pipen-runinfo 0.0.0

Generate running information for jobs in pipen pipelines

pipen-runinfo

Generate running information for jobs in pipen pipelines.

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. 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 running 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 running information. Default is False. This option could be either specified in the process-level or the pipeline-level. Only works for python.

Supported languages

python, R, bash, and fish.

Usage

The plugin will generate a job.runinfo file in the job directory of the pipeline, which contains the running information of the job.

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