commonnexus 1.9.1__tar.gz → 1.9.3__tar.gz

{commonnexus-1.9.1/src/commonnexus.egg-info → commonnexus-1.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: commonnexus
-Version: 1.9.1
+Version: 1.9.3
 Summary: A nexus (phylogenetics) file reader and writer (.nex, .trees)
 Home-page: https://github.com/dlce-eva/commonnexus
 Author: Robert Forkel
@@ -25,15 +25,33 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: License :: OSI Approved :: BSD License
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: newick>=1.8.1
 Provides-Extra: dev
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: wheel>=0.36; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: build; extra == "dev"
 Provides-Extra: test
+Requires-Dist: pytest>=5; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: coverage>=4.2; extra == "test"
 Provides-Extra: docs
-License-File: LICENSE
+Requires-Dist: sphinx<7; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-prompt; extra == "docs"
+Requires-Dist: sphinxcontrib-programoutput; extra == "docs"
+Requires-Dist: termgraph; extra == "docs"
 
 # commonnexus
 

{commonnexus-1.9.1 → commonnexus-1.9.3}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = commonnexus
-version = 1.9.1
+version = 1.9.3
 author = Robert Forkel
 author_email = robert_forkel@eva.mpg.de
 description = A nexus (phylogenetics) file reader and writer (.nex, .trees)
@@ -30,6 +30,8 @@ classifiers =
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
 	Programming Language :: Python :: 3.12
+	Programming Language :: Python :: 3.13
+	Programming Language :: Python :: 3.14
 	Programming Language :: Python :: Implementation :: CPython
 	Programming Language :: Python :: Implementation :: PyPy
 	License :: OSI Approved :: BSD License
@@ -98,7 +100,7 @@ show_missing = true
 skip_covered = true
 
 [tox:tox]
-envlist = py38, py39, py310, py311, py312
+envlist = py38, py39, py310, py311, py312, py313, py314
 isolated_build = true
 skip_missing_interpreter = true
 

{commonnexus-1.9.1 → commonnexus-1.9.3}/src/commonnexus/__init__.py

@@ -1,4 +1,4 @@
 from .nexus import Nexus, Config  # noqa: F401
 from commonnexus.blocks import Block  # noqa: F401
 
-__version__ = '1.9.1'
+__version__ = '1.9.3'

{commonnexus-1.9.1 → commonnexus-1.9.3}/src/commonnexus/blocks/characters.py

@@ -549,10 +549,15 @@ class Charstatelabels(Payload):
                 if isinstance(w, Token) and w.text == '/':
                     in_states = True
                     continue
+                if name:
+                    raise ValueError(
+                        'Illegal token in charstatelabel: "{}{}"'.format(name, w))
                 name = w
             except StopIteration:
                 break
         if num:
+            if name and name in names:
+                duplicate_charlabel(name, 'CHARSTATELABELS', nexus)
             self.characters.append(types.SimpleNamespace(number=num, name=name, states=states))
         elif comma:  # There was a comma, but no new label.
             warnings.warn('Trailing comma in CHARSTATELABELS command')

{commonnexus-1.9.1 → commonnexus-1.9.3}/src/commonnexus/blocks/trees.py

@@ -127,6 +127,25 @@ class Tree(Payload):
     NEXUS comment commands. The NEXUS standard places no restrictions on the number of taxa
     contained in each tree.
 
+    Sometimes, trees are annotated with additional information in a NEXUS comment such as
+
+    .. code-block::
+
+        TREE tree1 = [&R] [&clockrate=9.118820e-04] ((beetle,fly),spider);
+
+    Since comments may appear anywhere in NEXUS, this is valid content. However, such comments have
+    no semantics whatsoever; in particular they do not "belong" to any object, be it the Newick
+    tree or the NEXUS TREE wrapper. Instead, they are just added to the global list of comments in
+    a NEXUS file by `commonnexus`. Thus, to retrieve such a comment, one would have to search
+    through `Nexus.comments`, picking one that appears immediately after a `"&R"` comment:
+
+    .. code-block::
+
+        >>> from commonnexus import Nexus
+        >>> nex = Nexus('#nexus begin trees; tree 1 = [&R] [&clockrate] ((a,b)c); end;')
+        >>> nex.comments
+        ['&R', '&clockrate']
+
     :ivar str name: The name of the tree.
     :ivar typing.Union[bool, None] rooted: Flag indicating whether the tree is rooted (or `None` \
     if no information is given)
@@ -172,8 +191,11 @@ class Tree(Payload):
 
         while not nwk:
             t = next(tokens)
-            if t.type == TokenType.COMMENT and t.text.startswith('&'):
-                self._rooted = t.text
+            if t.type == TokenType.COMMENT:
+                if t.text.startswith('&') and t.text[1:] in {'U', 'R'}:
+                    self._rooted = t.text
+                else:
+                    pass
             if t.type == TokenType.PUNCTUATION and t.text == '(':
                 nwk = True
         assert nwk

{commonnexus-1.9.1 → commonnexus-1.9.3}/src/commonnexus/tokenizer.py

@@ -11,7 +11,7 @@ Punctuation
 
     The following punctuation marks have special properties: [ ] do not break a
     word; + and - are allowed as state symbols, but none of the rest are allowed; - is
-    considered punctuation except were it is the minus sign in a negative number.
+    considered punctuation except where it is the minus sign in a negative number.
 """
 import enum
 import itertools

{commonnexus-1.9.1 → commonnexus-1.9.3/src/commonnexus.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: commonnexus
-Version: 1.9.1
+Version: 1.9.3
 Summary: A nexus (phylogenetics) file reader and writer (.nex, .trees)
 Home-page: https://github.com/dlce-eva/commonnexus
 Author: Robert Forkel
@@ -25,15 +25,33 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: License :: OSI Approved :: BSD License
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: newick>=1.8.1
 Provides-Extra: dev
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: wheel>=0.36; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: build; extra == "dev"
 Provides-Extra: test
+Requires-Dist: pytest>=5; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: coverage>=4.2; extra == "test"
 Provides-Extra: docs
-License-File: LICENSE
+Requires-Dist: sphinx<7; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-prompt; extra == "docs"
+Requires-Dist: sphinxcontrib-programoutput; extra == "docs"
+Requires-Dist: termgraph; extra == "docs"
 
 # commonnexus
 

{commonnexus-1.9.1 → commonnexus-1.9.3}/tests/test_blocks_characters.py

@@ -267,3 +267,56 @@ def test_Data_with_mixed_charlabels(nexus):
     nex = nexus(DATA="DIMENSIONS NCHAR=2; CHARSTATELABELS 1 x, 2 ; MATRIX t1 1 1;")
     m = nex.characters.get_matrix()
     assert '2' in m['t1'], 'unspecified character label'
+
+
+def test_illegal_charstatelabel():
+    nex = Nexus("""\
+#NEXUS
+
+BEGIN DATA;
+    DIMENSIONS NTAX=3 NCHAR=3;
+    FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
+    CHARSTATELABELS
+        1 hand_1,
+        2 burn(tr.)_3,
+        3 claw(nail)_3
+        ;
+MATRIX
+A   001
+B   000
+C   000
+;
+END;""")
+    with pytest.raises(ValueError) as e:
+        _ = nex.DATA.CHARSTATELABELS
+    assert 'burn(' in str(e)
+
+    with pytest.raises(ValueError):
+        nex.validate()
+
+
+def test_duplicate_charstatelabels():
+    nex = Nexus("""\
+#NEXUS
+
+BEGIN DATA;
+    DIMENSIONS NTAX=3 NCHAR=3;
+    FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
+    CHARSTATELABELS
+        1 hand_1,
+        2 _3,
+        3 _3
+        ;
+MATRIX
+A   001
+B   000
+C   000
+;
+END;""")
+    with warnings.catch_warnings(record=True) as w:
+        _ = nex.DATA.CHARSTATELABELS
+        assert len(w) == 1, 'Expected 1 warning, got %r' % w
+
+    nex.cfg.strict = True
+    with pytest.raises(ValueError):
+        _ = nex.DATA.CHARSTATELABELS

{commonnexus-1.9.1 → commonnexus-1.9.3}/tests/test_blocks_trees.py

@@ -23,6 +23,14 @@ def test_Trees(nexus):
     assert nex.TREES.translate(tree).newick == '((Scarabaeus,Drosophila),Aranaeus)'
 
 
+def test_Trees_with_leading_comment(nexus):
+    nex = nexus(
+        TAXA="TAXLABELS Scarabaeus Drosophila Aranaeus;",
+        TREES="TREE tree1 = [&R] [&clockrate=9.118820e-04] ((beetle,fly),spider);")
+    assert nex.TREES.TREE.rooted
+    assert '&clockrate=9.118820e-04' in nex.comments
+
+
 def test_Tree_translate_with_taxa_from_linked_block(nexus):
     nex = nexus(
         TAXA="TITLE x; TAXLABELS A B C;",