Merge remote-tracking branch 'origin/master' into code-quality

# Conflicts:
#	ipython2cwl/cwltoolextractor.py

Author: giannisdoukas

.travis.yml

@@ -19,6 +19,7 @@ script:
   - pycodestyle --max-line-length=119 $(find ipython2cwl -name '*.py')
   - coverage run --source ipython2cwl -m unittest discover tests
   - coveralls
+  - make mypy
 matrix:
   include:
     - name: "Python 3.7 on macOS 10.13"

Makefile

@@ -0,0 +1,2 @@
+mypy:
+	 mypy $$(find ipython2cwl -name '*.py')

ipython2cwl/cwltoolextractor.py

@@ -31,8 +31,8 @@
 
 class AnnotatedVariablesExtractor(ast.NodeTransformer):
     """AnnotatedVariablesExtractor removes the typing annotations
-    from relative to ipython2cwl and identifies all the variables
-    relative to an ipython2cwl typing annotation."""
+        from relative to ipython2cwl and identifies all the variables
+        relative to an ipython2cwl typing annotation."""
     input_type_mapper: Dict[Tuple[str, ...], Tuple[str, str]] = {
         (CWLFilePathInput.__name__,): (
             'File',
@@ -308,14 +308,18 @@ def compile(self, filename: Path = Path('notebookAsCWLTool.tar')) -> str:
         """
         workdir = tempfile.mkdtemp()
         script_path = os.path.join(workdir, 'notebookTool')
-        cwl_path = os.path.join(workdir, 'tool.cwl')
+        cwl_path: str = os.path.join(workdir, 'tool.cwl')
         dockerfile_path = os.path.join(workdir, 'Dockerfile')
         setup_path = os.path.join(workdir, 'setup.py')
         requirements_path = os.path.join(workdir, 'requirements.txt')
-        with open(script_path, 'wb') as f:
-            f.write(self._wrap_script_to_method(self._tree, self._variables).encode())
-        with open(cwl_path, 'w') as f:
-            yaml.safe_dump(self.cwl_command_line_tool(), f, encoding='utf-8')
+        with open(script_path, 'wb') as script_fd:
+            script_fd.write(self._wrap_script_to_method(self._tree, self._variables).encode())
+        with open(cwl_path, 'w') as cwl_fd:
+            yaml.safe_dump(
+                self.cwl_command_line_tool(),
+                cwl_fd,
+                encoding='utf-8'
+            )
         dockerfile = DOCKERFILE_TEMPLATE.format(
             python_version=f'python:{".".join(platform.python_version_tuple())}'
         )

ipython2cwl/repo2cwl.py

@@ -9,11 +9,11 @@
 from typing import List, Optional, Tuple, Dict
 from urllib.parse import urlparse, ParseResult
 
-import git
-import nbformat
+import git  # type: ignore
+import nbformat  # type: ignore
 import yaml
 from git import Repo
-from repo2docker import Repo2Docker
+from repo2docker import Repo2Docker  # type: ignore
 
 from .cwltoolextractor import AnnotatedIPython2CWLToolConverter
 
@@ -68,8 +68,8 @@ def _store_jn_as_script(notebook_path: str, git_directory_absolute_path: str, bi
     return tool, script_relative_path
 
 
-def existing_path(path: str):
-    path = Path(path)
+def existing_path(path_str: str):
+    path: Path = Path(path_str)
     if not path.is_dir():
         raise argparse.ArgumentTypeError(f'Directory: {str(path)} does not exists')
     return path
@@ -159,7 +159,7 @@ def _repo2cwl(git_directory_path: Repo) -> Tuple[str, List[Dict]]:
             bin_path,
             r2d.output_image_spec
         )
-        if cwl_command_line_tool is None:
+        if cwl_command_line_tool is None or script_name is None:
             continue
         cwl_command_line_tool['baseCommand'] = os.path.join('/app', 'cwl', 'bin', script_name)
         tools.append(cwl_command_line_tool)

ipython2cwl/requirements_manager.py

@@ -1,6 +1,6 @@
 from typing import List
 
-from pip._internal.operations import freeze
+from pip._internal.operations import freeze  # type: ignore
 
 
 class RequirementsManager:

test-requirements.txt

@@ -6,3 +6,4 @@ gitpython>=3.1.3
 docker>=4.2.1
 git+https://github.com/giannisdoukas/cwltool.git#egg=cwltool
 pandas==1.0.5
+mypy

tests/repo-like/requirements.txt

@@ -1 +1 @@
-PyYAML==5.3.1
+PyYAML==5.3.1