-#!/usr/bin/env python
+#!/usr/bin/env python3
"""
Check lesson files and their contents.
import os
import glob
import re
-from optparse import OptionParser
+from argparse import ArgumentParser
from util import (Reporter, read_markdown, load_yaml, check_unwanted_files,
require)
# Where to look for source Markdown files.
SOURCE_DIRS = ['', '_episodes', '_extras']
+# Where to look for source Rmd files.
+SOURCE_RMD_DIRS = ['_episodes_rmd']
+
# Required files: each entry is ('path': YAML_required).
# FIXME: We do not yet validate whether any files have the required
# YAML headers, but should in the future.
# specially. This list must include all the Markdown files listed in the
# 'bin/initialize' script.
REQUIRED_FILES = {
- '%/CONDUCT.md': True,
+ '%/CODE_OF_CONDUCT.md': True,
'%/CONTRIBUTING.md': False,
'%/LICENSE.md': True,
'%/README.md': False,
args = parse_args()
args.reporter = Reporter()
check_config(args.reporter, args.source_dir)
+ check_source_rmd(args.reporter, args.source_dir, args.parser)
args.references = read_references(args.reporter, args.reference_path)
docs = read_all_markdown(args.source_dir, args.parser)
checker.check()
args.reporter.report()
+ if args.reporter.messages and not args.permissive:
+ exit(1)
def parse_args():
"""Parse command-line arguments."""
- parser = OptionParser()
- parser.add_option('-l', '--linelen',
- default=False,
- action="store_true",
- dest='line_lengths',
- help='Check line lengths')
- parser.add_option('-p', '--parser',
- default=None,
- dest='parser',
- help='path to Markdown parser')
- parser.add_option('-r', '--references',
- default=None,
- dest='reference_path',
- help='path to Markdown file of external references')
- parser.add_option('-s', '--source',
- default=os.curdir,
- dest='source_dir',
- help='source directory')
- parser.add_option('-w', '--whitespace',
- default=False,
- action="store_true",
- dest='trailing_whitespace',
- help='Check for trailing whitespace')
-
- args, extras = parser.parse_args()
+ parser = ArgumentParser(description="""Check episode files in a lesson.""")
+ parser.add_argument('-l', '--linelen',
+ default=False,
+ action="store_true",
+ dest='line_lengths',
+ help='Check line lengths')
+ parser.add_argument('-p', '--parser',
+ default=None,
+ dest='parser',
+ help='path to Markdown parser')
+ parser.add_argument('-r', '--references',
+ default=None,
+ dest='reference_path',
+ help='path to Markdown file of external references')
+ parser.add_argument('-s', '--source',
+ default=os.curdir,
+ dest='source_dir',
+ help='source directory')
+ parser.add_argument('-w', '--whitespace',
+ default=False,
+ action="store_true",
+ dest='trailing_whitespace',
+ help='Check for trailing whitespace')
+ parser.add_argument('--permissive',
+ default=False,
+ action="store_true",
+ dest='permissive',
+ help='Do not raise an error even if issues are detected')
+
+ args, extras = parser.parse_known_args()
require(args.parser is not None,
'Path to Markdown parser not provided')
require(not extras,
reporter.check_field(config_file, 'configuration',
config, 'kind', 'lesson')
reporter.check_field(config_file, 'configuration',
- config, 'carpentry', ('swc', 'dc', 'lc'))
+ config, 'carpentry', ('swc', 'dc', 'lc', 'cp'))
reporter.check_field(config_file, 'configuration', config, 'title')
reporter.check_field(config_file, 'configuration', config, 'email')
- reporter.check({'values': {'root': '..'}} in config.get('defaults', []),
+ for defaults in [
+ {'values': {'root': '.', 'layout': 'page'}},
+ {'values': {'root': '..', 'layout': 'episode'}, 'scope': {'type': 'episodes', 'path': ''}},
+ {'values': {'root': '..', 'layout': 'page'}, 'scope': {'type': 'extras', 'path': ''}}
+ ]:
+ reporter.check(defaults in config.get('defaults', []),
'configuration',
- '"root" not set to ".." in configuration')
-
+ '"root" not set to "." in configuration')
+
+def check_source_rmd(reporter, source_dir, parser):
+ """Check that Rmd episode files include `source: Rmd`"""
+
+ episode_rmd_dir = [os.path.join(source_dir, d) for d in SOURCE_RMD_DIRS]
+ episode_rmd_files = [os.path.join(d, '*.Rmd') for d in episode_rmd_dir]
+ results = {}
+ for pat in episode_rmd_files:
+ for f in glob.glob(pat):
+ data = read_markdown(parser, f)
+ dy = data['metadata']
+ if dy:
+ reporter.check_field(f, 'episode_rmd',
+ dy, 'source', 'Rmd')
def read_references(reporter, ref_path):
"""Read shared file of reference links, returning dictionary of valid references
for (pat, cls) in CHECKERS:
if pat.search(filename):
return cls(args, filename, **info)
+ return NotImplemented
-
-class CheckBase(object):
+class CheckBase:
"""Base class for checking Markdown files."""
def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
"""Cache arguments for checking."""
- super(CheckBase, self).__init__()
self.args = args
self.reporter = self.args.reporter # for convenience
self.filename = filename
return False
return True
- def get_val(self, node, *chain):
+ @staticmethod
+ def get_val(node, *chain):
"""Get value one or more levels down."""
curr = node
class CheckNonJekyll(CheckBase):
"""Check a file that isn't translated by Jekyll."""
- def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
- super(CheckNonJekyll, self).__init__(
- args, filename, metadata, metadata_len, text, lines, doc)
-
def check_metadata(self):
self.reporter.check(self.metadata is None,
self.filename,
"""Check the main index page."""
def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
- super(CheckIndex, self).__init__(args, filename,
- metadata, metadata_len, text, lines, doc)
+ super().__init__(args, filename, metadata, metadata_len, text, lines, doc)
self.layout = 'lesson'
def check_metadata(self):
- super(CheckIndex, self).check_metadata()
+ super().check_metadata()
self.reporter.check(self.metadata.get('root', '') == '.',
self.filename,
'Root not set to "."')
class CheckEpisode(CheckBase):
"""Check an episode page."""
- def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
- super(CheckEpisode, self).__init__(args, filename,
- metadata, metadata_len, text, lines, doc)
-
def check(self):
"""Run extra tests."""
- super(CheckEpisode, self).check()
+ super().check()
self.check_reference_inclusion()
def check_metadata(self):
- super(CheckEpisode, self).check_metadata()
+ super().check_metadata()
if self.metadata:
if 'layout' in self.metadata:
if self.metadata['layout'] == 'break':
self.check_metadata_fields(TEACHING_METADATA_FIELDS)
def check_metadata_fields(self, expected):
+ """Check metadata fields."""
for (name, type_) in expected:
if name not in self.metadata:
self.reporter.add(self.filename,
"""Check the reference page."""
def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
- super(CheckReference, self).__init__(
- args, filename, metadata, metadata_len, text, lines, doc)
+ super().__init__(args, filename, metadata, metadata_len, text, lines, doc)
self.layout = 'reference'
"""Check a generic page."""
def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
- super(CheckGeneric, self).__init__(args, filename,
- metadata, metadata_len, text, lines, doc)
- self.layout = 'page'
+ super().__init__(args, filename, metadata, metadata_len, text, lines, doc)
CHECKERS = [
(re.compile(r'index\.md'), CheckIndex),
(re.compile(r'reference\.md'), CheckReference),
(re.compile(r'_episodes/.*\.md'), CheckEpisode),
+ (re.compile(r'aio\.md'), CheckNonJekyll),
(re.compile(r'.*\.md'), CheckGeneric)
]
projects / rnaseq-cwl-training.git / blobdiff