ci/cd

pynxtools/dataconverter/convert.py

@@ -36,14 +36,29 @@
 
 from pynxtools.dataconverter.logger import logger as pynx_logger
 
+if sys.version_info >= (3, 10):
+    from importlib.metadata import entry_points
+else:
+    from importlib_metadata import entry_points
+
 
 def get_reader(reader_name) -> BaseReader:
     """Helper function to get the reader object from it's given name"""
     path_prefix = f"{os.path.dirname(__file__)}{os.sep}" if os.path.dirname(__file__) else ""
     path = os.path.join(path_prefix, "readers", reader_name, "reader.py")
     spec = importlib.util.spec_from_file_location("reader.py", path)
-    module = importlib.util.module_from_spec(spec)
-    spec.loader.exec_module(module)  # type: ignore[attr-defined]
+    try:
+        module = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(module)  # type: ignore[attr-defined]
+    except FileNotFoundError as exc:
+        # pylint: disable=unexpected-keyword-arg
+        importlib_module = entry_points(group='pynxtools.reader')
+        if (
+            importlib_module
+            and reader_name in map(lambda ep: ep.name, entry_points(group='pynxtools.reader'))
+        ):
+            return importlib_module[reader_name].load()
+        raise ValueError(f"The reader, {reader_name}, was not found.") from exc
     return module.READER  # type: ignore[attr-defined]
 
 
@@ -158,7 +173,7 @@ def transfer_data_into_template(input_file,
     return data
 
 
-# pylint: disable=too-many-arguments,too-many-locals
+# pylint: disable=too-many-arguments, W1203
 def convert(input_file: Tuple[str, ...],
             reader: str,
             nxdl: str,
@@ -211,12 +226,13 @@ def convert(input_file: Tuple[str, ...],
     if fair and data.undocumented.keys():
         logger.warning("There are undocumented paths in the template. This is not acceptable!")
         return
-    for path in data.undocumented.keys():
-        if "/@default" in path:
-            continue
-        logger.info(
-            f"NO DOCUMENTATION: The path, {path} is being written but has no documentation."
-        )
+    if undocumented:
+        for path in data.undocumented.keys():
+            if "/@default" in path:
+                continue
+            logger.info(
+                f"NO DOCUMENTATION: The path, {path} is being written but has no documentation."
+            )
     helpers.add_default_root_attributes(data=data, filename=os.path.basename(output))
     Writer(data=data, nxdl_f_path=nxdl_f_path, output_path=output).write()
 

pynxtools/dataconverter/helpers.py

@@ -33,7 +33,7 @@
 from pynxtools.nexus import nexus
 from pynxtools.nexus.nexus import NxdlAttributeError
 
-logger = logging.getLogger(__name__)
+pynx_logger = logging.getLogger(__name__)
 
 
 def is_a_lone_group(xml_element) -> bool:
@@ -447,7 +447,9 @@ def does_group_exist(path_to_group, data):
     return False
 
 
-def ensure_all_required_fields_exist(template, data, nxdl_root, logger):
+# pylint: disable=W1203
+def ensure_all_required_fields_exist(template, data,
+                                     nxdl_root, logger=pynx_logger):
     """Checks whether all the required fields are in the returned data object."""
     for path in template["required"]:
         entry_name = get_name_from_data_dict_entry(path[path.rindex('/') + 1:])
@@ -498,7 +500,9 @@ def try_undocumented(data, nxdl_root: ET.Element):
             pass
 
 
-def validate_data_dict(template, data, nxdl_root: ET.Element, logger):
+def validate_data_dict(template, data,
+                       nxdl_root: ET.Element,
+                       logger=pynx_logger):
     """Checks whether all the required paths from the template are returned in data dict."""
     assert nxdl_root is not None, "The NXDL file hasn't been loaded."
 
@@ -590,7 +594,7 @@ def convert_to_hill(atoms_typ):
     return atom_list + list(atoms_typ)
 
 
-def add_default_root_attributes(data, filename):
+def add_default_root_attributes(data, filename, logger=pynx_logger):
     """
     Takes a dict/Template and adds NXroot fields/attributes that are inherently available
     """