-#!/usr/bin/env python3
-
"""
Check lesson files and their contents.
"""
# 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,
- '%/CONTRIBUTING.md': False,
- '%/LICENSE.md': True,
- '%/README.md': False,
- '%/_extras/discuss.md': True,
- '%/_extras/guide.md': True,
- '%/index.md': True,
- '%/reference.md': True,
- '%/setup.md': True,
+ 'CODE_OF_CONDUCT.md': True,
+ 'CONTRIBUTING.md': False,
+ 'LICENSE.md': True,
+ 'README.md': False,
+ os.path.join('_extras', 'discuss.md'): True,
+ os.path.join('_extras', 'guide.md'): True,
+ 'index.md': True,
+ 'reference.md': True,
+ 'setup.md': True,
}
# Episode filename pattern.
-P_EPISODE_FILENAME = re.compile(r'/_episodes/(\d\d)-[-\w]+.md$')
+P_EPISODE_FILENAME = re.compile(r'(\d\d)-[-\w]+.md$')
# Pattern to match lines ending with whitespace.
P_TRAILING_WHITESPACE = re.compile(r'\s+$')
# Pattern to match reference links (to resolve internally-defined references).
P_INTERNAL_LINK_DEF = re.compile(r'^\[([^\]]+)\]:\s*(.+)')
+# Pattern to match {% include ... %} statements
+P_INTERNAL_INCLUDE_LINK = re.compile(r'^{% include ([^ ]*) %}$')
+
# What kinds of blockquotes are allowed?
KNOWN_BLOCKQUOTES = {
'callout',
+ 'caution',
'challenge',
'checklist',
'discussion',
'prereq',
'quotation',
'solution',
- 'testimonial'
+ 'testimonial',
+ 'warning'
}
# What kinds of code fragments are allowed?
+# Below we allow all 'language-*' code blocks
KNOWN_CODEBLOCKS = {
'error',
'output',
'source',
- 'language-bash',
- 'html',
- 'language-make',
- 'language-matlab',
- 'language-python',
- 'language-r',
- 'language-shell',
- 'language-sql'
+ 'warning'
}
# What fields are required in teaching episode metadata?
}
# How long are lines allowed to be?
+# Please keep this in sync with .editorconfig!
MAX_LINE_LEN = 100
args = parse_args()
args.reporter = Reporter()
- check_config(args.reporter, args.source_dir)
+ life_cycle = check_config(args.reporter, args.source_dir)
+ # pre-alpha lessons should report without error
+ if life_cycle == "pre-alpha":
+ args.permissive = True
+ 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)
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', 'incubator'))
reporter.check_field(config_file, 'configuration', config, 'title')
reporter.check_field(config_file, 'configuration', config, 'email')
reporter.check(defaults in config.get('defaults', []),
'configuration',
'"root" not set to "." in configuration')
-
+ return config['life_cycle']
+
+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
{symbolic_name : URL}
"""
+ if not ref_path:
+ raise Warning("No filename has been provided.")
+
result = {}
urls_seen = set()
- if ref_path:
- with open(ref_path, 'r') as reader:
- for (num, line) in enumerate(reader):
- line_num = num + 1
- m = P_INTERNAL_LINK_DEF.search(line)
- require(m,
- '{0}:{1} not valid reference:\n{2}'.format(ref_path, line_num, line.rstrip()))
- name = m.group(1)
- url = m.group(2)
- require(name,
- 'Empty reference at {0}:{1}'.format(ref_path, line_num))
- reporter.check(name not in result,
- ref_path,
- 'Duplicate reference {0} at line {1}',
- name, line_num)
- reporter.check(url not in urls_seen,
- ref_path,
- 'Duplicate definition of URL {0} at line {1}',
- url, line_num)
- result[name] = url
- urls_seen.add(url)
+
+ with open(ref_path, 'r', encoding='utf-8') as reader:
+ for (num, line) in enumerate(reader, 1):
+
+ if P_INTERNAL_INCLUDE_LINK.search(line): continue
+
+ m = P_INTERNAL_LINK_DEF.search(line)
+
+ message = '{}: {} not a valid reference: {}'
+ require(m, message.format(ref_path, num, line.rstrip()))
+
+ name = m.group(1)
+ url = m.group(2)
+
+ message = 'Empty reference at {0}:{1}'
+ require(name, message.format(ref_path, num))
+
+ unique_name = name not in result
+ unique_url = url not in urls_seen
+
+ reporter.check(unique_name,
+ ref_path,
+ 'Duplicate reference name {0} at line {1}',
+ name, num)
+
+ reporter.check(unique_url,
+ ref_path,
+ 'Duplicate definition of URL {0} at line {1}',
+ url, num)
+
+ result[name] = url
+ urls_seen.add(url)
+
return result
"""Are all required files present? Are extraneous files present?"""
# Check files with predictable names.
- required = [p.replace('%', source_dir) for p in REQUIRED_FILES]
+ required = [os.path.join(source_dir, p) for p in REQUIRED_FILES]
missing = set(required) - set(filenames_present)
for m in missing:
reporter.add(None, 'Missing required file {0}', m)
for filename in filenames_present:
if '_episodes' not in filename:
continue
- m = P_EPISODE_FILENAME.search(filename)
+
+ # split path to check episode name
+ base_name = os.path.basename(filename)
+ m = P_EPISODE_FILENAME.search(base_name)
if m and m.group(1):
seen.append(m.group(1))
else:
n > MAX_LINE_LEN) and (not l.startswith('!'))]
self.reporter.check(not over,
self.filename,
- 'Line(s) are too long: {0}',
+ 'Line(s) too long: {0}',
', '.join([str(i) for i in over]))
def check_trailing_whitespace(self):
for node in self.find_all(self.doc, {'type': 'codeblock'}):
cls = self.get_val(node, 'attr', 'class')
- self.reporter.check(cls in KNOWN_CODEBLOCKS,
+ self.reporter.check(cls in KNOWN_CODEBLOCKS or cls.startswith('language-'),
(self.filename, self.get_loc(node)),
'Unknown or missing code block type {0}',
cls)
(re.compile(r'README\.md'), CheckNonJekyll),
(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(os.path.join('_episodes', '*\.md')), CheckEpisode),
(re.compile(r'.*\.md'), CheckGeneric)
]
projects / rnaseq-cwl-training.git / blobdiff