def test_rmarkdown(clear_now_and_after):
"""Test action Rmarkdown"""
if not R_library('rmarkdown1').target_exists():
pytest.xfail('rmarkdown is not properly installed.')
clear_now_and_after("myreport.html")
execute_workflow(
r"""
[10]
report:
## Some random figure
Generated by matplotlib
[100]
# generate report
output: 'myreport.html'
Rmarkdown(output=_output[0])
""",
options={"report_output": "report.md"},
)
assert os.path.isfile("myreport.html")
def install_package(lib, libtype, dryrun=False, autoinstall=False):
groups = re.search('(.*?)\((.*?)\)', lib)
if groups is not None:
lib = groups.group(1).strip()
versions = [x.strip() for x in groups.group(2).split(',')]
# only allow for one version specification: in previous versions of DSC we support multiple versions
# but now restricting it to just one version because I think it is more confusing than helpful otherwise
version = versions[0]
else:
version = ""
if version and not (version.startswith('=') or version.startswith(">") or
version.startswith("<") or version.startswith("!=")):
version = f"=={version}"
if not dryrun:
logger.info(
f"{'Checking / installing' if autoinstall else 'Checking'} {libtype.replace('_', ' ')} {lib}{(' version' + version) if version else ''} ..."
)
if libtype == 'R_library':
from sos.targets_r import R_library
return R_library(f"{lib}{version}",
autoinstall=autoinstall).target_exists()
else:
from sos.targets_python import Py_Module
return Py_Module(f"{lib}{version}",
autoinstall=autoinstall).target_exists()
else:
return (lib, version)
def test_rmarkdown_to_stdout():
if not R_library('rmarkdown1').target_exists():
pytest.xfail('rmarkdown is not properly installed.')
execute_workflow(
r"""
# generate report
Rmarkdown:
# this is title
"""
)
def test_rmarkdown_with_input(clear_now_and_after):
if not R_library('rmarkdown1').target_exists():
pytest.xfail('rmarkdown is not properly installed.')
clear_now_and_after("myreport.html")
# Rmarkdown with specified input.
execute_workflow(
r"""
[10]
report: output='a.md'
## Some random figure
Generated by matplotlib
[100]
# generate report
output: 'myreport.html'
Rmarkdown(input='a.md', output=_output[0])
"""
)
assert os.path.isfile("myreport.html")
def test_rmarkdown_with_action_output(clear_now_and_after):
if not R_library('rmarkdown1').target_exists():
pytest.xfail('rmarkdown is not properly installed.')
clear_now_and_after("default_10.md", "default_20.md", "output.html")
execute_workflow(
r"""
[10]
report: output='default_10.md'
A_10
[20]
report: output='default_20.md'
A_20
[100]
# generate report
Rmarkdown(input=['default_10.md', 'default_20.md'], output='output.html')
""",
options={"report_output": "${step_name}.md"},
)
for f in ["default_10.md", "default_20.md", "output.html"]:
assert file_target(f).exists()
def prepare_bookdown(files, title, author, date, description, no_section_number,
split_by, url, url_edit, repo, pdf, output, pdf_args):
if not os.path.exists(os.path.join(env.tmp_dir, env.time) + '.deps'):
R_library('rstudio/bookdown')
R_library('rstudio/DT')
executable('pandoc')
os.system('touch %s' % os.path.join(env.tmp_dir, env.time) + '.deps')
#
if title:
idx['title'] = title
if author:
idx['author'] = author
if date:
idx['date'] = date
if description:
if os.path.isfile(description):
idx['description'] = open(description).read()
else:
idx['description'] = description
if url:
idx['url'] = url
else:
del idx['url']
if repo:
idx['github-repo'] = repo
cfg['repo'] = repo
else:
del idx['github-repo']
del cfg['repo']
idx['author'] = '© ' + idx['author']
out['bookdown::gitbook']['css'] = 'style.css'
out['bookdown::html_chapters']['css'] = ['style.css', 'toc.css']
out['bookdown::epub_book']['stylesheet'] = 'style.css'
if pdf:
out['bookdown::pdf_book']['includes']['in_header'] = os.path.join(env.tmp_dir, 'preamble.tex')
else:
del out['bookdown::pdf_book']
workdir = os.getcwd()
if output:
output = os.path.abspath(os.path.expanduser(output))
os.makedirs(output, exist_ok = True)
cfg['output_dir'] = os.path.basename(output)
workdir = os.path.dirname(output)
else:
os.makedirs(cfg['output_dir'], exist_ok = True)
out['bookdown::gitbook']['config']['toc']['before'] = '{}'.format(
out['bookdown::gitbook']['config']['toc']['before'].replace('VALUE', idx['title']))
out['bookdown::gitbook']['config']['toc']['after'] = '{}'.format(
out['bookdown::gitbook']['config']['toc']['after'].replace('VALUE',
'{} {}'.format(env.year, idx['author'])))
if split_by:
out['bookdown::gitbook']['split_by'] = split_by
if no_section_number:
out['bookdown::gitbook']['number_sections'] = 0
if pdf:
pdf = (pdf, cfg['output_dir'], '{} {} {} --toc 3 --long_ref --font_size 12 {}'.\
format('-a {}'.format(repr(author)) if author else '',
'-t {}'.format(repr(title)) if title else '',
'-d {}'.format(repr(date)) if date else '',
' '.join(pdf_args)))
# Move files around to resolve path problem for bookdown
filenames = ['index.rmd' if idx == 0 else '{}_{}'.format(str(idx).zfill(4), os.path.basename(x))
for idx, x in enumerate(files)]
filenames = [x if x.endswith('.rmd') else os.path.splitext(x)[0] + '.rmd' for x in filenames]
for x, y in zip(files[1:], filenames[1:]):
shutil.copy(x, os.path.join(workdir, y))
with open(files[0]) as f:
tmp = f.readlines()
if len(tmp) == 0:
tmp.append(' ')
if not (tmp[0].startswith('# ')):
name = os.path.splitext(os.path.basename(files[0]))[0].lstrip('0123456789.- ')
tmp = ['# ' + re.sub(r'\-|_', ' ', name) + '\n'] \
+ tmp
tmp = ''.join(tmp)
for i, fn in enumerate(files):
if i == 0:
continue
with cd(workdir):
with open(filenames[i]) as f:
lines = f.readlines()
if len(lines) == 0:
lines.append(' ')
if not (lines[0].startswith('# ')):
name = os.path.splitext(os.path.basename(fn))[0].lstrip('0123456789.- ')
lines = ['# ' + re.sub(r'\-|_', ' ', name) + '\n'] \
+ lines
with open(filenames[i], 'w') as f:
f.write(''.join(lines))
# write resources
with codecs.open(os.path.join(workdir, cfg['output_dir'], 'style.css'), 'w', encoding='UTF-8') as f:
f.write(style)
with codecs.open(os.path.join(workdir, cfg['output_dir'], 'toc.css'), 'w', encoding='UTF-8') as f:
f.write(toc)
with codecs.open(os.path.join(env.tmp_dir, 'preamble.tex'), 'w', encoding='UTF-8') as f:
f.write(tex)
error_msg = None
try:
with cd(workdir):
with open(filenames[0], 'w') as f:
f.write('---\n{}\n---\n{}'.format(dict2str(idx), tmp))
cfg['rmd_files']['html'] = list(filenames)
cfg['rmd_files']['latex'] = list(filenames)
with open('_output.yml', 'w') as f:
f.write(dict2str(out))
with open('_bookdown.yml', 'w') as f:
f.write(dict2str(cfg))
sos_file = os.path.join(env.tmp_dir, 'bookdown.sos')
with open(sos_file, 'w') as f:
f.write(get_sos(filenames, pdf, workdir))
os.system('sos run {}'.format(sos_file))
except Exception as e:
error_msg = e
os.remove(sos_file)
try:
with cd(workdir):
os.remove('_output.yml')
os.remove('_bookdown.yml')
for f in filenames:
os.remove(f)
except:
pass
if error_msg is not None:
raise RuntimeError(error_msg)