Merge pull request cogent3#1841 from GavinHuttley/develop

MAINT: remove some plugins from toml file, relates to cogent3#1636

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"

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()