# Controls
.PHONY : commands clean files
+.NOTPARALLEL:
all : commands
## commands : show all commands.
@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
## serve : run a local server.
-serve : lesson-rmd
+serve : lesson-md
${JEKYLL} serve
## site : build files but do not run a server.
-site : lesson-rmd
+site : lesson-md
${JEKYLL} build
# repo-check : check repository settings.
## ----------------------------------------
## Commands specific to lesson websites.
-.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
# RMarkdown files
RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
$(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
${DST}/license/index.html
-## lesson-rmd : convert Rmarkdown files to markdown
-lesson-rmd: $(RMD_SRC)
- @bin/knit_lessons.sh $(RMD_SRC)
+## lesson-md : convert Rmarkdown files to markdown
+lesson-md : ${RMD_DST}
+
+# Use of .NOTPARALLEL makes rule execute only once
+${RMD_DST} : ${RMD_SRC}
+ @bin/knit_lessons.sh ${RMD_SRC}
## lesson-check : validate lesson Markdown.
lesson-check :
- @bin/lesson_check.py -s . -p ${PARSER}
+ @bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
lesson-check-all :
{% comment %}
- Find previous and next episodes (if any).
-{% endcomment %}
-{% for episode in site.episodes %}
- {% if episode.url == page.url %}
- {% unless forloop.first %}
- {% assign prev_episode = prev %}
- {% endunless %}
- {% unless forloop.last %}
- {% assign next_episode = site.episodes[forloop.index] %}
- {% endunless %}
- {% endif %}
- {% assign prev = episode %}
-{% endfor %}
-
-{% comment %}
- Display title and prev/next links.
+ Navigation bar for an episode.
{% endcomment %}
<div class="row">
<div class="col-md-1">
<h3>
- {% if prev_episode %}
- <a href="{{ page.root }}{{ prev_episode.url }}"><span class="glyphicon glyphicon-menu-left" aria-hidden="true"></span><span class="sr-only">previous episode</span></a>
+ {% if page.previous.url %}
+ <a href="{{ page.root }}{{ page.previous.url }}"><span class="glyphicon glyphicon-menu-left" aria-hidden="true"></span><span class="sr-only">previous episode</span></a>
{% else %}
<a href="{{ page.root }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
{% endif %}
</div>
<div class="col-md-1">
<h3>
- {% if next_episode %}
- <a href="{{ page.root }}{{ next_episode.url }}"><span class="glyphicon glyphicon-menu-right" aria-hidden="true"></span><span class="sr-only">next episode</span></a>
+ {% if page.next.url %}
+ <a href="{{ page.root }}{{ page.next.url }}"><span class="glyphicon glyphicon-menu-right" aria-hidden="true"></span><span class="sr-only">next episode</span></a>
{% else %}
<a href="{{ page.root }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
{% endif %}
from util import Reporter, read_markdown, load_yaml, check_unwanted_files, require, IMAGE_FILE_SUFFIX
-__version__ = '0.2'
+__version__ = '0.3'
# Where to look for source Markdown files.
SOURCE_DIRS = ['', '_episodes', '_extras']
P_FIGURE_REFS = re.compile(r'<img[^>]+src="([^"]+)"[^>]*>')
# Pattern to match internally-defined Markdown links.
-P_INTERNALLY_DEFINED_LINK = re.compile(r'\[[^\]]+\]\[[^\]]+\]')
+P_INTERNAL_LINK_REF = re.compile(r'\[([^\]]+)\]\[([^\]]+)\]')
+
+# Pattern to match reference links (to resolve internally-defined references).
+P_INTERNAL_LINK_DEF = re.compile(r'^\[([^\]]+)\]:\s*(.+)')
# What kinds of blockquotes are allowed?
KNOWN_BLOCKQUOTES = {
args = parse_args()
args.reporter = Reporter()
check_config(args.reporter, args.source_dir)
+ 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_unwanted_files(args.source_dir, args.reporter)
checker = create_checker(args, filename, docs[filename])
checker.check()
check_figures(args.source_dir, args.reporter)
+
args.reporter.report()
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',
'"root" not set to ".." in configuration')
+def read_references(reporter, ref_path):
+ """Read shared file of reference links, returning dictionary of valid references
+ {symbolic_name : URL}
+ """
+
+ 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)
+ return result
+
+
def read_all_markdown(source_dir, parser):
"""Read source files, returning
{path : {'metadata':yaml, 'metadata_len':N, 'text':text, 'lines':[(i, line, len)], 'doc':doc}}
def check(self):
- """Run tests on metadata."""
+ """Run tests."""
self.check_metadata()
self.check_line_lengths()
def check_defined_link_references(self):
"""Check that defined links resolve in the file.
- Internally-defined links match the pattern [text][label]. If
- the label contains '{{...}}', it is hopefully a references to
- a configuration value - we should check that, but don't right
- now.
+ Internally-defined links match the pattern [text][label].
"""
result = set()
for node in self.find_all(self.doc, {'type' : 'text'}):
- for match in P_INTERNALLY_DEFINED_LINK.findall(node['value']):
- if '{{' not in match:
- result.add(match)
+ for match in P_INTERNAL_LINK_REF.findall(node['value']):
+ text = match[0]
+ link = match[1]
+ if link not in self.args.references:
+ result.add('"{0}"=>"{1}"'.format(text, link))
self.reporter.check(not result,
self.filename,
'Internally-defined links may be missing definitions: {0}',
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()
+ self.check_reference_inclusion()
+
+
def check_metadata(self):
super(CheckEpisode, self).check_metadata()
if self.metadata:
name, type(self.metadata[name]), type_)
+ def check_reference_inclusion(self):
+ """Check that links file has been included."""
+
+ if not self.args.reference_path:
+ return
+
+ for (i, last_line, line_len) in reversed(self.lines):
+ if last_line:
+ break
+
+ require(last_line,
+ 'No non-empty lines in {0}'.format(self.filename))
+
+ include_filename = os.path.split(self.args.reference_path)[-1]
+ if include_filename not in last_line:
+ self.reporter.add(self.filename,
+ 'episode does not include "{0}"',
+ include_filename)
+
+
class CheckReference(CheckBase):
"""Check the reference page."""
projects / rnaseq-cwl-training.git / commitdiff