rm ipython2cwl imports from code

ipython2cwl/cwltool.py

@@ -6,17 +6,17 @@
 import tempfile
 from collections import namedtuple
 from pathlib import Path
-from typing import Dict
+from typing import Dict, Any
 
 import astor
 import yaml
 
 from .iotypes import CWLFilePathInput, CWLBooleanInput, CWLIntInput, CWLStringInput, CWLFilePathOutput
 from .requirements_manager import RequirementsManager
 
-with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), 'template.dockerfile'])) as f:
+with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), 'templates', 'template.dockerfile'])) as f:
     DOCKERFILE_TEMPLATE = f.read()
-with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), 'template.setup.py'])) as f:
+with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), 'templates', 'template.setup'])) as f:
     SETUP_TEMPLATE = f.read()
 
 
@@ -82,6 +82,23 @@ def visit_AnnAssign(self, node):
             pass
         return node
 
+    def visit_Import(self, node: ast.Import):
+        names = []
+        for name in node.names:  # type: ast.alias
+            if name.name == 'ipython2cwl' or name.name.startswith('ipython2cwl.'):
+                continue
+            names.append(name)
+        if len(names) > 0:
+            node.names = names
+            return node
+        else:
+            return None
+
+    def visit_ImportFrom(self, node: ast.ImportFrom) -> Any:
+        if node.module == 'ipython2cwl' or node.module.startswith('ipython2cwl.'):
+            return None
+        return node
+
 
 class AnnotatedIPython2CWLToolConverter:
     """

ipython2cwl/ipython2cwl.py

@@ -1,21 +1,9 @@
 import argparse
-import os
 from pathlib import Path
 from typing import List, Optional
 
 import nbformat
-from pip._internal.operations import freeze
-
-with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), 'template.dockerfile'])) as f:
-    DOCKERFILE_TEMPLATE = f.read()
-
-
-def directory_type(directory_argument: str):
-    """Function to be used as a directory type for argparse argument."""
-    directory = Path(directory_argument)
-    if not directory.is_dir():
-        raise RuntimeError('directory does not exists')
-    return str(directory.absolute())
+from .cwltool import AnnotatedIPython2CWLToolConverter
 
 
 def main(argv: Optional[List[str]] = None):
@@ -24,28 +12,19 @@ def main(argv: Optional[List[str]] = None):
         argv = sys.argv
     parser = argparse.ArgumentParser()
     parser.add_argument('jn', type=argparse.FileType('r'), nargs=1)
-    parser.add_argument('-o', '--output-dir', type=directory_type, required=True)
+    parser.add_argument('-o', '--output', type=Path, required=True)
     args = parser.parse_args(argv[1:])
     notebook = nbformat.read(args.jn[0], as_version=4)
-    output_dir = args.output_dir
+    output: Path = args.output
     args.jn[0].close()
     script_code = '\n'.join(
         [f"\n\n# --------- cell - {i} ---------\n\n{cell.source}" for i, cell in
          enumerate(filter(lambda c: c.cell_type == 'code', notebook.cells), start=1)]
     )
-    print(script_code)
-    requirements = list(freeze.freeze())
-    with open(os.sep.join([output_dir, 'app.py']), 'w') as f:
-        f.write(script_code)
-    with open(os.sep.join([output_dir, 'requirements.txt']), 'w') as f:
-        f.write('\n'.join(requirements))
-    with open(os.sep.join([output_dir, 'Dockerfile']), 'w') as f:
-        f.write(
-            DOCKERFILE_TEMPLATE.format(
-                python_version=notebook.metadata.language_info.version,
-                source_code_directory=output_dir
-            )
-        )
+
+    converter = AnnotatedIPython2CWLToolConverter(script_code)
+    converter.compile(output)
+
     return 0
 
 

ipython2cwl/templates/template.setup

@@ -0,0 +1,12 @@
+from setuptools import setup
+
+name = 'JupyterAsATool'
+
+setup(
+    name=name,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: Apache Software License",
+    ],
+    scripts=['notebookTool']
+)

setup.py

@@ -28,7 +28,9 @@ def get_version(rel_path):
 setup(
     name=name,
     version=get_version(f"{name}/__init__.py"),
-    packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]),
+    packages=['ipython2cwl'],
+    package_dir={'ipython2cwl': 'ipython2cwl'},
+    package_data={'ipython2cwl': ['ipython2cwl/templates/*']},
     author='Yannis Doukas',
     author_email='giannisdoukas2311@gmail.com',
     description='Convert IPython Jupyter Notebooks to CWL tool',
@@ -47,7 +49,9 @@ def get_version(rel_path):
         "Programming Language :: Python :: 3.8",
     ],
     entry_points={
-        'console_scripts': ['jupyter-jn2cwl=ipython2cwl.ipython2cwl:main'],
+        'console_scripts': [
+            'jupyter-jn2cwl=ipython2cwl.ipython2cwl:main',
+        ],
     },
     install_requires=[
         'nbformat>=5.0.6',

tests/test_cwltool.py

@@ -170,6 +170,52 @@ def test_AnnotatedIPython2CWLToolConverter_wrap_script_to_method(self):
         locals()['main']('new message')
         self.assertEqual('new message', globals()['printed_message'])
 
+    def test_AnnotatedIPython2CWLToolConverter_wrap_script_to_method_removes_ipython2cwl_imports(self):
+        annotated_python_scripts = [
+            os.linesep.join([
+                'import ipython2cwl',
+                'print("hello world")'
+            ]),
+            os.linesep.join([
+                'import ipython2cwl as foo',
+                'print("hello world")'
+            ]),
+            os.linesep.join([
+                'import ipython2cwl.iotypes',
+                'print("hello world")'
+            ]),
+            os.linesep.join([
+                'from ipython2cwl import iotypes',
+                'print("hello world")'
+            ]),
+            os.linesep.join([
+                'from ipython2cwl.iotypes import CWLFilePathInput',
+                'print("hello world")'
+            ]),
+            os.linesep.join([
+                'from ipython2cwl.iotypes import CWLFilePathInput, CWLBooleanInput',
+                'print("hello world")'
+            ]),
+            os.linesep.join([
+                'import typing, ipython2cwl',
+                'print("hello world")'
+            ])
+        ]
+        for script in annotated_python_scripts:
+            conv = AnnotatedIPython2CWLToolConverter(script)
+            new_script = conv._wrap_script_to_method(conv._tree, conv._variables)
+            print('-' * 10)
+            print(script)
+            print('-' * 2)
+            print(new_script)
+            print('-' * 10)
+            self.assertNotIn('ipython2cwl', new_script)
+
+        self.assertIn('typing', os.linesep.join([
+            'import typing, ipython2cwl'
+            'print("hello world")'
+        ]))
+
     def test_AnnotatedIPython2CWLToolConverter_output_file_annotation(self):
         import tempfile
         root_dir = tempfile.mkdtemp()