Sync upstream lesson_check (carpentries-incubator#345)

* Sync upstream lesson_check

* Exclude `vendor` (not always hidden) from Jekyll

Author: tkphd

CODE_OF_CONDUCT.md

@@ -8,4 +8,7 @@ we pledge to follow the [Carpentry Code of Conduct][coc].
 Instances of abusive, harassing, or otherwise unacceptable behavior
 may be reported by following our [reporting guidelines][coc-reporting].
 
+[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
+[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
+
 {% include links.md %}

_config.yml

@@ -159,6 +159,7 @@ exclude:
   - bin/
   - .Rproj.user/
   - .vendor/
+  - vendor/
   - .docker-vendor/
 
 # Turn on built-in syntax highlighting.

_episodes/16-parallel.md

@@ -180,7 +180,7 @@ Pi: 3.140944, memory: 0.022351741790771484 GiB
 {{ site.local.prompt }} python pi-serial.py 100000000
 Pi: 3.14182724, memory: 2.2351741790771484 GiB
 ```
-{: .bash }
+{: .language-bash }
 
 Here we can see that the estimated amount of memory required scales linearly
 with the number of samples used.
@@ -278,7 +278,7 @@ Pi: 3.1425492, memory: 0.22351741790771484 GiB, time: 0.351212 s
 {{ site.local.prompt }} python pi-serial.py 100000000
 Pi: 3.14146608, memory: 2.2351741790771484 GiB, time: 3.735195 s
 ```
-{: .bash }
+{: .language-bash }
 
 Here we can see that the amount of time required scales approximately linearly
 with the number of samples used.

bin/lesson_check.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python3
-
 """
 Check lesson files and their contents.
 """
@@ -32,20 +30,20 @@
 # specially. This list must include all the Markdown files listed in the
 # 'bin/initialize' script.
 REQUIRED_FILES = {
-    '%/CODE_OF_CONDUCT.md': True,
-    '%/CONTRIBUTING.md': False,
-    '%/LICENSE.md': True,
-    '%/MAINTENANCE.md': False,
-    '%/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,
+    'MAINTENANCE.md': False,
+    '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+$')
@@ -79,32 +77,12 @@
 }
 
 # What kinds of code fragments are allowed?
+# We allow all 'language-*' code blocks below
 KNOWN_CODEBLOCKS = {
-    'bash',
     'error',
-    'html',
-    'language-bash',
-    'language-c',
-    'language-chapel',
-    'language-cpp',
-    'language-d',
-    'language-fortran',
-    'language-go',
-    'language-java',
-    'language-julia',
-    'language-lua',
-    'language-make',
-    'language-matlab',
-    'language-perl',
-    'language-python',
-    'language-r',
-    'language-rust',
-    'language-scala',
-    'language-shell',
-    'language-sql',
     'output',
-    'python',
-    'source'
+    'source',
+    'warning'
 }
 
 # What fields are required in teaching episode metadata?
@@ -134,9 +112,15 @@ def main():
 
     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)
+
+    args.references = {}
+    if not using_remote_theme(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, list(docs.keys()))
@@ -180,7 +164,7 @@ def parse_args():
                         default=False,
                         action="store_true",
                         dest='permissive',
-                        help='Do not raise an error even if there are issues')
+                        help='Do not raise an error even if issues are detected')
 
     args, extras = parser.parse_known_args()
     require(args.parser is not None,
@@ -190,6 +174,10 @@ def parse_args():
 
     return args
 
+def using_remote_theme(source_dir):
+    config_file = os.path.join(source_dir, '_config.yml')
+    config = load_yaml(config_file)
+    return 'remote_theme' in config
 
 def check_config(reporter, source_dir):
     """Check configuration file."""
@@ -211,6 +199,9 @@ def check_config(reporter, source_dir):
         reporter.check(defaults in config.get('defaults', []),
                    'configuration',
                    '"root" not set to "." in configuration')
+    if 'life_cycle' not in config:
+        config['life_cycle'] = None
+    return config['life_cycle']
 
 def check_source_rmd(reporter, source_dir, parser):
     """Check that Rmd episode files include `source: Rmd`"""
@@ -237,7 +228,7 @@ def read_references(reporter, ref_path):
     result = {}
     urls_seen = set()
 
-    with open(ref_path, 'r') as reader:
+    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
@@ -299,17 +290,20 @@ def check_fileset(source_dir, reporter, filenames_present):
     """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)
 
-    # Check episode files' names.
+    # Check names of episode files.
     seen = []
     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:
@@ -421,7 +415,8 @@ def check_codeblock_classes(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 is not None and (cls in KNOWN_CODEBLOCKS
+                                             or cls.startswith('language-')),
                                 (self.filename, self.get_loc(node)),
                                 'Unknown or missing code block type {0}',
                                 cls)
@@ -493,8 +488,6 @@ def get_loc(self, 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().__init__(args, filename, metadata, metadata_len, text, lines, doc)
 
     def check_metadata(self):
         self.reporter.check(self.metadata is None,
@@ -523,7 +516,8 @@ def check(self):
         """Run extra tests."""
 
         super().check()
-        self.check_reference_inclusion()
+        if not using_remote_theme():
+            self.check_reference_inclusion()
 
     def check_metadata(self):
         super().check_metadata()
@@ -563,6 +557,11 @@ def check_reference_inclusion(self):
         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):
@@ -586,7 +585,7 @@ def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
     (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(os.path.join('_episodes', '*\.md')), CheckEpisode),
     (re.compile(r'.*\.md'), CheckGeneric),
     (re.compile(r'.*\.snip'), CheckNonJekyll)
 ]