Merge pull request #4 from pd3/master

Add test generator script and update variant_calling and data_formats tests

tests/make-test.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+
+import os,sys,json,re
+
+def usage():
+    print('Usage: make-test.py [OPTIONS] index.ipynb answers.ipynb')
+    print('Options:')
+    print('   -o, --output FILE     Output file')
+    sys.exit(1)
+
+def parse_opts():
+    opts = {}
+    opts['files'] = []
+    args = sys.argv[1:]
+    while len(args):
+        if args[0]=='-o' or args[0]=='--output':
+            args = args[1:]
+            opts['outfile'] = args[0]
+        elif os.path.isfile(args[0]):
+            opts['files'].append(args[0])
+        else:
+            usage()
+        args = args[1:]
+    if len(opts['files']) == 0: usage()
+    if 'outfile' in opts: opts['fh'] = open(opts['outfile'],"w")
+    else: opts['fh'] = sys.stdout
+    return opts
+
+def process_file(opts,file):
+    nb = json.load(open(file))
+    opts['fh'].write("\n# "+file+"\n")
+    next_file = None
+    lines = []
+    for cell in nb['cells']:
+        if cell['cell_type'] == 'markdown':
+            for line in cell['source']:
+                m = re.search(r'\(([^(]+\.ipynb)\)',line); 
+                if m!=None: next_file = m.group(1)
+                m = re.search(r'^\s*`(.+)`\s*$',line)
+                if m!=None and m.group(1)!='`' : lines.append(m.group(1))
+        if cell['cell_type'] == 'code':
+            for line in cell['source']:
+                line = line.rstrip('\n')
+                if len(lines)>0 and lines[-1][-1]=='\\':
+                    lines[-1] = lines[-1].rstrip('\\')
+                    lines[-1] += line
+                else:
+                    lines.append(line)
+    for line in lines:
+        line = re.sub(r'\|\s*less -S\s*$', '| head',line)
+        line = re.sub(r'\|\s*less\s*$', '| head',line)
+        line = re.sub(r'less\s+-S\s+', 'tail ',line)
+        line = re.sub(r'less\s+', 'tail ',line)
+        opts['fh'].write(line+"\n")
+    opts['fh'].write("\n")
+    if next_file!=None:
+        dir = '.'
+        m = re.search(r'^(.*)/[^/]+$',file);
+        if m!=None and m.group(1)!='': dir = m.group(1)
+        opts['files'].append(dir+'/'+next_file)
+
+def main(opts):
+    opts['fh'].write("#!/bin/bash\n")
+    opts['fh'].write("set -e\n")
+    opts['fh'].write("set -x\n")
+
+    for file in opts['files']:
+        process_file(opts,file)
+
+    opts['fh'].close()
+
+if __name__ == "__main__":
+    opts = parse_opts()
+    main(opts)
+