Merge pull request #28 from bbglab/27-openvariant--failing-with-pytho…

…n-313

Openvariant | Failing with Python 3.13

.github/workflows/openvariant_tester.yml

@@ -27,10 +27,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+    - name: Set up the latest Python
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: "3.x"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

README.md

@@ -68,15 +68,14 @@ For more details check our [Installation](https://openvariant.readthedocs.io/en/
 
 ## Examples
 
-We offer a bunch of [examples](https://github.com/bbglab/openvariant/tree/master/examples) to be able to understand how OpenVariant can be applied. Also, check 
-[Examples](https://openvariant.readthedocs.io/en/latest/examples.html) section in OpenVariant's documentation.
+We provide a variety of [examples](https://github.com/bbglab/openvariant/tree/master/examples) to help to understand how OpenVariant can be applied. Explore the 
+[Examples](https://openvariant.readthedocs.io/en/latest/examples.html) section in OpenVariant's documentation for more details.
 
 ## Contributing
 
-Feel free to contribute as much as you want to the code.
+You're welcome to contribute to the code as much as you'd like!
 
-See [CONTRIBUTING](https://github.com/bbglab/openvariant/blob/master/CONTRIBUTING.md) for guidelines on contributing and respect your behaviour specified
-at [CODE OF CONDUCT](https://github.com/bbglab/openvariant/blob/master/CODE_OF_CONDUCT.md).
+Please review the guidelines outlined in the [Contributing](https://github.com/bbglab/openvariant/blob/master/CONTRIBUTING.md) document and adhere to the standards of conduct detailed in the [Code of Conduct](https://github.com/bbglab/openvariant/blob/master/CODE_OF_CONDUCT.md).
 
 ## License
 

openvariant/__init__.py

@@ -1,12 +1,22 @@
-import pkg_resources
+from multiprocessing import set_start_method
 
 from openvariant.annotation.annotation import Annotation
 from openvariant.tasks import cat, count, group_by
 from openvariant.variant import Variant
 from openvariant.find_files import findfiles
 
-version = pkg_resources.require("open-variant")[0].version
-__version__ = version
+try:
+    from importlib.metadata import version  # Python 3.8+
+except ImportError:
+    from importlib_metadata import version  # Backport for older versions
+
+__version__ = version("open-variant")
+
+# Set multiprocessing start method to 'spawn'
+try:
+    set_start_method('spawn', force=True)
+except RuntimeError:
+    pass
 
 __all__ = ['Annotation', 'Variant', 'cat', 'count', 'group_by', 'findfiles']
 

openvariant/annotation/annotation.py

@@ -9,7 +9,7 @@
 from typing import List
 from yaml import safe_load, YAMLError
 
-from openvariant.annotation.builder import AnnotationTypesBuilders
+from openvariant.utils.utils import import_class_from_module
 from openvariant.annotation.config_annotation import (AnnotationGeneralKeys, AnnotationKeys, AnnotationTypes,
                                                       ExcludesKeys, DEFAULT_FORMAT, DEFAULT_DELIMITER,
                                                       AnnotationFormat, AnnotationDelimiter)
@@ -166,8 +166,13 @@ def __init__(self, annotation_path: str) -> None:
         self._annotations: dict = {}
         for k in raw_annotation.get(AnnotationGeneralKeys.ANNOTATION.value, []):
 
+            class_name = k[AnnotationKeys.TYPE.value].upper()
+            module_name = "openvariant.annotation.builder"
+            ClassAnnotation = import_class_from_module(module_name, class_name)
+            instance = ClassAnnotation()
+
             self._annotations[k[AnnotationKeys.FIELD.value]] = \
-                AnnotationTypesBuilders[k[AnnotationKeys.TYPE.value].upper()].value(k, self._path)
+                instance(k, self._path)
 
         self._columns = raw_annotation.get(AnnotationGeneralKeys.COLUMNS.value, list(self.annotations.keys()))
         self._check_columns()