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import os
import traceback
import warnings
from os.path import join
from stat import ST_MTIME
import re
import runpy
from docutils import nodes
from docutils.parsers.rst.roles import set_classes
from subprocess import check_call, DEVNULL, CalledProcessError
from pathlib import Path
import matplotlib
matplotlib.use('Agg')
def mol_role(role, rawtext, text, lineno, inliner, options={}, content=[]):
n = []
t = ''
while text:
if text[0] == '_':
n.append(nodes.inline(text=t))
t = ''
m = re.match(r'\d+', text[1:])
if m is None:
raise RuntimeError('Expected one or more digits after "_"')
digits = m.group()
n.append(nodes.subscript(text=digits))
text = text[1 + len(digits):]
else:
t += text[0]
text = text[1:]
n.append(nodes.inline(text=t))
return n, []
def git_role_tmpl(urlroot,
role,
rawtext, text, lineno, inliner, options={}, content=[]):
if text[-1] == '>':
i = text.index('<')
name = text[:i - 1]
text = text[i + 1:-1]
else:
name = text
if name[0] == '~':
name = name.split('/')[-1]
text = text[1:]
if '?' in name:
name = name[:name.index('?')]
# Check if the link is broken
is_tag = text.startswith('..') # Tags are like :git:`3.19.1 <../3.19.1>`
path = os.path.join('..', text)
do_exists = os.path.exists(path)
if not (is_tag or do_exists):
msg = 'Broken link: {}: Non-existing path: {}'.format(rawtext, path)
msg = inliner.reporter.error(msg, line=lineno)
prb = inliner.problematic(rawtext, rawtext, msg)
return [prb], [msg]
ref = urlroot + text
set_classes(options)
node = nodes.reference(rawtext, name, refuri=ref,
**options)
return [node], []
def creates():
"""Generator for Python scripts and their output filenames."""
for dirpath, dirnames, filenames in sorted(os.walk('.')):
if dirpath.startswith('./build'):
# Skip files in the build/ folder
continue
for filename in filenames:
if filename.endswith('.py'):
path = join(dirpath, filename)
with open(path) as fd:
lines = fd.readlines()
if len(lines) == 0:
continue
if 'coding: utf-8' in lines[0]:
lines.pop(0)
outnames = []
for line in lines:
if line.startswith('# creates:'):
outnames.extend([file.rstrip(',')
for file in line.split()[2:]])
else:
break
if outnames:
yield dirpath, filename, outnames
def create_png_files(raise_exceptions=False):
from ase.utils import workdir
try:
check_call(['povray', '-h'], stderr=DEVNULL)
except (FileNotFoundError, CalledProcessError):
warnings.warn('No POVRAY!')
# Replace write_pov with write_png:
from ase.io import pov
from ase.io.png import write_png
def write_pov(filename, atoms,
povray_settings={}, isosurface_data=None,
**generic_projection_settings):
write_png(Path(filename).with_suffix('.png'), atoms,
**generic_projection_settings)
class DummyRenderer:
def render(self):
pass
return DummyRenderer()
pov.write_pov = write_pov
for dir, pyname, outnames in creates():
path = join(dir, pyname)
t0 = os.stat(path)[ST_MTIME]
run = False
for outname in outnames:
try:
t = os.stat(join(dir, outname))[ST_MTIME]
except OSError:
run = True
break
else:
if t < t0:
run = True
break
if run:
print('running:', path)
with workdir(dir):
import matplotlib.pyplot as plt
plt.figure()
try:
runpy.run_path(pyname)
except KeyboardInterrupt:
return
except Exception:
if raise_exceptions:
raise
else:
traceback.print_exc()
for n in plt.get_fignums():
plt.close(n)
for outname in outnames:
print(dir, outname)
def clean():
"""Remove all generated files."""
for dir, pyname, outnames in creates():
for outname in outnames:
if os.path.isfile(os.path.join(dir, outname)):
os.remove(os.path.join(dir, outname))
def visual_inspection():
"""Manually inspect generated files."""
import subprocess
images = []
text = []
pdf = []
for dir, pyname, outnames in creates():
for outname in outnames:
path = os.path.join(dir, outname)
ext = path.rsplit('.', 1)[1]
if ext == 'pdf':
pdf.append(path)
elif ext in ['csv', 'txt', 'out', 'css', 'LDA', 'rst']:
text.append(path)
else:
images.append(path)
subprocess.call(['eog'] + images)
subprocess.call(['evince'] + pdf)
subprocess.call(['more'] + text)
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser(description='Process generated files.')
parser.add_argument('command', nargs='?', default='list',
choices=['list', 'inspect', 'clean', 'run'])
args = parser.parse_args()
if args.command == 'clean':
clean()
elif args.command == 'list':
for dir, pyname, outnames in creates():
for outname in outnames:
print(os.path.join(dir, outname))
elif args.command == 'run':
create_png_files(raise_exceptions=True)
else:
visual_inspection()
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