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Merge pull request #370 from mkelley/setup-updates-202304
Setup updates 202304
2 parents 997d64d + 2853c0a commit 462f453

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‎.github/workflows/ci_cron_weekly.yml‎

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@@ -5,35 +5,45 @@ name: Weekly CI Tests
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on:
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schedule:
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# run at 6am UTC on Mondays
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- cron: '0 6 * * 1'
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# run at 5am UTC on Mondays
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- cron: '0 5 * * 1'
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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IS_CRON: 'true'
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jobs:
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weekly:
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tests:
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runs-on: ubuntu-latest
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env:
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ARCH_ON_CI: "normal"
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strategy:
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fail-fast: false
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matrix:
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include:
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- name: Check links in docs using tox
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toxenv: linkcheck
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- name: Check dev versions of key dependencies
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toxenv: py39-test-devdeps
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python: '3.11'
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toxenv: py311-test-devdeps
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toxposargs: --remote-data
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v2
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uses: actions/setup-python@v4
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with:
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python-version: 3.9
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python-version: ${{ matrix.python }}
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- name: Install base dependencies
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run: |
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python -m pip install --upgrade pip tox
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- name: Test with tox
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- name: Run tests
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env:
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ADS_DEV_KEY: ${{ secrets.ADS_DEV_KEY }}
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run: tox ${{ matrix.toxargs}} -e ${{ matrix.toxenv}} -- ${{ matrix.toxposargs}}
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run: tox ${{ matrix.toxargs }} -e ${{ matrix.toxenv }} -- ${{ matrix.toxposargs }}

‎.github/workflows/ci_tests.yml‎

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@@ -7,91 +7,72 @@ name: CI Tests
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on:
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push:
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branches:
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- main # GitHub now defaults to 'main' as the name of the primary branch. Change this as needed.
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# tags: # run CI if specific tags are pushed
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- main
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tags:
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- '*'
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pull_request:
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# branches: # only build on PRs against 'main' if you need to further limit when CI is run.
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# - main
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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ARCH_ON_CI: "normal"
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IS_CRON: "false"
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jobs:
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# Github Actions supports ubuntu, windows, and macos virtual environments:
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# https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners
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ci_tests:
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name: ${{ matrix.name }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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include:
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- name: Code style checks
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os: ubuntu-latest
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python: 3.x
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toxenv: codestyle
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- name: Python 3.7 with minimal dependencies
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os: ubuntu-latest
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python: 3.7
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toxenv: py37-test
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- name: Python 3.8 with all optional dependencies and coverage checking
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os: ubuntu-latest
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python: 3.8
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toxenv: py38-test-alldeps
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- name: OS X - Python 3.8 with all optional dependencies
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os: macos-latest
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python: 3.8
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toxenv: py38-test-alldeps
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tests:
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uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
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secrets:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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with:
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setenv: |
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ARCH_ON_CI: "normal"
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IS_CRON: "false"
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submodules: false
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coverage: ''
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envs: |
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- name: Code style checks
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linux: codestyle
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- name: Python 3.8 with all optional dependencies and coverage checking
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os: ubuntu-latest
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python: 3.8
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toxenv: py38-test-alldeps-cov
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- name: Python 3.11 with minimal dependencies and full coverage
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linux: py311-test-cov
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coverage: codecov
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# - name: Windows - Python 3.8 with all optional dependencies
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# os: windows-latest
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# python: 3.8
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# toxenv: py38-test-alldeps
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# - name: Python 3.7 with oldest supported version of all dependencies
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# os: ubuntu-16.04
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# python: 3.7
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# toxenv: py37-test-oldestdeps
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# - name: Python 3.8 with latest dev versions of key dependencies
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# os: ubuntu-latest
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# python: 3.8
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# toxenv: py38-test-devdeps
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# - name: Test building of Sphinx docs
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# os: ubuntu-latest
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# python: 3.x
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# toxenv: build_docs
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- name: Python 3.10 with all optional dependencies
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linux: py310-test-alldeps
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- name: Python 3.8 with oldest supported versions
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linux: py38-test-oldestdeps
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coverage: codecov
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macos-tests:
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name: Python 3.10 with all optional dependencies (MacOS)
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runs-on: macos-latest
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env:
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ARCH_ON_CI: "normal"
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Set up python ${{ matrix.python }} on ${{ matrix.os }}
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uses: actions/setup-python@v2
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- name: Set up python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python }}
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python-version: "3.10"
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- name: Set up gfortran on ${{ matrix.os }}
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if: runner.os == 'macos'
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run: |
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echo `which gfortran-11`
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sudo ln -sfn /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
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echo `which gfortran`
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gfortran --version
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- name: Install base dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install tox codecov
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python -m pip install tox
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- name: Test with tox
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run: tox ${{ matrix.toxargs }} -e ${{ matrix.toxenv }} -- ${{ matrix.toxposargs }}
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# This is an example of how to upload coverage to codecov
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# - name: Upload coverage to codecov
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# if: "contains(matrix.toxenv, '-cov')"
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# uses: codecov/codecov-action@v1
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# with:
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# file: ./coverage.xml
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run: tox -e py310-test-alldeps

‎.gitignore‎

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@@ -56,6 +56,7 @@ distribute-*.tar.gz
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.*.sw[op]
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*~
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\#*
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.hypothesis
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.project
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.pydevproject
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.settings

‎CHANGES.rst‎

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0.4.0 (release date TBD)
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========================
33

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* Dropped support for Python 3.7, minimum supported version is 3.8.
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6+
* Bumped minimum supported versions for `numpy` to 1.18, `astropy` to 4.3, `synphot`
7+
to 1.1, `astroquery` to 4.6.
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New Features
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------------
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@@ -12,6 +18,7 @@ sbpy.data
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- Added ``Orbit.D_criterion`` to evaluate the D-criterion between two sets
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of orbital elements. [#325]
21+
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- Added ``DataClass.__contains__`` to enable `in` operator for ``DataClass``
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objects. [#357]
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‎docs/sbpy/activity/dust.rst‎

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@@ -85,11 +85,11 @@ The `Afrho` class may be converted to a flux density, and the original value is
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`Afrho` works seamlessly with `sbpy`'s spectral calibration framework (:ref:`sbpy-calib`) when the `astropy` affiliated package `synphot` is installed. The solar flux density (via `~sbpy.calib.solar_fluxd`) is not required, but instead the spectral wavelengths or the system transmission of the instrument and filter:
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.. doctest-requires:: synphot
88+
.. doctest-requires:: synphot; astropy>=5.3
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>>> wave = [0.4, 0.5, 0.6] * u.um
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>>> print(afrho.to_fluxd(wave, aper, eph)) # doctest: +FLOAT_CMP
92-
[7.76770018e-14 1.05542873e-13 9.57978939e-14] W / (m2 um)
92+
[7.76770018e-14 1.05542873e-13 9.57978939e-14] W / (um m2)
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.. doctest-requires:: synphot
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‎docs/sbpy/calib.rst‎

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The `~astropy.utils.state.ScienceState` objects `~sbpy.calib.solar_fluxd` and `~sbpy.calib.vega_fluxd` control photometric calibration by filter name. These are completely independent of the spectroscopic calibration and can be used without the optional `synphot` package. The spectral flux densities (per unit wavelength) of the Sun and Vega are provided and enabled by default. Values and filters are from Willmer (2018):
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98+
.. testsetup::
99+
.. doctest-requires:: astropy<5.3
100+
101+
>>> from sbpy.calib import Sun, solar_fluxd, vega_fluxd
102+
>>> import sbpy.units as sbu
103+
104+
.. doctest-requires:: astropy>=5.3
105+
98106
>>> from sbpy.calib import Sun, solar_fluxd, vega_fluxd
99107
>>> import sbpy.units as sbu
100108
>>>
101109
>>> solar_fluxd.set('Willmer2018') # doctest: +IGNORE_OUTPUT
102110
>>> sun = Sun(None)
103111
>>> print(sun.observe('PS1 r')) # doctest: +FLOAT_CMP
104-
167.49428760264365 erg / (Angstrom cm2 s)
112+
167.49428760264365 erg / (Angstrom s cm2)
105113
>>> vega_fluxd.set('Willmer2018') # doctest: +IGNORE_OUTPUT
106114
>>> print(sun.observe('PS1 r', unit=sbu.VEGAmag)) # doctest: +FLOAT_CMP
107115
-27.05 mag(VEGA)
@@ -117,6 +125,8 @@ Users wanting to calibrate data with their own flux densities may do so. For ex
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Some sbpy calculations will require the effective wavelength or the pivot wavelength. These are optional parameters that may be specified with `~sbpy.calib.solar_fluxd` and `~sbpy.calib.vega_fluxd`:
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.. doctest-requires:: astropy>=5.3
129+
120130
>>> import astropy.units as u
121131
>>> from sbpy.calib import vega_fluxd, Vega
122132
>>>
@@ -133,15 +143,15 @@ Some sbpy calculations will require the effective wavelength or the pivot wavele
133143
... # doctest: +IGNORE_EXCEPTION_DETAIL
134144
Traceback (most recent call last):
135145
...
136-
UnitConversionError: 'Jy' (spectral flux density) and 'erg / (Angstrom cm2 s)' (spectral flux density wav) are not convertible Is "V(lambda pivot)" required and was it provided?
146+
UnitConversionError: 'Jy' (spectral flux density) and 'erg / (Angstrom s cm2)' (spectral flux density wav) are not convertible Is "V(lambda pivot)" required and was it provided?
137147
>>> vega_fluxd.set({
138148
... 'V': 3674.73 * u.Jy,
139149
... 'V(lambda eff)': 5476 * u.AA,
140150
... 'V(lambda pivot)': 5511 * u.AA
141151
... }) # doctest: +IGNORE_OUTPUT
142152
<ScienceState vega_fluxd: {'V': <Quantity 3674.73 Jy>, 'V(lambda eff)': <Quantity 5476. Angstrom>, 'V(lambda pivot)': <Quantity 5511. Angstrom>}>
143153
>>> print(vega.observe('V', unit='erg/(s cm2 AA)')) # doctest: +FLOAT_CMP
144-
3.62701e-9 erg / (Angstrom cm2 s)
154+
3.62701e-9 erg / (Angstrom s cm2)
145155

146156
Observe the Sun
147157
---------------
@@ -178,15 +188,23 @@ Compare interpolation and rebinning for the E490 low-resolution solar spectrum,
178188

179189
Inspect a sub-set of the data for this example.
180190

191+
.. doctest-requires:: astropy>=5.3
192+
181193
>>> wave = sun.wave[430:435]
182194
>>> S = sun.fluxd[430:435]
183195
>>> print(wave) # doctest: +FLOAT_CMP
184196
[5495. 5505. 5515. 5525. 5535.] Angstrom
185197
>>> print(S) # doctest: +FLOAT_CMP
186-
[1895. 1862. 1871. 1846. 1882.] W / (m2 um)
198+
[1895. 1862. 1871. 1846. 1882.] W / (um m2)
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188200
Interpolate with observe() and compare to the original values.
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202+
.. testsetup::
203+
.. doctest-requires:: astropy<5.3
204+
205+
>>> wave = sun.wave[430:435]
206+
>>> S = sun.fluxd[430:435] # for astropy<5.3
207+
190208
>>> S_interp = sun.observe(wave, interpolate=True)
191209
>>> np.allclose(S.value, S_interp.value)
192210
True

‎docs/sbpy/data/obs.rst‎

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@@ -8,28 +8,27 @@ Observational Data Objects (`sbpy.data.Obs`)
88
For instance, this class allows you to query observations reported to the Minor
99
Planet Center for a given target via `astroquery.mpc.MPCClass.get_observations`:
1010

11-
>>> from sbpy.data import Obs
12-
>>> data = Obs.from_mpc('2019 AA', id_type='asteroid designation') # doctest: +REMOTE_DATA
13-
>>> data # doctest: +REMOTE_DATA +SKIP
14-
<QTable masked=True length=33>
15-
number desig discovery note1 ... DEC mag band observatory
16-
... deg mag
17-
int64 str7 str1 str1 ... float64 float64 str1 str3
18-
------ ------- --------- ----- ... ------------------ ------- ---- -----------
19-
-- 2019 AA -- -- ... 42.32416944444445 20.2 G F51
20-
-- 2019 AA -- -- ... 42.32879722222223 20.3 G F51
21-
-- 2019 AA -- -- ... 42.333225000000006 20.3 G F51
22-
-- 2019 AA * -- ... 46.52321666666666 20.0 w F51
23-
-- 2019 AA -- -- ... 46.52748611111111 20.0 w F51
24-
-- 2019 AA -- -- ... 46.531755555555556 20.0 w F51
25-
... ... ... ... ... ... ... ... ...
26-
-- 2019 AA -- -- ... 46.706500000000005 20.2 V 033
27-
-- 2019 AA -- -- ... 46.70652777777778 20.2 V 033
28-
-- 2019 AA -- -- ... 49.73566111111111 20.1 i F52
29-
-- 2019 AA -- -- ... 49.73788888888889 20.1 i F52
30-
-- 2019 AA -- -- ... 49.74008611111111 20.1 i F52
31-
-- 2019 AA -- -- ... 49.742266666666666 20.2 i F52
11+
.. doctest-remote-data::
3212

13+
>>> from sbpy.data import Obs
14+
>>> data = Obs.from_mpc('2019 AA', id_type='asteroid designation')
15+
>>> data = data[:10] # limit the number of rows for this example
16+
>>> data # doctest: +SKIP
17+
<QTable length=10>
18+
number desig discovery note1 ... DEC mag band observatory
19+
... deg mag
20+
int64 str7 str1 str1 ... float64 float64 str1 str3
21+
------ ------- --------- ----- ... ------------------- ------- ---- -----------
22+
-- 2019 AA -- -- ... -2.6917250000000004 22.2 w F51
23+
-- 2019 AA -- -- ... -2.6893833333333337 22.1 w F51
24+
-- 2019 AA -- -- ... -2.6872222222222226 22.2 w F51
25+
-- 2019 AA -- -- ... 18.10141666666667 20.3 V 703
26+
-- 2019 AA -- -- ... 18.100916666666667 19.4 V 703
27+
-- 2019 AA -- -- ... 18.100555555555555 20.2 V 703
28+
-- 2019 AA -- -- ... 18.10086111111111 20.8 V 703
29+
-- 2019 AA -- -- ... 22.21022222222222 19.6 V G96
30+
-- 2019 AA -- -- ... 22.210083333333333 19.8 V G96
31+
-- 2019 AA -- -- ... 22.21022222222222 20.2 V G96
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3433
For a given `~sbpy.data.Obs` object, `~sbpy.data.Obs.supplement`
3534
allows you to supplement the information content of this object by
@@ -38,18 +37,17 @@ function makes use of the query functions that are part of
3837
`~sbpy.data.Ephem` and allows you to pick a service from which you
3938
would like to obtain the data.
4039

41-
>>> data.field_names # doctest: +REMOTE_DATA
40+
.. doctest-remote-data::
41+
42+
>>> data.field_names
4243
['number', 'desig', 'discovery', 'note1', 'note2', 'epoch', 'RA', 'DEC', 'mag', 'band', 'observatory']
43-
>>> data_sup = data.supplement(id_field='desig') # doctest: +REMOTE_DATA
44-
>>> data_sup.field_names # doctest: +REMOTE_DATA
44+
>>> data_sup = data.supplement(id_field='desig')
45+
>>> data_sup.field_names
4546
['number', 'desig', 'discovery', 'note1', 'note2', 'epoch', 'RA_obs', 'DEC_obs', 'mag', 'band', 'observatory', 'targetname', 'H', 'G', 'solar_presence', 'flags', 'RA', 'DEC', 'RA_app', 'DEC_app', 'RA*cos(Dec)_rate', 'DEC_rate', 'AZ', 'EL', 'AZ_rate', 'EL_rate', 'sat_X', 'sat_Y', 'sat_PANG', 'siderealtime', 'airmass', 'magextinct', 'V', 'surfbright', 'illumination', 'illum_defect', 'sat_sep', 'sat_vis', 'ang_width', 'PDObsLon', 'PDObsLat', 'PDSunLon', 'PDSunLat', 'SubSol_ang', 'SubSol_dist', 'NPole_ang', 'NPole_dist', 'EclLon', 'EclLat', 'r', 'r_rate', 'delta', 'delta_rate', 'lighttime', 'vel_sun', 'vel_obs', 'elong', 'elongFlag', 'alpha', 'lunar_elong', 'lunar_illum', 'sat_alpha', 'sunTargetPA', 'velocityPA', 'OrbPlaneAng', 'constellation', 'TDB-UT', 'ObsEclLon', 'ObsEclLat', 'NPole_RA', 'NPole_DEC', 'GlxLon', 'GlxLat', 'solartime', 'earth_lighttime', 'RA_3sigma', 'DEC_3sigma', 'SMAA_3sigma', 'SMIA_3sigma', 'Theta_3sigma', 'Area_3sigma', 'RSS_3sigma', 'r_3sigma', 'r_rate_3sigma', 'SBand_3sigma', 'XBand_3sigma', 'DoppDelay_3sigma', 'true_anom', 'hour_angle', 'alpha_true', 'PABLon', 'PABLat']
4647
>>> data_sup['r'] # doctest: +SKIP
47-
[1.87637455 1.87638696 1.87639935 1.8891401 1.88915504 1.88916999
48-
1.88918492 1.88963885 1.88964435 1.88965078 1.8896515 1.88965233
49-
1.88965306 1.88970198 1.88970271 1.88970353 1.88970426 1.88970508
50-
1.88970581 1.88978031 1.88978103 1.88978186 1.8897826 1.88978341
51-
1.88978415 1.88978497 1.88978569 1.88978653 1.88978725 1.90342431
52-
1.903438 1.90345164 1.90346529] AU
48+
<MaskedQuantity [1.74110682, 1.74111208, 1.74111672, 1.97466336,
49+
1.97465973, 1.97465603, 1.97465236, 1.98676694,
50+
1.98676467, 1.9867624 ] AU>
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5452
`~sbpy.data.Obs.supplement` queries in this case ephemerides from the
5553
JPL Horizons system (the default ``service`` to be used) and appends

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