pipen-runinfo 1.1.4

Generate running information for jobs in pipen pipelines

pipen-runinfo

Generate running information for jobs in pipen pipelines.

Including session info (packages and versions), time, and device info.

Install

pip install -U pipen-runinfo

Enable/Disable the plugin

The plugin is registered via entrypoints. It's by default enabled. To disable it: plugins=[..., "no:runinfo"], or uninstall this plugin.

Plugin options

• runinfo_lang: The name of the language to run the job script for session info. Default is None, which means it will be inferred from the proc.lang This should be a process-level option, unless you only have one single process in your pipeline.
• runinfo_path: Whether to include paths for the modules in the session information. Default is True. This option could be either specified in the process-level or the pipeline-level. Only works for python.
• runinfo_submod: Whether to include submodules in the session information. Default is False. This option could be either specified in the process-level or the pipeline-level. Only works for python.

Supported languages for session info

python, R, bash, and fish.

Usage

The plugin will generate 3 files in the job directory of the pipeline.

job.runinfo.session

The session information of the job, including the interpreter, packages and their versions.

Python

Generates a TSV file with the following columns:

• Name: The name of the module, or python itself
• __version__: The version fetched by module.__version__ or module.version
• importlib.metadata: The version fetched by importlib.metadata.version(package)
• Path: The path of the module (only if runinfo_path is True)

R

Generates a text file sessionInfo() output.

Bash

Generates a TSV file with the following columns:

• SHELL: The value of $SHELL
• BASH_VERSION: The value of $BASH_VERSION
• BASH_ARGV0: The value of $BASH_ARGV0
• BASH_SOURCE: The value of $BASH_SOURCE
• proc-exe: The real path of the executable from /proc/<pid>/exe
• proc-exe-version: The version of the executable from /proc/<pid>/exe --version

Fish

Generates a TSV file with the following columns:

• SHELL: The value of $SHELL
• FISH_VERSION: The value of $FISH_VERSION
• proc-exe: The real path of the executable from /proc/<pid>/exe
• proc-exe-version: The version of the executable from /proc/<pid>/exe --version

job.runinfo.time

The time spent on the job, and more, generated by time -v command.

job.runinfo.device

The device (cpu and memory) information of the job, generated by lscpu/lsmem command.