MNT: Infrastructure and other updates

astropy · Dec 5, 2023 · 6b14578 · 6b14578
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diff --git a/.flake8 b/.flake8
@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 100
diff --git a/.github/workflows/cron-tests.yml b/.github/workflows/cron-tests.yml
@@ -5,48 +5,31 @@
 name: Weekly Tests
 
 on:
+  pull_request:
+    # We also want this workflow triggered if the 'Extra CI' label is added
+    # or present when PR is updated
+    types:
+      - synchronize
+      - labeled
   schedule:
     # run every Monday at 6am UTC
     - cron: '0 6 * * 1'
 
-env:
-  TOXARGS: '-v'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  # Set up matrix to run tox tests across lists of os, python version, and tox environment
-  matrix_tests:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # Github actions supports ubuntu, windows, and macos virtual environments:
-        # https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners
-        #
-        # Only run on ubuntu by default, but can add other os's to the test matrix here.
-        # For example -- os: [ubuntu-latest, macos-latest, windows-latest]
-        include:
-          - os: ubuntu-latest
-            python: '3.11'
-            tox_env: 'linkcheck'
-          - os: ubuntu-latest
-            python: '3.12'
-            tox_env: 'py312-test-devdeps'
-          - os: ubuntu-latest
-            python: '3.12'
-            tox_env: 'py312-test-predeps'
+  tests:
+    if: (github.repository == 'astropy/specreduce' && (github.event_name == 'schedule' || github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'Extra CI')))
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      submodules: false
+      coverage: ''
+      envs: |
+        - name: Check URLs in docs
+          linux: linkcheck
 
-    steps:
-    - name: Check out repository
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-    - name: Set up python ${{ matrix.python }} with tox environment ${{ matrix.tox_env }} on ${{ matrix.os }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python }}
-    - name: Install base dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install tox
-    - name: Test with tox
-      run: |
-        tox -e ${{ matrix.tox_env }}
+        - name: Python 3.12 on Linux with pre-releases
+          linux: py312-test-alldeps-predeps
+          toxargs: -v
diff --git a/.github/workflows/tox-tests.yml b/.github/workflows/tox-tests.yml
@@ -11,64 +11,44 @@ on:
     tags:
       - '*'
   pull_request:
+  schedule:
+    # run every Monday at 6am UTC
+    - cron: '0 6 * * 1'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-env:
-  TOXARGS: '-v'
-
 jobs:
-  # Set up matrix to run tox tests across lists of os, python version, and tox environment
-  matrix_tests:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # Github actions supports ubuntu, windows, and macos virtual environments:
-        # https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners
-        #
-        # Only run on ubuntu by default, but can add other os's to the test matrix here.
-        # For example -- os: [ubuntu-latest, macos-latest, windows-latest]
-        include:
-          - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test-cov'
-          - os: ubuntu-latest
-            python: '3.11'
-            tox_env: 'py311-test'
-          - os: ubuntu-latest
-            python: '3.12'
-            tox_env: 'py312-test'
-          - os: macos-latest
-            python: '3.12'
-            tox_env: 'py312-test-devdeps'
-          - os: ubuntu-latest
-            python: '3.12'
-            tox_env: 'codestyle'
-          - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test-oldestdeps'
+  tests:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV }}
+    with:
+      submodules: false
+      coverage: ''
+      envs: |
+        - name: Codestyle
+          linux: codestyle
+
+        - name: Python 3.8 on Linux with oldest supported dependencies
+          linux: py38-test-oldestdeps
+          toxargs: -v
+
+        - name: Python 3.9 on Windows with minimal dependencies
+          windows: py39-test
+          toxargs: -v
+
+        - name: Python 3.10 on OSX with minimal dependencies
+          macos: py310-test
+          toxargs: -v
+
+        - name: Python 3.11 on Linux with all dependencies, remote data, and coverage
+          linux: py311-test-alldeps-cov
+          coverage: codecov
+          toxargs: -v
+          posargs: --remote-data=any
 
-    steps:
-    - name: Check out repository
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-    - name: Set up python ${{ matrix.python }} with tox environment ${{ matrix.tox_env }} on ${{ matrix.os }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python }}
-    - name: Install base dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install tox
-    - name: Test with tox
-      run: |
-        tox -e ${{ matrix.tox_env }}
-    - name: Upload coverage to codecov
-      if: "contains(matrix.tox_env, '-cov')"
-      uses: codecov/codecov-action@v3
-      with:
-        file: ./coverage.xml
-        verbose: true
+        - name: (Allowed Failure) Python 3.12 on Linux with dev dependencies
+          linux: py312-test-devdeps
+          toxargs: -v
diff --git a/.readthedocs.yml → .readthedocs.yaml b/.readthedocs.yml → .readthedocs.yaml
@@ -1,11 +1,11 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   apt_packages:
     - graphviz
   tools:
-    python: "3.10"
+    python: "3.11"
 
 sphinx:
   builder: html

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -5,30 +5,37 @@ New Features
 ^^^^^^^^^^^^
 
 - Added 'interpolated_profile' option for HorneExtract. If The ``interpolated_profile`` option
-is used, the image will be sampled in various wavelength bins (set by
-``n_bins_interpolated_profile``), averaged in those bins, and samples are then
-interpolated between (linear by default, interpolation degree can be set with
-the ``interp_degree_interpolated_profile`` parameter) to generate a continuously varying
-spatial profile that can be evaluated at any wavelength.[ #173]
+  is used, the image will be sampled in various wavelength bins (set by
+  ``n_bins_interpolated_profile``), averaged in those bins, and samples are then
+  interpolated between (linear by default, interpolation degree can be set with
+  the ``interp_degree_interpolated_profile`` parameter) to generate a continuously varying
+  spatial profile that can be evaluated at any wavelength. [#173]
 
 API Changes
 ^^^^^^^^^^^
 
-- Fit residuals exposed for wavelength calibration in WavelengthCalibration1D.fit_residuals. [#446]
+- Fit residuals exposed for wavelength calibration in ``WavelengthCalibration1D.fit_residuals``. [#446]
 
 Bug Fixes
 ^^^^^^^^^
 
 - Output 1D spectra from Background no longer include NaNs. Output 1D
-spectra from BoxcarExtract no longer include NaNs when none are present
-in the extraction window. NaNs in the window will still propagate to
-BoxcarExtract's extracted 1D spectrum. [#159]
+  spectra from BoxcarExtract no longer include NaNs when none are present
+  in the extraction window. NaNs in the window will still propagate to
+  BoxcarExtract's extracted 1D spectrum. [#159]
 
-- Backgrounds using median statistic properly ignore zero-weighted pixels
-[#159]
+- Backgrounds using median statistic properly ignore zero-weighted pixels.
+  [#159]
 
-- HorneExtract now accepts 'None' as a vaild option for bkgrd_prof [#171]
+- HorneExtract now accepts 'None' as a vaild option for ``bkgrd_prof``. [#171]
 
+Other changes
+^^^^^^^^^^^^^
+
+- The following packages are now optional dependencies because they are not
+  required for core functionality: ``matplotlib``, ``photutils``, ``synphot``.
+  To install them anyway, use the ``[all]`` specifier when you install specreduce; e.g.:
+  ``pip install specreduce[all]`` [#202]
 
 1.3.0 (2022-12-05)
 ------------------

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,16 +1,11 @@
 include README.rst
 include CHANGES.rst
-include setup.cfg
-include LICENSE.rst
 include pyproject.toml
 
-recursive-include specreduce *.pyx *.c *.pxd
 recursive-include docs *
 recursive-include licenses *
-recursive-include scripts *
 
+prune notebook_sandbox
 prune build
 prune docs/_build
 prune docs/api
-
-global-exclude *.pyc *.o
diff --git a/README.rst b/README.rst
@@ -1,22 +1,27 @@
 Specreduce
 ==========
 
-.. image:: https://github.com/astropy/specreduce/workflows/Python%20Tests/badge.svg
-    :target: https://github.com/astropy/specreduce/actions
+.. image:: https://github.com/astropy/specreduce/actions/workflows/tox-tests.yml/badge.svg?branch=main
+    :target: https://github.com/astropy/specreduce/actions/workflows/tox-tests.yml
     :alt: CI Status
 
+.. image:: https://codecov.io/gh/astropy/specreduce/graph/badge.svg?token=3fLGjZ2Pe0
+    :target: https://codecov.io/gh/astropy/specreduce
+    :alt: Coverage
+
 .. image:: https://readthedocs.org/projects/specreduce/badge/?version=latest
-    :target: http://specreduce.readthedocs.io/en/latest/?badge=latest
+    :target: http://specreduce.readthedocs.io/en/latest/
     :alt: Documentation Status
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6608788.svg
-   :target: https://doi.org/10.5281/zenodo.6608788
-   :alt: Zenodo DOI 10.5281/zenodo.6608788
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6608787.svg
+   :target: https://zenodo.org/doi/10.5281/zenodo.6608787
+   :alt: Zenodo DOI 10.5281/zenodo.6608787
 
 .. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
-    :target: http://www.astropy.org/
+   :target: http://www.astropy.org/
+   :alt: Powered by Astropy
 
-Specreduce is an Astropy affiliated package with the goal of providing a shared
+Specreduce is an Astropy coordinated package with the goal of providing a shared
 set of Python utilities that can be used to reduce and calibrate spectroscopic data.
 
 License

diff --git a/conftest.py b/conftest.py
@@ -0,0 +1,24 @@
+"""Need to repeat the astropy header config here for tox."""
+
+try:
+    from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS  # noqa: E501
+    ASTROPY_HEADER = True
+except ImportError:
+    ASTROPY_HEADER = False
+
+
+def pytest_configure(config):
+
+    if ASTROPY_HEADER:
+
+        config.option.astropy_header = True
+
+        # Customize the following lines to add/remove entries from the list of
+        # packages for which version numbers are displayed when running the tests.  # noqa: E501
+        PYTEST_HEADER_MODULES.pop('Pandas', None)
+        PYTEST_HEADER_MODULES['scikit-image'] = 'skimage'
+        PYTEST_HEADER_MODULES['photutils'] = 'photutils'
+        PYTEST_HEADER_MODULES['synphot'] = 'synphot'
+
+        from specreduce import __version__
+        TESTED_VERSIONS["specreduce"] = __version__
diff --git a/docs/conf.py b/docs/conf.py
@@ -25,24 +25,17 @@
 # Thus, any C-extensions that are needed to build the documentation will *not*
 # be accessible, and the documentation will not build correctly.
 
-import os
 import sys
 import datetime
-from importlib import import_module
+
+from specreduce import __version__
 
 try:
     from sphinx_astropy.conf.v1 import *  # noqa
 except ImportError:
     print('ERROR: the documentation requires the sphinx-astropy package to be installed')
     sys.exit(1)
 
-# Get configuration information from setup.cfg
-from configparser import ConfigParser
-conf = ConfigParser()
-
-conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')])
-setup_cfg = dict(conf.items('metadata'))
-
 # -- General configuration ----------------------------------------------------
 
 # By default, highlight as Python 3.
@@ -67,22 +60,19 @@
 # -- Project information ------------------------------------------------------
 
 # This does not *have* to match the package name, but typically does
-project = setup_cfg['name']
-author = setup_cfg['author']
+project = "specreduce"
+author = "Astropy Specreduce contributors"
 copyright = '{0}, {1}'.format(
-    datetime.datetime.now().year, setup_cfg['author'])
+    datetime.datetime.now().year, author)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-import_module(setup_cfg['name'])
-package = sys.modules[setup_cfg['name']]
-
 # The short X.Y version.
-version = package.__version__.split('-', 1)[0]
+version = __version__.split('-', 1)[0]
 # The full version, including alpha/beta/rc tags.
-release = package.__version__
+release = __version__
 
 
 # -- Options for HTML output --------------------------------------------------
@@ -154,19 +144,6 @@
 
 # -- Options for the edit_on_github extension ---------------------------------
 
-if setup_cfg.get('edit_on_github').lower() == 'true':
-
-    extensions += ['sphinx_astropy.ext.edit_on_github']
-
-    edit_on_github_project = setup_cfg['github_project']
-    edit_on_github_branch = "main"
-
-    edit_on_github_source_root = ""
-    edit_on_github_doc_root = "docs"
-
-# -- Resolving issue number to links in changelog -----------------------------
-github_issues_url = 'https://github.com/{0}/issues/'.format(setup_cfg['github_project'])
-
 # -- Turn on nitpicky mode for sphinx (to warn about references not found) ----
 #
 nitpicky = True