Merge pull request #135 from tgen/release-v1.6.2

Release v1.6.2

docs/releases/1.6.2.md

@@ -0,0 +1,11 @@
+# Jetstream v1.6.2 Release Notes
+
+# Major changes
+
+- Fixed issue #131
+- Fixed parsing of account info when the cluster does not supply accounting info
+- Fixed "RuntimeError: generator ignored GeneratorExit" exception handling
+
+# Dev Notes
+
+- Security issues resolved from dependabot

jetstream/__init__.py

@@ -8,7 +8,7 @@
 
 __author__ = 'Ryan Richholt'
 __email__ = 'rrichholt@tgen.org'
-__version__ = '1.6.1'
+__version__ = '1.6.2'
 
 
 # Configure parallel library dependencies (Used by numpy)

jetstream/backends/slurm.py

@@ -446,11 +446,11 @@ def launch_sacct(*job_ids, delimiter=sacct_delimiter, raw=False):
 def parse_sacct(data, delimiter=sacct_delimiter, id_pattern=job_id_pattern):
     """Parse stdout from sacct to a dictionary of job ids and data."""
     jobs = dict()
-    lines = iter(data.strip().splitlines())
-    header = next(lines).strip().split(delimiter)
+    lines = iter(data.splitlines())
+    header = next(lines).split(delimiter)
 
     for line in lines:
-        row = dict(zip(header, line.strip().split(delimiter)))
+        row = dict(zip(header, line.split(delimiter)))
 
         try:
             match = id_pattern.match(row['JobID'])

jetstream/pipelines.py

@@ -163,7 +163,7 @@ def find_pipelines(*dirs):
                     p = Pipeline(path)
                     log.debug(f'Found {p} at {path}')
                     yield p
-                except :
+                except Exception:
                     log.debug(f'Failed to load: {path}')
 
                 yield from find_pipelines(path)

jetstream/runner.py

@@ -237,8 +237,7 @@ def process_exec_directives(self, task):
         exec_directive = task.directives.get('exec')
 
         if exec_directive:
-            env = {'runner': self, 'task': task}
-            exec(exec_directive, None, env)
+            exec(exec_directive)
             self._workflow_graph = self.workflow.reload_graph()
             self._workflow_iterator = iter(self.workflow.graph)
 

requirements.txt

@@ -1,8 +1,8 @@
 confuse==1.0.0
 decorator==4.4.0
 filelock==3.0.12
-Jinja2==2.10.1
+Jinja2==2.11.3
 MarkupSafe==1.1.1
 networkx==2.3
-PyYAML==5.1.1
+PyYAML==5.4
 ulid-py==0.0.9

tests/templates/dependencies_3.jst

@@ -1,16 +1,16 @@
-# This template tests dynamic features with the exec directive. 
+# This template tests dynamic features with the exec directive.
 # During a run, add_tasks will add a new to the workflow. The
-# last task will wait for the new task to complete via the 
+# last task will wait for the new task to complete via the
 # after-re directive.
 # Expected stdout: "Hello, world! All done!"
 - name: start
-  cmd: printf 'Hello, ' 
+  cmd: printf 'Hello, '
 
 
 - name: add_tasks
   after: start
   exec: |
-    runner.workflow.new_task(
+    self.workflow.new_task(
         name='dynamic_task',
         cmd="printf 'world! '"
     )