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Fix PositionD parsing in config from strings like '123.1, 234.2', which had been doing the wrong thing. #1068

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Fix PositionD parsing in config from strings like '123.1, 234.2', which had been doing the wrong thing.

Fix PositionD parsing in config from strings like '123.1, 234.2', which had been doing the wrong thing. #1068

Workflow file for this run

.github/workflows/ci.yml at 7e50733
name: GalSim CI
on:
push:
branches:
- main
- runci
- releases/*
pull_request:
branches:
- main
- runci
- releases/*
jobs:
build:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# First all python versions in basic linux
os: [ ubuntu-latest ]
py: [ 3.7, 3.8, 3.9, "3.10", 3.11, 3.12 ]
CC: [ gcc ]
CXX: [ g++ ]
FFTW_DIR: [ "/usr/local/lib" ]
# Add some other particular combinations to test
include:
# Just one in MacOS, since GitHub actions seems to have some kind of
# system problem where seg faults happen randomly on their Mac machines.
# Usually just restarting will fix it, but that's annoying, so minimize
# that by only having one of these to fight with.
- os: macos-latest
py: "3.10"
CC: cc
CXX: c++
FFTW_DIR: "/opt/homebrew/lib/"
# Check one with clang compiler
- os: ubuntu-latest
py: "3.10"
CC: clang
CXX: clang++
FFTW_DIR: "/usr/local/lib/"
# And a pypy system.
# As of 12/1/2022, this is broken for astropy.
# pypy3 used to work, but that's Py 3.6, and GHA no longer supports it.
# Maybe revisit at some point. Or maybe don't care too much about pypy...
#- os: ubuntu-latest
#py: pypy-3.7
#CC: gcc
#CXX: g++
env:
FFTW_DIR: ${{ matrix.FFTW_DIR }}
steps:
- uses: actions/checkout@v4
with:
# Need this for git commands to work right.
# Also for codecov upload apparently.
fetch-depth: 0
- name: Print github context properties
run: |
echo 'event: ${{ github.event_name }}'
echo 'sha: ${{ github.sha }}'
echo 'ref: ${{ github.ref }}'
echo 'head_ref: ${{ github.head_ref }}'
echo 'base_ref: ${{ github.base_ref }}'
echo 'event.before: ${{ github.event.before }}'
echo 'event.after: ${{ github.event.after }}'
- name: Set up Python ${{ matrix.py }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.py }}
- name: Set up ccache
uses: hendrikmuhs/ccache-action@v1
with:
key: ${{ matrix.os }}-${{ matrix.py }}-${{ matrix.CXX }}
- name: Cache pip
uses: actions/cache@v4
with:
path: |
~/.cache/pip
$HOME/des_data
$HOME/Library/Caches/Homebrew
/usr/local/Cellar
key: ${{ runner.os }}-${{ matrix.py }}-pip-${{ hashFiles('requirements.txt') }}
restore-keys: |
${{ runner.os }}-${{ matrix.py }}-pip-
${{ runner.os }}-
- name: Install fftw, etc. on linux
if: matrix.os == 'ubuntu-latest'
run: |
echo ${{ matrix.os }}
sudo -H apt update -y
sudo -H apt install -y libfftw3-dev
ls $FFTW_DIR
# Easier if eigen is installed with apt-get, but on at least one system, check that
# it gets downloaded and installed properly if it isn't installed.
if ${{ matrix.py != 3.7 }}; then sudo -H apt install -y libeigen3-dev; fi
# Need this for the mpeg tests
sudo -H apt install -y ffmpeg
- name: Install fftw, etc. on MacOS
if: matrix.os == 'macos-latest'
# brew sometimes exits with 1 if things are already installed.
# continue-on-error should mean that this still counds as success for this step.
# but it doesn't seem to work right. Still counts as an error, it just moves
# on and finishes everything else before calling the whole job a failure. :(
# So we still need the || true bits below.
continue-on-error: true
run: |
echo ${{ matrix.os }}
# brew update takes forever to run. Hopefully won't need to enable this too often.
# Note: The || true bit here is because brew returns an error code if everything is
# already installed, which is goofy. So || true means these always give
# non-error values. If there really is an error, we should notice later
# when trying to use whatever package failed to install.
#brew update || true
brew install fftw wget || true
brew upgrade wget || true
brew link --overwrite fftw gcc wget || true
brew install eigen || true
brew link --overwrite eigen || true
ls $FFTW_DIR
- name: Download des_data
run: |
ls -l $HOME
if test -d $HOME/des_data; then ls -l $HOME/des_data; fi
if ! test -d $HOME/des_data || ! test -f $HOME/des_data/DECam_00154912_01.fits.fz; then wget --no-check-certificate http://www.sas.upenn.edu/~mjarvis/des_data.tar.gz; tar xfz des_data.tar.gz -C $HOME; fi
ln -s $HOME/des_data examples/des/
- name: Install basic dependencies
run: |
python -m pip install -U pip
# Do these three first to clarify potential conflicts
pip install -U numpy
pip install -U setuptools
pip install -U wheel
# Standard dependencies
pip install -U -r requirements.txt
# Extra packages needed for testing
pip install -U -r test_requirements.txt
pip install -U nose coverage
pip install -U matplotlib
- name: Install astroplan
# astroplan isn't yet numpy 2.0 compatible. So don't install that on 3.9+.
# I'm also getting errors with starlink, which I think may be related to
# numpy 2.0.
if: (matrix.py == 3.8) || (matrix.py == 3.9)
run: |
pip install -U astroplan
pip install -U starlink-pyast
- name: Install CPython-only dependencies
if: matrix.py != 'pypy-3.7'
run: |
# The only one left that doesn't seem to work right on pypy is starlink-pyast.
# (This is now above in numpy 1.x versions.)
#pip install -U starlink-pyast
# And now pandas is acting up on pypy.
# cf. https://github.com/pandas-dev/pandas/issues/44253
pip install -U pandas
- name: List all installed packages for reference
run: pip list
- name: Build GalSim
run: |
# The prefix is required for recent MacOS, because of System Integrity Protection.
# It's not necessary on Linux, but is harmless enough.
FFTW_DIR=$FFTW_DIR pip install -vvv .
- name: Check download_cosmos only if it changed. (And only on 1 runner)
if: matrix.py == 3.7 && github.base_ref != ''
run: |
git status
git --no-pager log --graph --pretty=oneline --abbrev-commit | head -50
echo git --no-pager diff origin/${{ github.base_ref }}...${{ github.event.after }} --name-only
git --no-pager diff origin/${{ github.base_ref }}...${{ github.event.after }} --name-only
if git --no-pager diff origin/${{ github.base_ref }}...${{ github.event.after }} --name-only | grep -Fxq 'galsim/download_cosmos.py'; then galsim_download_cosmos -s 23.5 -v1; fi
- name: Run unit tests
run: |
cd tests
coverage run -m pytest -v
pytest -v run_examples.py
cd .. # N.B. This seems to happen automatically if omitted.
# Less confusing to include it explicitly.
- name: Check shared library
if: matrix.py == 3.8
run: |
# On a few systems (arbitrarily py3.8, where we also chec mac and clang),
# check the shared library creation and link.
GALSIM_BUILD_SHARED=1 python setup.py install
# These directories/files should now exist.
echo "Look for the shared library:"
test -d build/shared_clib
ls build/shared_clib
ls build/shared_clib/libgalsim.*
# For now, use `python setup.py test` to test linking to the shared library.
# We run some C++ tests there, and we use the shared library for linking.
# Caveats:
# 1. The C++ tests are not very comprehensive, so it won't catch all errors.
# 2. Apparently setup.py test is deprecated. I'm getting warnings when I run
# it that indicate it may go away at some point. So whenever that happens,
# we'll have to revisit this test to find another way to build and run
# the C++ tests.
GALSIM_TEST_PY=0 python setup.py test
- name: Upload coverage to codecov
if: matrix.py != 'pypy-3.7'
run: |
cd tests
pwd -P
ls -la
coverage combine || true # (Not necessary I think, but just in case.)
coverage report
ls -la
#codecov # This didn't work.
# cf. https://community.codecov.io/t/github-not-getting-codecov-report-after-switching-from-travis-to-github-actions-for-ci/
# The solution was to switch to the bash uploader line instead.
bash <(curl -s https://codecov.io/bash)
cd ..
- name: Pre-cache cleanup
continue-on-error: true
run: |
# This was helpful in Travis. Not sure how important it is in GHA.
rm -rfv $HOME/.cache/pip/log
rm -rfv $HOME/.cache/pip/http
if ${{ runner.os == 'macOS' }}; then brew cleanup || true; fi