Merge pull request #69 from weaverba137/endian-test

Fix failing test on bigendian devices

.github/workflows/ci_cron_weekly.yml

@@ -11,7 +11,7 @@ jobs:
   # Testing links in documents is a good example of something to run on a schedule
   # to catch links that stop working for some reason.
   doc_test:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python to build docs with sphinx

.github/workflows/ci_tests.yml

@@ -37,7 +37,7 @@ jobs:
             python: 3.8
             toxenv: py38-test-alldeps-cov
 
-          - name: OS X - Python 3.8 with all optional dependencies
+          - name: macOS - Python 3.8 with all optional dependencies
             os: macos-latest
             python: 3.8
             toxenv: py38-test-alldeps

.gitignore

@@ -36,6 +36,7 @@ docs/_build
 .flooignore
 
 # Visual Studio Code project files
+.env
 .vscode
 
 # Packages/installer info

.readthedocs.yml

@@ -1,16 +1,27 @@
-# See https://docs.readthedocs.io/en/latest/yaml-config.html
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
 version: 2
 
 build:
-    image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
 
+# Optionally declare the Python requirements required to build your docs
 python:
-    version: 3.7
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-                - docs
-                - all
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - all
 
+# If using Sphinx, optionally build your docs in additional formats such as PDF
 formats: []

pydl/pydlspec2d/spec2d.py

@@ -436,7 +436,7 @@ def filter_thru(flux, waveimg=None, wset=None, mask=None,
     pixnorm, logdiff = traceset2xy(diffset)
     logdiff = np.absolute(logdiff)
     if mask is not None:
-        flux_interp = djs_maskinterp(flux, mask, iaxis=0)
+        flux_interp = djs_maskinterp(flux, mask, axis=0)
     res = np.zeros((nTrace, len(ffiles)), dtype=flux.dtype)
     for i, f in enumerate(ffiles):
         filter_data = ascii.read(f, comment='#.*', names=('lam', 'respt',

pydl/pydlutils/tests/test_mangle.py

@@ -11,16 +11,13 @@ class TestMangle(object):
     """Test the functions in pydl.pydlutils.mangle.
     """
 
-    def setup(self):
+    def setup_method(self):
         self.poly_fits = get_pkg_data_filename('t/polygon.fits')
         self.no_id_fits = get_pkg_data_filename('t/polygon_no_id.fits')
         self.one_cap_fits = get_pkg_data_filename('t/polygon_one_cap.fits')
         self.poly_ply = get_pkg_data_filename('t/polygon.ply')
         self.bad_ply = get_pkg_data_filename('t/median_data.txt')
 
-    def teardown(self):
-        pass
-
     def test_ManglePolygon(self):
         #
         # Zero caps

pydl/pydlutils/tests/test_sdss.py

@@ -13,7 +13,7 @@ class TestSDSS(object):
     """Test the functions in pydl.pydlutils.sdss.
     """
 
-    def setup(self):
+    def setup_method(self):
         pydl.pydlutils.sdss.maskbits = set_maskbits(
             maskbits_file=get_pkg_data_filename('t/testMaskbits.par'))
         self.opbadfields = np.array([
@@ -28,9 +28,6 @@ def setup(self):
         pydl.pydlutils.sdss.opbadfields = self.opbadfields
         return
 
-    def teardown(self):
-        pass
-
     def test_default_skyversion(self):
         assert default_skyversion() == 2
 

pydl/pydlutils/tests/test_trace.py

@@ -13,15 +13,15 @@ class TestTrace(object):
     """Test the functions in pydl.pydlutils.trace.
     """
 
-    def setup(self):
+    def setup_method(self):
         # extracted from spFrame-b1-00057618.fits
 
         self.sdss = fits.open(get_pkg_data_filename('t/sdss_traceset.fits'))
         # extracted from spFrame-r1-00180406.fits
         self.boss = fits.open(get_pkg_data_filename('t/boss_traceset.fits'))
         return
 
-    def teardown(self):
+    def teardown_method(self):
         self.sdss.close()
         self.boss.close()
         return

pydl/pydlutils/tests/test_yanny.py

@@ -2,6 +2,8 @@
 # -*- coding: utf-8 -*-
 import warnings
 import json
+import stat
+import sys
 from os import chmod, remove
 from os.path import exists, join
 from shutil import copy, rmtree
@@ -29,7 +31,7 @@ class YannyTestCase(object):
     """
     save_temp = False
 
-    def setup(self):
+    def setup_method(self):
         self.temp_dir = mkdtemp(prefix='yanny-test-')
         # Ignore deprecation warnings--this only affects Python 2.5 and 2.6,
         # since deprecation warnings are ignored by defualt on 2.7
@@ -39,7 +41,7 @@ def setup(self):
         with open(get_pkg_data_filename("t/yanny_data.json")) as js:
             self.test_data = json.load(js)
 
-    def teardown(self):
+    def teardown_method(self):
         warnings.resetwarnings()
         if not self.save_temp:
             if hasattr(self, 'temp_dir') and exists(self.temp_dir):
@@ -82,7 +84,11 @@ def json2dtype(self, data):
                 stuff.append(tuple([str(k[0]), str(k[1]), tuple(k[2])]))
             else:
                 stuff.append(tuple([str(k[0]), str(k[1])]))
-        return np.dtype(stuff)
+        d = np.dtype(stuff)
+        if sys.byteorder == 'little':
+            return d
+        else:
+            return d.newbyteorder()
 
 
 class TestYanny(YannyTestCase):

setup.cfg

@@ -42,8 +42,6 @@ all =
 test =
     pytest-astropy
     pytest-mock
-astropy20 =
-    pytest-mock<2
 docs =
     sphinx-astropy
 

tox.ini

@@ -3,27 +3,23 @@ envlist =
     py{36,37,38}-test{,-alldeps,-devdeps}{,-cov}
     py{36,37,38}-test-numpy{116,117,118}
     py{36,37,38}-test-astropy{30,40,lts}
-    astropy20
     build_docs
     linkcheck
     codestyle
 requires =
     setuptools >= 30.3.0
     pip >= 19.3.1
     setuptools_scm
-    tox-pypi-filter >= 0.12
 isolated_build = true
+indexserver =
+    NIGHTLY = https://pypi.anaconda.org/scipy-wheels-nightly/simple
 
 [testenv]
-
-# The following option combined with the use of the tox-pypi-filter above allows
-# project-wide pinning of dependencies, e.g. if new versions of pytest do not
-# work correctly with pytest-astropy plugins. Most of the time the pinnings file
-# should be empty.
-pypi_filter = https://raw.githubusercontent.com/astropy/ci-helpers/master/pip_pinnings.txt
+# Suppress display of matplotlib plots generated during docs build
+setenv = MPLBACKEND=agg
 
 # Pass through the following environment variables which may be needed for the CI
-passenv = HOME WINDIR LC_ALL LC_CTYPE CC CI GITHUB_* COVERALLS_*
+passenv = HOME,WINDIR,LC_ALL,LC_CTYPE,CC,CI,GITHUB_*,COVERALLS_*
 
 # Run the tests in a temporary directory to make sure that we don't import
 # this package from the source tree
@@ -52,6 +48,7 @@ description =
 
 # The following provides some specific pinnings for key packages
 deps =
+
     cov: coveralls
 
     numpy116: numpy==1.16.*
@@ -62,7 +59,7 @@ deps =
     astropy40: astropy==4.0.*
     astropylts: astropy==4.0.*
 
-    devdeps: git+https://github.com/numpy/numpy.git#egg=numpy
+    devdeps: :NIGHTLY:numpy
     devdeps: git+https://github.com/astropy/astropy.git#egg=astropy
 
 # The following indicates which extras_require from setup.cfg will be installed
@@ -76,18 +73,6 @@ commands =
     cov: pytest --pyargs pydl {toxinidir}/docs --cov pydl --cov-config={toxinidir}/setup.cfg {posargs}
     cov: coveralls
 
-[testenv:astropy20]
-description = run tests with astropy2.0.*
-extras = astropy20
-deps =
-    astropy==2.0.*
-    numpy==1.14.*
-    pytest<3.7
-    pytest-mock<2
-commands =
-    pip freeze
-    pytest -p astropy.tests.pytest_repeat -p astropy.extern.plugins.pytest_doctestplus.plugin -p astropy.extern.plugins.pytest_openfiles.plugin -p astropy.extern.plugins.pytest_remotedata.plugin --traceconfig --pyargs pydl {toxinidir}/docs {posargs}
-
 [testenv:build_docs]
 changedir = docs
 description = invoke sphinx-build to build the HTML docs