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Merge pull request #47 from henrikef/master
github actions instead of travis ci
2 parents 4126b48 + e240e15 commit f250eea

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‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name: "\U0001F41B Bug Report"
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about: "If something isn't working as expected \U0001F914."
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is. What data are you using and how was it obtained?
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*NOTE:* This is for BUG reports and not questions about generic data analysis.
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**To Reproduce**
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Please provide enough information for someone else to reporoduce this bug. That means e.g. a script + (links to) necessary files + any command line options, or an ipython notebook or something similar.
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Log files**
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Add log files or copy & paste the entire terminal output.
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**Desktop (please complete the following information):**
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- OS: [e.g. iOS]
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- Version [e.g. 22]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: true
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contact_links:
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- name: GitHub Community Support
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url: https://github.community/
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about: Please ask and answer questions here.
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- name: GitHub Security Bug Bounty
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url: https://bounty.github.com/
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about: Please report security vulnerabilities here.

‎.github/ISSUE_TEMPLATE/data-analysis-question.md

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---
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name: "\U0001F52D Data Analysis Question"
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about: "I am trying to analyze some data with 3ML/HAL and I am stuck!"
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title: ''
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labels:
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assignees: ''
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---
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## Data Analysis Question
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**To reproduce**
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Please let us know which data file, instrument response function etc. you are using, and include your model(s) and analysis script.
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‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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name: "\U0001F680 Feature Request"
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about: "I have a suggestion (and may want to implement it \U0001F642)!"
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title: ''
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labels: ''
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assignees: ''
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---
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## Feature Request
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I have an issue when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen. Add any considered drawbacks.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Teachability, Documentation, Adoption, Migration Strategy**
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If you can, explain how users will be able to use this and possibly write out a version the docs.
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Maybe a screenshot or design?

‎.github/workflows/build_and_test.yml

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name: CI
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on:
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push:
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# paths-ignore:
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# - 'CHANGELOG.md'
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pull_request:
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schedule:
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- cron: "0 11 * * *"
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jobs:
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skip_duplicate:
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runs-on: ubuntu-latest
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outputs:
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should_skip: ${{ steps.skip_check.outputs.should_skip }}
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steps:
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- id: skip_check
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uses: fkirc/skip-duplicate-actions@master
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with:
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github_token: ${{ github.token }}
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concurrent_skipping: never
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skip_after_successful_duplicate: true
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paths_ignore: '["**/README.md", "**/docs/**"]'
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do_not_skip: '["pull_request", "schedule"]'
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test-conda:
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name: Test on Conda
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needs: skip_duplicate
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if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
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strategy:
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matrix:
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os: ["ubuntu-latest", "macos-latest"]
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python-version: [3.7]
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Cache conda
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uses: actions/cache@v1
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with:
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path: ~/conda_pkgs_dir
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key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('environment-ci.yml') }}
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: test_env
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python-version: ${{ matrix.python-version }}
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channels: conda-forge, xspecmodels, threeml, defaults
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environment-file: ci/environment.yml
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- name: Init Env
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shell: bash -l {0}
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run: |
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# Make sure we fail in case of error
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if [[ ${{matrix.os}} == ubuntu-latest ]];
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then
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miniconda_os=Linux
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compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"
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else # osx
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miniconda_os=MacOSX
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compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"
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# On macOS we also need the conda libx11 libraries used to build xspec
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# We also need to pin down ncurses, for now only on macos.
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xorg="xorg-libx11"
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fi
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# Get the version in the __version__ environment variable
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#python ci/set_minor_version.py --patch $TRAVIS_BUILD_NUMBER --version_file threeML/version.py
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#export PKG_VERSION=$(cd threeML && python -c "import version;print(version.__version__)")
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export PKG_VERSION=$(python -c "import versioneer;print(versioneer.get_version())")
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echo "HOME= ${HOME}"
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echo "Building ${PKG_VERSION} ..."
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echo "Python version: ${{matrix.python-version}}"
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#libgfortranver="3.0"
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#NUMPYVER=1.15
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MATPLOTLIBVER=2
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XSPECVER="6.25"
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xspec_channel=xspecmodels
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# Figure out requested dependencies
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if [ -n "${MATPLOTLIBVER}" ]; then MATPLOTLIB="matplotlib=${MATPLOTLIBVER}"; fi
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if [ -n "${NUMPYVER}" ]; then NUMPY="numpy=${NUMPYVER}"; fi
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if [ -n "${XSPECVER}" ];
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then export XSPEC="xspec-modelsonly=${XSPECVER} ${xorg}";
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fi
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PKG="pytest>=3.6 pandas>=0.23 ultranest interpolation>=2.1.5"
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conda install ${PKG} codecov pytest-cov git ${MATPLOTLIB} ${NUMPY} ${XSPEC} astropy ${compilers} scipy astropy astromodels threeML numba reproject root emcee pymultinest ultranest flake8
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pip install --no-binary :all: root_numpy
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- name: Conda list
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shell: bash -l {0}
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run: |
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conda list
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- name: install it
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shell: bash -l {0}
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run: |
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pip install -e .
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- name: Lint with flake8
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shell: bash -l {0}
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: test it
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shell: bash -l {0}
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run: |
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python -m pytest -vv
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env:
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OMP_NUM_THREADS: 1
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MKL_NUM_THREADS: 1
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NUMEXPR_NUM_THREADS: 1
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MPLBACKEND: "Agg"
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test-master:
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name: Test with master threeML/astromodels
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needs: skip_duplicate
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if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
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strategy:
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matrix:
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os: ["ubuntu-latest", "macos-latest"]
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python-version: [3.7]
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Cache conda
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uses: actions/cache@v1
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with:
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path: ~/conda_pkgs_dir
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key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('environment-ci.yml') }}
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: test_env
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python-version: ${{ matrix.python-version }}
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channels: conda-forge, xspecmodels, threeml, defaults
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environment-file: ci/environment.yml
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- name: Init Env
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shell: bash -l {0}
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run: |
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# Make sure we fail in case of error
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if [[ ${{matrix.os}} == ubuntu-latest ]];
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then
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miniconda_os=Linux
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compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"
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else # osx
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miniconda_os=MacOSX
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compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"
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# On macOS we also need the conda libx11 libraries used to build xspec
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# We also need to pin down ncurses, for now only on macos.
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xorg="xorg-libx11"
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fi
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# Get the version in the __version__ environment variable
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#python ci/set_minor_version.py --patch $TRAVIS_BUILD_NUMBER --version_file threeML/version.py
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#export PKG_VERSION=$(cd threeML && python -c "import version;print(version.__version__)")
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export PKG_VERSION=$(python -c "import versioneer;print(versioneer.get_version())")
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echo "HOME= ${HOME}"
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echo "Building ${PKG_VERSION} ..."
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echo "Python version: ${{matrix.python-version}}"
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#libgfortranver="3.0"
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#NUMPYVER=1.15
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MATPLOTLIBVER=2
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XSPECVER="6.25"
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xspec_channel=xspecmodels
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# Figure out requested dependencies
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if [ -n "${MATPLOTLIBVER}" ]; then MATPLOTLIB="matplotlib=${MATPLOTLIBVER}"; fi
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if [ -n "${NUMPYVER}" ]; then NUMPY="numpy=${NUMPYVER}"; fi
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if [ -n "${XSPECVER}" ];
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then export XSPEC="xspec-modelsonly=${XSPECVER} ${xorg}";
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fi
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PKG="pytest>=3.6 pandas>=0.23 ultranest interpolation>=2.1.5"
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conda install ${PKG} codecov pytest-cov git ${MATPLOTLIB} ${NUMPY} ${XSPEC} astropy ${compilers} scipy astropy astromodels threeML numba reproject root emcee pymultinest ultranest flake8
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pip install --no-binary :all: root_numpy
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pip uninstall astromodels threeML -y
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pip install git+https://github.com/threeml/astromodels.git
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pip install git+https://github.com/threeml/threeML.git
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- name: Conda list
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shell: bash -l {0}
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run: |
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conda list
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- name: install it
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shell: bash -l {0}
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run: |
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pip install -e .
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- name: Lint with flake8
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shell: bash -l {0}
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: test it
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shell: bash -l {0}
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run: |
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python -m pytest -vv
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env:
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OMP_NUM_THREADS: 1
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MKL_NUM_THREADS: 1
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NUMEXPR_NUM_THREADS: 1
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MPLBACKEND: "Agg"

‎.github/workflows/issues.yml

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name: Close stale issues and PRs
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on:
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schedule:
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- cron: 30 1 * * *
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jobs:
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stale:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/stale@v3
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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stale-issue-message: 'This issue has become stale. Is there an update? We will close in 14 days'
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stale-pr-message: 'This PR has become stale. Please check the status'
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stale-issue-label: 'no-issue-activity'
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days-before-stale: 90
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days-before-close: 14

‎ci/environment.yml

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# environment file fo CI testing
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name: test_env
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channels:
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- conda-forge
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- threeml
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- xspecmodels
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- defaults
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dependencies:
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- pip
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- pytest
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- pytest-cov
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- coverage
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- setuptools
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- python
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- numpy>=1.15
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- scipy>=0.18
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- emcee>=3
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- astropy>=1.0.3
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- matplotlib
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- uncertainties
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- pyyaml>=5.1
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- dill
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- iminuit>=1.2,<2
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- astromodels>=2
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- astroquery
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- corner>=1.0.2
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- pandas>=0.23
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- requests
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- speclite
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- pymultinest
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- ultranest
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- dynesty>=1
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- pygmo>=2.4
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- ipywidgets
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- ipython
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- ipyparallel
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- numba
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- xz
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- py
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- pytest
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- numexpr
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- ipopt
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- numdifftools
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- tqdm
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- astromodels
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- threeml
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- future
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- xspec-modelsonly==6.25
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- root
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- numba
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- reproject

‎hawc_hal/obsolete/image_to_healpix.py

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import six
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from scipy.ndimage import map_coordinates
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from astropy import units as u
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def image_to_healpix(data, wcs_in, coord_system_out,
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nside, pixels_id, order='bilinear', nested=False,
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fill_value=UNSEEN, pixels_to_be_zeroed=None, full=False):

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