Update from scikit-bio/scikit-bio@c8461d4

scikit-bio · Mar 28, 2024 · 24cb6ef · 24cb6ef
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diff --git a/docs/0.6.0/.buildinfo b/docs/0.6.0/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 176ff4286e1c8bcf023c49c2a0e4ff39
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/0.6.0/_images/diversity-1.png b/docs/0.6.0/_images/diversity-1.png
diff --git a/docs/0.6.0/_images/diversity-2_00.png b/docs/0.6.0/_images/diversity-2_00.png
diff --git a/docs/0.6.0/_images/diversity-2_01.png b/docs/0.6.0/_images/diversity-2_01.png
diff --git a/docs/0.6.0/_images/diversity-3_00.png b/docs/0.6.0/_images/diversity-3_00.png
diff --git a/docs/0.6.0/_images/diversity-3_01.png b/docs/0.6.0/_images/diversity-3_01.png
diff --git a/docs/0.6.0/_images/diversity-3_02.png b/docs/0.6.0/_images/diversity-3_02.png
diff --git a/docs/0.6.0/_images/skbio-sequence-SubstitutionMatrix-plot-1.png b/docs/0.6.0/_images/skbio-sequence-SubstitutionMatrix-plot-1.png
diff --git a/docs/0.6.0/_images/skbio-stats-distance-DissimilarityMatrix-plot-1.png b/docs/0.6.0/_images/skbio-stats-distance-DissimilarityMatrix-plot-1.png
diff --git a/docs/0.6.0/_images/skbio-stats-distance-DistanceMatrix-plot-1.png b/docs/0.6.0/_images/skbio-stats-distance-DistanceMatrix-plot-1.png
diff --git a/docs/0.6.0/_images/skbio-stats-ordination-OrdinationResults-plot-1.png b/docs/0.6.0/_images/skbio-stats-ordination-OrdinationResults-plot-1.png
diff --git a/docs/0.6.0/_sources/alignment.rst.txt b/docs/0.6.0/_sources/alignment.rst.txt
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+.. automodule:: skbio.alignment
diff --git a/docs/0.6.0/_sources/diversity.rst.txt b/docs/0.6.0/_sources/diversity.rst.txt
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+.. automodule:: skbio.diversity
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__eq__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__eq__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__eq__
+=========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__eq__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__ge__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__ge__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__ge__
+=========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__ge__
diff --git a/...0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__getitem__.rst.txt b/...0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__getitem__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__getitem__
+==============================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__getitem__
diff --git a/....6.0/_sources/generated/skbio.alignment.AlignmentStructure.__getstate__.rst.txt b/....6.0/_sources/generated/skbio.alignment.AlignmentStructure.__getstate__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__getstate__
+===============================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__getstate__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__gt__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__gt__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__gt__
+=========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__gt__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__hash__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__hash__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__hash__
+===========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__hash__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__le__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__le__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__le__
+=========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__le__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__lt__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__lt__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__lt__
+=========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__lt__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__ne__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__ne__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__ne__
+=========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__ne__
diff --git a/....6.0/_sources/generated/skbio.alignment.AlignmentStructure.__setstate__.rst.txt b/....6.0/_sources/generated/skbio.alignment.AlignmentStructure.__setstate__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__setstate__
+===============================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__setstate__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__str__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.__str__.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.__str__
+==========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.__str__
diff --git a/...6.0/_sources/generated/skbio.alignment.AlignmentStructure.is_zero_based.rst.txt b/...6.0/_sources/generated/skbio.alignment.AlignmentStructure.is_zero_based.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.is_zero_based
+================================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.is_zero_based
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.AlignmentStructure.rst.txt
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+
+skbio.alignment.AlignmentStructure
+==================================
+
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+.. currentmodule:: skbio.alignment
+
+.. autoclass:: AlignmentStructure
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~AlignmentStructure.aligned_query_sequence
+      ~AlignmentStructure.aligned_target_sequence
+      ~AlignmentStructure.cigar
+      ~AlignmentStructure.optimal_alignment_score
+      ~AlignmentStructure.query_begin
+      ~AlignmentStructure.query_end
+      ~AlignmentStructure.query_sequence
+      ~AlignmentStructure.suboptimal_alignment_score
+      ~AlignmentStructure.target_begin
+      ~AlignmentStructure.target_end_optimal
+      ~AlignmentStructure.target_end_suboptimal
+      ~AlignmentStructure.target_sequence
+
+
+
+   .. rubric:: Built-ins
+
+   .. autosummary::
+      :toctree:
+
+      ~AlignmentStructure.__eq__
+      ~AlignmentStructure.__ge__
+      ~AlignmentStructure.__getitem__
+      ~AlignmentStructure.__getstate__
+      ~AlignmentStructure.__gt__
+      ~AlignmentStructure.__hash__
+      ~AlignmentStructure.__le__
+      ~AlignmentStructure.__lt__
+      ~AlignmentStructure.__ne__
+      ~AlignmentStructure.__setstate__
+      ~AlignmentStructure.__str__
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree:
+
+
+
+      ~AlignmentStructure.is_zero_based
+
+
+      ~AlignmentStructure.set_zero_based
+
+
diff --git a/....0/_sources/generated/skbio.alignment.AlignmentStructure.set_zero_based.rst.txt b/....0/_sources/generated/skbio.alignment.AlignmentStructure.set_zero_based.rst.txt
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+:orphan:
+
+skbio.alignment.AlignmentStructure.set_zero_based
+=================================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: AlignmentStructure.set_zero_based
diff --git a/.../0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__call__.rst.txt b/.../0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__call__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__call__
+=============================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__call__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__eq__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__eq__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__eq__
+===========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__eq__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__ge__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__ge__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__ge__
+===========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__ge__
diff --git a/....0/_sources/generated/skbio.alignment.StripedSmithWaterman.__getstate__.rst.txt b/....0/_sources/generated/skbio.alignment.StripedSmithWaterman.__getstate__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__getstate__
+=================================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__getstate__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__gt__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__gt__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__gt__
+===========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__gt__
diff --git a/.../0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__hash__.rst.txt b/.../0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__hash__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__hash__
+=============================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__hash__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__le__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__le__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__le__
+===========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__le__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__lt__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__lt__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__lt__
+===========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__lt__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__ne__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__ne__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__ne__
+===========================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__ne__
diff --git a/....0/_sources/generated/skbio.alignment.StripedSmithWaterman.__setstate__.rst.txt b/....0/_sources/generated/skbio.alignment.StripedSmithWaterman.__setstate__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__setstate__
+=================================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__setstate__
diff --git a/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__str__.rst.txt b/docs/0.6.0/_sources/generated/skbio.alignment.StripedSmithWaterman.__str__.rst.txt
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+:orphan:
+
+skbio.alignment.StripedSmithWaterman.__str__
+============================================
+
+.. currentmodule:: skbio.alignment
+
+.. automethod:: StripedSmithWaterman.__str__