forked from pool/python-sherpa
Dirk Mueller
14bc0b2cc6
* Update to version 4.13.0. * Add sherpa-numpy-1.20.patch: Fix test errors with numpy 1.20 [gh#sherpa/sherpa#/1092]; patch committed upstream. * Disable python 3.6 flavour: dependency numpy not supported. OBS-URL: https://build.opensuse.org/request/show/873000 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-sherpa?expand=0&rev=13
201 lines
7.2 KiB
Diff
201 lines
7.2 KiB
Diff
From 1ca81268c560b712677f91c98c5481ef473bfa0e Mon Sep 17 00:00:00 2001
|
|
From: Douglas Burke <dburke.gw@gmail.com>
|
|
Date: Sun, 31 Jan 2021 19:03:24 -0500
|
|
Subject: [PATCH 1/3] Whitelist np.bool/int/float warning from NumPy 1.20 in
|
|
tests
|
|
|
|
As well as white-listing the warnings I've had to tweak one set
|
|
of tests which was explicitly checking the warning messages
|
|
(and so needed to ignore the known warnings).
|
|
---
|
|
.../astro/tests/test_astro_data_swift_unit.py | 21 ++++++----
|
|
sherpa/conftest.py | 38 +++++++++++++++----
|
|
2 files changed, 43 insertions(+), 16 deletions(-)
|
|
|
|
Index: sherpa-4.13.0/sherpa/astro/tests/test_astro_data_swift_unit.py
|
|
===================================================================
|
|
--- sherpa-4.13.0.orig/sherpa/astro/tests/test_astro_data_swift_unit.py
|
|
+++ sherpa-4.13.0/sherpa/astro/tests/test_astro_data_swift_unit.py
|
|
@@ -172,7 +172,12 @@ def test_read_pha_fails_rmf(make_data_pa
|
|
assert emsg in str(excinfo.value)
|
|
|
|
|
|
-def validate_replacement_warning(ws, rtype, label):
|
|
+def validate_replacement_warning(ws, rtype, label, is_known_warning):
|
|
+ """Check that there is one expected warning."""
|
|
+
|
|
+ # Filter out the "allowed" warnings.
|
|
+ #
|
|
+ ws = [w for w in ws if not is_known_warning(w)]
|
|
|
|
assert len(ws) == 1
|
|
w = ws[0]
|
|
@@ -185,7 +190,7 @@ def validate_replacement_warning(ws, rty
|
|
|
|
@requires_data
|
|
@requires_fits
|
|
-def test_read_arf(make_data_path):
|
|
+def test_read_arf(make_data_path, is_known_warning):
|
|
"""Can we read in a Swift ARF."""
|
|
|
|
infile = make_data_path(ARFFILE)
|
|
@@ -194,7 +199,7 @@ def test_read_arf(make_data_path):
|
|
warnings.simplefilter("always")
|
|
arf = io.read_arf(infile)
|
|
|
|
- validate_replacement_warning(ws, 'ARF', infile)
|
|
+ validate_replacement_warning(ws, 'ARF', infile, is_known_warning)
|
|
|
|
assert isinstance(arf, DataARF)
|
|
|
|
@@ -262,7 +267,7 @@ def test_read_arf_fails_rmf(make_data_pa
|
|
|
|
@requires_data
|
|
@requires_fits
|
|
-def test_read_rmf(make_data_path):
|
|
+def test_read_rmf(make_data_path, is_known_warning):
|
|
"""Can we read in a Swift RMF."""
|
|
|
|
infile = make_data_path(RMFFILE)
|
|
@@ -271,7 +276,7 @@ def test_read_rmf(make_data_path):
|
|
warnings.simplefilter("always")
|
|
rmf = io.read_rmf(infile)
|
|
|
|
- validate_replacement_warning(ws, 'RMF', infile)
|
|
+ validate_replacement_warning(ws, 'RMF', infile, is_known_warning)
|
|
|
|
assert isinstance(rmf, DataRMF)
|
|
|
|
@@ -362,7 +367,7 @@ def test_read_rmf_fails_arf(make_data_pa
|
|
|
|
@requires_data
|
|
@requires_fits
|
|
-def test_can_use_swift_data(make_data_path):
|
|
+def test_can_use_swift_data(make_data_path, is_known_warning):
|
|
"""A basic check that we can read in and use the Swift data.
|
|
|
|
Unlike the previous tests, that directly access the io module,
|
|
@@ -383,14 +388,14 @@ def test_can_use_swift_data(make_data_pa
|
|
warnings.simplefilter("always")
|
|
ui.load_rmf(rmffile)
|
|
|
|
- validate_replacement_warning(ws, 'RMF', rmffile)
|
|
+ validate_replacement_warning(ws, 'RMF', rmffile, is_known_warning)
|
|
|
|
arffile = make_data_path(ARFFILE)
|
|
with warnings.catch_warnings(record=True) as ws:
|
|
warnings.simplefilter("always")
|
|
ui.load_arf(arffile)
|
|
|
|
- validate_replacement_warning(ws, 'ARF', arffile)
|
|
+ validate_replacement_warning(ws, 'ARF', arffile, is_known_warning)
|
|
|
|
assert ui.get_analysis() == 'energy'
|
|
|
|
Index: sherpa-4.13.0/sherpa/conftest.py
|
|
===================================================================
|
|
--- sherpa-4.13.0.orig/sherpa/conftest.py
|
|
+++ sherpa-4.13.0/sherpa/conftest.py
|
|
@@ -116,7 +116,12 @@ known_warnings = {
|
|
# Matplotlib version 2 warnings (from HTML notebook represention)
|
|
#
|
|
r'np.asscalar\(a\) is deprecated since NumPy v1.16, use a.item\(\) instead',
|
|
- r"Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working"
|
|
+ r"Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working",
|
|
+
|
|
+ # numpy 1.20 bool/float issue
|
|
+ r'`np.bool` is a deprecated alias for the builtin `bool`. .*',
|
|
+ r'`np.int` is a deprecated alias for the builtin `int`. .*',
|
|
+ r'`np.float` is a deprecated alias for the builtin `float`. .*',
|
|
],
|
|
UserWarning:
|
|
[
|
|
@@ -140,18 +145,11 @@ known_warnings = {
|
|
# See https://github.com/ContinuumIO/anaconda-issues/issues/6678
|
|
r"numpy.dtype size changed, may indicate binary " +
|
|
r"incompatibility. Expected 96, got 88",
|
|
- # I am getting the following from astropy with at least python 2.7 during the conda tests
|
|
- r"numpy.ufunc size changed, may indicate binary ",
|
|
+ # See https://github.com/numpy/numpy/pull/432
|
|
+ r"numpy.ufunc size changed",
|
|
+ # numpy 1.20 shows this in some tests
|
|
+ r"numpy.ndarray size changed, may indicate binary "
|
|
],
|
|
- VisibleDeprecationWarning:
|
|
- [],
|
|
-}
|
|
-
|
|
-# Since Sherpa now requires Python 3.5 at a minumum, the following
|
|
-# are always added, but kept as a separate dict and then merged
|
|
-# to make it clearer where they came from.
|
|
-#
|
|
-python3_warnings = {
|
|
ResourceWarning:
|
|
[
|
|
r"unclosed file .*king_kernel.txt.* closefd=True>",
|
|
@@ -166,17 +164,9 @@ python3_warnings = {
|
|
r"unclosed file .*/dev/null.* closefd=True>",
|
|
r"unclosed file .*table.txt.* closefd=True>",
|
|
],
|
|
- RuntimeWarning:
|
|
- [r"invalid value encountered in sqrt",
|
|
- # See https://github.com/ContinuumIO/anaconda-issues/issues/6678
|
|
- r"numpy.dtype size changed, may indicate binary " +
|
|
- r"incompatibility. Expected 96, got 88",
|
|
- # See https://github.com/numpy/numpy/pull/432
|
|
- r"numpy.ufunc size changed"
|
|
- ],
|
|
+ VisibleDeprecationWarning:
|
|
+ [],
|
|
}
|
|
-known_warnings.update(python3_warnings)
|
|
-
|
|
|
|
if have_astropy:
|
|
astropy_warnings = {
|
|
@@ -230,13 +220,8 @@ def capture_all_warnings(request, recwar
|
|
pytestconfig injected service for accessing the configuration data
|
|
|
|
"""
|
|
- def known(warning):
|
|
- message = warning.message
|
|
- for known_warning in known_warnings[type(message)]:
|
|
- pattern = re.compile(known_warning)
|
|
- if pattern.match(str(message)):
|
|
- return True
|
|
- return False
|
|
+
|
|
+ known = check_known_warning
|
|
|
|
def fin():
|
|
warnings = [w for w in recwarn.list
|
|
@@ -263,6 +248,28 @@ def capture_all_warnings(request, recwar
|
|
request.addfinalizer(fin)
|
|
|
|
|
|
+def check_known_warning(warning):
|
|
+ """Return True if this is an "allowed" warning."""
|
|
+
|
|
+ message = warning.message
|
|
+ for known_warning in known_warnings[type(message)]:
|
|
+ pattern = re.compile(known_warning)
|
|
+ if pattern.match(str(message)):
|
|
+ return True
|
|
+
|
|
+ return False
|
|
+
|
|
+
|
|
+@pytest.fixture
|
|
+def is_known_warning():
|
|
+ """Returns a function that returns True if this is an "allowed" warning.
|
|
+
|
|
+ It is not expected that this will see much use.
|
|
+ """
|
|
+
|
|
+ return check_known_warning
|
|
+
|
|
+
|
|
def pytest_configure(config):
|
|
"""
|
|
This configuration hook overrides the default mechanism for test data self-discovery, if the --test-data command line
|