cokelaer / sequana_pipetools / 33759827905

91%

master: 83%

Build Type

push

github

Committed by cokelaer

Commit Message

Document all modules, fix stale docstrings and test python 3.12

The reference documentation only included 4 modules. All modules are now
documented and the RST issues that this revealed are fixed: bullet lists
missing a blank line in profile.py and misc.py, and a .. plot:: directive
in DOTParser that required an extension not enabled in conf.py. Sphinx
now builds without any warning (the deprecated get_html_theme_path call
was removed as well).

Several docstrings still referred to the old monolithic sequana package:
wrong import paths, a ModuleFinderSingleton class that does not exist,
a sample_func example using SequanaManager instead of PipelineManager,
and a Pipeline docstring claiming the snakefile must be a .rules file.
The error message raised for an unknown pipeline pointed to two dead
URLs and now explains that pipelines are independent packages.

Finally, python 3.12 is added to the CI matrix (it was already declared
in the classifiers), the github actions are updated to a supported
version, and a few flake8 warnings are fixed (ambiguous variable name,
membership test, unused variable). Note that diagnose.py and monitor.py
had their __future__ import placed before their docstring, which made
the module documentation invisible.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01XTLCWttPDsZBJTKQMGaqSP

Coverage Stats

4 of 4 new or added lines in 3 files covered. (100.0%)

123 existing lines in 9 files now uncovered.

2137 of 2363 relevant lines covered (90.44%)

3.62 hits per line