Fix cutoff documentation of DistanceCalculator classes (#474)

* Fix cutoff documentation of DistanceCalculator classes

* Fix incompatibility with adjustText 1.0

* Update CHANGELOG

* Update CHANGELOG

* Adjusttext compatibility with both new and old versions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -22,6 +22,12 @@ and this project adheres to [Semantic Versioning][].
     in `pp.ir_dist` now uses the `FastAlignmentDistanceCalculator` with only the lenght-based filter activated.
     Using the `"fastalignment"` activates the heuristic, which is significantly faster, but results in some false-negatives.
 
+### Documentation
+
+-   The default values of the distance calculator classes in `ir_dist.metrics` was unclear. The default value is now
+    set in the classes. In `pp.ir_dist` and `ir_dist.sequence_dist`, no cutoff argument is passed to the metrics
+    objects, unless one is explicitly specified (previously `None` was passed by default).
+
 ## v0.14.0
 
 ### Breaking changes

src/scirpy/ir_dist/__init__.py

@@ -51,7 +51,7 @@ def IrNeighbors(*args, **kwargs):
       * `alignment` -- Distance based on pairwise sequence alignments using the
         BLOSUM62 matrix. This option is incompatible with nucleotide sequences.
         See :class:`~scirpy.ir_dist.metrics.FastAlignmentDistanceCalculator`.
-        * `fastalignment` -- Distance based on pairwise sequence alignments using the
+      * `fastalignment` -- Distance based on pairwise sequence alignments using the
         BLOSUM62 matrix. Faster implementation of `alignment` with some loss.
         This option is incompatible with nucleotide sequences.
         See :class:`~scirpy.ir_dist.metrics.FastAlignmentDistanceCalculator`.
@@ -82,18 +82,22 @@ def _get_distance_calculator(metric: MetricType, cutoff: Union[int, None], *, n_
         metric = "identity"
         cutoff = 0
 
+    # Let's rely on the default set by the class if cutoff is None
+    if cutoff is not None:
+        kwargs["cutoff"] = cutoff
+
     if isinstance(metric, metrics.DistanceCalculator):
         dist_calc = metric
     elif metric == "alignment":
-        dist_calc = metrics.FastAlignmentDistanceCalculator(cutoff=cutoff, n_jobs=n_jobs, estimated_penalty=0, **kwargs)
+        dist_calc = metrics.FastAlignmentDistanceCalculator(n_jobs=n_jobs, estimated_penalty=0, **kwargs)
     elif metric == "fastalignment":
-        dist_calc = metrics.FastAlignmentDistanceCalculator(cutoff=cutoff, n_jobs=n_jobs, **kwargs)
+        dist_calc = metrics.FastAlignmentDistanceCalculator(n_jobs=n_jobs, **kwargs)
     elif metric == "identity":
-        dist_calc = metrics.IdentityDistanceCalculator(cutoff=cutoff, **kwargs)
+        dist_calc = metrics.IdentityDistanceCalculator(**kwargs)
     elif metric == "levenshtein":
-        dist_calc = metrics.LevenshteinDistanceCalculator(cutoff=cutoff, n_jobs=n_jobs, **kwargs)
+        dist_calc = metrics.LevenshteinDistanceCalculator(n_jobs=n_jobs, **kwargs)
     elif metric == "hamming":
-        dist_calc = metrics.HammingDistanceCalculator(cutoff=cutoff, n_jobs=n_jobs, **kwargs)
+        dist_calc = metrics.HammingDistanceCalculator(n_jobs=n_jobs, **kwargs)
     else:
         raise ValueError("Invalid distance metric.")
 

src/scirpy/ir_dist/metrics.py

@@ -243,7 +243,7 @@ class IdentityDistanceCalculator(DistanceCalculator):
         will be ignored and is always 0.
     """
 
-    def __init__(self, cutoff: Union[int, None] = 0):
+    def __init__(self, cutoff: int = 0):
         cutoff = 0
         super().__init__(cutoff)
 
@@ -295,9 +295,7 @@ class LevenshteinDistanceCalculator(ParallelDistanceCalculator):
     {params}
     """
 
-    def __init__(self, cutoff: Union[None, int] = None, **kwargs):
-        if cutoff is None:
-            cutoff = 2
+    def __init__(self, cutoff: int = 2, **kwargs):
         super().__init__(cutoff, **kwargs)
 
     def _compute_block(self, seqs1, seqs2, origin):
@@ -344,9 +342,7 @@ class HammingDistanceCalculator(ParallelDistanceCalculator):
     {params}
     """
 
-    def __init__(self, cutoff: Union[None, int] = None, **kwargs):
-        if cutoff is None:
-            cutoff = 2
+    def __init__(self, cutoff: int = 2, **kwargs):
         super().__init__(cutoff, **kwargs)
 
     def _compute_block(self, seqs1, seqs2, origin):
@@ -420,16 +416,14 @@ class AlignmentDistanceCalculator(ParallelDistanceCalculator):
     )
     def __init__(
         self,
-        cutoff: Union[None, int] = None,
+        cutoff: int = 10,
         *,
         n_jobs: Union[int, None] = None,
         block_size: int = 50,
         subst_mat: str = "blosum62",
         gap_open: int = 11,
         gap_extend: int = 11,
     ):
-        if cutoff is None:
-            cutoff = 10
         super().__init__(cutoff, n_jobs=n_jobs, block_size=block_size)
         self.subst_mat = subst_mat
         self.gap_open = gap_open
@@ -558,7 +552,7 @@ class FastAlignmentDistanceCalculator(ParallelDistanceCalculator):
 
     def __init__(
         self,
-        cutoff: Union[None, int] = None,
+        cutoff: int = 10,
         *,
         n_jobs: Union[int, None] = None,
         block_size: int = 50,
@@ -567,8 +561,6 @@ def __init__(
         gap_extend: int = 11,
         estimated_penalty: float = None,
     ):
-        if cutoff is None:
-            cutoff = 10
         super().__init__(cutoff, n_jobs=n_jobs, block_size=block_size)
         self.subst_mat = subst_mat
         self.gap_open = gap_open