Use scverse-misc for deprecations - #735
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Replace the home-grown `scirpy.util.deprecated` decorator and the ad-hoc
`warnings.warn` calls with the `deprecated` and `deprecated_arg` decorators
from `scverse-misc`, which also add a deprecation notice to the API docs.
`scverse-misc` is added as a hard dependency (no extras required; the
`[sphinx]` extra remains in the `doc` dependency group).
Deprecated functions:
* `ir_dist.tcr_dist` (0.5.0)
* `ir_dist.metrics.AlignmentDistanceCalculator` (0.15.0). The decorator moves
from `__init__` to the class so the notice appears in the class docs.
Deprecated arguments:
* `clip_at` of `tl.clonal_expansion` and `pl.clonal_expansion` (0.14.0)
* `block_size` of the `ParallelDistanceCalculator`s (0.15.0)
* `include_fields` (0.13.0) and `use_umi_count_col` (0.16.0) of the
`io.read_*` functions
* `cached`/`cache_path` of `datasets.vdjdb` and `datasets.iedb` (0.24.0)
The latter two groups previously did not emit any warning at all and now
consistently raise a `FutureWarning`.
Since `deprecated_arg` warns whenever the deprecated argument is passed
(irrespective of its value), internal calls must not forward it:
`pl.clonal_expansion` now converts `clip_at` into `breakpoints` itself instead
of passing it on to `tl.clonal_expansion`, and the alignment distance
calculators no longer forward the ignored `block_size` to their base class.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #735 +/- ##
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+ Coverage 78.20% 78.32% +0.12%
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Files 51 51
Lines 4620 4628 +8
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+ Hits 3613 3625 +12
+ Misses 1007 1003 -4
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Replace the home-grown
scirpy.util.deprecateddecorator and the ad-hocwarnings.warncalls with thedeprecatedanddeprecated_argdecoratorsfrom
scverse-misc, which also add a deprecation notice to the API docs.scverse-miscis added as a hard dependency (no extras required; the[sphinx]extra remains in thedocdependency group).Deprecated functions:
ir_dist.tcr_dist(0.5.0)ir_dist.metrics.AlignmentDistanceCalculator(0.15.0). The decorator movesfrom
__init__to the class so the notice appears in the class docs.Deprecated arguments:
clip_atoftl.clonal_expansionandpl.clonal_expansion(0.14.0)block_sizeof theParallelDistanceCalculators (0.15.0)include_fields(0.13.0) anduse_umi_count_col(0.16.0) of theio.read_*functionscached/cache_pathofdatasets.vdjdbanddatasets.iedb(0.24.0)The latter two groups previously did not emit any warning at all and now
consistently raise a
FutureWarning.Since
deprecated_argwarns whenever the deprecated argument is passed(irrespective of its value), internal calls must not forward it:
pl.clonal_expansionnow convertsclip_atintobreakpointsitself insteadof passing it on to
tl.clonal_expansion, and the alignment distancecalculators no longer forward the ignored
block_sizeto their base class.Co-Authored-By: Claude Opus 5 (1M context) noreply@anthropic.com
Closes #704