config
config#
- showyourwork.config.as_dict(x, depth=0, maxdepth=30)#
Replaces nested instances of OrderedDicts with regular dicts in a dictionary.
This is useful when parsing a config generated from a YAML file with inconsistent use of hyphens.
- Parameters
x – A dictionary or dictionary-like mapping generated from reading a YAML file.
depth (int, optional) – Default is
0
.maxdepth (int, optional) – Default is
30
.
- showyourwork.config.edit_yaml(file)#
A context used to edit a YAML file in place.
- Parameters
file (str) – The full path to the YAML file.
- showyourwork.config.get_run_type()#
Return the type of the current Snakemake run.
Options are:
clean
build
tarball
preprocess
other
- Returns
The type of the current run (one of the options listed above).
- Return type
str
- showyourwork.config.get_upstream_dependencies(file, dependencies, depth=0)#
Collect user-defined dependencies of a file recursively. Returns a list of strings.
- showyourwork.config.parse_config()#
Parse the current config and fill in defaults.
- showyourwork.config.parse_overleaf()#
Parse Overleaf configuration options and fill in defaults.
- showyourwork.config.render_config(cwd='.')#
Render any jinja templates in
showyourwork.yml
, combine withzenodo.yml
, and save the processed config to a temporary YAML file.This temporary YAML file is then used as the configfile for the Snakemake workflow.
- Parameters
cwd (str, optional) – The path to the working directory.
- Returns
The user config.
- Return type
dict