Merge pull request #521 from GavinHuttley/develop

pre-release code maintenance

src/cogent3/align/pairwise.py

@@ -15,7 +15,6 @@
 from cogent3.core.alignment import Aligned
 from cogent3.evolve.likelihood_tree import LikelihoodTreeEdge
 from cogent3.util.modules import ExpectedImportError, importVersionedModule
-from cogent3.util.warning import deprecated, discontinued
 
 from .indel_positions import leaf2pog
 

src/cogent3/core/annotation.py

@@ -432,10 +432,9 @@ class Source(_Feature):
     type = "source"
 
     def __init__(self, seq, map, accession, basemap):
-        self._serialisable = locals()
-        for key in ("self", "__class__", "kw"):
-            self._serialisable.pop(key, None)
-        self._serialisable
+        d = locals()
+        exclude = ("self", "__class__")
+        self._serialisable = {k: v for k, v in d.items() if k not in exclude}
 
         self.accession = accession
         self.name = repr(basemap) + " of " + accession

src/cogent3/core/location.py

@@ -236,9 +236,9 @@ def __init__(
         value=None,
         reverse=False,
     ):
-        self._serialisable = locals()
-        for key in ("self", "__class__", "__slots__"):
-            self._serialisable.pop(key, None)
+        d = locals()
+        x = ("self", "__class__", "__slots__")
+        self._serialisable = {k: v for k, v in d.items() if k not in x}
 
         self._new_init(start, end, reverse)
         self.tidy_start = tidy_start
@@ -253,10 +253,9 @@ def _new_init(self, start, end=None, reverse=False):
         If end is not supplied, it is set to start + 1 (providing a 1-element
         range).
         reverse defaults to False.
-
-        This should replace the current __init__ method when deprecated vars
-        are removed.
         """
+        # This should replace the current __init__ method when deprecated vars
+        # are removed.
         # special handling in case we were passed another Span
         if isinstance(start, Span):
             assert end is None
@@ -480,9 +479,9 @@ class _LostSpan(object):
     terminal = False
 
     def __init__(self, length, value=None):
-        self._serialisable = locals()
-        for key in ("self", "__class__", "__slots__"):
-            self._serialisable.pop(key, None)
+        d = locals()
+        exclude = ("self", "__class__", "__slots__")
+        self._serialisable = {k: v for k, v in d.items() if k not in exclude}
 
         self.length = length
         self.value = value
@@ -563,9 +562,9 @@ def __init__(
         termini_unknown=False,
     ):
         assert parent_length is not None
-        self._serialisable = locals()
-        for key in ("self", "__class__", "__slots__"):
-            self._serialisable.pop(key, None)
+        d = locals()
+        exclude = ("self", "__class__", "__slots__")
+        self._serialisable = {k: v for k, v in d.items() if k not in exclude}
 
         if spans is None:
             spans = []

src/cogent3/evolve/likelihood_function.py

@@ -20,12 +20,7 @@
 from cogent3.recalculation.definition import ParameterController
 from cogent3.util import table
 from cogent3.util.dict_array import DictArrayTemplate
-from cogent3.util.misc import (
-    adjusted_gt_minprob,
-    adjusted_within_bounds,
-    get_object_provenance,
-)
-from cogent3.util.warning import deprecated, discontinued
+from cogent3.util.misc import adjusted_gt_minprob, get_object_provenance
 
 
 __author__ = "Peter Maxwell"

src/cogent3/evolve/parameter_controller.py

@@ -18,7 +18,6 @@
 from cogent3.maths.stats.information_criteria import aic, bic
 from cogent3.recalculation.scope import _indexed
 from cogent3.util.misc import adjusted_gt_minprob
-from cogent3.util.warning import deprecated, discontinued
 
 
 __author__ = "Peter Maxwell"
@@ -72,9 +71,9 @@ def __init__(
         **kw,
     ):
         # cache of arguments used to construct
-        self._serialisable = locals()
-        for key in ("self", "__class__", "kw"):
-            self._serialisable.pop(key)
+        d = locals()
+        exclude = ("self", "__class__", "kw")
+        self._serialisable = {k: v for k, v in d.items() if k not in exclude}
         self._serialisable.update(kw)
 
         self.model = self._model = model

src/cogent3/evolve/substitution_model.py

@@ -170,8 +170,9 @@ def __init__(
            tuple-alphabet (including codon) motif probs are used.
 
         """
-        self._serialisable = locals()
-        self._serialisable.pop("self")
+        d = locals()
+        exclude = ("self", "__class__")
+        self._serialisable = {k: v for k, v in d.items() if k not in exclude}
         # MISC
         assert len(alphabet) < 65, (
             "Alphabet too big. Try explicitly " "setting alphabet to PROTEIN or DNA"
@@ -469,8 +470,10 @@ def __init__(
         """
 
         _SubstitutionModel.__init__(self, alphabet, **kw)
-        self._serialisable.update(locals())
-        self._serialisable.pop("self")
+        d = locals()
+        exclude = ("self", "__class__")
+        d = {k: v for k, v in d.items() if k not in exclude}
+        self._serialisable.update(d)
         alphabet = self.get_alphabet()  # as may be altered by recode_gaps etc.
 
         # BINS
@@ -679,8 +682,10 @@ def __init__(self, alphabet, rate_matrix, **kw):
          - rate_matrix: The instantaneous rate matrix
         """
         _ContinuousSubstitutionModel.__init__(self, alphabet, **kw)
-        self._serialisable.update(locals())
-        self._serialisable.pop("self")
+        d = locals()
+        exclude = ("self", "__class__")
+        d = {k: v for k, v in d.items() if k not in exclude}
+        self._serialisable.update(d)
 
         alphabet = self.get_alphabet()  # as may be altered by recode_gaps etc.
         N = len(alphabet)
@@ -710,8 +715,10 @@ def __init__(self, alphabet, predicates=None, scales=None, **kw):
         self._canned_predicates = None
         _ContinuousSubstitutionModel.__init__(self, alphabet, **kw)
 
-        self._serialisable.update(locals())
-        self._serialisable.pop("self")
+        d = locals()
+        exclude = ("self", "__class__")
+        d = {k: v for k, v in d.items() if k not in exclude}
+        self._serialisable.update(d)
 
         (predicate_masks, predicate_order) = self._adapt_predicates(predicates or [])
 

src/cogent3/phylo/nj.py

@@ -283,12 +283,10 @@ def _show_progress():
     return ScoredTreeCollection(result)
 
 
-def nj(dists, no_negatives=True, show_progress=True):
+def nj(dists, show_progress=True):
     """Arguments:
         - dists: dict of (name1, name2): distance
-        - no_negatives: negative branch lengths will be set to 0
     """
-    assert no_negatives, "no_negatives=False is deprecated"
     (result,) = gnj(dists, keep=1, show_progress=show_progress)
     (score, tree) = result
     return tree