Merge branch 'cogent3:develop' into feature/issue-1682

pyproject.toml

@@ -176,12 +176,8 @@ new_fragment_template="file: changelog.d/templates/new.md.j2"
 entry_title_template="file: changelog.d/templates/title.md.j2"
 
 [project.entry-points."cogent3.app"]
-compress = "cogent3.app.io:compress"
 concat = "cogent3.app.sample:concat"
-decompress = "cogent3.app.io:decompress"
 fixed_length = "cogent3.app.sample:fixed_length"
-from_json = "cogent3.app.io:from_json"
-from_primitive = "cogent3.app.io:from_primitive"
 load_aligned = "cogent3.app.io:load_aligned"
 load_db = "cogent3.app.io:load_db"
 load_json = "cogent3.app.io:load_json"
@@ -192,16 +188,12 @@ omit_bad_seqs = "cogent3.app.sample:omit_bad_seqs"
 omit_degenerates = "cogent3.app.sample:omit_degenerates"
 omit_duplicated = "cogent3.app.sample:omit_duplicated"
 omit_gap_pos = "cogent3.app.sample:omit_gap_pos"
-pickle_it = "cogent3.app.io:pickle_it"
 select_translatable = "cogent3.app.translate:select_translatable"
 take_codon_positions = "cogent3.app.sample:take_codon_positions"
 take_n_seqs = "cogent3.app.sample:take_n_seqs"
 take_named_seqs = "cogent3.app.sample:take_named_seqs"
-to_json = "cogent3.app.io:to_json"
-to_primitive = "cogent3.app.io:to_primitive"
 translate_seqs = "cogent3.app.translate:translate_seqs"
 trim_stop_codons = "cogent3.app.sample:trim_stop_codons"
-unpickle_it = "cogent3.app.io:unpickle_it"
 write_db = "cogent3.app.io:write_db"
 write_json = "cogent3.app.io:write_json"
 write_seqs = "cogent3.app.io:write_seqs"

src/cogent3/core/alignment.py

@@ -1608,41 +1608,42 @@ def strand_symmetry(self, motif_length=1):
 
     def dotplot(
         self,
-        name1=None,
-        name2=None,
-        window=20,
-        threshold=None,
-        k=None,
-        min_gap=0,
-        width=500,
-        title=None,
-        rc=False,
-        show_progress=False,
+        name1: Optional[str] = None,
+        name2: Optional[str] = None,
+        window: int = 20,
+        threshold: Optional[int] = None,
+        k: Optional[int] = None,
+        min_gap: int = 0,
+        width: int = 500,
+        title: Optional[str] = None,
+        rc: bool = False,
+        show_progress: bool = False,
     ):
         """make a dotplot between specified sequences. Random sequences
         chosen if names not provided.
 
         Parameters
         ----------
-        name1, name2 : str or None
-            names of sequences. If one is not provided, a random choice is made
-        window : int
-            k-mer size for comparison between sequences
-        threshold : int
+        name1, name2
+            names of sequences. If not provided, a random choice is made
+        window
+            segment size for comparison between sequences
+        threshold
             windows where the sequences are identical >= threshold are a match
-        k : int
+        k
             size of k-mer to break sequences into. Larger values increase
-            speed but reduce resolution. If not specified, is computed as the
-            maximum of (window-threshold), (window % k) * k <= threshold.
-        min_gap : int
+            speed but reduce resolution. If not specified, and
+            window == threshold, then k is set to window. Otherwise, it is
+            computed as the maximum of {threshold // (window - threshold), 5}.
+        min_gap
             permitted gap for joining adjacent line segments, default is no gap
             joining
-        width : int
+        width
             figure width. Figure height is computed based on the ratio of
             len(seq1) / len(seq2)
         title
             title for the plot
-        rc : bool or None
+        rc
             include dotplot of reverse compliment also. Only applies to Nucleic
             acids moltypes
 

src/cogent3/draw/dotplot.py

@@ -129,8 +129,9 @@ def __init__(
             windows where the sequences are identical >= threshold are a match
         k : int
             size of k-mer to break sequences into. Larger values increase
-            speed but reduce resolution. If not specified, is computed as the
-            maximum of (window-threshold), (window % k) * k <= threshold.
+            speed but reduce resolution. If not specified, and
+            window == threshold, then k is set to window. Otherwise, it is
+            computed as the maximum of {threshold // (window - threshold), 5}.
         min_gap : int
             permitted gap for joining adjacent line segments, default is no gap
             joining

tests/test_app/test_init.py

@@ -133,10 +133,10 @@ def test_get_app_kwargs():
 
 
 def test_app_help(capsys):
-    app_help("compress")
+    app_help("concat")
     got = capsys.readouterr().out
     assert "Options" in got
-    assert got.count("bytes") >= 2  # both input and output types are bytes
+    assert got.count("SerialisableType") == 1  # output type
 
 
 @pytest.mark.parametrize(

tests/test_app/test_io.py

@@ -608,27 +608,27 @@ def test_default_serialiser_deserialiser(data):
 
 
 def test_to_json():
-    to_j = get_app("to_json")
+    to_j = io_app.to_json()
     data = {"a": [0, 1]}
     assert to_j(data) == json.dumps(data)
 
 
 def test_from_json():
-    from_j = get_app("from_json")
+    from_j = io_app.from_json()
     assert from_j('{"a": [0, 1]}') == {"a": [0, 1]}
 
 
 def test_to_from_json():
-    to_j = get_app("to_json")
-    from_j = get_app("from_json")
+    to_j = io_app.to_json()
+    from_j = io_app.from_json()
     app = to_j + from_j
     data = {"a": [0, 1]}
     assert app(data) == data
     assert app(data) is not data
 
 
 def test_to_json_combines():
-    app = get_app("to_primitive") + get_app("to_json")
+    app = io_app.to_primitive() + io_app.to_json()
     assert app(DNA) == DNA.to_json()