fix arguments for ipython

Author: giannisdoukas

.gitignore

@@ -244,4 +244,5 @@ cython_debug/
 /tests/jn/output/
 tmp.py
 /html/
-cwlbuild
+cwlbuild
+/tests/repo-like/result.yaml

examples/compiled_tool/Dockerfile

@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -33,7 +33,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -85,6 +85,32 @@
     "fig.figure.savefig(after_transform_data)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Traceback (most recent call last):\r\n",
+      "  File \"/Users/dks/.pyenv/versions/3.6.10/bin/jupyter-jn2cwl\", line 33, in <module>\r\n",
+      "    sys.exit(load_entry_point('ipython2cwl', 'console_scripts', 'jupyter-jn2cwl')())\r\n",
+      "  File \"/Users/dks/Workspaces/IPython2CWL/ipython2cwl/ipython2cwl.py\", line 32, in main\r\n",
+      "    converter = AnnotatedIPython2CWLToolConverter(script_code)\r\n",
+      "  File \"/Users/dks/Workspaces/IPython2CWL/ipython2cwl/cwltoolextractor.py\", line 133, in __init__\r\n",
+      "    self._tree = ast.fix_missing_locations(extractor.visit(ast.parse(self._code)))\r\n",
+      "  File \"/Users/dks/.pyenv/versions/3.6.10/lib/python3.6/ast.py\", line 35, in parse\r\n",
+      "    return compile(source, filename, mode, PyCF_ONLY_AST)\r\n",
+      "TypeError: compile() arg 1 must be a string, bytes or AST object\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "# !jupyter-jn2cwl -o compiled_tool intro.ipynb"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},