help functionality on report now works

tests/io/test_io_tree.py

@@ -4,16 +4,133 @@
 from topiary.io.tree import read_tree
 from topiary.io.tree import _map_tree_to_tree
 from topiary.io.tree import load_trees
+from topiary.io.tree import write_trees
+
+import os
+import re
 
 def test_read_tree():
 
     pass
 
-
 def test__map_tree_to_tree():
 
     pass
 
 def test_load_trees():
 
-    pass
+    pass
+
+def test_write_trees(small_phylo,tmpdir):
+
+    cwd = os.getcwd()
+    os.chdir(tmpdir)
+
+    # Reconciled trees
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="reconciled")
+    newick = write_trees(T)
+    split_trees = newick.split(";")[:-1]
+    assert len(split_trees) == 4
+
+    expected = ["100","S","a5","0.999999"]
+    for i in range(4):
+        last_value = split_trees[i].split(")")[-2].split(":")[0]
+        assert last_value == expected[i]
+
+    # gene trees
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="gene")
+    newick = write_trees(T)
+    split_trees = newick.split(";")[:-1]
+    assert len(split_trees) == 3
+
+    expected = ["100","a10","0.997959"]
+    for i in range(3):
+        last_value = split_trees[i].split(")")[-2].split(":")[0]
+        assert last_value == expected[i]
+
+    # Only anc_pp
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="reconciled")
+    newick = write_trees(T,
+                         anc_pp=True,
+                         anc_label=False,
+                         bs_support=False,
+                         event=False)
+    split_trees = newick.split(";")[:-1]
+    assert len(split_trees) == 1
+    last_value = split_trees[0].split(")")[-2].split(":")[0]
+    assert last_value == "0.999999"
+
+    # Only anc_label
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="reconciled")
+    newick = write_trees(T,
+                         anc_pp=False,
+                         anc_label=True,
+                         bs_support=False,
+                         event=False)
+    split_trees = newick.split(";")[:-1]
+    assert len(split_trees) == 1
+    last_value = split_trees[0].split(")")[-2].split(":")[0]
+    assert last_value == "a5"
+
+    # Only bs_support
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="reconciled")
+    newick = write_trees(T,
+                         anc_pp=False,
+                         anc_label=False,
+                         bs_support=True,
+                         event=False)
+    split_trees = newick.split(";")[:-1]
+    assert len(split_trees) == 1
+    last_value = split_trees[0].split(")")[-2].split(":")[0]
+    assert last_value == "100"
+
+    # Only event
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="reconciled")
+    newick = write_trees(T,
+                         anc_pp=False,
+                         anc_label=False,
+                         bs_support=False,
+                         event=True)
+    split_trees = newick.split(";")[:-1]
+    assert len(split_trees) == 1
+    last_value = split_trees[0].split(")")[-2].split(":")[0]
+    assert last_value == "S"
+
+    # Write to file
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="reconciled")
+    newick = write_trees(T,out_file="test.newick")
+    f = open("test.newick","r")
+    lines = f.readlines()
+    f.close()
+    assert len(lines) == 4
+    assert sum([line.strip()[-1] == ";" for line in lines]) == 4
+
+    # Try to write to existing
+    with pytest.raises(FileExistsError):
+        newick = write_trees(T,out_file="test.newick")
+
+    # Overwrite
+    newick = write_trees(T,out_file="test.newick",overwrite=True)
+
+    # Try to write onto a directory
+    os.mkdir("test")
+    with pytest.raises(FileExistsError):
+        newick = write_trees(T,out_file="test",overwrite=True)
+
+    # name_dict
+    T = load_trees(small_phylo["06_reconciled-tree-bootstraps/output"],prefix="reconciled")
+
+    # Build simple name_dict
+    name_dict = {}
+    for n in T.traverse():
+        if n.is_leaf():
+            name_dict[n.name] = re.sub("x","Y",n.name)
+
+    # Make sure replacement happened
+    newick = write_trees(T,name_dict=name_dict)
+    found = re.search("Y",newick)
+    assert found is not None
+    found = re.search("x",newick)
+    assert found is None
+
+    os.chdir(cwd)

tests/reports/test_elements.py

@@ -355,6 +355,20 @@ def test_create_icon_row():
     assert np.array_equal(parser.tag_dict["a"][0][1]["title"],["some","words"])
     assert parser.tag_dict["img"][0][1]["src"][0] == ".assets/pdf_icon.svg"
 
+    out = create_icon_row(["stupid.newick"],["some words"])
+    parser = _load_check_html(out)
+
+    assert parser.tag_dict["a"][0][1]["href"][0] == "stupid.newick"
+    assert np.array_equal(parser.tag_dict["a"][0][1]["title"],["some","words"])
+    assert parser.tag_dict["img"][0][1]["src"][0] == ".assets/newick_icon.svg"
+
+    out = create_icon_row(["stupid.fasta"],["some words"])
+    parser = _load_check_html(out)
+
+    assert parser.tag_dict["a"][0][1]["href"][0] == "stupid.fasta"
+    assert np.array_equal(parser.tag_dict["a"][0][1]["title"],["some","words"])
+    assert parser.tag_dict["img"][0][1]["src"][0] == ".assets/fasta_icon.svg"
+
     out = create_icon_row(["stupid.doc"],["some words"])
     parser = _load_check_html(out)
 

topiary/draw/core.py

@@ -154,9 +154,9 @@ def create_name_dict(df,tip_columns=None,separator="|",disambiguate=True):
     tip_columns : list, optional
         columns in dataframe to use to create human-readable names for tips on
         tree. For example, :code:`tip_columns = ["species","nickname"]` would
-        give names like :code:`"Homo sapiens|LY96"`. If None, try
-        :code:`["species","nickname"]`. If nickname is not in dataframe,
-        fall back to :code:`["species",f"{name[:10]}..."]`.
+        give names like :code:`"Homo sapiens|LY96"`. If None, try 
+        :code:`["species","recip_paralog"], then :code:`["species","nickname"]`,
+        then :code:`["species",f"{name[:10]}..."]`.
     separator : str
         separator to use between pretty names. Cannot be "#,;:'\")(" as these
         are used in newick format.
@@ -181,12 +181,11 @@ def create_name_dict(df,tip_columns=None,separator="|",disambiguate=True):
 
     local_df = df.loc[df.keep,:]
     if tip_columns is None:
-
-        try:
-            local_df.nickname
+        if "recip_paralog" in df.columns:
+            tip_columns = ["species","recip_paralog"]
+        elif "nickname" in df.columns:
             tip_columns = ["species","nickname"]
-        except AttributeError:
-
+        else:
             local_df = df.copy()
             trunc_name = []
             for i in range(len(local_df)):

topiary/draw/tree.py

@@ -171,14 +171,6 @@ def tree(calculation,
     if df is None:
         df = supervisor.df
 
-    if tip_columns is None:
-        if "recip_paralog" in df.columns:
-            recip_columns = ["species","recip_paralog"]
-        elif "nickname" in df.columns:
-            recip_columns = ["species","nickname"]
-        else:
-            recip_columns = ["species","name"]
-
     # Create dictionary mapping between uid and pretty name format
     name_dict = create_name_dict(df=df,
                                  tip_columns=tip_columns,