Fix Python scripts for Windows: UTF-8 encoding (#485)

[rnaseq-cwl-training.git] / bin / lesson_check.py

diff --git a/bin/lesson_check.py b/bin/lesson_check.py
old mode 100755 (executable)
new mode 100644 (file)
index b0b5581..b76d35b
--- a/bin/lesson_check.py
+++ b/bin/lesson_check.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python3
-
 """
 Check lesson files and their contents.
 """
@@ -29,19 +27,19 @@ SOURCE_RMD_DIRS = ['_episodes_rmd']
 # 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,
-    '%/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+$')
@@ -55,6 +53,9 @@ 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*(.+)')
 
+# Pattern to match {% include ... %} statements
+P_INTERNAL_INCLUDE_LINK = re.compile(r'^{% include ([^ ]*) %}$')
+
 # What kinds of blockquotes are allowed?
 KNOWN_BLOCKQUOTES = {
     'callout',
@@ -208,29 +209,44 @@ def read_references(reporter, ref_path):
     {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
 
 
@@ -254,7 +270,7 @@ 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)
@@ -264,7 +280,10 @@ def check_fileset(source_dir, reporter, filenames_present):
     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:
@@ -538,8 +557,7 @@ CHECKERS = [
     (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)
 ]