Merge branch 'dev' into new_pipestat

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.

pypiper/_version.py

@@ -1 +1 @@
-__version__ = "0.13.2"
+__version__ = "0.13.3a1"

pypiper/manager.py

@@ -728,6 +728,7 @@ 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",
         )
 
@@ -1425,6 +1426,7 @@ 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"],
+
                     status_identifier="waiting",
                 )
                 first_message_flag = True

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()

requirements/requirements-pypiper.txt

@@ -4,4 +4,4 @@ psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.4.0
+pipestat>=0.6.0a1