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ENH: attached rate and motif parameters to cogent3 tree object #49

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Merged
merged 15 commits into from
Sep 27, 2024
Merged

ENH: attached rate and motif parameters to cogent3 tree object #49

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bf33ea5
NEW: intrude edge params to a tree object
YapengLang Aug 23, 2024
770f9c9
ENH: attach rate and motif params to tree object for non-lie model
YapengLang Aug 23, 2024
27fac13
TST: add tests for tree params
YapengLang Aug 23, 2024
57e7591
MAINT: formatting
YapengLang Aug 23, 2024
cbe079a
ENH: reform rate pars to be consistent with cogent3
YapengLang Aug 26, 2024
603a6c0
TST: added test for the parameters when fit_tree are called
YapengLang Aug 26, 2024
52a5641
TST: modified tests for corresponding rate parameters
YapengLang Aug 26, 2024
ecc7911
ENH: splitted function for processing yaml and reforming pars
YapengLang Aug 27, 2024
33ad493
TST: modified tests for yaml processing
YapengLang Aug 27, 2024
b1bb3c3
MAINT: changed names of functions and commented
YapengLang Sep 25, 2024
f5d11e1
TST: restricted the values for checking parameters fits
YapengLang Sep 25, 2024
ab7988b
TST: added type annotations for tree yaml tests
YapengLang Sep 25, 2024
f66ed0c
MAINT: renamed `_format_edge_pars` and included type casting when pro…
YapengLang Sep 26, 2024
6191e64
TST: modified test for cogent3 tree edge params
YapengLang Sep 26, 2024
32ee9fa
TST: changed the relative tolerance as 1e-2 for rate parameters compa…
YapengLang Sep 26, 2024
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TST: added type annotations for tree yaml tests
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@YapengLang
YapengLang committed Sep 27, 2024
commit ab7988b6fcf913767c38e697f32f11ee9490272b
4 changes: 2 additions & 2 deletions tests/test_iqtree/test_tree_yaml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ def newick_not_in_candidates() -> dict[str, Any]:


@pytest.fixture()
def standard_yaml():
def standard_yaml() -> dict[str, Any]:
return {
"CandidateSet": {
0: "-6736.94578464 (0:0.0063211201,1:0.0029675780,(2:0.0228519739,3:0.3072009029):0.01373649616);",
Expand Down Expand Up @@ -77,7 +77,7 @@ def test_newick_not_in_candidates(newick_not_in_candidates: dict[str, Any]) -> N
)


def test_edge_params(standard_yaml):
def test_edge_params(standard_yaml: dict[str, Any]) -> None:
params = {
"rates": "1, 3.82025079, 1, 1, 3.82025079, 1",
"state_freq": "0.3628523161, 0.1852938562, 0.2173913044, 0.2344625233",
Expand Down