From 0c9b16f123d5df4c4ea1c0b18c8276b540f70493 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Tue, 5 Sep 2023 15:52:44 +0200
Subject: [PATCH 01/39] try getting just stage name, but fall back to str
 representation of stage; close #197

---
 pypiper/pipeline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pypiper/pipeline.py b/pypiper/pipeline.py
index 69474c2..a5546ce 100644
--- a/pypiper/pipeline.py
+++ b/pypiper/pipeline.py
@@ -314,7 +314,7 @@ def run(self, start_point=None, stop_before=None, stop_after=None):
             # between results from different stages.
             skip_mode = False
 
-            print("Running stage: {}".format(stage))
+            print(f"Running stage: {getattr(stage, "name", str(stage))}")
 
             stage.run()
             self.executed.append(stage)

From 0b430c7ab416f35389a85683c56c2258adb31e60 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 4 Oct 2023 15:56:14 -0400
Subject: [PATCH 02/39] version 0.13.3a1 for pipestat 0.6.0a1

---
 docs/changelog.md                     |  4 ++++
 pypiper/_version.py                   |  2 +-
 pypiper/manager.py                    | 21 ++++++++++++---------
 pypiper/utils.py                      | 12 ++++++------
 requirements/requirements-pypiper.txt |  2 +-
 5 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index d7281c6..81a0729 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.13.3a1] -- 2023-10-04
+### Fixed
+- refactor for pipestat 0.6.0a1
+
 ## [0.13.2] -- 2023-08-02
 ### Fixed
 - fixed self.new_start overriding checkpoints.
diff --git a/pypiper/_version.py b/pypiper/_version.py
index 83ce76f..78a3de9 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.13.2"
+__version__ = "0.13.3a1"
diff --git a/pypiper/manager.py b/pypiper/manager.py
index c3f4cf6..65adad4 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -344,7 +344,7 @@ def _get_arg(args_dict, arg_name):
             return None if arg_name not in args_dict else args_dict[arg_name]
 
         self._pipestat_manager = PipestatManager(
-            sample_name=self.pipestat_sample_name
+            record_identifier=self.pipestat_sample_name
             or _get_arg(args_dict, "pipestat_sample_name")
             or DEFAULT_SAMPLE_NAME,
             pipeline_name=self.name,
@@ -724,7 +724,8 @@ def start_pipeline(self, args=None, multi=False):
         self.info("\n----------------------------------------\n")
         self.status = "running"
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier="running"
+            record_identifier=self._pipestat_manager.sample_name,
+            status_identifier="running",
         )
 
         # Record the start in PIPE_profile and PIPE_commands output files so we
@@ -770,7 +771,8 @@ def _set_status_flag(self, status):
         prev_status = self.status
         self.status = status
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier=status
+            record_identifier=self._pipestat_manager.sample_name,
+            status_identifier=status,
         )
         self.debug("\nChanged status from {} to {}.".format(prev_status, self.status))
 
@@ -1419,7 +1421,7 @@ def _wait_for_lock(self, lock_file):
                 )
                 # self._set_status_flag(WAIT_FLAG)
                 self.pipestat.set_status(
-                    sample_name=self._pipestat_manager.sample_name,
+                    record_identifier=self._pipestat_manager.sample_name,
                     status_identifier="waiting",
                 )
                 first_message_flag = True
@@ -1443,7 +1445,7 @@ def _wait_for_lock(self, lock_file):
             self.timestamp("File unlocked.")
             # self._set_status_flag(RUN_FLAG)
             self.pipestat.set_status(
-                sample_name=self._pipestat_manager.sample_name,
+                record_identifier=self._pipestat_manager.sample_name,
                 status_identifier="running",
             )
 
@@ -1602,7 +1604,7 @@ def report_result(self, key, value, nolog=False, result_formatter=None):
 
         reported_result = self.pipestat.report(
             values={key: value},
-            sample_name=self.pipestat_sample_name,
+            record_identifier=self.pipestat_sample_name,
             result_formatter=rf,
         )
 
@@ -1684,7 +1686,7 @@ def report_object(
         val = {key: message_raw.replace("\t", " ")}
 
         reported_result = self.pipestat.report(
-            values=val, sample_name=self.pipestat_sample_name, result_formatter=rf
+            values=val, record_identifier=self.pipestat_sample_name, result_formatter=rf
         )
         if not nolog:
             for r in reported_result:
@@ -2026,7 +2028,7 @@ def fail_pipeline(self, exc, dynamic_recover=False):
             self.info("Failure reason: " + str(exc))
             # self._set_status_flag(FAIL_FLAG)
             self.pipestat.set_status(
-                sample_name=self._pipestat_manager.sample_name,
+                record_identifier=self._pipestat_manager.sample_name,
                 status_identifier="failed",
             )
 
@@ -2087,7 +2089,8 @@ def stop_pipeline(self, status=COMPLETE_FLAG):
         """
         # self._set_status_flag(status)
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier=status
+            record_identifier=self._pipestat_manager.sample_name,
+            status_identifier=status,
         )
         self._cleanup()
         elapsed_time_this_run = str(
diff --git a/pypiper/utils.py b/pypiper/utils.py
index 2c5ac75..3d64071 100644
--- a/pypiper/utils.py
+++ b/pypiper/utils.py
@@ -387,20 +387,20 @@ def split_by_pipes(cmd):
     cmdlist = []
     newcmd = str()
     for char in cmd:
-        if char is "{":
+        if char == "{":
             stack_brace.append("{")
-        elif char is "}":
+        elif char == "}":
             stack_brace.pop()
-        elif char is "(":
+        elif char == "(":
             stack_paren.append("(")
-        elif char is ")":
+        elif char == ")":
             stack_paren.pop()
 
         if len(stack_brace) > 0 or len(stack_paren) > 0:
             # We are inside a parenthetic of some kind; emit character
             # no matter what it is
             newcmd += char
-        elif char is "|":
+        elif char == "|":
             # if it's a pipe, finish the command and start a new one
             cmdlist.append(newcmd)
             newcmd = str()
@@ -1110,7 +1110,7 @@ def _add_args(parser, args, required):
     return parser
 
 
-def result_formatter_markdown(pipeline_name, sample_name, res_id, value) -> str:
+def result_formatter_markdown(pipeline_name, record_identifier, res_id, value) -> str:
     """
     Returns Markdown formatted value as string
     """
diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
index 886be3e..04e6661 100644
--- a/requirements/requirements-pypiper.txt
+++ b/requirements/requirements-pypiper.txt
@@ -4,4 +4,4 @@ psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.4.0
+pipestat>=0.6.0a1

From d9c818d3135e924d8696ab1ea9deeba8a92f67a8 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Tue, 7 Nov 2023 22:44:07 +0100
Subject: [PATCH 03/39] updated to pipestat 0.6.0

---
 pypiper/manager.py | 47 ++++++++++++++++++++++++++--------------------
 pypiper/utils.py   |  4 +++-
 2 files changed, 30 insertions(+), 21 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index c3f4cf6..57af110 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -330,7 +330,6 @@ def __init__(
 
         # pipestat setup
         self.pipestat_sample_name = pipestat_sample_name or DEFAULT_SAMPLE_NAME
-        # getattr(self, "sample_name", DEFAULT_SAMPLE_NAME)
 
         # don't force default pipestat_results_file value unless
         # pipestat config not provided
@@ -344,7 +343,7 @@ def _get_arg(args_dict, arg_name):
             return None if arg_name not in args_dict else args_dict[arg_name]
 
         self._pipestat_manager = PipestatManager(
-            sample_name=self.pipestat_sample_name
+            record_identifier=self.pipestat_sample_name
             or _get_arg(args_dict, "pipestat_sample_name")
             or DEFAULT_SAMPLE_NAME,
             pipeline_name=self.name,
@@ -437,7 +436,7 @@ def _completed(self):
         :return bool: Whether the managed pipeline is in a completed state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.sample_name)
+            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
             == COMPLETE_FLAG
         )
 
@@ -448,7 +447,10 @@ def _failed(self):
 
         :return bool: Whether the managed pipeline is in a failed state.
         """
-        return self.pipestat.get_status(self._pipestat_manager.sample_name) == FAIL_FLAG
+        return (
+            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            == FAIL_FLAG
+        )
 
     @property
     def halted(self):
@@ -457,7 +459,8 @@ def halted(self):
         :return bool: Whether the managed pipeline is in a paused/halted state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.sample_name) == PAUSE_FLAG
+            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            == PAUSE_FLAG
         )
 
     @property
@@ -724,7 +727,8 @@ def start_pipeline(self, args=None, multi=False):
         self.info("\n----------------------------------------\n")
         self.status = "running"
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier="running"
+            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            status_identifier="running",
         )
 
         # Record the start in PIPE_profile and PIPE_commands output files so we
@@ -770,7 +774,8 @@ def _set_status_flag(self, status):
         prev_status = self.status
         self.status = status
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier=status
+            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            status_identifier=status,
         )
         self.debug("\nChanged status from {} to {}.".format(prev_status, self.status))
 
@@ -786,7 +791,7 @@ def _flag_file_path(self, status=None):
         """
 
         flag_file_name = "{}_{}_{}".format(
-            self._pipestat_manager["_pipeline_name"],
+            self._pipestat_manager.cfg["pipeline_name"],
             self.pipestat_sample_name,
             flag_name(status or self.status),
         )
@@ -1419,7 +1424,7 @@ def _wait_for_lock(self, lock_file):
                 )
                 # self._set_status_flag(WAIT_FLAG)
                 self.pipestat.set_status(
-                    sample_name=self._pipestat_manager.sample_name,
+                    record_identifier=self._pipestat_manager.cfg["record_identifier"],
                     status_identifier="waiting",
                 )
                 first_message_flag = True
@@ -1443,7 +1448,7 @@ def _wait_for_lock(self, lock_file):
             self.timestamp("File unlocked.")
             # self._set_status_flag(RUN_FLAG)
             self.pipestat.set_status(
-                sample_name=self._pipestat_manager.sample_name,
+                record_identifier=self._pipestat_manager.cfg["record_identifier"],
                 status_identifier="running",
             )
 
@@ -1602,7 +1607,7 @@ def report_result(self, key, value, nolog=False, result_formatter=None):
 
         reported_result = self.pipestat.report(
             values={key: value},
-            sample_name=self.pipestat_sample_name,
+            record_identifier=self.pipestat_sample_name,
             result_formatter=rf,
         )
 
@@ -1684,7 +1689,7 @@ def report_object(
         val = {key: message_raw.replace("\t", " ")}
 
         reported_result = self.pipestat.report(
-            values=val, sample_name=self.pipestat_sample_name, result_formatter=rf
+            values=val, record_identifier=self.pipestat_sample_name, result_formatter=rf
         )
         if not nolog:
             for r in reported_result:
@@ -1851,10 +1856,12 @@ def _refresh_stats(self):
             _, data = read_yaml_data(path=self.pipeline_stats_file, what="stats_file")
             print(data)
             pipeline_key = list(
-                data[self.pipestat["_pipeline_name"]][self.pipestat["_pipeline_type"]]
+                data[self._pipestat_manager.cfg["pipeline_name"]][
+                    self.pipestat["_pipeline_type"]
+                ]
             )[0]
             if self.name == pipeline_key:
-                for key, value in data[self.pipestat["_pipeline_name"]][
+                for key, value in data[self._pipestat_manager.cfg["pipeline_name"]][
                     self.pipestat["_pipeline_type"]
                 ][pipeline_key].items():
                     self.stats_dict[key] = value.strip()
@@ -1989,12 +1996,12 @@ def complete(self):
         """Stop a completely finished pipeline."""
         self.stop_pipeline(status=COMPLETE_FLAG)
 
-    def fail_pipeline(self, exc, dynamic_recover=False):
+    def fail_pipeline(self, exc: Exception, dynamic_recover: bool = False):
         """
         If the pipeline does not complete, this function will stop the pipeline gracefully.
         It sets the status flag to failed and skips the normal success completion procedure.
 
-        :param Exception e: Exception to raise.
+        :param Exception exc: Exception to raise.
         :param bool dynamic_recover: Whether to recover e.g. for job termination.
         """
         # Take care of any active running subprocess
@@ -2024,9 +2031,8 @@ def fail_pipeline(self, exc, dynamic_recover=False):
             total_time = datetime.timedelta(seconds=self.time_elapsed(self.starttime))
             self.info("Total time: " + str(total_time))
             self.info("Failure reason: " + str(exc))
-            # self._set_status_flag(FAIL_FLAG)
             self.pipestat.set_status(
-                sample_name=self._pipestat_manager.sample_name,
+                record_identifier=self._pipestat_manager.cfg["record_identifier"],
                 status_identifier="failed",
             )
 
@@ -2087,7 +2093,8 @@ def stop_pipeline(self, status=COMPLETE_FLAG):
         """
         # self._set_status_flag(status)
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier=status
+            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            status_identifier=status,
         )
         self._cleanup()
         elapsed_time_this_run = str(
@@ -2457,7 +2464,7 @@ def _cleanup(self, dry_run=False):
                 for fn in glob.glob(self.outfolder + flag_name("*"))
                 if COMPLETE_FLAG not in os.path.basename(fn)
                 and not "{}_{}_{}".format(
-                    self._pipestat_manager["_pipeline_name"],
+                    self._pipestat_manager.cfg["pipeline_name"],
                     self.pipestat_sample_name,
                     run_flag,
                 )
diff --git a/pypiper/utils.py b/pypiper/utils.py
index 2c5ac75..54677c8 100644
--- a/pypiper/utils.py
+++ b/pypiper/utils.py
@@ -1110,9 +1110,11 @@ def _add_args(parser, args, required):
     return parser
 
 
-def result_formatter_markdown(pipeline_name, sample_name, res_id, value) -> str:
+def result_formatter_markdown(pipeline_name, record_identifier, res_id, value) -> str:
     """
     Returns Markdown formatted value as string
+
+    # Pipeline_name and record_identifier should be kept because pipestat needs it
     """
 
     message_markdown = "\n> `{key}`\t{value}\t_RES_".format(key=res_id, value=value)

From e00e8d8d930f22cc3b0312ed0f066db6027ebb88 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Tue, 7 Nov 2023 22:49:45 +0100
Subject: [PATCH 04/39] updated requirements

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

diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
index 04e6661..0b74f55 100644
--- a/requirements/requirements-pypiper.txt
+++ b/requirements/requirements-pypiper.txt
@@ -1,7 +1,6 @@
-attmap>=0.12.5
 logmuse>=0.2.4
 psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.6.0a1
+pipestat>=0.6.0a4

From 39b6e9931f19cc46ecf95c9432a58ea5bc6c37b3 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Tue, 7 Nov 2023 22:56:38 +0100
Subject: [PATCH 05/39] testing, drop python 3.7

---
 .github/workflows/run-pytest.yml | 2 +-
 pypiper/manager.py               | 2 --
 setup.py                         | 5 ++++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
index 6bf573b..cc3d35d 100644
--- a/.github/workflows/run-pytest.yml
+++ b/.github/workflows/run-pytest.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.10"]
         os: [ubuntu-latest]
 
     steps:
diff --git a/pypiper/manager.py b/pypiper/manager.py
index fa73352..57af110 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -728,7 +728,6 @@ def start_pipeline(self, args=None, multi=False):
         self.status = "running"
         self.pipestat.set_status(
             record_identifier=self._pipestat_manager.cfg["record_identifier"],
-
             status_identifier="running",
         )
 
@@ -1426,7 +1425,6 @@ def _wait_for_lock(self, lock_file):
                 # self._set_status_flag(WAIT_FLAG)
                 self.pipestat.set_status(
                     record_identifier=self._pipestat_manager.cfg["record_identifier"],
-
                     status_identifier="waiting",
                 )
                 first_message_flag = True
diff --git a/setup.py b/setup.py
index d485071..06a9d08 100644
--- a/setup.py
+++ b/setup.py
@@ -56,7 +56,10 @@ def read_reqs_file(reqs_name):
     classifiers=[
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python :: 2.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
     author="Nathan Sheffield, Johanna Klughammer, Andre Rendeiro",

From 1c2c844dacf29c1d693af20e57f20e9cc1b60d4d Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 8 Nov 2023 14:34:47 -0500
Subject: [PATCH 06/39] fix f-string quote issue for python 3.10

---
 pypiper/pipeline.py                   | 2 +-
 requirements/requirements-pypiper.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pypiper/pipeline.py b/pypiper/pipeline.py
index 652d6bf..95d31f2 100644
--- a/pypiper/pipeline.py
+++ b/pypiper/pipeline.py
@@ -330,7 +330,7 @@ def run(self, start_point=None, stop_before=None, stop_after=None):
             # between results from different stages.
             skip_mode = False
 
-            print(f"Running stage: {getattr(stage, "name", str(stage))}")
+            print(f"Running stage: {getattr(stage, 'name', str(stage))}")
 
             stage.run()
             self.executed.append(stage)
diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
index 0b74f55..dd3bca5 100644
--- a/requirements/requirements-pypiper.txt
+++ b/requirements/requirements-pypiper.txt
@@ -3,4 +3,4 @@ psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.6.0a4
+pipestat>=0.6.0a5

From 5b4668291cea761f5ca1de3750207291b21b5d6b Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Fri, 10 Nov 2023 14:48:31 -0500
Subject: [PATCH 07/39] minor refactor to use pipestat properties instead of
 cfg dict

---
 pypiper/manager.py | 42 ++++++++++++++++++++++--------------------
 1 file changed, 22 insertions(+), 20 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 57af110..660ed85 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -329,7 +329,7 @@ def __init__(
         signal.signal(signal.SIGTERM, self._signal_term_handler)
 
         # pipestat setup
-        self.pipestat_sample_name = pipestat_sample_name or DEFAULT_SAMPLE_NAME
+        self.pipestat_record_identifier = pipestat_sample_name or DEFAULT_SAMPLE_NAME
 
         # don't force default pipestat_results_file value unless
         # pipestat config not provided
@@ -343,7 +343,7 @@ def _get_arg(args_dict, arg_name):
             return None if arg_name not in args_dict else args_dict[arg_name]
 
         self._pipestat_manager = PipestatManager(
-            record_identifier=self.pipestat_sample_name
+            record_identifier=self.pipestat_record_identifier
             or _get_arg(args_dict, "pipestat_sample_name")
             or DEFAULT_SAMPLE_NAME,
             pipeline_name=self.name,
@@ -436,7 +436,7 @@ def _completed(self):
         :return bool: Whether the managed pipeline is in a completed state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            self.pipestat.get_status(self._pipestat_manager.record_identifier)
             == COMPLETE_FLAG
         )
 
@@ -448,7 +448,7 @@ def _failed(self):
         :return bool: Whether the managed pipeline is in a failed state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            self.pipestat.get_status(self._pipestat_manager.record_identifier)
             == FAIL_FLAG
         )
 
@@ -459,7 +459,7 @@ def halted(self):
         :return bool: Whether the managed pipeline is in a paused/halted state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            self.pipestat.get_status(self._pipestat_manager.record_identifier)
             == PAUSE_FLAG
         )
 
@@ -723,11 +723,11 @@ def start_pipeline(self, args=None, multi=False):
         results = self._pipestat_manager.__str__().split("\n")
         for i in results:
             self.info("* " + i)
-        self.info("* Sample name: " + self.pipestat_sample_name + "\n")
+        self.info("* Sample name: " + self.pipestat_record_identifier + "\n")
         self.info("\n----------------------------------------\n")
         self.status = "running"
         self.pipestat.set_status(
-            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            record_identifier=self._pipestat_manager.record_identifier,
             status_identifier="running",
         )
 
@@ -774,7 +774,7 @@ def _set_status_flag(self, status):
         prev_status = self.status
         self.status = status
         self.pipestat.set_status(
-            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            record_identifier=self._pipestat_manager.record_identifier,
             status_identifier=status,
         )
         self.debug("\nChanged status from {} to {}.".format(prev_status, self.status))
@@ -791,8 +791,8 @@ def _flag_file_path(self, status=None):
         """
 
         flag_file_name = "{}_{}_{}".format(
-            self._pipestat_manager.cfg["pipeline_name"],
-            self.pipestat_sample_name,
+            self._pipestat_manager.pipeline_name,
+            self.pipestat_record_identifier,
             flag_name(status or self.status),
         )
         return pipeline_filepath(self, filename=flag_file_name)
@@ -1424,7 +1424,7 @@ def _wait_for_lock(self, lock_file):
                 )
                 # self._set_status_flag(WAIT_FLAG)
                 self.pipestat.set_status(
-                    record_identifier=self._pipestat_manager.cfg["record_identifier"],
+                    record_identifier=self._pipestat_manager.record_identifier,
                     status_identifier="waiting",
                 )
                 first_message_flag = True
@@ -1448,7 +1448,7 @@ def _wait_for_lock(self, lock_file):
             self.timestamp("File unlocked.")
             # self._set_status_flag(RUN_FLAG)
             self.pipestat.set_status(
-                record_identifier=self._pipestat_manager.cfg["record_identifier"],
+                record_identifier=self._pipestat_manager.record_identifier,
                 status_identifier="running",
             )
 
@@ -1607,7 +1607,7 @@ def report_result(self, key, value, nolog=False, result_formatter=None):
 
         reported_result = self.pipestat.report(
             values={key: value},
-            record_identifier=self.pipestat_sample_name,
+            record_identifier=self.pipestat_record_identifier,
             result_formatter=rf,
         )
 
@@ -1689,7 +1689,9 @@ def report_object(
         val = {key: message_raw.replace("\t", " ")}
 
         reported_result = self.pipestat.report(
-            values=val, record_identifier=self.pipestat_sample_name, result_formatter=rf
+            values=val,
+            record_identifier=self.pipestat_record_identifier,
+            result_formatter=rf,
         )
         if not nolog:
             for r in reported_result:
@@ -1856,12 +1858,12 @@ def _refresh_stats(self):
             _, data = read_yaml_data(path=self.pipeline_stats_file, what="stats_file")
             print(data)
             pipeline_key = list(
-                data[self._pipestat_manager.cfg["pipeline_name"]][
+                data[self._pipestat_manager.pipeline_name][
                     self.pipestat["_pipeline_type"]
                 ]
             )[0]
             if self.name == pipeline_key:
-                for key, value in data[self._pipestat_manager.cfg["pipeline_name"]][
+                for key, value in data[self._pipestat_manager.pipeline_name][
                     self.pipestat["_pipeline_type"]
                 ][pipeline_key].items():
                     self.stats_dict[key] = value.strip()
@@ -2032,7 +2034,7 @@ def fail_pipeline(self, exc: Exception, dynamic_recover: bool = False):
             self.info("Total time: " + str(total_time))
             self.info("Failure reason: " + str(exc))
             self.pipestat.set_status(
-                record_identifier=self._pipestat_manager.cfg["record_identifier"],
+                record_identifier=self._pipestat_manager.record_identifier,
                 status_identifier="failed",
             )
 
@@ -2093,7 +2095,7 @@ def stop_pipeline(self, status=COMPLETE_FLAG):
         """
         # self._set_status_flag(status)
         self.pipestat.set_status(
-            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            record_identifier=self._pipestat_manager.record_identifier,
             status_identifier=status,
         )
         self._cleanup()
@@ -2464,8 +2466,8 @@ def _cleanup(self, dry_run=False):
                 for fn in glob.glob(self.outfolder + flag_name("*"))
                 if COMPLETE_FLAG not in os.path.basename(fn)
                 and not "{}_{}_{}".format(
-                    self._pipestat_manager.cfg["pipeline_name"],
-                    self.pipestat_sample_name,
+                    self._pipestat_manager.pipeline_name,
+                    self.pipestat_record_identifier,
                     run_flag,
                 )
                 == os.path.basename(fn)

From d360ba1425d6dfd2cc37232835517bbbb72c138d Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Fri, 10 Nov 2023 14:54:22 -0500
Subject: [PATCH 08/39] update changelog and version number

---
 docs/changelog.md   | 6 ++++++
 pypiper/_version.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index 81a0729..472efbe 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.13.3a2] -- 2023-11-xx
+### Changed
+- minor refactor for pipestat 0.6.0 release
+- drop python 2.7
+- updated requirements
+
 ## [0.13.3a1] -- 2023-10-04
 ### Fixed
 - refactor for pipestat 0.6.0a1
diff --git a/pypiper/_version.py b/pypiper/_version.py
index 78a3de9..7c16d15 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.13.3a1"
+__version__ = "0.13.3a2"

From 4ea21c2bb99e66e0b85a101af31a900ab0162f1c Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Tue, 14 Nov 2023 08:46:02 -0500
Subject: [PATCH 09/39] update v0.13.3 and changelog

---
 docs/changelog.md   | 10 ++++------
 pypiper/_version.py |  2 +-
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index 472efbe..d0fe4f9 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,14 +1,12 @@
 # Changelog
 
-## [0.13.3a2] -- 2023-11-xx
+## [0.13.3] -- 2023-11-xx
 ### Changed
-- minor refactor for pipestat 0.6.0 release
+- refactor for pipestat v0.6.0 release
 - drop python 2.7
 - updated requirements
-
-## [0.13.3a1] -- 2023-10-04
-### Fixed
-- refactor for pipestat 0.6.0a1
+- ### Fixed
+- fixed #196 and #197
 
 ## [0.13.2] -- 2023-08-02
 ### Fixed
diff --git a/pypiper/_version.py b/pypiper/_version.py
index 7c16d15..26c36ca 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.13.3a2"
+__version__ = "0.13.3"

From ed6b7fb43140526d831ce976d68f6c554efaf166 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Tue, 14 Nov 2023 16:06:06 -0500
Subject: [PATCH 10/39] fix _refresh_stats bug and change version to 0.14.0

---
 docs/changelog.md   |  2 +-
 pypiper/_version.py |  2 +-
 pypiper/manager.py  | 15 ++++++++-------
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index d0fe4f9..fb4b8c7 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,6 +1,6 @@
 # Changelog
 
-## [0.13.3] -- 2023-11-xx
+## [0.14.0] -- 2023-11-xx
 ### Changed
 - refactor for pipestat v0.6.0 release
 - drop python 2.7
diff --git a/pypiper/_version.py b/pypiper/_version.py
index 26c36ca..9e78220 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.13.3"
+__version__ = "0.14.0"
diff --git a/pypiper/manager.py b/pypiper/manager.py
index 660ed85..d3c058d 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -1856,17 +1856,18 @@ def _refresh_stats(self):
 
         if os.path.isfile(self.pipeline_stats_file):
             _, data = read_yaml_data(path=self.pipeline_stats_file, what="stats_file")
-            print(data)
-            pipeline_key = list(
+            record_identifier = list(
                 data[self._pipestat_manager.pipeline_name][
-                    self.pipestat["_pipeline_type"]
+                    self._pipestat_manager.pipeline_type
                 ]
             )[0]
-            if self.name == pipeline_key:
+
+            # Confirm that the loaded stats file is the same namespace as the pipeline manager
+            if record_identifier == self._pipestat_manager.record_identifier:
                 for key, value in data[self._pipestat_manager.pipeline_name][
-                    self.pipestat["_pipeline_type"]
-                ][pipeline_key].items():
-                    self.stats_dict[key] = value.strip()
+                    self._pipestat_manager.pipeline_type
+                ][record_identifier].items():
+                    self.stats_dict[key] = value
 
     def get_stat(self, key):
         """

From b0c5f8d5a06c039e2b9df7fc5a60407dd2a4ddfe Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 15 Nov 2023 15:14:52 -0500
Subject: [PATCH 11/39] potential fix for #201

---
 pypiper/manager.py | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index d3c058d..c87ec9c 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -1587,7 +1587,9 @@ def _report_profile(
         with open(self.pipeline_profile_file, "a") as myfile:
             myfile.write(message_raw + "\n")
 
-    def report_result(self, key, value, nolog=False, result_formatter=None):
+    def report_result(
+        self, key, value, nolog=False, result_formatter=None, force_overwrite=False
+    ):
         """
         Writes a key:value pair to self.pipeline_stats_file.
 
@@ -1597,6 +1599,7 @@ def report_result(self, key, value, nolog=False, result_formatter=None):
             logfile. Use sparingly in case you will be printing the result in a
             different format.
         :param str result_formatter: function for formatting via pipestat backend
+        :param bool force_overwrite: overwrite results if they already exist?
         :return str reported_result: the reported result is returned as a list of formatted strings.
 
         """
@@ -1609,11 +1612,17 @@ def report_result(self, key, value, nolog=False, result_formatter=None):
             values={key: value},
             record_identifier=self.pipestat_record_identifier,
             result_formatter=rf,
+            force_overwrite=force_overwrite,
         )
 
         if not nolog:
-            for r in reported_result:
-                self.info(r)
+            if isinstance(
+                reported_result, bool
+            ):  # Pipestat can return False if results are NOT reported.
+                self.info("Result successfully reported? " + str(reported_result))
+            else:
+                for r in reported_result:
+                    self.info(r)
 
         return reported_result
 
@@ -1626,6 +1635,7 @@ def report_object(
         annotation=None,
         nolog=False,
         result_formatter=None,
+        force_overwrite=False,
     ):
         """
         Writes a key:value pair to self.pipeline_stats_file. Note: this function
@@ -1646,6 +1656,7 @@ def report_object(
             logfile. Use sparingly in case you will be printing the result in a
             different format.
         :param str result_formatter: function for formatting via pipestat backend
+        :param bool force_overwrite: overwrite results if they already exist?
         :return str reported_result: the reported result is returned as a list of formatted strings.
         """
         warnings.warn(
@@ -1692,11 +1703,17 @@ def report_object(
             values=val,
             record_identifier=self.pipestat_record_identifier,
             result_formatter=rf,
+            force_overwrite=force_overwrite,
         )
+
         if not nolog:
-            for r in reported_result:
-                self.info(r)
-        return reported_result
+            if isinstance(
+                reported_result, bool
+            ):  # Pipestat can return False if results are NOT reported.
+                self.info("Result successfully reported? " + str(reported_result))
+            else:
+                for r in reported_result:
+                    self.info(r)
 
     def _safe_write_to_file(self, file, message):
         """

From d7b9c8c70d6e87805b0257d5cf510dba4e2c153a Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 15 Nov 2023 15:17:13 -0500
Subject: [PATCH 12/39] changelog

---
 docs/changelog.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/changelog.md b/docs/changelog.md
index fb4b8c7..2c21384 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -7,6 +7,8 @@
 - updated requirements
 - ### Fixed
 - fixed #196 and #197
+- ### Added
+- added `force_overwrite` to `report_result` and `report_object`
 
 ## [0.13.2] -- 2023-08-02
 ### Fixed

From f92d034b5d5ee4c01f4d7e7077d883a79d93b30e Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 15 Nov 2023 18:12:54 -0500
Subject: [PATCH 13/39] v0.14.0a1 prerelease

---
 pypiper/_version.py                   | 2 +-
 requirements/requirements-pypiper.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pypiper/_version.py b/pypiper/_version.py
index 9e78220..679c8ec 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.14.0"
+__version__ = "0.14.0a1"
diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
index dd3bca5..17bf456 100644
--- a/requirements/requirements-pypiper.txt
+++ b/requirements/requirements-pypiper.txt
@@ -3,4 +3,4 @@ psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.6.0a5
+pipestat>=0.6.0a7

From 1a677dad34ffe77dd14cff1034d02e9fde09c117 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Mon, 20 Nov 2023 14:41:28 -0500
Subject: [PATCH 14/39] report_object -> change message_raw to be a values dict
 to conform with pipestat output schemas

---
 pypiper/manager.py | 29 +++++++----------------------
 1 file changed, 7 insertions(+), 22 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index c87ec9c..d9ae454 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -1675,29 +1675,14 @@ def report_object(
             anchor_text = str(key).strip()
         # better to use a relative path in this file
         # convert any absolute paths into relative paths
-        relative_filename = (
-            os.path.relpath(filename, self.outfolder)
-            if os.path.isabs(filename)
-            else filename
-        )
-
-        if anchor_image:
-            relative_anchor_image = (
-                os.path.relpath(anchor_image, self.outfolder)
-                if os.path.isabs(anchor_image)
-                else anchor_image
-            )
-        else:
-            relative_anchor_image = "None"
 
-        message_raw = "{filename}\t{anchor_text}\t{anchor_image}\t{annotation}".format(
-            filename=relative_filename,
-            anchor_text=anchor_text,
-            anchor_image=relative_anchor_image,
-            annotation=annotation,
-        )
-
-        val = {key: message_raw.replace("\t", " ")}
+        values = {
+            "path": filename,
+            "thumbnail_path": anchor_image,
+            "title": anchor_text,
+            "annotation": annotation,
+        }
+        val = {key: values}
 
         reported_result = self.pipestat.report(
             values=val,

From ed95993f5031dc4e25f8fb162b7184e26786177a Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Mon, 20 Nov 2023 17:26:41 -0500
Subject: [PATCH 15/39] self.pipestat_results_file should take priority over
 self.pipeline_stats_file related to
 https://github.com/databio/pepatac/issues/257

---
 pypiper/manager.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index d9ae454..903badc 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -338,6 +338,9 @@ def __init__(
                 self, filename="pipestat_results.yaml"
             )
 
+        if pipestat_results_file:
+            self.pipestat_results_file = pipestat_results_file
+
         def _get_arg(args_dict, arg_name):
             """safely get argument from arg dict -- return None if doesn't exist"""
             return None if arg_name not in args_dict else args_dict[arg_name]
@@ -350,8 +353,9 @@ def _get_arg(args_dict, arg_name):
             schema_path=pipestat_schema
             or _get_arg(args_dict, "pipestat_schema")
             or default_pipestat_output_schema(sys.argv[0]),
-            results_file_path=self.pipeline_stats_file
-            or _get_arg(args_dict, "pipestat_results_file"),
+            results_file_path=self.pipestat_results_file
+            or _get_arg(args_dict, "pipestat_results_file")
+            or self.pipeline_stats_file,
             config_file=pipestat_config or _get_arg(args_dict, "pipestat_config"),
             multi_pipelines=multi,
         )

From cc8407089f8df7aac666ed68727b69d7bd369bba Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Mon, 27 Nov 2023 12:22:49 -0500
Subject: [PATCH 16/39] make pipestat_results_file = pipeline_stats_file if it
 is not provided

---
 pypiper/manager.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 903badc..5b6bb3c 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -334,11 +334,8 @@ def __init__(
         # don't force default pipestat_results_file value unless
         # pipestat config not provided
         if pipestat_config is None and pipestat_results_file is None:
-            pipestat_results_file = pipeline_filepath(
-                self, filename="pipestat_results.yaml"
-            )
-
-        if pipestat_results_file:
+            self.pipestat_results_file = self.pipeline_stats_file
+        elif pipestat_results_file:
             self.pipestat_results_file = pipestat_results_file
 
         def _get_arg(args_dict, arg_name):

From 2de4e842d6ba555cc1f18473403c04085dc586b2 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Mon, 27 Nov 2023 13:06:49 -0500
Subject: [PATCH 17/39] set pipeline_stats_file if pipestat_results_file IS
 provided, remove checking for the first record_identifier during get_stat

---
 pypiper/manager.py | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 5b6bb3c..1a4b1ab 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -337,6 +337,7 @@ def __init__(
             self.pipestat_results_file = self.pipeline_stats_file
         elif pipestat_results_file:
             self.pipestat_results_file = pipestat_results_file
+            self.pipeline_stats_file = self.pipestat_results_file
 
         def _get_arg(args_dict, arg_name):
             """safely get argument from arg dict -- return None if doesn't exist"""
@@ -1859,18 +1860,11 @@ def _refresh_stats(self):
 
         if os.path.isfile(self.pipeline_stats_file):
             _, data = read_yaml_data(path=self.pipeline_stats_file, what="stats_file")
-            record_identifier = list(
-                data[self._pipestat_manager.pipeline_name][
-                    self._pipestat_manager.pipeline_type
-                ]
-            )[0]
-
-            # Confirm that the loaded stats file is the same namespace as the pipeline manager
-            if record_identifier == self._pipestat_manager.record_identifier:
-                for key, value in data[self._pipestat_manager.pipeline_name][
-                    self._pipestat_manager.pipeline_type
-                ][record_identifier].items():
-                    self.stats_dict[key] = value
+
+            for key, value in data[self._pipestat_manager.pipeline_name][
+                self._pipestat_manager.pipeline_type
+            ][self._pipestat_manager.record_identifier].items():
+                self.stats_dict[key] = value
 
     def get_stat(self, key):
         """

From d5446448656d6f52b637c4f4cb739b5b7a385777 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Fri, 8 Dec 2023 18:38:25 -0500
Subject: [PATCH 18/39] add pipestat_pipeline_type, defaulting to sample

---
 pypiper/manager.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 1a4b1ab..67441d6 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -141,6 +141,7 @@ def __init__(
         pipestat_schema=None,
         pipestat_results_file=None,
         pipestat_config=None,
+        pipestat_pipeline_type=None,
         pipestat_result_formatter=None,
         **kwargs,
     ):
@@ -330,6 +331,7 @@ def __init__(
 
         # pipestat setup
         self.pipestat_record_identifier = pipestat_sample_name or DEFAULT_SAMPLE_NAME
+        self.pipestat_pipeline_type = pipestat_pipeline_type or "sample"
 
         # don't force default pipestat_results_file value unless
         # pipestat config not provided
@@ -356,6 +358,7 @@ def _get_arg(args_dict, arg_name):
             or self.pipeline_stats_file,
             config_file=pipestat_config or _get_arg(args_dict, "pipestat_config"),
             multi_pipelines=multi,
+            pipeline_type=self.pipestat_pipeline_type,
         )
 
         self.start_pipeline(args, multi)

From 649c985ed4d74034aaba2056307faf016037d1fc Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Thu, 14 Dec 2023 10:56:15 -0500
Subject: [PATCH 19/39] pipestat req version bump, v0.14.0a2 bump for
 pre-release

---
 pypiper/_version.py                   | 2 +-
 requirements/requirements-docs.txt    | 2 +-
 requirements/requirements-pypiper.txt | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pypiper/_version.py b/pypiper/_version.py
index 679c8ec..04ffdb1 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.14.0a1"
+__version__ = "0.14.0a2"
diff --git a/requirements/requirements-docs.txt b/requirements/requirements-docs.txt
index 4471914..45b990b 100644
--- a/requirements/requirements-docs.txt
+++ b/requirements/requirements-docs.txt
@@ -2,5 +2,5 @@ mkdocs>=1.0
 markdown-include
 pydoc-markdown
 piper
-pipestat>=0.4.0
+pipestat>=0.6.0a9
 https://github.com/databio/mkdocs-databio/archive/master.zip
\ No newline at end of file
diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
index 17bf456..2b9fe4b 100644
--- a/requirements/requirements-pypiper.txt
+++ b/requirements/requirements-pypiper.txt
@@ -3,4 +3,4 @@ psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.6.0a7
+pipestat>=0.6.0a9

From 9349aa8279433b1acac144318d9593f2cdbeb737 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Fri, 22 Dec 2023 11:37:37 -0500
Subject: [PATCH 20/39] v0.14.0 release prep

---
 docs/changelog.md                     | 4 +++-
 pypiper/_version.py                   | 2 +-
 requirements/requirements-docs.txt    | 2 +-
 requirements/requirements-pypiper.txt | 2 +-
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index 2c21384..edbdfef 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,14 +1,16 @@
 # Changelog
 
-## [0.14.0] -- 2023-11-xx
+## [0.14.0] -- 2023-12-22
 ### Changed
 - refactor for pipestat v0.6.0 release
 - drop python 2.7
 - updated requirements
+- changed message_raw to be a value_dict when reporting to conform to pipestat
 - ### Fixed
 - fixed #196 and #197
 - ### Added
 - added `force_overwrite` to `report_result` and `report_object`
+- added pipestat_pipeline_type, defaulting to sample-level
 
 ## [0.13.2] -- 2023-08-02
 ### Fixed
diff --git a/pypiper/_version.py b/pypiper/_version.py
index 04ffdb1..9e78220 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.14.0a2"
+__version__ = "0.14.0"
diff --git a/requirements/requirements-docs.txt b/requirements/requirements-docs.txt
index 45b990b..ef5b4e6 100644
--- a/requirements/requirements-docs.txt
+++ b/requirements/requirements-docs.txt
@@ -2,5 +2,5 @@ mkdocs>=1.0
 markdown-include
 pydoc-markdown
 piper
-pipestat>=0.6.0a9
+pipestat>=0.6.0
 https://github.com/databio/mkdocs-databio/archive/master.zip
\ No newline at end of file
diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
index 2b9fe4b..9a35f34 100644
--- a/requirements/requirements-pypiper.txt
+++ b/requirements/requirements-pypiper.txt
@@ -3,4 +3,4 @@ psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.6.0a9
+pipestat>=0.6.0

From b7d3f6bc8cb1b88a9d14a6af5ef1bab9d228ae1d Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Tue, 16 Jan 2024 21:11:35 -0500
Subject: [PATCH 21/39] https updates

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 046003d..7e6db31 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
 
 [![Documentation Status](https://readthedocs.org/projects/pypiper/badge/?version=latest)](http://pypiper.readthedocs.org/en/latest/?badge=latest)
 [![Build Status](https://github.com/databio/pypiper/actions/workflows/run-pytest.yml/badge.svg)](https://github.com/databio/pypiper/actions/workflows/run-pytest.yml)
-[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
+[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 [![pypi-badge](https://img.shields.io/pypi/v/piper)](https://pypi.org/project/piper)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 

From 87f1074bc781d94eef45758c5f7cbab6d48d7a88 Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Sat, 17 Feb 2024 14:42:07 -0500
Subject: [PATCH 22/39] log outfile directly, and clean up logging code. Fix
 #210

---
 .gitignore         |  3 ++
 pypiper/manager.py | 95 ++++++++++++----------------------------------
 2 files changed, 27 insertions(+), 71 deletions(-)

diff --git a/.gitignore b/.gitignore
index bc05997..c1e53a2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -86,3 +86,6 @@ piper.egg-info/
 
 *ipynb_checkpoints*
 *.egg-info*
+
+
+example_pipelines/pipeline_output
diff --git a/pypiper/manager.py b/pypiper/manager.py
index 67441d6..d18eabc 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -631,88 +631,41 @@ def start_pipeline(self, args=None, multi=False):
         # Print out a header section in the pipeline log:
         # Wrap things in backticks to prevent markdown from interpreting underscores as emphasis.
         # print("----------------------------------------")
-        self.info("### Pipeline run code and environment:\n")
-        self.info(
-            "* " + "Command".rjust(20) + ":  " + "`" + str(" ".join(sys.argv)) + "`"
-        )
-        self.info("* " + "Compute host".rjust(20) + ":  " + platform.node())
-        self.info("* " + "Working dir".rjust(20) + ":  " + os.getcwd())
-        self.info("* " + "Outfolder".rjust(20) + ":  " + self.outfolder)
+        def logfmt(key, value=None, padding=16):
+            padded_key = key.rjust(padding)
+            formatted_val = f"`{value}`" if value else ""
+            return f"* {padded_key}: {formatted_val}"
 
-        self.timestamp("* " + "Pipeline started at".rjust(20) + ":  ")
+        self.info("### Pipeline run code and environment:\n")
+        self.info(logfmt("Command", str(" ".join(sys.argv))))
+        self.info(logfmt("Compute host", platform.node()))
+        self.info(logfmt("Working dir", os.getcwd()))
+        self.info(logfmt("Outfolder", self.outfolder))
+        self.info(logfmt("Log file", self.pipeline_log_file))
+        self.timestamp(logfmt("Start time"))
 
         self.info("\n### Version log:\n")
-        self.info("* " + "Python version".rjust(20) + ":  " + platform.python_version())
+        self.info(logfmt("Python version", platform.python_version()))
         try:
-            self.info(
-                "* "
-                + "Pypiper dir".rjust(20)
-                + ":  "
-                + "`"
-                + gitvars["pypiper_dir"].strip()
-                + "`"
-            )
-            self.info("* " + "Pypiper version".rjust(20) + ":  " + __version__)
-            self.info(
-                "* " + "Pypiper hash".rjust(20) + ":  " + str(gitvars["pypiper_hash"])
-            )
-            self.info(
-                "* "
-                + "Pypiper branch".rjust(20)
-                + ":  "
-                + str(gitvars["pypiper_branch"])
-            )
-            self.info(
-                "* " + "Pypiper date".rjust(20) + ":  " + str(gitvars["pypiper_date"])
-            )
+            self.info(logfmt("Pypiper dir", gitvars["pypiper_dir"].strip()))
+            self.info(logfmt("Pypiper version", __version__))
+            self.info(logfmt("Pypiper hash", gitvars["pypiper_hash"]))
+            self.info(logfmt("Pypiper branch", gitvars["pypiper_branch"]))
+            self.info(logfmt("Pypiper date", gitvars["pypiper_date"]))
             if gitvars["pypiper_diff"]:
-                self.info(
-                    "* "
-                    + "Pypiper diff".rjust(20)
-                    + ":  "
-                    + str(gitvars["pypiper_diff"])
-                )
+                self.info(logfmt("Pypiper diff", gitvars["pypiper_diff"]))
         except KeyError:
             # It is ok if keys aren't set, it means pypiper isn't in a  git repo.
             pass
 
         try:
-            self.info(
-                "* "
-                + "Pipeline dir".rjust(20)
-                + ":  "
-                + "`"
-                + gitvars["pipe_dir"].strip()
-                + "`"
-            )
-            self.info(
-                "* " + "Pipeline version".rjust(20) + ":  " + str(self.pl_version)
-            )
-            self.info(
-                "* "
-                + "Pipeline hash".rjust(20)
-                + ":  "
-                + str(gitvars["pipe_hash"]).strip()
-            )
-            self.info(
-                "* "
-                + "Pipeline branch".rjust(20)
-                + ":  "
-                + str(gitvars["pipe_branch"]).strip()
-            )
-            self.info(
-                "* "
-                + "Pipeline date".rjust(20)
-                + ":  "
-                + str(gitvars["pipe_date"]).strip()
-            )
+            self.info(logfmt("Pipeline dir", gitvars["pipe_dir"].strip()))
+            self.info(logfmt("Pipeline version", self.pl_version))
+            self.info(logfmt("Pipeline hash", gitvars["pipe_hash"]).strip())
+            self.info(logfmt("Pipeline branch", gitvars["pipe_branch"]).strip())
+            self.info(logfmt("Pipeline date", gitvars["pipe_date"]).strip())
             if gitvars["pipe_diff"] != "":
-                self.info(
-                    "* "
-                    + "Pipeline diff".rjust(20)
-                    + ":  "
-                    + str(gitvars["pipe_diff"]).strip()
-                )
+                self.info(logfmt("Pipeline diff", gitvars["pipe_diff"]).strip())
         except KeyError:
             # It is ok if keys aren't set, it means the pipeline isn't a git repo.
             pass

From 65ed31d91b5f8f6977361cb04e5e27372648bd0f Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Sat, 17 Feb 2024 14:48:07 -0500
Subject: [PATCH 23/39] use f-strings in example pipelines

---
 example_pipelines/basic.py         | 4 ++--
 example_pipelines/hello_pypiper.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/example_pipelines/basic.py b/example_pipelines/basic.py
index 34a0d37..c7497b2 100755
--- a/example_pipelines/basic.py
+++ b/example_pipelines/basic.py
@@ -26,7 +26,7 @@
 tgt = "pipeline_output/test.out"
 
 # build the command
-cmd = "shuf -i 1-500000000 -n 10000000 > " + tgt
+cmd = f"shuf -i 1-500000000 -n 10000000 > {tgt}"
 
 # and run with run().
 pm.run(cmd, target=tgt)
@@ -34,7 +34,7 @@
 # Now copy the data into a new file.
 # first specify target file and build command:
 tgt = "pipeline_output/copied.out"
-cmd = "cp pipeline_output/test.out " + tgt
+cmd = f"cp pipeline_output/test.out {tgt}"
 pm.run(cmd, target=tgt)
 
 # You can also string multiple commands together, which will execute
diff --git a/example_pipelines/hello_pypiper.py b/example_pipelines/hello_pypiper.py
index 88abecf..17d424a 100755
--- a/example_pipelines/hello_pypiper.py
+++ b/example_pipelines/hello_pypiper.py
@@ -12,7 +12,7 @@
 
 # Now build a command-line command however you like, and pass it to pm.run()
 target_file = "hello_pypiper_results/output.txt"
-cmd = "echo 'Hello, Pypiper!' > " + target_file
+cmd = f"echo 'Hello, Pypiper!' > {target_file}"
 pm.run(cmd, target_file)
 
 pm.stop_pipeline()

From bddeddcb220dc0ab8515945b6e514dd6ccd77d0a Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 14:01:41 +0100
Subject: [PATCH 24/39] simplify syntax

---
 pypiper/manager.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 67441d6..7e9dc2d 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -193,10 +193,7 @@ def __init__(
         # If no starting point was specified, assume that the pipeline's
         # execution is to begin right away and set the internal flag so that
         # run() is let loose to execute instructions given.
-        if not self.start_point:
-            self._active = True
-        else:
-            self._active = False
+        self._active = not self.start_point
 
         # Pipeline-level variables to track global state and pipeline stats
         # Pipeline settings

From 005869e2a2896b99fa573d726d0c2594fdd04141 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 14:03:44 +0100
Subject: [PATCH 25/39] separate what can and can't cause exception

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

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 7e9dc2d..7a73f0c 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -223,10 +223,11 @@ def __init__(
             logger_kwargs.setdefault("name", default_logname)
             try:
                 self._logger = logmuse.logger_via_cli(args)
-                self.debug("Logger set with logmuse.logger_via_cli")
             except logmuse.est.AbsentOptionException:
                 self._logger = logmuse.init_logger("pypiper", level="DEBUG")
                 self.debug("logger_via_cli failed; Logger set with logmuse.init_logger")
+            else:
+                self.debug("Logger set with logmuse.logger_via_cli")
 
         # Keep track of an ID for the number of processes attempted
         self.proc_count = 0

From d8504f6bf972c1d38e603f535af84e69edef8b9b Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 14:12:15 +0100
Subject: [PATCH 26/39] copy the kwargs to avoid modification

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

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 7a73f0c..00c6653 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -8,6 +8,7 @@
 """
 
 import atexit
+import copy
 import datetime
 import errno
 import glob
@@ -208,7 +209,7 @@ def __init__(
         self.testmode = params["testmode"]
 
         # Set up logger
-        logger_kwargs = logger_kwargs or {}
+        logger_kwargs = copy.deepcopy(logger_kwargs) or {}
         default_logname = ".".join([__name__, self.__class__.__name__, self.name])
         if not args:
             # strict is only for logger_via_cli.

From 28a608aa36fb34ddab13e3f5eeeda04652b18579 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 14:12:45 +0100
Subject: [PATCH 27/39] homogenize messaging about logger establishment

---
 pypiper/manager.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 00c6653..0f160ae 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -224,11 +224,13 @@ def __init__(
             logger_kwargs.setdefault("name", default_logname)
             try:
                 self._logger = logmuse.logger_via_cli(args)
-            except logmuse.est.AbsentOptionException:
+            except logmuse.est.AbsentOptionException as e:
                 self._logger = logmuse.init_logger("pypiper", level="DEBUG")
-                self.debug("logger_via_cli failed; Logger set with logmuse.init_logger")
+                logger_builder_method = "init_logger"
+                self.debug(f"logger_via_cli failed: {e}")
             else:
-                self.debug("Logger set with logmuse.logger_via_cli")
+                logger_builder_method = "logger_via_cli"
+            self.debug(f"Logger set with logmuse.{logger_builder_method}")
 
         # Keep track of an ID for the number of processes attempted
         self.proc_count = 0

From 9b2ccbc5f83894b1731a45b9ca282c160591a12f Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 15:00:42 +0100
Subject: [PATCH 28/39] organize logger construction for pipeline manager, and
 homogenize treatment of arguments across branches

---
 pypiper/manager.py | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 0f160ae..76bb306 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -209,28 +209,27 @@ def __init__(
         self.testmode = params["testmode"]
 
         # Set up logger
-        logger_kwargs = copy.deepcopy(logger_kwargs) or {}
+        logger_kwargs = logger_kwargs or {}
         default_logname = ".".join([__name__, self.__class__.__name__, self.name])
-        if not args:
+        self._logger = None
+        if args:
+            logger_builder_method = "logger_via_cli"
+            try:
+                self._logger = logmuse.logger_via_cli(args, **logger_kwargs)
+            except logmuse.est.AbsentOptionException as e:
+                # Defer logger construction to init_logger.
+                self.debug(f"logger_via_cli failed: {e}")
+        if self._logger is None:
+            logger_builder_method = "init_logger"
+            # covers cases of bool(args) being False, or failure of logger_via_cli.
             # strict is only for logger_via_cli.
-            kwds = {k: v for k, v in logger_kwargs.items() if k != "strict"}
+            logger_kwargs = {k: v for k, v in logger_kwargs.items() if k != "strict"}
             try:
-                name = kwds.pop("name")
+                name = logger_kwargs.pop("name")
             except KeyError:
                 name = default_logname
-            self._logger = logmuse.init_logger(name, **kwds)
-            self.debug("Logger set with logmuse.init_logger")
-        else:
-            logger_kwargs.setdefault("name", default_logname)
-            try:
-                self._logger = logmuse.logger_via_cli(args)
-            except logmuse.est.AbsentOptionException as e:
-                self._logger = logmuse.init_logger("pypiper", level="DEBUG")
-                logger_builder_method = "init_logger"
-                self.debug(f"logger_via_cli failed: {e}")
-            else:
-                logger_builder_method = "logger_via_cli"
-            self.debug(f"Logger set with logmuse.{logger_builder_method}")
+            self._logger = logmuse.init_logger(name, **logger_kwargs)
+        self.debug(f"Logger set with logmuse.{logger_builder_method}")
 
         # Keep track of an ID for the number of processes attempted
         self.proc_count = 0

From 76ffdc6ba7988b5e62d510c09e37b052d0f5167a Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 15:00:58 +0100
Subject: [PATCH 29/39] tweak syntax

---
 pypiper/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pypiper/utils.py b/pypiper/utils.py
index 8973466..37b396c 100644
--- a/pypiper/utils.py
+++ b/pypiper/utils.py
@@ -788,7 +788,7 @@ def pipeline_filepath(pm, filename=None, suffix=None):
 
     if filename is None and suffix is None:
         raise TypeError(
-            "Provide filename and/or suffix to create " "path to a pipeline file."
+            "Provide filename and/or suffix to create path to a pipeline file."
         )
 
     filename = (filename or pm.name) + (suffix or "")

From 7baa056fda3d35a83c022565223b9f75f38ec466 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 15:01:20 +0100
Subject: [PATCH 30/39] use default strict=False behavior for logger via CLI

---
 pypiper/manager.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 76bb306..80b8d1e 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -215,7 +215,7 @@ def __init__(
         if args:
             logger_builder_method = "logger_via_cli"
             try:
-                self._logger = logmuse.logger_via_cli(args, **logger_kwargs)
+                self._logger = logger_via_cli(args, **logger_kwargs)
             except logmuse.est.AbsentOptionException as e:
                 # Defer logger construction to init_logger.
                 self.debug(f"logger_via_cli failed: {e}")
@@ -229,7 +229,7 @@ def __init__(
             except KeyError:
                 name = default_logname
             self._logger = logmuse.init_logger(name, **logger_kwargs)
-        self.debug(f"Logger set with logmuse.{logger_builder_method}")
+        self.debug(f"Logger set with {logger_builder_method}")
 
         # Keep track of an ID for the number of processes attempted
         self.proc_count = 0

From a83025bc550f8d224bf3e352c26cbe6c8400dfc8 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 15:05:48 +0100
Subject: [PATCH 31/39] move up logfile setting to set up solution for #212

---
 pypiper/manager.py | 9 +++++----
 pypiper/utils.py   | 2 --
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 80b8d1e..7473d97 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -8,7 +8,6 @@
 """
 
 import atexit
-import copy
 import datetime
 import errno
 import glob
@@ -208,6 +207,11 @@ def __init__(
         self.output_parent = params["output_parent"]
         self.testmode = params["testmode"]
 
+        # Establish the log file to check safety with logging keyword arguments.
+        # Establish the output folder since it's required for the log file.
+        self.outfolder = os.path.join(outfolder, "")  # trailing slash
+        self.pipeline_log_file = pipeline_filepath(self, suffix="_log.md")
+
         # Set up logger
         logger_kwargs = logger_kwargs or {}
         default_logname = ".".join([__name__, self.__class__.__name__, self.name])
@@ -276,10 +280,7 @@ def __init__(
         #   self.output_parent = os.path.join(os.getcwd(), self.output_parent)
 
         # File paths:
-        self.outfolder = os.path.join(outfolder, "")  # trailing slash
         self.make_sure_path_exists(self.outfolder)
-        self.pipeline_log_file = pipeline_filepath(self, suffix="_log.md")
-
         self.pipeline_profile_file = pipeline_filepath(self, suffix="_profile.tsv")
 
         # Stats and figures are general and so lack the pipeline name.
diff --git a/pypiper/utils.py b/pypiper/utils.py
index 37b396c..1c65f59 100644
--- a/pypiper/utils.py
+++ b/pypiper/utils.py
@@ -785,12 +785,10 @@ def pipeline_filepath(pm, filename=None, suffix=None):
         filename as given or determined by the pipeline name, and suffix
         appended if given.
     """
-
     if filename is None and suffix is None:
         raise TypeError(
             "Provide filename and/or suffix to create path to a pipeline file."
         )
-
     filename = (filename or pm.name) + (suffix or "")
 
     # Note that Pipeline and PipelineManager define the same outfolder.

From ba423a428ff8279b508951efdc20d1206c1f14c1 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 15:08:48 +0100
Subject: [PATCH 32/39] check that logfile for logger doesn't match manager's
 own logfile; #212

---
 pypiper/manager.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 7473d97..6cae014 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -214,6 +214,10 @@ def __init__(
 
         # Set up logger
         logger_kwargs = logger_kwargs or {}
+        if logger_kwargs.get("logfile") == self.pipeline_log_file:
+            raise ValueError(
+                f"The logfile given for the pipeline manager's logger matches that which will be used by the manager itself: {self.pipeline_log_file}"
+            )
         default_logname = ".".join([__name__, self.__class__.__name__, self.name])
         self._logger = None
         if args:

From 97821e986a5c248cba2dd885ace7d34bf3d5f3e5 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 15:16:23 +0100
Subject: [PATCH 33/39] test solution for #212

---
 pypiper/manager.py                            |  3 ++-
 .../test_manager_constructor.py               | 19 ++++++++++++++++++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 6cae014..df661b3 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -58,6 +58,7 @@
 
 
 LOCK_PREFIX = "lock."
+LOGFILE_SUFFIX = "_log.md"
 
 
 class Unbuffered(object):
@@ -210,7 +211,7 @@ def __init__(
         # Establish the log file to check safety with logging keyword arguments.
         # Establish the output folder since it's required for the log file.
         self.outfolder = os.path.join(outfolder, "")  # trailing slash
-        self.pipeline_log_file = pipeline_filepath(self, suffix="_log.md")
+        self.pipeline_log_file = pipeline_filepath(self, suffix=LOGFILE_SUFFIX)
 
         # Set up logger
         logger_kwargs = logger_kwargs or {}
diff --git a/tests/pipeline_manager/test_manager_constructor.py b/tests/pipeline_manager/test_manager_constructor.py
index 0792bf1..b327fb2 100644
--- a/tests/pipeline_manager/test_manager_constructor.py
+++ b/tests/pipeline_manager/test_manager_constructor.py
@@ -1,10 +1,11 @@
 """ Test effects of construction of a pipeline manager. """
 
 import argparse
+import os
 
 import pytest
 
-from pypiper.manager import CHECKPOINT_SPECIFICATIONS
+from pypiper.manager import CHECKPOINT_SPECIFICATIONS, LOGFILE_SUFFIX
 from tests.helpers import named_param
 
 __author__ = "Vince Reuter"
@@ -24,6 +25,22 @@ def test_manager_starts_in_null_checkpoint_state(get_pipe_manager, checkpoint_ty
     assert getattr(pm, checkpoint_type) is None
 
 
+def test_logger_logfile_collision_with_manager_logfile_is_expected_error__issue_212(
+    get_pipe_manager, tmpdir
+):
+    pipe_name = "test_issue212"
+    with pytest.raises(ValueError) as err_ctx:
+        get_pipe_manager(
+            name=pipe_name,
+            logger_kwargs={
+                "logfile": os.path.join(tmpdir.strpath, pipe_name + LOGFILE_SUFFIX)
+            },
+        )
+    assert str(err_ctx.value).startswith(
+        f"The logfile given for the pipeline manager's logger matches that which will be used by the manager itself"
+    )
+
+
 class ManagerConstructorCheckpointSpecificationTests:
     """Tests for manager's constructor's ability to parse and set
     checkpoint specifications, which can determine aspects of control flow."""

From fcb02facd2da19b3e129769a67729f35a571696d Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Sun, 18 Feb 2024 15:50:28 +0100
Subject: [PATCH 34/39] apply new black formatting

---
 pypiper/const.py | 1 -
 pypiper/ngstk.py | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/pypiper/const.py b/pypiper/const.py
index 2749529..0bfbdb6 100644
--- a/pypiper/const.py
+++ b/pypiper/const.py
@@ -1,6 +1,5 @@
 """ Pypiper constants. """
 
-
 CHECKPOINT_EXTENSION = ".checkpoint"
 DEFAULT_SAMPLE_NAME = "DEFAULT_SAMPLE_NAME"
 PIPELINE_CHECKPOINT_DELIMITER = "_"
diff --git a/pypiper/ngstk.py b/pypiper/ngstk.py
index 329b321..b607913 100755
--- a/pypiper/ngstk.py
+++ b/pypiper/ngstk.py
@@ -153,8 +153,7 @@ def get_file_size(self, filenames):
             return sum([self.get_file_size(filename) for filename in filenames])
 
         return round(
-            sum([float(os.stat(f).st_size) for f in filenames.split(" ")])
-            / (1024**2),
+            sum([float(os.stat(f).st_size) for f in filenames.split(" ")]) / (1024**2),
             4,
         )
 

From 94806df7f097e70ec93afe43853f7212ec50c63e Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Mon, 19 Feb 2024 09:49:28 -0500
Subject: [PATCH 35/39] Fix #213, remove pipestat_project_name, refactor
 pipestat_sample_name to pipestat_record_identifier, update doc strings

---
 docs/changelog.md  |  6 ++++++
 pypiper/manager.py | 13 ++++++++++---
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index edbdfef..42d8f16 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.15.0] -- 2024-xx-xx
+### Changed
+- remove pipestat_project_name from PipelineManager parameters
+- refactor pipestat_sample_name to pipestat_record_identifier in PipelineManager parameters
+
+
 ## [0.14.0] -- 2023-12-22
 ### Changed
 - refactor for pipestat v0.6.0 release
diff --git a/pypiper/manager.py b/pypiper/manager.py
index d18eabc..ce1e385 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -112,6 +112,12 @@ class PipelineManager(object):
         protect from a case in which a restart begins upstream of a stage
         for which a checkpoint file already exists, but that depends on the
         upstream stage and thus should be rerun if it's "parent" is rerun.
+    :param str pipestat_record_identifier: record_identifier to report results via pipestat
+    :param str pipestat_schema: output schema used by pipestat to report results
+    :param str pipestat_results_file: path to file backend for reporting results
+    :param str pipestat_config_file: path to pipestat configuration file
+    :param str pipestat_pipeline_type: Sample or Project level pipeline
+    :param pipestat_result_formatter: function used to style reported results, defaults to result_formatter_markdown
     :raise TypeError: if start or stop point(s) are provided both directly and
         via args namespace, or if both stopping types (exclusive/prospective
         and inclusive/retrospective) are provided.
@@ -136,8 +142,7 @@ def __init__(
         output_parent=None,
         overwrite_checkpoints=False,
         logger_kwargs=None,
-        pipestat_project_name=None,
-        pipestat_sample_name=None,
+        pipestat_record_identifier=None,
         pipestat_schema=None,
         pipestat_results_file=None,
         pipestat_config=None,
@@ -330,7 +335,9 @@ def __init__(
         signal.signal(signal.SIGTERM, self._signal_term_handler)
 
         # pipestat setup
-        self.pipestat_record_identifier = pipestat_sample_name or DEFAULT_SAMPLE_NAME
+        self.pipestat_record_identifier = (
+            pipestat_record_identifier or DEFAULT_SAMPLE_NAME
+        )
         self.pipestat_pipeline_type = pipestat_pipeline_type or "sample"
 
         # don't force default pipestat_results_file value unless

From 04abc1fba2325b6c418dc2d82ba90ddaf79d1950 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Thu, 4 Apr 2024 13:23:47 -0400
Subject: [PATCH 36/39] #209 Switch force_overwrite to default to True

---
 pypiper/manager.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index 5aad867..e4e72cb 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -1559,7 +1559,7 @@ def _report_profile(
             myfile.write(message_raw + "\n")
 
     def report_result(
-        self, key, value, nolog=False, result_formatter=None, force_overwrite=False
+        self, key, value, nolog=False, result_formatter=None, force_overwrite=True
     ):
         """
         Writes a key:value pair to self.pipeline_stats_file.
@@ -1606,7 +1606,7 @@ def report_object(
         annotation=None,
         nolog=False,
         result_formatter=None,
-        force_overwrite=False,
+        force_overwrite=True,
     ):
         """
         Writes a key:value pair to self.pipeline_stats_file. Note: this function

From 5413eecc040da9d41c81959a80cf4049db6a359b Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Thu, 4 Apr 2024 14:00:03 -0400
Subject: [PATCH 37/39] version bump on requirements #216

---
 pypiper/manager.py                    | 4 ++--
 pypiper/ngstk.py                      | 3 ++-
 requirements/requirements-docs.txt    | 2 +-
 requirements/requirements-pypiper.txt | 6 +++---
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index e4e72cb..965945b 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -52,7 +52,7 @@
     default_pipestat_output_schema,
     result_formatter_markdown,
 )
-from pipestat.helpers import read_yaml_data
+from yacman import load_yaml
 
 __all__ = ["PipelineManager"]
 
@@ -1828,7 +1828,7 @@ def _refresh_stats(self):
         """
 
         if os.path.isfile(self.pipeline_stats_file):
-            _, data = read_yaml_data(path=self.pipeline_stats_file, what="stats_file")
+            data = load_yaml(filepath=self.pipeline_stats_file)
 
             for key, value in data[self._pipestat_manager.pipeline_name][
                 self._pipestat_manager.pipeline_type
diff --git a/pypiper/ngstk.py b/pypiper/ngstk.py
index b607913..329b321 100755
--- a/pypiper/ngstk.py
+++ b/pypiper/ngstk.py
@@ -153,7 +153,8 @@ def get_file_size(self, filenames):
             return sum([self.get_file_size(filename) for filename in filenames])
 
         return round(
-            sum([float(os.stat(f).st_size) for f in filenames.split(" ")]) / (1024**2),
+            sum([float(os.stat(f).st_size) for f in filenames.split(" ")])
+            / (1024**2),
             4,
         )
 
diff --git a/requirements/requirements-docs.txt b/requirements/requirements-docs.txt
index ef5b4e6..9ae381f 100644
--- a/requirements/requirements-docs.txt
+++ b/requirements/requirements-docs.txt
@@ -2,5 +2,5 @@ mkdocs>=1.0
 markdown-include
 pydoc-markdown
 piper
-pipestat>=0.6.0
+pipestat>=0.9.0a1
 https://github.com/databio/mkdocs-databio/archive/master.zip
\ No newline at end of file
diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
index 9a35f34..180ad3d 100644
--- a/requirements/requirements-pypiper.txt
+++ b/requirements/requirements-pypiper.txt
@@ -1,6 +1,6 @@
 logmuse>=0.2.4
 psutil
 pandas
-ubiquerg>=0.4.5
-yacman
-pipestat>=0.6.0
+ubiquerg>=0.8.0
+yacman>=0.9.3
+pipestat>=0.9.0a1

From 3e102133327be3c76366ba49903afd9e1ee78831 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Fri, 19 Apr 2024 09:49:32 -0400
Subject: [PATCH 38/39] update version and changelog for 0.14.1 release

---
 docs/changelog.md   | 4 +++-
 pypiper/_version.py | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index 42d8f16..feba103 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,9 +1,11 @@
 # Changelog
 
-## [0.15.0] -- 2024-xx-xx
+## [0.14.1] -- 2024-04-19
 ### Changed
 - remove pipestat_project_name from PipelineManager parameters
 - refactor pipestat_sample_name to pipestat_record_identifier in PipelineManager parameters
+- update requirements for pipestat 0.9.0, ubiquerg 0.8.0, and yacman 0.9.3
+- set `force_overwrite` to default to true, Issue #209
 
 
 ## [0.14.0] -- 2023-12-22
diff --git a/pypiper/_version.py b/pypiper/_version.py
index 9e78220..f075dd3 100644
--- a/pypiper/_version.py
+++ b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.14.0"
+__version__ = "0.14.1"

From 703580d2f99c04d65b0a2ed57a14813fb96997a7 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Fri, 19 Apr 2024 09:53:19 -0400
Subject: [PATCH 39/39] lint

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

diff --git a/pypiper/ngstk.py b/pypiper/ngstk.py
index 329b321..b607913 100755
--- a/pypiper/ngstk.py
+++ b/pypiper/ngstk.py
@@ -153,8 +153,7 @@ def get_file_size(self, filenames):
             return sum([self.get_file_size(filename) for filename in filenames])
 
         return round(
-            sum([float(os.stat(f).st_size) for f in filenames.split(" ")])
-            / (1024**2),
+            sum([float(os.stat(f).st_size) for f in filenames.split(" ")]) / (1024**2),
             4,
         )