jpas_forecast: make photo-z scatter sigma0 configurable #3177

Workflow file for this run

.github/workflows/build_check.yml at d66b6da

	name: Build and Check

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

	env:
	CONDA_ENV: numcosmo_developer
	CACHE_VERSION: 0

	jobs:

	build-gcc-ubuntu:
	name: (ubuntu, apt, pip)
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v6
	with:
	python-version: '3.12'
	- name: Install pre-requisites
	run: \|
	sudo apt-get update
	sudo apt-get install gobject-introspection gir1.2-glib-2.0 gir1.2-glib-2.0-dev libgirepository-2.0-dev gcc gfortran pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-dev libcfitsio-dev libfyaml-dev libnlopt-dev libhdf5-dev libopenmpi-dev libcairo2-dev uncrustify
	pip install meson ninja pytest pytest-lazy-fixtures numpy scipy pygobject typer matplotlib --break-system-packages
	- name: Ensure clear Jupyter Notebooks
	uses: ResearchSoftwareActions/[email protected]
	- name: Configure NumCosmo
	run: meson setup build -Dbuildtype=release -Dnumcosmo_py=true -Dfftw-planner=estimate -Ddocumentation=false --prefix=/usr \|\| (cat build/meson-logs/meson-log.txt && exit 1)
	- name: Building NumCosmo
	run: meson compile -C build
	- name: Checking indentation
	run: \|
	uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/.c numcosmo/.h
	uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/math/.c numcosmo/math/.h
	uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/model/.c numcosmo/model/.h
	uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/xcor/.c numcosmo/xcor/.h
	- name: Test python examples
	run: \|
	source build/numcosmo_export.sh
	cd examples
	python example_simple.py
	python example_cbe.py
	- name: Test example compilation using non-installed library
	run: \|
	source build/numcosmo_export.sh
	cd examples
	gcc -D_GNU_SOURCE -Wall example_simple.c -o example_simple -lnumcosmo -lgsl -lm $(pkg-config glib-2.0 gobject-2.0 --libs --cflags)
	gcc -D_GNU_SOURCE -Wall example_ca.c -o example_ca -lnumcosmo -lgsl -lm $(pkg-config glib-2.0 gobject-2.0 --libs --cflags)
	./example_simple
	./example_ca
	- name: Check NumCosmo
	run: meson test -v -C build --num-processes=2 \|\| (cat build/meson-logs/testlog.txt && exit 1)
	- name: Create a NumCosmo tarball
	run: meson dist -C build --no-tests
	- name: Upload a Build Artifact
	uses: actions/upload-artifact@v4
	with:
	name: release
	path: build/meson-dist/numcosmo-*.tar.xz
	- name: Test example compilation using installed library
	run: \|
	meson install -C build --destdir=install_tmp
	sudo cp -a build/install_tmp/* /
	cd examples
	gcc -D_GNU_SOURCE -Wall example_simple.c -o example_simple $(pkg-config numcosmo --libs --cflags)
	gcc -D_GNU_SOURCE -Wall example_ca.c -o example_ca $(pkg-config numcosmo --libs --cflags)
	./example_simple
	./example_ca

	build-gcc-macos:
	name: (macos, brew, pip)
	runs-on: macos-latest
	env:
	CC: gcc-14
	FC: gfortran-14
	F77: gfortran-14
	F90: gfortran-14
	LIBRARY_PATH: /usr/local/lib:/opt/homebrew/Cellar/gmp/6.3.0/lib
	LD_LIBRARY_PATH: /usr/local/lib:/opt/homebrew/Cellar/gmp/6.3.0/lib
	DYLD_LIBRARY_PATH: /usr/local/lib:/opt/homebrew/Cellar/gmp/6.3.0/lib
	CPATH: /usr/local/include

	steps:
	- uses: actions/checkout@v4
	- name: Brew install pre-requisites
	run: \|
	brew uninstall --ignore-dependencies --force [email protected]
	brew install python3 gobject-introspection pygobject3 numpy scipy python-matplotlib meson ninja gsl gmp mpfr fftw cfitsio libfyaml nlopt gfortran glib openblas
	- name: Pip install pre-requisites
	run: \|
	python3 -m pip install pytest pytest-lazy-fixtures typer pydantic --break-system-packages
	- name: Ensure clear Jupyter Notebooks
	uses: ResearchSoftwareActions/[email protected]
	- name: Fix libfyaml.pc
	run: \|
	pc=$(pkg-config --variable=pcfiledir libfyaml)/libfyaml.pc
	sed -i '' 's/none required//g' "$pc" \|\| true
	- name: Dump pkg-config info (cfitsio + libfyaml)
	run: \|
	set -x

	echo "which pkg-config:"
	which pkg-config \|\| true

	echo "version:"
	pkg-config --version \|\| true

	echo "env:"
	echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH"
	echo "PKG_CONFIG_LIBDIR=$PKG_CONFIG_LIBDIR"

	echo "---- cfitsio ----"
	pkg-config --libs cfitsio \|\| true
	pkg-config --cflags cfitsio \|\| true
	pkg-config --variable=pcfiledir cfitsio \|\| true
	pkg-config --debug --libs cfitsio \|\| true

	echo "---- libfyaml ----"
	pkg-config --libs libfyaml \|\| true
	pkg-config --cflags libfyaml \|\| true
	pkg-config --variable=pcfiledir libfyaml \|\| true
	pkg-config --debug --libs libfyaml \|\| true
	- name: Configure NumCosmo
	run: \|
	meson setup build -Dbuildtype=release -Dnumcosmo_py=true -Dfftw-planner=estimate -Dmpi=disabled --prefix=/usr \|\| (cat build/meson-logs/meson-log.txt && exit 1)
	- name: Building NumCosmo
	run: \|
	meson compile -C build
	- name: Test python examples
	run: \|
	source build/numcosmo_export.sh
	cd examples
	python3 example_simple.py
	python3 example_cbe.py
	cd ..
	pytest -xvs tests/python --run-sphere-map -m sphere_map
	- name: Check NumCosmo
	run: \|
	meson test -v -C build --num-processes=2 \|\| (cat build/meson-logs/testlog.txt && exit 1)

	build-miniforge:
	name: (${{ matrix.os }}, py${{ matrix.python-version }}, ${{ matrix.mpi }}, Miniforge)
	runs-on: ${{ matrix.os }}-latest
	strategy:
	matrix:
	os: ["ubuntu", "macos"]
	python-version: ["3.12"]
	mpi: ["openmpi", "mpich"]
	exclude:
	- os: "macos"
	mpi: "openmpi"
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- uses: actions/checkout@v4
	- name: Setup miniforge
	uses: conda-incubator/setup-miniconda@v4
	with:
	miniforge-version: latest
	python-version: ${{ matrix.python-version }}
	activate-environment: ${{ env.CONDA_ENV }}
	- name: Cache date
	id: get-date
	run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
	- name: Cache Conda env
	uses: actions/cache/restore@v4
	id: cache
	with:
	path: ${{ env.CONDA }}/envs
	key: conda-${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ matrix.mpi }}-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-v${{ env.CACHE_VERSION }}
	- name: Update environment
	if: steps.cache.outputs.cache-hit != 'true'
	run: \|
	conda env update -q -v -n ${{ env.CONDA_ENV }} -f environment.yml
	which python
	conda list
	conda remove -q -v -n numcosmo_developer openmpi
	conda install -q -v -n numcosmo_developer ${{ matrix.mpi }}
	conda install -q -v -n numcosmo_developer libfabric-devel
	conda list
	- name: Save conda-forge cache
	if: steps.cache.outputs.cache-hit != 'true'
	id: cache-primes-save
	uses: actions/cache/save@v4
	with:
	path: ${{ env.CONDA }}/envs
	key: ${{ steps.cache.outputs.cache-primary-key }}
	- name: Setting up NumCosmo
	run: \|
	conda activate numcosmo_developer
	meson setup build -Dbuildtype=release -Dnumcosmo_py=true -Dfftw-planner=estimate --libdir=$CONDA_PREFIX/lib --prefix=$CONDA_PREFIX \|\| (cat build/meson-logs/meson-log.txt && exit 1)
	- name: Building NumCosmo
	run: \|
	meson compile -C build
	- name: Installing NumCosmo
	run: \|
	meson install -C build
	cd examples
	python example_simple.py
	python example_cbe.py
	numcosmo generate planck18 test_exp_gen.yaml --data-type TT
	- name: Running black check
	run: \|
	black --check numcosmo_py
	- name: Running flake8
	run: \|
	flake8 numcosmo_py
	- name: Running mypy
	run: \|
	mypy --exclude '.meson.\|numcosmo_py/generate_stubs\.py' -p numcosmo_py
	#- name: Checking indentation
	# run: \|
	# uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/.c numcosmo/.h
	#- name: Running pylint
	# run: \|
	# pylint --rcfile .pylintrc numcosmo_py
	- name: Check NumCosmo
	run: meson test -v -C build --num-processes=2 \|\| (cat build/meson-logs/testlog.txt && exit 1)

	build-miniforge-coverage:
	name: Cov-${{ matrix.suites }} (py${{ matrix.python-version }}, openmpi)
	runs-on: ${{ matrix.os }}-latest
	strategy:
	matrix:
	os: ["ubuntu"]
	python-version: ["3.12"]
	suites: ["python", "c", "stats-dist", "fit-esmcmc", "powspec", "data-cluster-wl", "py-powspec", "py-xcor"]
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- uses: actions/checkout@v4
	- name: Setup miniforge
	uses: conda-incubator/setup-miniconda@v4
	with:
	miniforge-version: latest
	python-version: ${{ matrix.python-version }}
	activate-environment: ${{ env.CONDA_ENV }}
	- name: Cache date
	id: get-date
	run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
	- name: Cache Conda env
	uses: actions/cache/restore@v4
	id: cache
	with:
	path: ${{ env.CONDA }}/envs
	key: conda-${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-v${{ env.CACHE_VERSION }}
	- name: Update environment
	if: steps.cache.outputs.cache-hit != 'true'
	run: \|
	conda env update -q -v -n ${{ env.CONDA_ENV }} -f environment.yml
	conda list
	- name: Save conda-forge cache
	if: steps.cache.outputs.cache-hit != 'true'
	id: cache-primes-save
	uses: actions/cache/save@v4
	with:
	path: ${{ env.CONDA }}/envs
	key: ${{ steps.cache.outputs.cache-primary-key }}
	- name: Setting up NumCosmo
	run: \|
	conda activate numcosmo_developer
	meson setup build -Dbuildtype=debug -Db_coverage=true -Dnumcosmo_py=true -Dfftw-planner=estimate -Dnumcosmo_debug=disabled --libdir=$CONDA_PREFIX/lib --prefix=$CONDA_PREFIX \|\| (cat build/meson-logs/meson-log.txt && exit 1)
	- name: Building NumCosmo
	run: \|
	meson compile -C build
	- name: Check and coverage
	# First run to generate the coverage base
	# Second run to generate the coverage for the tests
	# Third run to merge the coverage base and the coverage for the tests
	run: \|
	lcov --config-file .lcovrc --no-external --capture --initial --directory build --directory numcosmo --directory tests --base-directory $(pwd)/build --output-file numcosmo-coverage-base.info
	meson test -v -C build --timeout-multiplier 0 --num-processes=2 --suite=${{ matrix.suites }} \|\| (cat build/meson-logs/testlog.txt && exit 1)
	lcov --config-file .lcovrc --no-external --capture --directory build --directory numcosmo --directory tests --base-directory $(pwd)/build --output-file numcosmo-coverage-tests.info
	lcov --config-file .lcovrc --add-tracefile numcosmo-coverage-base.info --add-tracefile numcosmo-coverage-tests.info --output-file numcosmo-coverage-full.info
	lcov --config-file .lcovrc --remove numcosmo-coverage-full.info '/class/' '/levmar/' '/libcuba/' '/plc/' '/sundials/' '/toeplitz/' '/tools/' --output-file numcosmo-coverage.info
	- name: CodeCov
	uses: codecov/codecov-action@v4
	with:
	disable_search: true
	fail_ci_if_error: true
	files: ./numcosmo-coverage.info,./build/coverage.xml
	token: ${{ secrets.CODECOV_TOKEN }}
	verbose: true
	#- name: Generate coverage
	# # For some reason, gcovr is ignoring the configured gcovr.cfg file
	# # ninja coverage -C build -v -d stats -d explain
	# run: \|
	# gcovr --root . --object-directory build --config gcovr.cfg --xml-pretty -o build/meson-logs/coverage.xml
	#- name: Coveralls
	# uses: coverallsapp/github-action@v2
	# with:
	# files: ./numcosmo-coverage.info
	# format: lcov
	# github-token: ${{ secrets.GITHUB_TOKEN }}

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jpas_forecast: make photo-z scatter sigma0 configurable #3177

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jpas_forecast: make photo-z scatter sigma0 configurable #3177

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