	conda install ${compilers} jupytext jupyterthemes jupyter_latex_envs emcee pymultinest ultranest

	- name: Install the package
	shell: bash -l {0}
	run: \|
	pip install "black<24"
	pip install --upgrade speclite
	pip install git+https://github.com/threeml/hawc_hal.git
	if [[ "${ISDEV}" == "true" ]]; then
	pip install --upgrade --pre astromodels
	#pip install git+https://github.com/threeML/astromodels.git@dev
	else
	pip install --upgrade astromodels
	fi
	pip install -e .
	env:
	ISDEV: ${{contains(github.ref, 'dev') \|\| contains(github.base_ref, 'dev')}}
	- name: Execute the notebooks
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# copy the doc configuration over
	mkdir -p ~/.config/threeML
	cp threeML/data/doc_config.yml ~/.config/threeML/

	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/hal_example.md
	mv docs/md_docs/slow_execute/hal_example.ipynb docs/notebooks/
	ls docs/notebooks
	env:
	OMP_NUM_THREADS: 1
	MKL_NUM_THREADS: 1
	NUMEXPR_NUM_THREADS: 1
	MPLBACKEND: "Agg"

	- uses: actions/upload-artifact@v4
	with:
	name: notebooks-for-hal-${{ github.sha }}
	path: docs/notebooks

	fermi_notebooks:
	name: "Build the Fermi notebooks"
	runs-on: macos-12
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if etc/example-environment.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: conda-fermi_notebooks-python-3.7-${{ hashFiles('ci/environment_fermi.yml') }}

	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	auto-activate-base: false
	#mamba-version: "*"
	activate-environment: test_env
	python-version: 3.9
	channels: conda-forge, fermi, threeml, defaults
	environment-file: ci/environment_fermi.yml
	use-only-tar-bz2: true

	- name: Init Environment
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# miniconda_os=Linux
	# compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"

	miniconda_os=MacOSX
	compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"

	brew update
	brew install --cask basictex

	eval "$(/usr/libexec/path_helper)"
	#sudo apt-get install texlive

	conda install ${compilers} jupytext jupyterthemes jupyter_latex_envs emcee pymultinest ultranest

	- name: Install the package
	shell: bash -l {0}
	run: \|
	pip install "black<24" fermipy
	pip install --upgrade speclite

	if [[ "${ISDEV}" == "true" ]]; then
	pip install --upgrade --pre astromodels
	#pip install git+https://github.com/threeML/astromodels.git@dev
	else
	pip install --upgrade astromodels
	fi
	pip install -e .
	env:
	ISDEV: ${{contains(github.ref, 'dev') \|\| contains(github.base_ref, 'dev')}}

	- name: Execute the notebooks
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# copy the doc configuration over
	mkdir -p ~/.config/threeML
	cp threeML/data/doc_config.yml ~/.config/threeML/


	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/Fermipy_LAT.md

	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/LAT_Transient_Builder_Example.md

	#jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/optimizer_docs.md

	mv docs/md_docs/slow_execute/*.ipynb docs/notebooks/
	ls docs/notebooks

	env:
	OMP_NUM_THREADS: 1
	MKL_NUM_THREADS: 1
	NUMEXPR_NUM_THREADS: 1
	MPLBACKEND: "Agg"

	- uses: actions/upload-artifact@v4
	with:
	name: notebooks-for-fermi-${{ github.sha }}
	path: docs/notebooks

	xspec_notebooks:
	name: "Build the XSPEC notebooks"
	runs-on: macos-12
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if etc/example-environment.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: conda-xspec_notebooks-python-3.9-${{ hashFiles('ci/environment_xspec.yml') }}

	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	auto-activate-base: false
	miniforge-variant: Mambaforge
	activate-environment: test_env
	python-version: 3.9
	channels: threeml, conda-forge, xspecmodels, defaults
	environment-file: ci/environment_xspec.yml
	use-only-tar-bz2: true

	- name: Init Environment
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# miniconda_os=Linux
	# compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"

	miniconda_os=MacOSX
	compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"

	brew update
	brew install --cask basictex

	eval "$(/usr/libexec/path_helper)"
	#sudo apt-get install texlive

	mamba install ${compilers} jupytext jupyterthemes jupyter_latex_envs emcee pymultinest ultranest

	- name: Install the package
	shell: bash -l {0}
	run: \|
	pip install zeus_mcmc dynesty "black<24"
	pip install --upgrade speclite
	#pip install git+https://github.com/desihub/speclite.git
	if [[ "${ISDEV}" == "true" ]]; then
	pip install --upgrade --pre astromodels
	#pip install git+https://github.com/threeML/astromodels.git@dev
	else
	pip install --upgrade astromodels
	fi
	pip install -e .
	env:
	ISDEV: ${{contains(github.ref, 'dev') \|\| contains(github.base_ref, 'dev')}}
	- name: Execute the notebooks
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# copy the doc configuration over
	mkdir -p ~/.config/threeML
	cp threeML/data/doc_config.yml ~/.config/threeML/

	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/xspec_models.md
	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/joint_fitting_xrt_and_gbm_xspec_models.md
	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/Photometry_demo.md

	mv docs/md_docs/slow_execute/*.ipynb docs/notebooks/
	ls docs/notebooks

	env:
	OMP_NUM_THREADS: 1
	MKL_NUM_THREADS: 1
	NUMEXPR_NUM_THREADS: 1
	MPLBACKEND: "Agg"

	- uses: actions/upload-artifact@v4
	with:
	name: notebooks-for-xspec-${{ github.sha }}
	path: docs/notebooks

	multinest_notebooks:
	name: "Build the multinest notebooks"
	runs-on: macos-12
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if etc/example-environment.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: conda-hal_notebooks-python-3.7-${{ hashFiles('ci/environment_hal.yml') }}

	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	auto-activate-base: false
	#mamba-version: "*"
	activate-environment: test_env
	python-version: ${{ matrix.python-version }}
	channels: conda-forge, threeml, defaults
	environment-file: ci/environment_hal.yml
	use-only-tar-bz2: true

	- name: Init Environment
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# miniconda_os=Linux
	# compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"

	miniconda_os=MacOSX
	compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"

	brew update
	brew install --cask basictex

	eval "$(/usr/libexec/path_helper)"
	#sudo apt-get install texlive

	conda install ${compilers} jupytext jupyterthemes jupyter_latex_envs emcee ultranest

	- name: Install the package
	shell: bash -l {0}
	run: \|
	pip install zeus_mcmc dynesty "black<24"
	pip install --upgrade speclite
	#pip install git+https://github.com/desihub/speclite.git
	#pip install --no-binary :all: root_numpy

	if [[ "${ISDEV}" == "true" ]]; then
	pip install --upgrade --pre astromodels
	#pip install git+https://github.com/threeML/astromodels.git@dev
	else
	pip install --upgrade astromodels
	fi
	pip install -e .
	env:
	ISDEV: ${{contains(github.ref, 'dev') \|\| contains(github.base_ref, 'dev')}}

	- name: Execute the notebooks
	shell: bash -l {0}
	run: \|
	# Make sure we fail in case of error
	set -e
	# copy the doc configuration over
	mkdir -p ~/.config/threeML
	cp threeML/data/doc_config.yml ~/.config/threeML/

	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/Bayesian_tutorial.md

	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/sampler_docs.md

	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/Minimization_tutorial.md
	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/grb080916C.md

	jupytext --to ipynb --pipe black --execute docs/md_docs/slow_execute/joint_BAT_gbm_demo.md


	mv docs/md_docs/slow_execute/*.ipynb docs/notebooks/
	ls docs/notebooks


	env:
	OMP_NUM_THREADS: 1
	MKL_NUM_THREADS: 1
	NUMEXPR_NUM_THREADS: 1
	MPLBACKEND: "Agg"

	- uses: actions/upload-artifact@v4
	with:
	name: notebooks-for-multinest-${{ github.sha }}
	path: docs/notebooks



	upload_notebooks:
	needs: [fast_notebooks, fermi_notebooks, hal_notebooks, xspec_notebooks, multinest_notebooks]
	name: "Upload notebooks and trigger RTD"
	runs-on: macos-12

	steps:
	- name: Checkout
	uses: actions/checkout@v4


	- uses: actions/download-artifact@master
	with:
	name: notebooks-for-fermi-${{ github.sha }}
	path: docs/notebooks

	- uses: actions/download-artifact@master
	with:
	name: notebooks-for-fast-${{ github.sha }}
	path: docs/notebooks

	- uses: actions/download-artifact@master
	with:
	name: notebooks-for-hal-${{ github.sha }}
	path: docs/notebooks

	- uses: actions/download-artifact@master
	with:
	name: notebooks-for-xspec-${{ github.sha }}
	path: docs/notebooks

	- uses: actions/download-artifact@master
	with:
	name: notebooks-for-multinest-${{ github.sha }}
	path: docs/notebooks

	- name: Check that all notebooks are there
	shell: bash -l {0}
	run: \|

	ls docs/notebooks

	- uses: actions/upload-artifact@v4
	with:
	name: notebooks-for-${{ github.sha }}
	path: docs/notebooks

	- name: Sleep for 10 min
	uses: juliangruber/sleep-action@v1
	with:
	time: 10m

	- name: Trigger RTDs build
	uses: dfm/rtds-action@main
	with:
	webhook_url: ${{ secrets.RTDS_WEBHOOK_URL }}
	webhook_token: ${{ secrets.RTDS_WEBHOOK_TOKEN }}
	commit_ref: ${{ github.ref }}


	api_doc:
	name: "Create the API stubs"
	runs-on: macos-12
	steps:
	- uses: actions/checkout@v4
	with:
	persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
	fetch-depth: 0 # otherwise, you will failed to push refs to dest repo

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.9

	- name: Build the API doc
	run: \|

	brew install c-blosc
	brew install hdf5

	pip3 install cython tempita
	pip3 install cython blosc2 h5py
	pip3 install numpy scipy numba astropy pandas
	pip3 install wheel pkgconfig numexpr

	#python setup.py develop
	pip3 install -e .

	brew install sphinx-doc pandoc

	pip3 install mock recommonmark
	pip3 install sphinx-rtd-dark-mode
	pip3 install -U sphinx


	sphinx-apidoc -f -o docs/api/ threeML


	- uses: actions/upload-artifact@v4
	with:
	name: api-stubs-for-${{ github.sha }}
	path: docs/api




	build_docs:
	name: "Build the Documentation"
	runs-on: macos-12
	needs: [upload_notebooks, api_doc]
	steps:


	- uses: actions/checkout@v4
	with:
	persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
	fetch-depth: 0 # otherwise, you will failed to push refs to dest repo

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.9

	- name: Install package
	run: \|

	brew install c-blosc
	brew install hdf5

	pip3 install wheel pkgconfig
	pip3 install tempita
	pip3 install cython blosc2 h5py
	pip3 install numpy scipy numba astropy

	brew install sphinx-doc pandoc

	pip3 install mock recommonmark
	pip3 install sphinx-rtd-dark-mode sphinx-math-dollar
	pip3 install -U sphinx
	pip3 install -r docs/requirements.txt

	if [[ "${ISDEV}" == "true" ]]; then
	pip install --upgrade --pre astromodels
	#pip install git+https://github.com/threeML/astromodels.git@dev
	else
	pip install --upgrade astromodels
	fi
	pip install -e .

	rm -rf docs/md_docs/*
	env:
	ISDEV: ${{contains(github.ref, 'dev') \|\| contains(github.base_ref, 'dev')}}

	- uses: actions/download-artifact@master
	with:
	name: notebooks-for-${{ github.sha }}
	path: docs/notebooks


	- uses: actions/download-artifact@master
	with:
	name: api-stubs-for-${{ github.sha }}
	path: docs/notebooks/api


	- name: Build and Commit
	uses: sphinx-notes/pages@v2
	with:
	documentation_path: docs
	sphinx_version: 5.1.1
	requirements_path: docs/requirements.txt


	- name: Push changes
	if: github.event_name == 'push' #&& startsWith(github.event.ref, 'refs/tags')
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	branch: gh-pages

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Update configparser SafeConfigParser and readfp, new in python 3.12 #1

Workflow file

Update configparser SafeConfigParser and readfp, new in python 3.12 #1

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Workflow file for this run