Release 0.12.8

[khoroshevskyi]

Changes:

• Updated docs
• Fixed parsing nested items. [143]
• Added pypiper to requirements [142]
• Fixed white spaces in reference genome string [141]
• Added version in CLI help [135]
• Updated SRA convert to use looper > 2.0.0 and fully automate process

[Copilot]

Pull Request Overview

This release bumps the version to 0.12.8, reorganizes Looper and pipeline interface templates, and enhances the CLI and requirements for automated SRA conversion.

• Bump package version and include --version in both CLI and sraconvert commands
• Move pipeline and Looper YAML templates into geofetch/templates and update path resolution
• Add (p)ypiper requirement and upgrade CI actions

Reviewed Changes

Copilot reviewed 15 out of 22 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
requirements/requirements-all.txt	Added new dependency for automated SRA conversion
pipeline_interface_convert_v1.yaml & pipeline_interface_convert.yaml	Removed legacy pipeline interface definitions
manual_testing.py	Added a simple example script for manual testing
geofetch/templates/*	Introduced new Looper and pipeline interface templates
geofetch/sraconvert.py	Switched to VersionInHelpParser and added a --version flag
geofetch/const.py	Defined TEMPLATES_DIR and new template name constants
geofetch/geofetch.py	Updated all template file lookups to use TEMPLATES_DIR
MANIFEST.in	Updated to include everything under geofetch/templates/
.looper.yaml	Added an example local Looper config file
.github/workflows/black.yml	Upgraded actions/checkout and actions/setup-python versions
geofetch/cli.py	Switched main CLI to VersionInHelpParser and embedded version
geofetch/_version.py	Bumped __version__ to 0.12.8

Comments suppressed due to low confidence (5)

requirements/requirements-all.txt:10

• The project code imports pypiper, but the requirement is listed as piper. It should be pypiper>=0.14.4 to match the actual package name.

piper>=0.14.4

geofetch/const.py:52

• [nitpick] The constant LOOPER_SRA_CONVERT suggests an SRA conversion template but holds the Looper config template filename. Consider renaming to LOOPER_CONFIG_TEMPLATE_NAME for clarity.

LOOPER_SRA_CONVERT = "looper_config_template.yaml"

.looper.yaml:4

• [nitpick] This example config references pipeline_interface_convert.yaml at the repo root, but that file has been removed. You may want to point to the template under geofetch/templates or remove this tracked example.

  - /home/bnt4me/virginia/repos/geofetch/pipeline_interface_convert.yaml

manual_testing.py:1

• [nitpick] This example script lacks a module docstring or comments explaining its purpose and usage. Consider adding a top-level docstring to clarify how to run and what it demonstrates.

from geofetch import Geofetcher

geofetch/sraconvert.py:75

• This version flag references __version__ but __version__ is not imported in this module, which will raise a NameError. Import it from geofetch._version or adjust accordingly.

    parser.add_argument(

[donaldcampbelljr]

Looks great!

[donaldcampbelljr]

This is minor, but I'd recommend simplifying variable names like this to key instead of key_in_list. Given the logic, it is implied, and so, the name is perhaps a bit redundant.

[donaldcampbelljr]

Why did we change from using ArgumentParser to a class from ubiquerg?