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 57af110..fa73352 100644 --- a/pypiper/manager.py +++ b/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 diff --git a/pypiper/utils.py b/pypiper/utils.py index 54677c8..8973466 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() 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