Merge pull request dendrograms#193 from astrofrog/fix-ci

Fix tests/continuous integration

.github/workflows/main.yml

@@ -11,9 +11,9 @@ jobs:
       envs: |
         - linux: codestyle
           pytest: false
-        - linux: py37-test-oldestdeps
-        - macos: py38-test
+        - linux: py38-test-oldestdeps
+        - macos: py39-test
         - windows: py39-test
         - linux: py310-test
-        - linux: py310-test-devdeps
+        - linux: py311-test-devdeps
       coverage: 'codecov'

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: '3.7'
+    python: '3.8'
 
 python:
   install:

astrodendro/analysis.py

@@ -462,7 +462,7 @@ def v_rms(self):
         0 following the Numpy convention - the third axis in the FITS
         convention).
         """
-        dv = self.velocity_scale or u.pixel
+        dv = self.velocity_scale if self.velocity_scale is not None else u.pixel
         ax = [0, 0, 0]
         ax[self.vaxis] = 1
         return dv * np.sqrt(self.stat.mom2_along(tuple(ax)))

astrodendro/io/util.py

@@ -91,7 +91,7 @@ def _construct_tree(repr):
             idx = int(idx)
             structure_indices = indices_by_structure[idx]
             f = flux_by_structure[idx]
-            if type(repr[idx]) == tuple:
+            if type(repr[idx]) is tuple:
                 sub_structures_repr = repr[idx][0]  # Parsed representation of sub structures
                 sub_structures = _construct_tree(sub_structures_repr)
                 for i in sub_structures:

astrodendro/tests/test_analysis.py

@@ -6,24 +6,14 @@
 from numpy.testing import assert_allclose
 import astropy.units as u
 from astropy.wcs import WCS
-
+from astropy.tests.helper import assert_quantity_allclose as assert_allclose_quantity
 
 from ._testdata import data
 from ..analysis import (ScalarStatistic, PPVStatistic, ppv_catalog,
                         Metadata, PPStatistic, pp_catalog)
 from .. import Dendrogram, periodic_neighbours
 from ..structure import Structure
 
-
-def assert_allclose_quantity(a, b):
-    if not isinstance(a, u.Quantity):
-        raise TypeError("a is not a quantity")
-    if not isinstance(b, u.Quantity):
-        raise TypeError("b is not a quantity")
-    assert_allclose(a.value, b.value)
-    assert a.unit == b.unit
-
-
 wcs_2d = WCS(header=dict(cdelt1=1, crval1=0, crpix1=1,
                          cdelt2=2, crval2=0, crpix2=1))
 wcs_3d = WCS(header=dict(cdelt1=1, crval1=0, crpix1=1,

astrodendro/tests/test_flux.py

@@ -6,10 +6,6 @@
 from ..flux import compute_flux
 
 
-def strip_parentheses(string):
-    return string.replace('(', '').replace(')', '')
-
-
 COMBINATIONS = \
     [
         (np.array([1, 2, 3]) * u.Jy, u.Jy, {}, 6 * u.Jy),
@@ -31,50 +27,41 @@ def test_compute_flux(input_quantities, output_unit, keywords, output):
 
 
 def test_monochromatic_wav_missing():
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='wavelength is needed to convert from erg'):
         compute_flux(np.array([1, 2, 3]) * u.erg / u.cm ** 2 / u.s / u.micron, u.Jy)
-    assert exc.value.args[0] == 'wavelength is needed to convert from erg / (cm2 micron s) to Jy'
 
 
 def test_monochromatic_wav_invalid_units():
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='wavelength should be a physical length'):
         compute_flux(np.array([1, 2, 3]) * u.erg / u.cm ** 2 / u.s / u.micron, u.Jy, wavelength=3 * u.L)
-    assert exc.value.args[0] == 'wavelength should be a physical length'
 
 
 def test_surface_brightness_scale_missing():
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='spatial_scale is needed to convert from Jy'):
         compute_flux(np.array([1, 2, 3]) * u.Jy / u.arcsec ** 2, u.Jy)
-    assert strip_parentheses(exc.value.args[0]) == 'spatial_scale is needed to convert from Jy / arcsec2 to Jy'
 
 
 def test_surface_brightness_invalid_units():
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='spatial_scale should be an angle'):
         compute_flux(np.array([1, 2, 3]) * u.Jy / u.arcsec ** 2, u.Jy, spatial_scale=3 * u.m)
-    assert exc.value.args[0] == 'spatial_scale should be an angle'
 
 
 def test_per_beam_scale_missing():
 
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='spatial_scale is needed to convert from Jy / beam to Jy'):
         compute_flux(np.array([1, 2, 3]) * u.Jy / u.beam, u.Jy, beam_major=3 * u.arcsec, beam_minor=2. * u.arcsec)
-    assert strip_parentheses(exc.value.args[0]) == 'spatial_scale is needed to convert from Jy / beam to Jy'
 
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='beam_major is needed to convert from Jy / beam to Jy'):
         compute_flux(np.array([1, 2, 3]) * u.Jy / u.beam, u.Jy, spatial_scale=3 * u.arcsec, beam_minor=2. * u.arcsec)
-    assert strip_parentheses(exc.value.args[0]) == 'beam_major is needed to convert from Jy / beam to Jy'
 
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='beam_minor is needed to convert from Jy / beam to Jy'):
         compute_flux(np.array([1, 2, 3]) * u.Jy / u.beam, u.Jy, spatial_scale=3 * u.arcsec, beam_major=2. * u.arcsec)
-    assert strip_parentheses(exc.value.args[0]) == 'beam_minor is needed to convert from Jy / beam to Jy'
 
 
 def test_per_beam_invalid_units():
 
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='beam_major should be an angle'):
         compute_flux(np.array([1, 2, 3]) * u.Jy / u.beam, u.Jy, spatial_scale=3 * u.arcsec, beam_major=3 * u.m, beam_minor=2. * u.arcsec)
-    assert exc.value.args[0] == 'beam_major should be an angle'
 
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(ValueError, match='beam_minor should be an angle'):
         compute_flux(np.array([1, 2, 3]) * u.Jy / u.beam, u.Jy, spatial_scale=3 * u.arcsec, beam_major=3 * u.arcsec, beam_minor=2. * u.m)
-    assert exc.value.args[0] == 'beam_minor should be an angle'

astrodendro/tests/test_index.py

@@ -8,10 +8,10 @@ def assert_permuted_fancyindex(x, y):
     """ Assert that two fancy indices (tuples of integer ndarrays)
     are permutations of each other
     """
-    if not isinstance(x, tuple) or not(isinstance(x[0], np.ndarray)):
+    if not isinstance(x, tuple) or not (isinstance(x[0], np.ndarray)):
         raise TypeError("First argument not a fancy index: %s" % x)
 
-    if not isinstance(y, tuple) or not(isinstance(y[0], np.ndarray)):
+    if not isinstance(y, tuple) or not (isinstance(y[0], np.ndarray)):
         raise TypeError("Second argument not a fancy index: %s" % y)
 
     dtype = [('%i' % i, 'i') for i in range(len(x))]

setup.cfg

@@ -14,20 +14,20 @@ github_project = dendrograms/astrodendro
 [options]
 zip_safe = False
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8
 setup_requires = setuptools_scm
 install_requires =
-    numpy>1.16
-    astropy>4
-    matplotlib>3
-    h5py>3
+    numpy>=1.20
+    astropy>=5.0
+    matplotlib>=3.3
+    h5py>=3
 
 [options.extras_require]
 test =
     pytest
     pytest-cov
 docs =
-    sphinx
+    sphinx<7
     numpydoc
     sphinx-astropy
     aplpy

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{37,38,39,310}-test{,-alldeps,-devdeps}{,-cov}
+    py{38,39,310,311}-test{,-alldeps,-devdeps}{,-cov}
     build_docs
     linkcheck
     codestyle
@@ -12,8 +12,7 @@ isolated_build = true
 [testenv]
 setenv =
     MPLBACKEND=agg
-    devdeps: PIP_EXTRA_INDEX_URL = https://pypi.anaconda.org/astropy/simple https://pypi.anaconda.org/scipy-wheels-nightly/simple
-passenv = HOME WINDIR LC_ALL LC_CTYPE CC CI TRAVIS
+    devdeps: PIP_EXTRA_INDEX_URL = https://pypi.anaconda.org/astropy/simple https://pypi.anaconda.org/scientific-python-nightly-wheels/
 changedir = .tmp/{envname}
 description =
     run tests
@@ -26,10 +25,10 @@ deps =
     cov: coverage
     devdeps: numpy>=0.0.dev0
     devdeps: astropy>=0.0.dev0
-    oldestdeps: astropy==4.0.*
+    oldestdeps: astropy==5.0.*
     oldestdeps: h5py==3.0.*
-    oldestdeps: matplotlib==3.0.*
-    oldestdeps: numpy==1.16.*
+    oldestdeps: matplotlib==3.3.*
+    oldestdeps: numpy==1.20.*
 
 extras =
     test