commonnexus 1.9.0__tar.gz → 1.9.1__tar.gz

{commonnexus-1.9.0 → commonnexus-1.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: commonnexus
-Version: 1.9.0
+Version: 1.9.1
 Summary: A nexus (phylogenetics) file reader and writer (.nex, .trees)
 Home-page: https://github.com/dlce-eva/commonnexus
 Author: Robert Forkel
@@ -83,14 +83,15 @@ and writing NEXUS
 >>> print(Nexus.from_blocks(Data.from_data(nex.CHARACTERS.get_matrix())))
 #NEXUS
 BEGIN DATA;
-	DIMENSIONS NCHAR=10;
-	FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
-	MATRIX 
-    t1 1001010000
-    t2 0101000100
-    t3 0011101010
-    t4 0001100001
-    t5 0001100001;
+DIMENSIONS NCHAR=10;
+FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
+MATRIX 
+t1 1001010000
+t2 0101000100
+t3 0011101010
+t4 0001100001
+t5 0001100001
+;
 END;
 ```
 

{commonnexus-1.9.0 → commonnexus-1.9.1}/README.md

@@ -46,14 +46,15 @@ and writing NEXUS
 >>> print(Nexus.from_blocks(Data.from_data(nex.CHARACTERS.get_matrix())))
 #NEXUS
 BEGIN DATA;
-	DIMENSIONS NCHAR=10;
-	FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
-	MATRIX 
-    t1 1001010000
-    t2 0101000100
-    t3 0011101010
-    t4 0001100001
-    t5 0001100001;
+DIMENSIONS NCHAR=10;
+FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
+MATRIX 
+t1 1001010000
+t2 0101000100
+t3 0011101010
+t4 0001100001
+t5 0001100001
+;
 END;
 ```
 

{commonnexus-1.9.0 → commonnexus-1.9.1}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = commonnexus
-version = 1.9.0
+version = 1.9.1
 author = Robert Forkel
 author_email = robert_forkel@eva.mpg.de
 description = A nexus (phylogenetics) file reader and writer (.nex, .trees)

{commonnexus-1.9.0 → commonnexus-1.9.1}/src/commonnexus/__init__.py

@@ -1,4 +1,4 @@
 from .nexus import Nexus, Config  # noqa: F401
 from commonnexus.blocks import Block  # noqa: F401
 
-__version__ = '1.9.0'
+__version__ = '1.9.1'

{commonnexus-1.9.0 → commonnexus-1.9.1}/src/commonnexus/nexus.py

@@ -5,6 +5,7 @@ import collections
 import dataclasses
 
 from .tokenizer import TokenType, iter_tokens, get_name
+from .util import log_or_raise
 from commonnexus.command import Command
 from commonnexus.blocks import Block
 
@@ -45,7 +46,7 @@ class Config:
 
 class Nexus(list):
     """
-    A NEXUS object implemented as list of tokens with methods to access newick constituents.
+    A NEXUS object implemented as list of commands with methods to read and write blocks.
 
     From the spec:
 
@@ -95,6 +96,7 @@ class Nexus(list):
         """
         self.cfg = config or Config(**kw)
         self.trailing_whitespace = []
+        self.leading = []
         self.block_implementations = {}
         for cls in Block.__subclasses__():
             self.block_implementations[cls.__name__.upper()] = cls
@@ -120,7 +122,10 @@ class Nexus(list):
                     if token.is_semicolon:
                         commands.append(Command(tuple(tokens)))
                         tokens = []
-            self.trailing_whitespace = tokens
+            if commands:
+                self.trailing_whitespace = tokens
+            else:
+                self.leading = tokens
             s = commands
         list.__init__(self, s)
 
@@ -211,6 +216,7 @@ class Nexus(list):
             END;
         """
         return NEXUS \
+            + ''.join(str(t) for t in self.leading) \
             + ''.join(''.join(str(t) for t in cmd) for cmd in self) \
             + ''.join(str(t) for t in self.trailing_whitespace)
 
@@ -224,8 +230,10 @@ class Nexus(list):
         p.write_text(text, encoding=self.cfg.encoding)
 
     def iter_comments(self):
+        yield from (t for t in self.leading if t.type == TokenType.COMMENT)
         for cmd in self:
             yield from (t for t in cmd if t.type == TokenType.COMMENT)
+        yield from (t for t in self.trailing_whitespace if t.type == TokenType.COMMENT)
 
     @property
     def comments(self) -> typing.List[str]:
@@ -262,6 +270,8 @@ class Nexus(list):
 
     def validate(self, log=None):
         valid = True
+        if any(t.type not in {TokenType.WHITESPACE, TokenType.COMMENT} for t in self.leading):
+            log_or_raise('Invalid token in preamble', log=log)
         for block in self.iter_blocks():
             #
             # FIXME: we can do a lot of validation here! If block.__commands__ is a list, there is
@@ -269,6 +279,9 @@ class Nexus(list):
             # If Payload.__multivalued__ == False, only one command instance is allowed, ...
             #
             valid = valid and block.validate(log=log)
+        if any(t.type not in {TokenType.WHITESPACE, TokenType.COMMENT}
+               for t in self.trailing_whitespace):
+            log_or_raise('Invalid token in text after the last command', log=log)
         return valid
 
     def get_numbers(self, object_name, items):

{commonnexus-1.9.0 → commonnexus-1.9.1}/src/commonnexus.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: commonnexus
-Version: 1.9.0
+Version: 1.9.1
 Summary: A nexus (phylogenetics) file reader and writer (.nex, .trees)
 Home-page: https://github.com/dlce-eva/commonnexus
 Author: Robert Forkel
@@ -83,14 +83,15 @@ and writing NEXUS
 >>> print(Nexus.from_blocks(Data.from_data(nex.CHARACTERS.get_matrix())))
 #NEXUS
 BEGIN DATA;
-	DIMENSIONS NCHAR=10;
-	FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
-	MATRIX 
-    t1 1001010000
-    t2 0101000100
-    t3 0011101010
-    t4 0001100001
-    t5 0001100001;
+DIMENSIONS NCHAR=10;
+FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
+MATRIX 
+t1 1001010000
+t2 0101000100
+t3 0011101010
+t4 0001100001
+t5 0001100001
+;
 END;
 ```
 

{commonnexus-1.9.0 → commonnexus-1.9.1}/tests/test_nexus.py

@@ -161,3 +161,18 @@ def test_Booleans_With_Values(fixture_dir):
 def test_Mesquite_multitaxa(fixture_dir):
     nex = Nexus.from_file(fixture_dir / 'multitaxa_mesquite.nex')
     assert [char.get_matrix() for char in nex.blocks['CHARACTERS']]
+
+
+def test_comments():
+    nex = Nexus('#NEXUS\n[comment]')
+    assert nex.comments == ['comment']
+    nex.append_block(Block.from_commands([], name='b', comment='block comment'))
+    assert nex.comments == ['comment', 'block comment']
+
+    with pytest.raises(ValueError):
+        nex = Nexus('#NEXUS\n[comment]]')
+        nex.validate()
+
+    with pytest.raises(ValueError):
+        nex = Nexus('#NEXUS\nBEGIN b; end;[comment]]')
+        nex.validate()