commonnexus 1.9.1__py2.py3-none-any.whl → 1.9.3__py2.py3-none-any.whl

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/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/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/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.dist-info → commonnexus-1.9.3.dist-info}/METADATA

@@ -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
@@ -25,31 +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)
+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: docs
-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'
+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'
+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
+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.dist-info → commonnexus-1.9.3.dist-info}/RECORD

@@ -1,20 +1,20 @@
-commonnexus/__init__.py,sha256=PjK3pLfL2O6-bT7dktuGDSQufBuU5J5VLsg9yRZVBPI,121
+commonnexus/__init__.py,sha256=ioVKrxHKY4GKtzmrSBlCjpRvF-GQMMPxXZUNPIk5aeA,121
 commonnexus/__main__.py,sha256=k07DsoCHCRw2Wi0HzXCmvNCSt8cddDEGCBlnHZorm6k,4361
 commonnexus/cli_util.py,sha256=pmqd3Fs2Wef7hRf0Z6koZ1Bg6-16FZUMOYZ8cMTY5Ig,3710
 commonnexus/command.py,sha256=5ZbW3wQY1GO6fChK7aqOzwjKBRxkPlKdUf09JbYEy9c,4284
 commonnexus/nexus.py,sha256=rsfxX_cM4aOxS5p-lu39U2ZEcHswDoXPGGiVBiiVAMA,18380
-commonnexus/tokenizer.py,sha256=8G2nP-xNN1gBd2a_7qxGDhHloCzoH4YE063p01FLTuk,11459
+commonnexus/tokenizer.py,sha256=a_zcTLhEc2KW2KCbVFXF-KoZlJg5TTfN9PIh7qnnIuk,11460
 commonnexus/util.py,sha256=WomyVUggYJON5T9uNuIZ_Bxm16UJHIhO737SjKcFYO0,168
 commonnexus/blocks/__init__.py,sha256=ehKEEc_E62zhlkvbp0p3asY56QkLuhqk7wYd1AqQuKI,602
 commonnexus/blocks/assumptions.py,sha256=SNURUIUNP86SgTTdfLVTnGQ0FJDnd3I6FTz3jT9A7aw,11215
 commonnexus/blocks/base.py,sha256=-sMfVczf7gWQ-hc9eV2pOgDgZUs9osrbDu_LbTPTgGM,8562
-commonnexus/blocks/characters.py,sha256=PvNHn11UdwCSNpAWZo_McowAzLlCqVhhxGRUF08T6Xs,59877
+commonnexus/blocks/characters.py,sha256=5zvGPUi6J9ES9hc-1flKb_OJzkhdqXn_1lbL_QbSfag,60130
 commonnexus/blocks/codons.py,sha256=Gox96r1Y3y8wmJIP1KhchfAepMC8BZB4Y7O2BTOcybc,7365
 commonnexus/blocks/distances.py,sha256=E1XnkOhn4NKwhKQS3APhcKJ6HR6B33O2q6rdzQ0n4wU,16018
 commonnexus/blocks/notes.py,sha256=6YctkCTgGAtOWKQ08LgzKXW_X0E1Oe5OgkqcF6iR5LY,8502
 commonnexus/blocks/sets.py,sha256=iLtOgDSAbgkh8JeVi7kdMK4lTuAZMXdZUaE7cU2Mrio,7699
 commonnexus/blocks/taxa.py,sha256=Pzhing1_KKTQPKB4pAXVFMOb6O1kDsPH5VEFn1mc7Ls,3241
-commonnexus/blocks/trees.py,sha256=C0Oa1px9h4MK-_XkRlJATqrMwDKTk12zmaH1gpo4NoA,17642
+commonnexus/blocks/trees.py,sha256=IBbLx4MPayLMKowdTCGj2H0Gw0XxySw0GsB3e54lfY4,18614
 commonnexus/blocks/unaligned.py,sha256=7objnIbG4zjb7v2LbaU1kS44auw4KGlhh1hTE94qGvc,2240
 commonnexus/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 commonnexus/commands/characters.py,sha256=VF458aKOVxFQc4ipOwoWkhZY29EuPCpSVxFY8QtDSY0,5977
@@ -28,9 +28,9 @@ commonnexus/tools/__init__.py,sha256=X8dv4VrjAo5C8VJdUXMrKviDLUrwXbawE5SJiQ--2uQ
 commonnexus/tools/combine.py,sha256=5vPQKcqA2acFji2lZc_xNZr1Xm2F3TPmfQk-fa9GA60,3048
 commonnexus/tools/matrix.py,sha256=3e2n_beug3MZyzXDgawjxxh1QfiM7KVp757OepCjQR0,11492
 commonnexus/tools/normalise.py,sha256=RdAasznob1aIY4B5z0Ir3jm9T5Yj_nbFzdtFtUM553U,6131
-commonnexus-1.9.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-commonnexus-1.9.1.dist-info/METADATA,sha256=wTiq1lHknPwEw9KXEd_2EB_UG_45v_jWmYBNhLFpTVE,5357
-commonnexus-1.9.1.dist-info/WHEEL,sha256=bb2Ot9scclHKMOLDEHY6B2sicWOgugjFKaJsT7vwMQo,110
-commonnexus-1.9.1.dist-info/entry_points.txt,sha256=0CbsOaqe6jaHnG1rpheuIISCZvFp1G1oBgDym82rpAo,58
-commonnexus-1.9.1.dist-info/top_level.txt,sha256=SiWuQrmGciG5Ivhrqz6ueU1Sxv-fzudflsMof81-I54,12
-commonnexus-1.9.1.dist-info/RECORD,,
+commonnexus-1.9.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+commonnexus-1.9.3.dist-info/METADATA,sha256=EY-NI_Fw5fmRZYFrNeGsgQ0WJVloJexMxPPVoWMm2IE,5429
+commonnexus-1.9.3.dist-info/WHEEL,sha256=9Hm2OB-j1QcCUq9Jguht7ayGIIZBRTdOXD1qg9cCgPM,109
+commonnexus-1.9.3.dist-info/entry_points.txt,sha256=0CbsOaqe6jaHnG1rpheuIISCZvFp1G1oBgDym82rpAo,58
+commonnexus-1.9.3.dist-info/top_level.txt,sha256=SiWuQrmGciG5Ivhrqz6ueU1Sxv-fzudflsMof81-I54,12
+commonnexus-1.9.3.dist-info/RECORD,,

{commonnexus-1.9.1.dist-info → commonnexus-1.9.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any