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#!/usr/bin/env python
"""Run the py->rst conversion and run all examples.
Steps are:
analyze example index file for example py filenames
check for any filenames in example directory not included
do py to rst conversion, writing into build directory
run
"""
# -----------------------------------------------------------------------------
# Library imports
# -----------------------------------------------------------------------------
# Stdlib imports
import os
import os.path as op
import sys
import shutil
import io
from subprocess import check_call
from glob import glob
from time import time
# Third-party imports
# We must configure the mpl backend before making any further mpl imports
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from matplotlib._pylab_helpers import Gcf
import dipy
# -----------------------------------------------------------------------------
# Function defintions
# -----------------------------------------------------------------------------
# These global variables let show() be called by the scripts in the usual
# manner, but when generating examples, we override it to write the figures to
# files with a known name (derived from the script name) plus a counter
figure_basename = None
# We must change the show command to save instead
def show():
allfm = Gcf.get_all_fig_managers()
for fcount, fm in enumerate(allfm):
fm.canvas.figure.savefig('%s_%02i.png' %
(figure_basename, fcount + 1))
_mpl_show = plt.show
plt.show = show
# -----------------------------------------------------------------------------
# Main script
# -----------------------------------------------------------------------------
# Where things are
DOC_PATH = op.abspath('..')
EG_INDEX_FNAME = op.join(DOC_PATH, 'examples_index.rst')
EG_SRC_DIR = op.join(DOC_PATH, 'examples')
# Work in examples directory
# os.chdir(op.join(DOC_PATH, 'examples_built'))
if not os.getcwd().endswith(op.join('doc', 'examples_built')):
raise OSError('This must be run from the doc directory')
# Copy the py files; check they are in the examples list and warn if not
with io.open(EG_INDEX_FNAME, 'rt', encoding="utf8") as f:
eg_index_contents = f.read()
# Here I am adding an extra step. The list of examples to be executed need
# also to be added in the following file (valid_examples.txt). This helps
# with debugging the examples and the documentation only a few examples at
# the time.
flist_name = op.join(op.dirname(os.getcwd()), 'examples',
'valid_examples.txt')
with io.open(flist_name, "r", encoding="utf8") as flist:
validated_examples = flist.readlines()
# Parse "#" in lines
validated_examples = [line.split("#", 1)[0] for line in validated_examples]
# Remove leading and trailing white space from example names
validated_examples = [line.strip() for line in validated_examples]
# Remove blank lines
validated_examples = list(filter(None, validated_examples))
for example in validated_examples:
fullpath = op.join(EG_SRC_DIR, example)
if not example.endswith(".py"):
print("%s not a python file, skipping." % example)
continue
elif not op.isfile(fullpath):
print("Cannot find file, %s, skipping." % example)
continue
shutil.copyfile(fullpath, example)
# Check that example file is included in the docs
file_root = example[:-3]
if file_root not in eg_index_contents:
msg = "Example, %s, not in index file %s."
msg = msg % (example, EG_INDEX_FNAME)
print(msg)
# Run the conversion from .py to rst file
check_call('{} ../../tools/ex2rst'.format(sys.executable) +
' --project dipy --outdir . .', shell=True)
# added the path so that scripts can import other scripts on the same directory
sys.path.insert(0, os.getcwd())
if not op.isdir('fig'):
os.mkdir('fig')
use_xvfb = os.environ.get('TEST_WITH_XVFB', False)
use_memprof = os.environ.get('TEST_WITH_MEMPROF', False)
if use_xvfb:
try:
from xvfbwrapper import Xvfb
except ImportError:
raise RuntimeError("You are trying to run a documentation build",
"with 'TEST_WITH_XVFB' set to True, but ",
"xvfbwrapper is not available. Please install",
"xvfbwrapper and try again")
display = Xvfb(width=1920, height=1080)
display.start()
if use_memprof:
try:
import memory_profiler
except ImportError:
raise RuntimeError("You are trying to run a documentation build",
"with 'TEST_WITH_MEMPROF' set to True, but ",
"memory_profiler is not available. Please install",
"memory_profiler and try again")
name = ''
def run_script():
namespace = {}
t1 = time()
with io.open(script, encoding="utf8") as f:
exec(f.read(), namespace)
t2 = time()
print("That took %.2f seconds to run" % (t2 - t1))
plt.close('all')
del namespace
# Execute each python script in the directory:
for script in validated_examples:
figure_basename = op.join('fig', op.splitext(script)[0])
if use_memprof:
print("memory profiling ", script)
memory_profiler.profile(run_script)()
else:
print('*************************************************************')
print(script)
print('*************************************************************')
run_script()
if use_xvfb:
display.stop()
# clean up stray images, pickles, npy files, etc
for globber in ('*.nii.gz', '*.dpy', '*.npy', '*.pkl', '*.mat', '*.img',
'*.hdr'):
for fname in glob(globber):
os.unlink(fname)
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