From 7887306998198ca7471953a590ae5d127792436b Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 5 May 2024 02:29:20 +0200
Subject: [PATCH 1/4] remove unused line that's now accomplished in subroutine

---
 pypiper/manager.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 965945b..da12953 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -1290,7 +1290,6 @@ def proc_wrapup(i):
             sleeptime = min((sleeptime + 0.25) * 3, 60 / len(processes))
 
         # All jobs are done, print a final closing and job info
-        stop_time = time.time()
         proc_message = "Command completed. {info}"
         info = (
             "Elapsed time: "

From 07fb60f474c4e3e330172ad53bfc6e21e1346bb6 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 5 May 2024 02:30:01 +0200
Subject: [PATCH 2/4] remove only-once-used variable binding

---
 pypiper/manager.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index da12953..657dd39 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -1290,7 +1290,6 @@ def proc_wrapup(i):
             sleeptime = min((sleeptime + 0.25) * 3, 60 / len(processes))
 
         # All jobs are done, print a final closing and job info
-        proc_message = "Command completed. {info}"
         info = (
             "Elapsed time: "
             + str(datetime.timedelta(seconds=self.time_elapsed(start_time)))
@@ -1307,7 +1306,7 @@ def proc_wrapup(i):
 
         info += "\n"  # finish out the
         self.info("</pre>")
-        self.info(proc_message.format(info=info))
+        self.info("Command completed. {info}".format(info=info))
 
         for rc in returncodes:
             if rc != 0:

From 90fb7ad532b3f954fc649fd99ad33dc318a01f56 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 5 May 2024 02:32:46 +0200
Subject: [PATCH 3/4] allow Stage to be nofail, close #218

---
 pypiper/pipeline.py |  5 ++++-
 pypiper/stage.py    | 14 +++++++++++++-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/pypiper/pipeline.py b/pypiper/pipeline.py
index 95d31f2..ab3f8d9 100644
--- a/pypiper/pipeline.py
+++ b/pypiper/pipeline.py
@@ -332,7 +332,10 @@ def run(self, start_point=None, stop_before=None, stop_after=None):
 
             print(f"Running stage: {getattr(stage, 'name', str(stage))}")
 
-            stage.run()
+            try:
+                stage.run()
+            except Exception as e:
+                self.manager._triage_error(e, nofail=stage.nofail)
             self.executed.append(stage)
             self.checkpoint(stage)
 
diff --git a/pypiper/stage.py b/pypiper/stage.py
index 6f1d551..929becf 100644
--- a/pypiper/stage.py
+++ b/pypiper/stage.py
@@ -17,7 +17,16 @@ class Stage(object):
     collection of commands that is checkpointed.
     """
 
-    def __init__(self, func, f_args=None, f_kwargs=None, name=None, checkpoint=True):
+    def __init__(
+        self,
+        func,
+        f_args=None,
+        f_kwargs=None,
+        name=None,
+        checkpoint=True,
+        *,
+        nofail=False
+    ):
         """
         A function, perhaps with arguments, defines the stage.
 
@@ -26,6 +35,8 @@ def __init__(self, func, f_args=None, f_kwargs=None, name=None, checkpoint=True)
         :param dict f_kwargs: Keyword arguments for func
         :param str name: name for the phase/stage
         :param callable func: Object that defines how the stage will execute.
+        :param bool nofail: Allow a failure of this stage to not fail the pipeline
+            in which it's running
         """
         if isinstance(func, Stage):
             raise TypeError("Cannot create Stage from Stage")
@@ -35,6 +46,7 @@ def __init__(self, func, f_args=None, f_kwargs=None, name=None, checkpoint=True)
         self.f_kwargs = f_kwargs or dict()
         self.name = name or func.__name__
         self.checkpoint = checkpoint
+        self.nofail = nofail
 
     @property
     def checkpoint_name(self):

From 7fa5a67181b589f0e67c68090dc15b72ae7d39c2 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 5 May 2024 02:39:48 +0200
Subject: [PATCH 4/4] add a requirements file tracking extra dev dependencies

---
 requirements/requirements-dev-extra.txt | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 requirements/requirements-dev-extra.txt

diff --git a/requirements/requirements-dev-extra.txt b/requirements/requirements-dev-extra.txt
new file mode 100644
index 0000000..7e66a17
--- /dev/null
+++ b/requirements/requirements-dev-extra.txt
@@ -0,0 +1 @@
+black