Make most arguments keyword-only, enforced by PLR0917 (#1288)

[selmanozleyen]

fixes: #1288 plus I also removed notes-dev.md as it's old. I also added some items to the contribution guide.

The rule: every public function takes only its data object positionally (adata, *, ...), everything after it is keyword-only. Private helpers that take an AnnData or SpatialData first follow the same rule; other private helpers only need to pass PLR0917.

The ones I didn't include:

• @old_positionals on released public functions: anything in v1.8.3 keeps accepting old positional calls, with a FutureWarning that says the positional form stops working in v1.9.0.
• None on squidpy.experimental: the experimental API makes no stability promise.
• None on unreleased functions: the spatial_neighbors_* builders and the Incorporating feedback on niche refactor #1284 niche flavors have no old calls to support.
• None on private functions: internal callers were updated to pass keywords.
• calculate_niche left as is: it's deprecated and removed in v1.9.0, and a second wrapper would stack warnings.
• ImageContainer left as is: it's exempted per file until it's deprecated.

Tests changed because

• Test calls that passed now-keyword-only arguments positionally were switched to keywords, so they don't hit the FutureWarning or the TypeError.
• New test: an old positional call still works and warns (tests/utils/test_old_positionals.py).
• test_niche.py filters calculate_niche's deprecation warning, since those tests exercise the umbrella on purpose until v1.9.0. One test still asserts the warning.
• Tests are exempt from PLR0917, since pytest passes fixtures by name.

Follow-ups

• Update the tutorials in squidpy-tutorials: 17 sq.im.calculate_image_features(adata, img, …) calls and 2 sq.gr.centrality_scores(adata, "…") calls, plus positional calls to pl.spatial_scatter, pl.spatial_segment, pl.var_by_distance, pl.extract and tl.sliding_window, now warn.
• Remove the @old_positionals shims in v1.9.0.
• Deal with ImageContainer when it's deprecated; it's currently exempt from the rule per file.
• Replace the deprecated skimage, pandas and anndata calls in src (binary_closing, square, area_threshold, skimage.io plugins, pandas copy=, uns_keys).

[codecov]

Codecov Report

❌ Patch coverage is 94.32624% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.74%. Comparing base (1936a92) to head (75b4beb).

Files with missing lines	Patch %	Lines
src/squidpy/gr/_nhood.py	81.81%	4 Missing ⚠️
src/squidpy/gr/_ligrec.py	66.66%	2 Missing ⚠️
src/squidpy/im/_container.py	50.00%	1 Missing ⚠️
src/squidpy/tl/_var_by_distance.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1297      +/-   ##
==========================================
+ Coverage   78.63%   78.74%   +0.10%     
==========================================
  Files          64       64              
  Lines        9604     9653      +49     
  Branches     1613     1613              
==========================================
+ Hits         7552     7601      +49     
  Misses       1497     1497              
  Partials      555      555              

Files with missing lines	Coverage Δ
src/squidpy/_compat.py	77.77% <100.00%> (+4.44%)	⬆️
src/squidpy/_utils.py	72.11% <100.00%> (+0.11%)	⬆️
...uidpy/experimental/im/_calculate_image_features.py	89.42% <100.00%> (ø)
src/squidpy/experimental/im/_detect_tissue.py	67.77% <100.00%> (ø)
src/squidpy/experimental/im/_make_tiles.py	73.97% <100.00%> (ø)
src/squidpy/experimental/im/_qc_image.py	82.48% <100.00%> (ø)
src/squidpy/experimental/im/_stain/_normalize.py	93.75% <100.00%> (ø)
src/squidpy/experimental/im/_utils.py	67.26% <ø> (ø)
src/squidpy/experimental/pl/_qc_image.py	60.22% <ø> (ø)
src/squidpy/experimental/pl/_tiling_qc.py	64.70% <ø> (ø)
... and 23 more

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