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Merge branch 'use-scriptrunner' into main-master
* use-scriptrunner: RF: change "below" to "above" for higher directory BF: workaround missing __package__ in Python 3.2 RF: move script test machinery into own module
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‎nibabel/tests/scriptrunner.py

Lines changed: 167 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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""" Module to help tests check script output
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Provides class to be instantiated in tests that check scripts. Usually works
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something like this in a test module::
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from .scriptrunner import ScriptRunner
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runner = ScriptRunner()
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Then, in the tests, something like::
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code, stdout, stderr = runner.run_command(['my-script', my_arg])
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assert_equal(code, 0)
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assert_equal(stdout, b'This script ran OK')
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"""
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import sys
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import os
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from os.path import (dirname, join as pjoin, isfile, isdir, realpath, pathsep)
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from subprocess import Popen, PIPE
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try: # Python 2
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string_types = basestring,
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except NameError: # Python 3
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string_types = str,
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def _get_package():
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""" Workaround for missing ``__package__`` in Python 3.2
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"""
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if '__package__' in globals() and not __package__ is None:
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return __package__
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return __name__.split('.', 1)[0]
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# Same as __package__ for Python 2.6, 2.7 and >= 3.3
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MY_PACKAGE=_get_package()
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def local_script_dir(script_sdir):
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""" Get local script directory if running in development dir, else None
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"""
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# Check for presence of scripts in development directory. ``realpath``
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# allows for the situation where the development directory has been linked
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# into the path.
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package_path = dirname(__import__(MY_PACKAGE).__file__)
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above_us = realpath(pjoin(package_path, '..'))
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devel_script_dir = pjoin(above_us, script_sdir)
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if isfile(pjoin(above_us, 'setup.py')) and isdir(devel_script_dir):
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return devel_script_dir
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return None
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def local_module_dir(module_name):
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""" Get local module directory if running in development dir, else None
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"""
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mod = __import__(module_name)
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containing_path = dirname(dirname(realpath(mod.__file__)))
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if containing_path == realpath(os.getcwd()):
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return containing_path
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return None
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class ScriptRunner(object):
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""" Class to run scripts and return output
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Finds local scripts and local modules if running in the development
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directory, otherwise finds system scripts and modules.
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"""
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def __init__(self,
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script_sdir = 'scripts',
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module_sdir = MY_PACKAGE,
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debug_print_var = None,
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output_processor = lambda x : x
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):
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""" Init ScriptRunner instance
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Parameters
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----------
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script_sdir : str, optional
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Name of subdirectory in top-level directory (directory containing
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setup.py), to find scripts in development tree. Typically
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'scripts', but might be 'bin'.
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module_sdir : str, optional
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Name of subdirectory in top-level directory (directory containing
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setup.py), to find main package directory.
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debug_print_vsr : str, optional
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Name of environment variable that indicates whether to do debug
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printing or no.
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output_processor : callable
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Callable to run on the stdout, stderr outputs before returning
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them. Use this to convert bytes to unicode, strip whitespace, etc.
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"""
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self.local_script_dir = local_script_dir(script_sdir)
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self.local_module_dir = local_module_dir(module_sdir)
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if debug_print_var is None:
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debug_print_var = '{0}_DEBUG_PRINT'.format(module_sdir.upper())
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self.debug_print = os.environ.get(debug_print_var, False)
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self.output_processor = output_processor
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def run_command(self, cmd, check_code=True):
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""" Run command sequence `cmd` returning exit code, stdout, stderr
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Parameters
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----------
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cmd : str or sequence
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string with command name or sequence of strings defining command
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check_code : {True, False}, optional
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If True, raise error for non-zero return code
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Returns
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-------
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returncode : int
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return code from execution of `cmd`
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stdout : bytes (python 3) or str (python 2)
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stdout from `cmd`
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stderr : bytes (python 3) or str (python 2)
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stderr from `cmd`
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"""
119+
if isinstance(cmd, string_types):
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cmd = [cmd]
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else:
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cmd = list(cmd)
123+
if not self.local_script_dir is None:
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# Windows can't run script files without extensions natively so we need
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# to run local scripts (no extensions) via the Python interpreter. On
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# Unix, we might have the wrong incantation for the Python interpreter
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# in the hash bang first line in the source file. So, either way, run
128+
# the script through the Python interpreter
129+
cmd = [sys.executable,
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pjoin(self.local_script_dir, cmd[0])] + cmd[1:]
131+
elif os.name == 'nt':
132+
# Need .bat file extension for windows
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cmd[0] += '.bat'
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if os.name == 'nt':
135+
# Quote all arguments because they might be files with spaces
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# The quotes delimit the arguments on Windows. On Unix the list
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# elements are each separate arguments.
138+
cmd = ['"{0}"'.format(c) for c in cmd]
139+
if self.debug_print:
140+
print("Running command '%s'" % cmd)
141+
env = os.environ
142+
if not self.local_module_dir is None:
143+
# module likely comes from the current working directory. We might need
144+
# that directory on the path if we're running the scripts from a
145+
# temporary directory
146+
env = env.copy()
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pypath = env.get('PYTHONPATH', None)
148+
if pypath is None:
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env['PYTHONPATH'] = self.local_module_dir
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else:
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env['PYTHONPATH'] = self.local_module_dir + pathsep + pypath
152+
proc = Popen(cmd, stdout=PIPE, stderr=PIPE, env=env)
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stdout, stderr = proc.communicate()
154+
if proc.poll() == None:
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proc.terminate()
156+
if check_code and proc.returncode != 0:
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raise RuntimeError(
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"""Command "{0}" failed with
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stdout
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------
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{1}
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stderr
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------
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{2}
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""".format(cmd, stdout, stderr))
166+
opp = self.output_processor
167+
return proc.returncode, opp(stdout), opp(stderr)

‎nibabel/tests/test_scripts.py

Lines changed: 26 additions & 69 deletions
Original file line numberDiff line numberDiff line change
@@ -2,19 +2,14 @@
22
# vi: set ft=python sts=4 ts=4 sw=4 et:
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""" Test scripts
44
5-
If we appear to be running from the development directory, use the scripts in
6-
the top-level folder ``scripts``. Otherwise try and get the scripts from the
7-
path
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Test running scripts
86
"""
97
from __future__ import division, print_function, absolute_import
108

11-
import sys
129
import os
13-
from os.path import dirname, join as pjoin, isfile, isdir, abspath, realpath, pardir
10+
from os.path import dirname, join as pjoin, abspath
1411
import re
1512

16-
from subprocess import Popen, PIPE
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1813
import numpy as np
1914

2015
from ..tmpdirs import InTemporaryDirectory
@@ -24,95 +19,58 @@
2419

2520
from numpy.testing import assert_almost_equal
2621

22+
from .scriptrunner import ScriptRunner
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24+
25+
def _proc_stdout(stdout):
26+
stdout_str = stdout.decode('latin1').strip()
27+
return stdout_str.replace(os.linesep, '\n')
28+
29+
30+
runner = ScriptRunner(
31+
script_sdir = 'bin',
32+
debug_print_var = 'NIPY_DEBUG_PRINT',
33+
output_processor=_proc_stdout)
34+
run_command = runner.run_command
35+
36+
2737
def script_test(func):
2838
# Decorator to label test as a script_test
2939
func.script_test = True
3040
return func
3141
script_test.__test__ = False # It's not a test
3242

33-
# Need shell to get path to correct executables
34-
USE_SHELL = True
35-
36-
DEBUG_PRINT = os.environ.get('NIPY_DEBUG_PRINT', False)
37-
3843
DATA_PATH = abspath(pjoin(dirname(__file__), 'data'))
39-
IMPORT_PATH = abspath(pjoin(dirname(__file__), pardir, pardir))
40-
41-
def local_script_dir(script_sdir):
42-
# Check for presence of scripts in development directory. ``realpath``
43-
# checks for the situation where the development directory has been linked
44-
# into the path.
45-
below_us_2 = realpath(pjoin(dirname(__file__), '..', '..'))
46-
devel_script_dir = pjoin(below_us_2, script_sdir)
47-
if isfile(pjoin(below_us_2, 'setup.py')) and isdir(devel_script_dir):
48-
return devel_script_dir
49-
return None
50-
51-
LOCAL_SCRIPT_DIR = local_script_dir('bin')
52-
53-
def run_command(cmd):
54-
if LOCAL_SCRIPT_DIR is None:
55-
env = None
56-
else: # We are running scripts local to the source tree (not installed)
57-
# Windows can't run script files without extensions natively so we need
58-
# to run local scripts (no extensions) via the Python interpreter. On
59-
# Unix, we might have the wrong incantation for the Python interpreter
60-
# in the hash bang first line in the source file. So, either way, run
61-
# the script through the Python interpreter
62-
cmd = "%s %s" % (sys.executable, pjoin(LOCAL_SCRIPT_DIR, cmd))
63-
# If we're testing local script files, point subprocess to consider
64-
# current nibabel in favor of possibly installed different version
65-
env = {'PYTHONPATH': '%s:%s'
66-
% (IMPORT_PATH, os.environ.get('PYTHONPATH', ''))}
67-
if DEBUG_PRINT:
68-
print("Running command '%s'" % cmd)
69-
proc = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=USE_SHELL,
70-
env=env)
71-
stdout, stderr = proc.communicate()
72-
if proc.poll() == None:
73-
proc.terminate()
74-
if proc.returncode != 0:
75-
raise RuntimeError('Command "%s" failed with stdout\n%s\nstderr\n%s\n'
76-
% (cmd, stdout, stderr))
77-
return proc.returncode, stdout, stderr
78-
79-
80-
def _proc_stdout(stdout):
81-
stdout_str = stdout.decode('latin1').strip()
82-
return stdout_str.replace(os.linesep, '\n')
83-
8444

8545
@script_test
8646
def test_nib_ls():
8747
# test nib-ls script
8848
fname = pjoin(DATA_PATH, 'example4d.nii.gz')
8949
expected_re = (" (int16|[<>]i2) \[128, 96, 24, 2\] "
9050
"2.00x2.00x2.20x2000.00 #exts: 2 sform$")
91-
# Need to quote out path in case it has spaces
92-
cmd = 'nib-ls "%s"' % (fname)
51+
cmd = ['nib-ls', fname]
9352
code, stdout, stderr = run_command(cmd)
94-
res = _proc_stdout(stdout)
95-
assert_equal(fname, res[:len(fname)])
96-
assert_not_equal(re.match(expected_re, res[len(fname):]), None)
53+
assert_equal(fname, stdout[:len(fname)])
54+
assert_not_equal(re.match(expected_re, stdout[len(fname):]), None)
9755

9856

9957
@script_test
10058
def test_nib_nifti_dx():
10159
# Test nib-nifti-dx script
10260
clean_hdr = pjoin(DATA_PATH, 'nifti1.hdr')
103-
cmd = 'nib-nifti-dx "%s"' % (clean_hdr,)
61+
cmd = ['nib-nifti-dx', clean_hdr]
10462
code, stdout, stderr = run_command(cmd)
105-
assert_equal(stdout.strip().decode('latin1'), 'Header for "%s" is clean' % clean_hdr)
63+
assert_equal(stdout.strip(), 'Header for "%s" is clean' % clean_hdr)
10664
dirty_hdr = pjoin(DATA_PATH, 'analyze.hdr')
107-
cmd = 'nib-nifti-dx "%s"' % (dirty_hdr,)
65+
cmd = ['nib-nifti-dx', dirty_hdr]
10866
code, stdout, stderr = run_command(cmd)
10967
expected = """Picky header check output for "%s"
11068
11169
pixdim[0] (qfac) should be 1 (default) or -1
11270
magic string "" is not valid
11371
sform_code 11776 not valid""" % (dirty_hdr,)
11472
# Split strings to remove line endings
115-
assert_equal(_proc_stdout(stdout), expected)
73+
assert_equal(stdout, expected)
11674

11775

11876
def vox_size(affine):
@@ -122,14 +80,13 @@ def vox_size(affine):
12280
@script_test
12381
def test_parrec2nii():
12482
# Test parrec2nii script
125-
cmd = 'parrec2nii --help'
83+
cmd = ['parrec2nii', '--help']
12684
code, stdout, stderr = run_command(cmd)
127-
stdout = stdout.decode('latin1')
12885
assert_true(stdout.startswith('Usage'))
12986
in_fname = pjoin(DATA_PATH, 'phantom_EPI_asc_CLEAR_2_1.PAR')
13087
out_froot = 'phantom_EPI_asc_CLEAR_2_1.nii'
13188
with InTemporaryDirectory():
132-
run_command('parrec2nii "{0}"'.format(in_fname))
89+
run_command(['parrec2nii', in_fname])
13390
img = load(out_froot)
13491
assert_equal(img.shape, (64, 64, 9, 3))
13592
assert_equal(img.get_data_dtype(), np.dtype(np.int16))

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