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

[CHANGED] not all apps need to be made available as plugins

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(