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MNT: Infrastructure and other updates (#202)
* MNT: Infrastructure and other updates. Replace broken URL and deprecated np.trapz usage. Ignore link that is blocking CI check. * Clean up test header * DOC: Style logo like specutils
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‎.flake8

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[flake8]
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max-line-length = 100

‎.github/workflows/cron-tests.yml

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name: Weekly Tests
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on:
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pull_request:
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# We also want this workflow triggered if the 'Extra CI' label is added
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# or present when PR is updated
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types:
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- synchronize
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- labeled
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schedule:
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# run every Monday at 6am UTC
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- cron: '0 6 * * 1'
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env:
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TOXARGS: '-v'
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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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jobs:
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# Set up matrix to run tox tests across lists of os, python version, and tox environment
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matrix_tests:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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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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#
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# Only run on ubuntu by default, but can add other os's to the test matrix here.
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# For example -- os: [ubuntu-latest, macos-latest, windows-latest]
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include:
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- os: ubuntu-latest
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python: '3.11'
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tox_env: 'linkcheck'
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- os: ubuntu-latest
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python: '3.12'
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tox_env: 'py312-test-devdeps'
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- os: ubuntu-latest
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python: '3.12'
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tox_env: 'py312-test-predeps'
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tests:
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if: (github.repository == 'astropy/specreduce' && (github.event_name == 'schedule' || github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'Extra CI')))
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uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
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with:
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submodules: false
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coverage: ''
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envs: |
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- name: Check URLs in docs
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linux: linkcheck
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steps:
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- name: Check out repository
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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 }} with tox environment ${{ matrix.tox_env }} on ${{ matrix.os }}
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uses: actions/setup-python@v3
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with:
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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
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python -m pip install tox
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- name: Test with tox
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run: |
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tox -e ${{ matrix.tox_env }}
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- name: Python 3.12 on Linux with pre-releases
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linux: py312-test-alldeps-predeps
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toxargs: -v

‎.github/workflows/tox-tests.yml

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tags:
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- '*'
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pull_request:
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schedule:
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# run every Monday at 6am UTC
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- cron: '0 6 * * 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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TOXARGS: '-v'
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jobs:
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# Set up matrix to run tox tests across lists of os, python version, and tox environment
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matrix_tests:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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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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#
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# Only run on ubuntu by default, but can add other os's to the test matrix here.
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# For example -- os: [ubuntu-latest, macos-latest, windows-latest]
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include:
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- os: ubuntu-latest
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python: '3.10'
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tox_env: 'py310-test-cov'
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- os: ubuntu-latest
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python: '3.11'
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tox_env: 'py311-test'
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- os: ubuntu-latest
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python: '3.12'
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tox_env: 'py312-test'
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- os: macos-latest
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python: '3.12'
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tox_env: 'py312-test-devdeps'
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- os: ubuntu-latest
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python: '3.12'
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tox_env: 'codestyle'
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- os: ubuntu-latest
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python: '3.10'
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tox_env: 'py310-test-oldestdeps'
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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 }}
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with:
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submodules: false
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coverage: ''
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envs: |
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- name: Codestyle
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linux: codestyle
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- name: Python 3.8 on Linux with oldest supported dependencies
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linux: py38-test-alldeps-oldestdeps
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toxargs: -v
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- name: Python 3.9 on Windows with minimal dependencies
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windows: py39-test
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toxargs: -v
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- name: Python 3.10 on OSX with minimal dependencies
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macos: py310-test
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toxargs: -v
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- name: Python 3.11 on Linux with all dependencies, remote data, and coverage
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linux: py311-test-alldeps-cov
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coverage: codecov
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toxargs: -v
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posargs: --remote-data=any
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steps:
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- name: Check out repository
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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 }} with tox environment ${{ matrix.tox_env }} on ${{ matrix.os }}
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uses: actions/setup-python@v3
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with:
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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
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python -m pip install tox
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- name: Test with tox
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run: |
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tox -e ${{ matrix.tox_env }}
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- name: Upload coverage to codecov
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if: "contains(matrix.tox_env, '-cov')"
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uses: codecov/codecov-action@v3
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with:
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file: ./coverage.xml
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verbose: true
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- name: (Allowed Failure) Python 3.12 on Linux with dev dependencies
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linux: py312-test-devdeps
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toxargs: -v

‎.readthedocs.yml ‎.readthedocs.yaml

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version: 2
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build:
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os: ubuntu-20.04
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os: ubuntu-22.04
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apt_packages:
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- graphviz
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tools:
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python: "3.10"
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python: "3.11"
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sphinx:
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builder: html

‎CHANGES.rst

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^^^^^^^^^^^^
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- Added 'interpolated_profile' option for HorneExtract. If The ``interpolated_profile`` option
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is used, the image will be sampled in various wavelength bins (set by
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``n_bins_interpolated_profile``), averaged in those bins, and samples are then
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interpolated between (linear by default, interpolation degree can be set with
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the ``interp_degree_interpolated_profile`` parameter) to generate a continuously varying
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spatial profile that can be evaluated at any wavelength.[ #173]
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is used, the image will be sampled in various wavelength bins (set by
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``n_bins_interpolated_profile``), averaged in those bins, and samples are then
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interpolated between (linear by default, interpolation degree can be set with
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the ``interp_degree_interpolated_profile`` parameter) to generate a continuously varying
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spatial profile that can be evaluated at any wavelength. [#173]
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API Changes
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^^^^^^^^^^^
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- Fit residuals exposed for wavelength calibration in WavelengthCalibration1D.fit_residuals. [#446]
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- Fit residuals exposed for wavelength calibration in ``WavelengthCalibration1D.fit_residuals``. [#446]
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Bug Fixes
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^^^^^^^^^
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- Output 1D spectra from Background no longer include NaNs. Output 1D
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spectra from BoxcarExtract no longer include NaNs when none are present
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in the extraction window. NaNs in the window will still propagate to
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BoxcarExtract's extracted 1D spectrum. [#159]
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spectra from BoxcarExtract no longer include NaNs when none are present
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in the extraction window. NaNs in the window will still propagate to
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BoxcarExtract's extracted 1D spectrum. [#159]
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- Backgrounds using median statistic properly ignore zero-weighted pixels
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[#159]
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- Backgrounds using median statistic properly ignore zero-weighted pixels.
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[#159]
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- HorneExtract now accepts 'None' as a vaild option for bkgrd_prof [#171]
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- HorneExtract now accepts 'None' as a vaild option for ``bkgrd_prof``. [#171]
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Other changes
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^^^^^^^^^^^^^
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- The following packages are now optional dependencies because they are not
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required for core functionality: ``matplotlib``, ``photutils``, ``synphot``.
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To install them anyway, use the ``[all]`` specifier when you install specreduce; e.g.:
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``pip install specreduce[all]`` [#202]
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1.3.0 (2022-12-05)
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------------------

‎MANIFEST.in

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include README.rst
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include CHANGES.rst
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include setup.cfg
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include LICENSE.rst
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include pyproject.toml
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recursive-include specreduce *.pyx *.c *.pxd
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recursive-include docs *
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recursive-include licenses *
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recursive-include scripts *
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prune notebook_sandbox
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prune build
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prune docs/_build
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prune docs/api
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global-exclude *.pyc *.o

‎README.rst

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Specreduce
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==========
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.. image:: https://github.com/astropy/specreduce/workflows/Python%20Tests/badge.svg
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:target: https://github.com/astropy/specreduce/actions
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.. image:: https://github.com/astropy/specreduce/actions/workflows/tox-tests.yml/badge.svg?branch=main
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:target: https://github.com/astropy/specreduce/actions/workflows/tox-tests.yml
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:alt: CI Status
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.. image:: https://codecov.io/gh/astropy/specreduce/graph/badge.svg?token=3fLGjZ2Pe0
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:target: https://codecov.io/gh/astropy/specreduce
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:alt: Coverage
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.. image:: https://readthedocs.org/projects/specreduce/badge/?version=latest
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:target: http://specreduce.readthedocs.io/en/latest/?badge=latest
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:target: http://specreduce.readthedocs.io/en/latest/
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:alt: Documentation Status
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.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6608788.svg
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:target: https://doi.org/10.5281/zenodo.6608788
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:alt: Zenodo DOI 10.5281/zenodo.6608788
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.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6608787.svg
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:target: https://zenodo.org/doi/10.5281/zenodo.6608787
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:alt: Zenodo DOI 10.5281/zenodo.6608787
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.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
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:target: http://www.astropy.org/
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:target: http://www.astropy.org/
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:alt: Powered by Astropy
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Specreduce is an Astropy affiliated package with the goal of providing a shared
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Specreduce is an Astropy coordinated package with the goal of providing a shared
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set of Python utilities that can be used to reduce and calibrate spectroscopic data.
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License

‎conftest.py

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"""Need to repeat the astropy header config here for tox."""
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try:
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from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
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ASTROPY_HEADER = True
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except ImportError:
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ASTROPY_HEADER = False
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def pytest_configure(config):
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if ASTROPY_HEADER:
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config.option.astropy_header = True
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# Customize the following lines to add/remove entries from the list of
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# packages for which version numbers are displayed when running the tests.
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PYTEST_HEADER_MODULES.pop('Pandas', None)
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PYTEST_HEADER_MODULES.pop('h5py', None)
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PYTEST_HEADER_MODULES['astropy'] = 'astropy'
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PYTEST_HEADER_MODULES['specutils'] = 'specutils'
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PYTEST_HEADER_MODULES['photutils'] = 'photutils'
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PYTEST_HEADER_MODULES['synphot'] = 'synphot'
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from specreduce import __version__
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TESTED_VERSIONS["specreduce"] = __version__

‎docs/_static/logo_icon.ico

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‎docs/_static/logo_icon.png

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‎docs/_static/specreduce.css

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@import url("bootstrap-astropy.css");
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div.topbar a.brand {
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background: transparent url("logo_icon.png") no-repeat 8px 3px;
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background-image: url("logo_icon.png"), none;
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background-size: 32px 32px;
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}
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#logotext1 {
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color: #519EA8;
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}
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#logotext2 {
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color: #FF5000;
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}

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