junifer 0.0.6.dev44__tar.gz → 0.0.6.dev51__tar.gz

{junifer-0.0.6.dev44 → junifer-0.0.6.dev51}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev44
+Version: 0.0.6.dev51
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.6.dev51/docs/changes/newsfragments/367.enh

@@ -0,0 +1 @@
+Allow for external python files in the ``with`` section of the yaml to import other files by `Fede Raimondo`_

{junifer-0.0.6.dev44 → junifer-0.0.6.dev51}/docs/extending/extension.rst

@@ -28,8 +28,25 @@ This is the ideal place to include ``junifer`` extensions.
 
 .. important::
 
-   Some ``junifer`` commands will not consider files imported from files included
-   in the ``with`` statement. If ``my_file.py`` imports ``my_other_file.py``,
-   some of the ``junifer`` commands will not consider ``my_other_file.py``. Either
-   place all the code in one file or add multiple files to the ``with``
-   statement.
+   Some ``junifer`` commands will not consider files imported from files
+   included in the ``with`` statement, unless this is known to junifer. If
+   ``my_file.py`` imports ``my_other_file.py``, the ``run`` command will work,
+   but ``queue`` will not create a proper job. This is because we need to 
+   let junifer know that ``my_other_file.py`` is also part of the code. To do
+   so, we need to include a special function in ``my_file.py`` which tells
+   ``junifer`` about the dependencies of the module:
+
+   .. code-block:: python
+
+      def junifer_module_deps() -> List[str]:
+        """Return the dependencies of the module.
+
+        Returns
+        -------
+        list of str
+            The list of dependencies.
+
+        """
+
+        return ["my_other_file.py"]
+

{junifer-0.0.6.dev44 → junifer-0.0.6.dev51}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev44'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev44')
+__version__ = version = '0.0.6.dev51'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev51')

{junifer-0.0.6.dev44 → junifer-0.0.6.dev51}/junifer/cli/parser.py

@@ -18,7 +18,7 @@ from ..utils import logger, raise_error, warn_with_log, yaml
 __all__ = ["parse_yaml", "parse_elements"]
 
 
-def parse_yaml(filepath: Union[str, Path]) -> Dict:
+def parse_yaml(filepath: Union[str, Path]) -> Dict:  # noqa: C901
     """Parse YAML.
 
     Parameters
@@ -65,14 +65,35 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
                     raise_error(
                         f"File in 'with' section does not exist: {file_path}"
                     )
+                # Add the parent directory to the sys.path so that the
+                # any imports from this module work correctly
+                t_path = str(file_path.parent)
+                if t_path not in sys.path:
+                    sys.path.append(str(file_path.parent))
+
                 spec = importlib.util.spec_from_file_location(
                     t_module, file_path
                 )
                 module = importlib.util.module_from_spec(spec)  # type: ignore
                 sys.modules[t_module] = module
                 spec.loader.exec_module(module)  # type: ignore
+
                 # Add absolute path to final list
                 final_to_load.append(str(file_path.resolve()))
+
+                # Check if the module has junifer_module_deps function
+                if hasattr(module, "junifer_module_deps"):
+                    logger.debug(
+                        f"Module {t_module} has junifer_module_deps function"
+                    )
+                    # Get the dependencies
+                    deps = module.junifer_module_deps()
+                    # Add the dependencies to the final list
+                    for dep in deps:
+                        if dep not in final_to_load:
+                            final_to_load.append(
+                                str((file_path.parent / dep).resolve())
+                            )
             else:
                 logger.info(f"Importing module: {t_module}")
                 importlib.import_module(t_module)

{junifer-0.0.6.dev44 → junifer-0.0.6.dev51}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev44
+Version: 0.0.6.dev51
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.6.dev44 → junifer-0.0.6.dev51}/junifer.egg-info/SOURCES.txt

@@ -66,6 +66,7 @@ docs/changes/newsfragments/358.doc
 docs/changes/newsfragments/359.doc
 docs/changes/newsfragments/360.bugfix
 docs/changes/newsfragments/361.misc
+docs/changes/newsfragments/367.enh
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst