Check lesson files and their contents.
"""
-from __future__ import print_function
-import sys
+
import os
import glob
-import json
import re
from optparse import OptionParser
-from util import Reporter, read_markdown, load_yaml, check_unwanted_files, require, IMAGE_FILE_SUFFIX
+from util import (Reporter, read_markdown, load_yaml, check_unwanted_files,
+ require)
__version__ = '0.3'
# FIXME: We do not yet validate whether any files have the required
# YAML headers, but should in the future.
# The '%' is replaced with the source directory path for checking.
-# Episodes are handled specially, and extra files in '_extras' are also handled specially.
-# This list must include all the Markdown files listed in the 'bin/initialize' script.
+# Episodes are handled specially, and extra files in '_extras' are also handled
+# 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/figures.md': True,
'%/_extras/guide.md': True,
'%/index.md': True,
'%/reference.md': True,
'error',
'output',
'source',
- 'bash',
- 'make',
- 'matlab',
- 'python',
- 'r',
- 'sql'
+ 'language-bash',
+ 'html',
+ 'language-make',
+ 'language-matlab',
+ 'language-python',
+ 'language-r',
+ 'language-shell',
+ 'language-sql'
}
# What fields are required in teaching episode metadata?
# How long are lines allowed to be?
MAX_LINE_LEN = 100
+
def main():
"""Main driver."""
args.references = read_references(args.reporter, args.reference_path)
docs = read_all_markdown(args.source_dir, args.parser)
- check_fileset(args.source_dir, args.reporter, docs.keys())
+ check_fileset(args.source_dir, args.reporter, list(docs.keys()))
check_unwanted_files(args.source_dir, args.reporter)
- for filename in docs.keys():
+ for filename in list(docs.keys()):
checker = create_checker(args, filename, docs[filename])
checker.check()
- check_figures(args.source_dir, args.reporter)
args.reporter.report()
config_file = os.path.join(source_dir, '_config.yml')
config = load_yaml(config_file)
- reporter.check_field(config_file, 'configuration', config, 'kind', 'lesson')
- reporter.check_field(config_file, 'configuration', config, 'carpentry', ('swc', 'dc', 'lc'))
+ reporter.check_field(config_file, 'configuration',
+ config, 'kind', 'lesson')
+ reporter.check_field(config_file, 'configuration',
+ config, 'carpentry', ('swc', 'dc', 'lc'))
reporter.check_field(config_file, 'configuration', config, 'title')
- reporter.check_field(config_file, 'configuration', config, 'contact')
+ reporter.check_field(config_file, 'configuration', config, 'email')
reporter.check({'values': {'root': '..'}} in config.get('defaults', []),
'configuration',
if m and m.group(1):
seen.append(m.group(1))
else:
- reporter.add(None, 'Episode {0} has badly-formatted filename', filename)
+ reporter.add(
+ None, 'Episode {0} has badly-formatted filename', filename)
# Check for duplicate episode numbers.
reporter.check(len(seen) == len(set(seen)),
- None,
- 'Duplicate episode numbers {0} vs {1}',
- sorted(seen), sorted(set(seen)))
+ None,
+ 'Duplicate episode numbers {0} vs {1}',
+ sorted(seen), sorted(set(seen)))
# Check that numbers are consecutive.
- seen = [int(s) for s in seen]
- seen.sort()
+ seen = sorted([int(s) for s in seen])
clean = True
for i in range(len(seen) - 1):
clean = clean and ((seen[i+1] - seen[i]) == 1)
seen)
-def check_figures(source_dir, reporter):
- """Check that all figures are present and referenced."""
-
- # Get references.
- try:
- all_figures_html = os.path.join(source_dir, '_includes', 'all_figures.html')
- with open(all_figures_html, 'r') as reader:
- text = reader.read()
- figures = P_FIGURE_REFS.findall(text)
- referenced = [os.path.split(f)[1] for f in figures if '/fig/' in f]
- except FileNotFoundError as e:
- reporter.add(all_figures_html,
- 'File not found')
- return
-
- # Get actual image files (ignore non-image files).
- fig_dir_path = os.path.join(source_dir, 'fig')
- actual = [f for f in os.listdir(fig_dir_path) if os.path.splitext(f)[1] in IMAGE_FILE_SUFFIX]
-
- # Report differences.
- unexpected = set(actual) - set(referenced)
- reporter.check(not unexpected,
- None,
- 'Unexpected image files: {0}',
- ', '.join(sorted(unexpected)))
- missing = set(referenced) - set(actual)
- reporter.check(not missing,
- None,
- 'Missing image files: {0}',
- ', '.join(sorted(missing)))
-
-
def create_checker(args, filename, info):
"""Create appropriate checker for file."""
super(CheckBase, self).__init__()
self.args = args
- self.reporter = self.args.reporter # for convenience
+ self.reporter = self.args.reporter # for convenience
self.filename = filename
self.metadata = metadata
self.metadata_len = metadata_len
self.layout = None
-
def check(self):
"""Run tests."""
self.check_codeblock_classes()
self.check_defined_link_references()
-
def check_metadata(self):
"""Check the YAML metadata."""
'Missing metadata entirely')
if self.metadata and (self.layout is not None):
- self.reporter.check_field(self.filename, 'metadata', self.metadata, 'layout', self.layout)
-
+ self.reporter.check_field(
+ self.filename, 'metadata', self.metadata, 'layout', self.layout)
def check_line_lengths(self):
"""Check the raw text of the lesson body."""
if self.args.line_lengths:
- over = [i for (i, l, n) in self.lines if (n > MAX_LINE_LEN) and (not l.startswith('!'))]
+ over = [i for (i, l, n) in self.lines if (
+ n > MAX_LINE_LEN) and (not l.startswith('!'))]
self.reporter.check(not over,
self.filename,
'Line(s) are too long: {0}',
', '.join([str(i) for i in over]))
-
def check_trailing_whitespace(self):
"""Check for whitespace at the ends of lines."""
if self.args.trailing_whitespace:
- trailing = [i for (i, l, n) in self.lines if P_TRAILING_WHITESPACE.match(l)]
+ trailing = [
+ i for (i, l, n) in self.lines if P_TRAILING_WHITESPACE.match(l)]
self.reporter.check(not trailing,
self.filename,
'Line(s) end with whitespace: {0}',
', '.join([str(i) for i in trailing]))
-
def check_blockquote_classes(self):
"""Check that all blockquotes have known classes."""
- for node in self.find_all(self.doc, {'type' : 'blockquote'}):
+ for node in self.find_all(self.doc, {'type': 'blockquote'}):
cls = self.get_val(node, 'attr', 'class')
self.reporter.check(cls in KNOWN_BLOCKQUOTES,
(self.filename, self.get_loc(node)),
'Unknown or missing blockquote type {0}',
cls)
-
def check_codeblock_classes(self):
"""Check that all code blocks have known classes."""
- for node in self.find_all(self.doc, {'type' : 'codeblock'}):
+ 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.filename, self.get_loc(node)),
'Unknown or missing code block type {0}',
cls)
-
def check_defined_link_references(self):
"""Check that defined links resolve in the file.
"""
result = set()
- for node in self.find_all(self.doc, {'type' : 'text'}):
+ for node in self.find_all(self.doc, {'type': 'text'}):
for match in P_INTERNAL_LINK_REF.findall(node['value']):
text = match[0]
link = match[1]
'Internally-defined links may be missing definitions: {0}',
', '.join(sorted(result)))
-
def find_all(self, node, pattern, accum=None):
"""Find all matches for a pattern."""
- assert type(pattern) == dict, 'Patterns must be dictionaries'
+ assert isinstance(pattern, dict), 'Patterns must be dictionaries'
if accum is None:
accum = []
if self.match(node, pattern):
self.find_all(child, pattern, accum)
return accum
-
def match(self, node, pattern):
"""Does this node match the given pattern?"""
if key not in node:
return False
val = pattern[key]
- if type(val) == str:
+ if isinstance(val, str):
if node[key] != val:
return False
- elif type(val) == dict:
+ elif isinstance(val, dict):
if not self.match(node[key], val):
return False
return True
-
def get_val(self, node, *chain):
"""Get value one or more levels down."""
break
return curr
-
def get_loc(self, node):
"""Convenience method to get node's line number."""
"""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)
-
+ super(CheckNonJekyll, self).__init__(
+ args, filename, metadata, metadata_len, text, lines, doc)
def check_metadata(self):
self.reporter.check(self.metadata is None,
"""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(CheckIndex, self).__init__(args, filename,
+ metadata, metadata_len, text, lines, doc)
self.layout = 'lesson'
def check_metadata(self):
"""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)
-
+ super(CheckEpisode, self).__init__(args, filename,
+ metadata, metadata_len, text, lines, doc)
def check(self):
"""Run extra tests."""
super(CheckEpisode, self).check()
self.check_reference_inclusion()
-
def check_metadata(self):
super(CheckEpisode, self).check_metadata()
if self.metadata:
else:
self.check_metadata_fields(TEACHING_METADATA_FIELDS)
-
def check_metadata_fields(self, expected):
for (name, type_) in expected:
if name not in self.metadata:
self.reporter.add(self.filename,
'Missing metadata field {0}',
name)
- elif type(self.metadata[name]) != type_:
+ elif not isinstance(self.metadata[name], type_):
self.reporter.add(self.filename,
'"{0}" has wrong type in metadata ({1} instead of {2})',
name, type(self.metadata[name]), type_)
-
def check_reference_inclusion(self):
"""Check that links file has been included."""
"""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(CheckReference, self).__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)
+ super(CheckGeneric, self).__init__(args, filename,
+ metadata, metadata_len, text, lines, doc)
self.layout = 'page'
projects / rnaseq-cwl-training.git / blobdiff