Merge pull request #2321 from dhomeier/py311-ci

Add check for FITS files mistaken as ASCII to ``astropy_table_read`` for Python 3.11 compatibility

.github/workflows/ci_workflows.yml

@@ -1,4 +1,4 @@
-name: CI Workflows
+name: CI Tests
 
 on:
   push:
@@ -24,18 +24,21 @@ jobs:
     with:
       coverage: codecov
       display: true
-      # The Linux PyQt 5.15 installation requires apt-getting its xcb deps and headless X11 display
+      # Linux PyQt 5.15 and 6.x installations require apt-getting xcb and EGL deps
+      # and headless X11 display; as of Python 3.11 Scipy and h5py also need their own deps.
       libraries: |
         apt:
           - '^libxcb.*-dev'
           - libxkbcommon-x11-dev
           - libegl1-mesa
+          - libopenblas-dev
+          - libhdf5-dev
         brew:
           - enchant
 
       envs: |
         # Standard tests
-        # Linux builds - test on all supported PyQt5 and PySide2 versions,
+        # Linux builds - test on all supported PyQt5/6 and PySide2/6 versions,
         # and include all dependencies in some builds
         - linux: py38-test-pyqt514-all
         - linux: py38-test-pyside514
@@ -44,44 +47,55 @@ jobs:
         - linux: py310-test-pyside63
         - linux: py310-test-pyqt63-all
         - linux: py310-test-pyqt64-all
+        - linux: py311-test-pyqt514
 
         # Documentation build
         - linux: py38-docs-pyqt514
           coverage: false
         - macos: py39-docs-pyqt515
           coverage: false
 
-        # Test a few configurations on MacOS X
+        # Test a few configurations on macOS
         - macos: py38-test-pyqt514-all
         - macos: py310-test-pyqt515
         - macos: py310-test-pyside63
         - macos: py310-test-pyqt64
+        - macos: py311-test-pyqt515
 
         # Test some configurations on Windows
         - windows: py38-test-pyqt514
         - windows: py310-test-pyqt63
 
         # Test against latest developer versions of some packages
         - linux: py310-test-pyqt515-dev-all
+        - linux: py311-test-pyqt64-dev
 
   allowed_failures:
     needs: initial_checks
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
       coverage: codecov
       display: true
-      # Linux PyQt 5.15 and 6.3 installations require apt-getting xcb and EGL deps
       libraries: |
         apt:
           - '^libxcb.*-dev'
           - libxkbcommon-x11-dev
           - libegl1-mesa
+          - libopenblas-dev
+          - libhdf5-dev
         brew:
           - enchant
+          - hdf5
       envs: |
         # PySide6 6.4 failures due to https://github.com/spyder-ide/qtpy/issues/373
+        # and https://github.com/matplotlib/matplotlib/issues/24155
+        # Python 3.11.0 failing on Windows in test_image.py on
+        # > assert df.find_factory(fname) is df.img_data
         - linux: py310-test-pyside64
         - windows: py310-test-pyside64
+        - linux: py311-test-pyside64
+        - macos: py311-test-pyside64
+        - windows: py311-test-pyqt515
 
         # Windows docs build
         - windows: py310-docs-pyqt515
@@ -95,7 +109,7 @@ jobs:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
     with:
       # Setup PyQt5 deps and headless X server as per pyvista/setup-headless-display-action@v1
-      libraries: '^libxcb.*-dev libxkbcommon-x11-dev libgl1-mesa-glx xvfb'
+      libraries: '^libxcb.*-dev libxkbcommon-x11-dev libgl1-mesa-glx libopenblas-dev libhdf5-dev xvfb'
       test_extras: 'test,qt'
       test_command: Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 & sleep 3; DISPLAY=:99.0 pytest --pyargs glue
     secrets:

README.rst

@@ -46,7 +46,7 @@ License
 Glue is licensed under the `BSD
 License <https://github.com/glue-viz/glue/blob/master/LICENSE>`__.
 
-.. |Actions Status| image:: https://github.com/glue-viz/glue/workflows/CI%20Workflows/badge.svg
+.. |Actions Status| image:: https://github.com/glue-viz/glue/actions/workflows/ci_workflows.yml/badge.svg
     :target: https://github.com/glue-viz/glue/actions
     :alt: Glue's GitHub Actions CI Status
 .. |Coverage Status| image:: https://codecov.io/gh/glue-viz/glue/branch/master/graph/badge.svg

glue/core/data_factories/astropy_table.py

@@ -40,7 +40,10 @@ def astropy_table_read(*args, **kwargs):
     # also more generally, we should first try the ASCII readers.
     if 'format' not in kwargs:
         try:
-            return Table.read(*args, format='ascii', **kwargs)
+            t = Table.read(*args, format='ascii', **kwargs)
+            # Double-check for certain FITS files that may be read in as ASCII in Python 3.11
+            if not (len(t) == 1 and [c.value[0] for c in t.itercols()][:3] == ['SIMPLE', '=', 'T']):
+                return t
         except Exception:
             pass
 

setup.cfg

@@ -39,9 +39,9 @@ install_requires =
     ipykernel>=4.0,!=5.0.0,!=5.1.0
     qtconsole>=4.3
     dill>=0.2
+    h5py>=2.10; python_version<'3.11'
     xlrd>=1.2
     openpyxl>=3.0
-    h5py>=2.10
     mpl-scatter-density>=0.7
     pvextractor>=0.2
 
@@ -74,6 +74,7 @@ all =
     scikit-image
     PyAVM
     astrodendro
+    h5py>=2.10
     spectral-cube
     # See https://github.com/python-pillow/Pillow/issues/4509
     # for why we exclude pillow 7.1.0
@@ -97,6 +98,7 @@ test =
     pytest-cov
     pytest-faulthandler
     pytest-flake8
+    h5py>=2.10; platform_system=="Linux"
     objgraph
 
 [options.package_data]

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{38,39,310}-{codestyle,test,docs}-{pyqt514,pyqt515,pyside514,pyside515,pyqt63,pyside63}-all-{dev,legacy}
+    py{38,39,310,311}-{codestyle,test,docs}-{pyqt514,pyqt515,pyside514,pyside515,pyqt63,pyside63}-all-{dev,legacy}
 requires = pip >= 18.0
            setuptools >= 30.3.0