cpg-utils 5.4.1__tar.gz → 5.4.3__tar.gz

{cpg_utils-5.4.1 → cpg_utils-5.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cpg-utils
-Version: 5.4.1
+Version: 5.4.3
 Summary: Library of convenience functions specific to the CPG
 Home-page: https://github.com/populationgenomics/cpg-utils
 License: MIT

{cpg_utils-5.4.1 → cpg_utils-5.4.3}/cpg_utils/hail_batch.py

@@ -189,12 +189,16 @@ class Batch(hb.Batch):
 
         self.total_job_num += 1
 
+        # Multiple jobs in the batch might reference the same attributes dict
+        # object. Avoid modifying the dict object (e.g. with pop() or update())
+        # to avoid changing the attributes of subsequently processed jobs.
+
         attributes = attributes or {}
         stage = attributes.get('stage')
         dataset = attributes.get('dataset')
         sequencing_group = attributes.get('sequencing_group')
         participant_id = attributes.get('participant_id')
-        sequencing_groups: set[str] = set(attributes.pop('sequencing_groups', []) or [])
+        sequencing_groups: set[str] = set(attributes.get('sequencing_groups') or [])
         if sequencing_group:
             sequencing_groups.add(sequencing_group)
         part = attributes.get('part')
@@ -234,10 +238,14 @@ class Batch(hb.Batch):
         self.job_by_tool[tool]['job_n'] += 1
         self.job_by_tool[tool]['sequencing_groups'] |= sequencing_groups
 
+        # Ensure all the returned attribute values are presented as strings
+        fixed_attrs = {
+            k: str(v) for k, v in attributes.items() if k != 'sequencing_groups'
+        }
+
         seqgroups_str = str(sorted(sequencing_groups))
-        attributes.update(self._pack_attribute('sequencing_groups', seqgroups_str))
+        fixed_attrs.update(self._pack_attribute('sequencing_groups', seqgroups_str))
 
-        fixed_attrs = {k: str(v) for k, v in attributes.items()}
         return name, fixed_attrs
 
     def run(self, **kwargs: Any):

{cpg_utils-5.4.1 → cpg_utils-5.4.3}/cpg_utils/slack.py

@@ -66,14 +66,21 @@ def send_message(text: str) -> None:
         logging.error(f'Error posting to Slack: {err}')
 
 
-def upload_file(content: bytes, comment: str) -> None:
+def upload_file(
+    content: bytes,
+    comment: str,
+    title: str | None = None,
+    filename: str | None = None,
+) -> None:
     """Uploads `content` to Slack with the given text `comment`, reading credentials from the config."""
     slack_client = _get_slack_sdk().WebClient(token=_get_token())
     try:
-        slack_client.files_upload(
-            channels=_get_channel(),
+        slack_client.files_upload_v2(
+            channel=_get_channel(),
             content=content,
             initial_comment=comment,
+            title=title,
+            filename=filename,
         )
     except _get_slack_sdk().errors.SlackApiError as err:
         logging.error(f'Error posting to Slack: {err}')

{cpg_utils-5.4.1 → cpg_utils-5.4.3}/cpg_utils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cpg-utils
-Version: 5.4.1
+Version: 5.4.3
 Summary: Library of convenience functions specific to the CPG
 Home-page: https://github.com/populationgenomics/cpg-utils
 License: MIT

{cpg_utils-5.4.1 → cpg_utils-5.4.3}/setup.py

@@ -8,7 +8,7 @@ with open('README.md') as f:
 setup(
     name='cpg-utils',
     # This tag is automatically updated by bumpversion
-    version='5.4.1',
+    version='5.4.3',
     description='Library of convenience functions specific to the CPG',
     long_description=long_description,
     long_description_content_type='text/markdown',