tutorials v2

[josenimo]

No description provided.

[codecov]

Codecov Report

Attention: Patch coverage is 7.54717% with 49 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/opendvp/plotting/rankplot.py	6.52%	43 Missing ⚠️
src/opendvp/plotting/density.py	14.28%	6 Missing ⚠️

@@            Coverage Diff             @@
##             main      #63      +/-   ##
==========================================
- Coverage   63.61%   63.02%   -0.59%     
==========================================
  Files          53       53              
  Lines        2105     2131      +26     
==========================================
+ Hits         1339     1343       +4     
- Misses        766      788      +22     

Files with missing lines	Coverage Δ
src/opendvp/plotting/volcano.py	100.00% <ø> (ø)
src/opendvp/plotting/density.py	30.00% <14.28%> (+0.37%)	⬆️
src/opendvp/plotting/rankplot.py	17.18% <6.52%> (-2.33%)	⬇️

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull Request Overview

This PR updates the tutorial content to version 2 and refactors key plotting functions with new filtering, logging, and defaults.

• Refactor rankplot.py to support a min_presence_fraction filter, group validation, dynamic colors, and logging.
• Simplify density.py figure/axis setup with an internal_ax flag and precise type hints.
• Update documentation and notebooks: swap tutorial order, fix code fences, correct relative paths, reset execution counts.
• Add a new dependency spatialdata-plot in pyproject.toml.

Reviewed Changes

Copilot reviewed 9 out of 14 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/opendvp/plotting/volcano.py	Removed a stray comment.
src/opendvp/plotting/rankplot.py	Major refactor: min_presence filter, logging, default params.
src/opendvp/plotting/density.py	Streamline fig/ax logic, add Axes annotation.
pyproject.toml	Added new dependency spatialdata-plot.
docs/index.md	Fixed code fence formatting and list items.
docs/Tutorials/index.md	Swapped tutorial headings and updated links.
docs/Tutorials/…/*.ipynb	Updated notebook titles, relative paths, and cleared outputs.

Comments suppressed due to low confidence (2)

src/opendvp/plotting/rankplot.py:44

• The order of parameters in the docstring does not match the function signature (min_presence_fraction appears after group_colors in the doc but before groups in the signature). Updating the doc order will reduce confusion.

    min_presence_fraction : float, optional

src/opendvp/plotting/rankplot.py:55

• [nitpick] The default figure size was changed from (10, 6) to (5, 5), which may reduce plot readability. Consider restoring the previous size or making it configurable.

        fig, ax = plt.subplots(figsize=(5, 5))

[Copilot]

This new dependency is added without a version pin. For reproducibility, consider specifying a version constraint for "spatialdata-plot."

Suggested change

	"spatialdata-plot",
	"spatialdata-plot>=1.0.0,<2.0.0",